title: KDM2B_CXXCfl_TAM_nucRNA_rep3

data_processing:
Paired-end reads were first aligned using Bowtie 2 (with ‘--very-fast’, ‘--no-mixed’ and ‘--no-discordant’ options) to the concatenated mm10 and dm6 rRNA genomic sequence (GenBank: BK000964.3 and M21017.1) to filter out reads mapping to rRNA. All unmapped reads were aligned to concatenated mm10 and dm6 genomes using STAR (Dobin et al., 2013). To improve mapping of intronic sequences, reads that failed to map using STAR were aligned using Bowtie 2, with ‘--sensitive-local’, ‘--no-mixed’ and ‘--no-discordant’ options. PCR duplicates were removed using SAMtools (Li et al., 2009).
To internally calibrate RNA-seq, we spiked a fixed number of Drosophila SG4 cells into each sample. DESeq2 was used with a custom R script to identify significant changes in gene expression (Love et al. 2014). In order to calibrate to the spike-in genome, Drosophila reads were first pre-normalised according to the exact dm6/mm10 spike-in ratio derived from the matched input gDNA sample. Drosophila read counts were then generated for a set of unique dm6 refGene genes and used to calculate DESeq2 size factors. These size factors were supplied for DESeq2 normalisation of raw mm10 read counts for a custom non-redundant mm10 gene set of 20,633 genes. P-adj < 0.05 and fold change > 1.4 thresholds were used to determine significant changes.
For data visualisation, mm10 reads were randomly subsampled according to the calculated DESeq2 Drosophila size factors.
Genome_build: mm10
Supplementary_files_format_and_content: Stranded bigWig files generated with genomeCoverageBed from BEDTools (Quinlan 2014). These represent genome coverage for merged biological replicates which have been normalised using spike-in downsampling factors.
Supplementary_files_format_and_content: DESeq2 results tables with normalised read counts, estimated log2 fold changes and statistical parameters of differential gene expression analysis.

molecule: nuclear RNA

source_name: Mouse embryonic stem cells with Drosophila SG4 cell spike-in, tamoxifen treated, nuclear RNA-seq

extract_protocol:
1x10^7 mESCs were mixed with 2.5x10^6 Drosophila SG4 cells in PBS. Cells were lysed in 1 ml HS lysis buffer (0.05% NP40, 50mM KCl, 10 mM MgSO4.7H20, 5mM HEPES, 1mM PMSF, 3mM DTT, 1xPIC). Nuclei were recovered by centrifugation at 1000 g for 5min and washed three times in 1 ml resuspension buffer (10mM NaCl, 10mM Tris pH 7.4, 3mM MgCl2). Nuclear integrity was assessed using 0.4% trypan blue staining (ThermoFisher). Nuclear RNA was prepared from 4x10^6 nuclei using TRIzol reagent according to the manufacturer’s protocol (Invitrogen), then treated with the TURBO DNA-free kit (ThermoFisher). RNA quality was assessed using the 2100 Bioanalyzer RNA 6000 Pico kit (Agilent), then RNA was depleted of rRNA using the NEBNext rRNA depletion kit. To quantitate the exact SG4 cell: mESC mixing ratio for each individual sample, genomic DNA was isolated from a small aliquot of nuclei by phenol-chloroform extraction. Genomic DNA was then tagmented using Tn5 transposase, and genomic DNA libraries were prepared alongside ATAC-seq libraries, for which ATAC was performed using another aliquot of the same nuclei. Genomic DNA libraries therefore serve as input controls for both cnRNA-seq and cATAC-seq experiments. Further details can be found in the ATACseq SubSeries.
RNA-seq libraries were prepared using the NEBNext Ultra Directional RNA-seq kit (NEB), following the manufacturer’s protocol and using NEBNext Multiplex Oligos (NEB). Libraries were sequenced using the Illumina NextSeq 500 platform with 80 bp paired-end reads in biological triplicate or quadruplicate.


title: KDM2AB_CXXCfl_UNT_RNAP_NTD_rep1

status: Public on Jul 03 2019

type: SRA

city: Oxford

first: Anne

last: Turberfield

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

library_source: genomic

data_processing:
For RNAPII, KDM2A and KDM2B  cChIP-seq reads were aligned to concatenated mm10 and hg19 genomes and for histone ChIP-seq reads were aligned to the mouse mm10 genome, using Bowtie 2 with the ‘-- no-mixed’ and ‘-- no-discordant’ options (Langmead and Salzberg 2012). Reads that were mapped more than once were discarded, and PCR duplicates were removed using SAMTools (Li et al. 2009).
To internally calibrate RNAPII, KDM2A and KDM2B cChIP-seq, we spiked a fixed number of HEK293T cells into each sample. For data visualisation and annotation of genomic intervals, mm10 reads were randomly subsampled by a factor that reflects the total number of spike-in reads in the same sample, as previously described (Bonhoure et al. 2014; Orlando et al. 2014; Hu et al. 2015). To account for any variation in the exact spike-in cell: mESC mixing ratio between biological replicates, the subsampling factors were additionally corrected according to the ratio of hg19/mm10 total read counts in the matched input sample.
For each condition, biological replicates were merged for downstream applications. Genome coverage tracks were generated using the pileup function from MACS2 (Zhang et al. 2008). Bigwig tracks of H3K36me2 normalised to H3 were generated from merged bigwig files using the deepTools bigwigCompare function with ‘--operation ratio’ setting (Ramírez et al. 2016).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files representing genome coverage for merged replicates.

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse embryonic stem cells with human HEK293T cell spike-in, untreated, RNAPII-NTD ChIP-seq

growth_protocol: Mouse embryonic stem cells were cultured on gelatine-coated dishes at 37oC and 5% CO2 in Dulbecco’s Modified Eagle Medium (Life Technologies) supplemented with 15% fetal bovine serum (Labtech), 2mM L-glutamine (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), 1x non-essential amino acids (Life Technologies), 1x penicillin-streptomycin (Life Technologies), and 10 ng/ml leukemia-inhibitory factor. Human HEK293T cells were grown at 37oC and 5% CO2 in DMEM supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 0.5 mM beta-mercaptoethanol and 1x penicillin-streptomycin.

extract_protocol: For histone H3 and H3K36me2 ChIP, 1x107 mESCs were crosslinked for 10 min in 1% formaldehyde. Reactions were quenched by addition of 125 mM glycine. The released nuclei were washed twice in PBS, then resuspended in lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl pH 8.1 and 1xPIC) and incubated on ice for 30 min. For KDM2A/B ChIP, 5x107 mESCs were resuspended in PBS and mixed with 2x106 HEK293T cells. Cells were crosslinked in 2 mM disuccinimidyl glutarate (Thermo Scientific) for 45 min at 25°C with gentle rotation, then in 1% formaldehyde for 12.5 min (methanol-free, Life Technologies). Reactions were quenched by addition of 125 mM glycine, and crosslinked cells were resuspended in lysis buffer (50mM HEPES-KOH pH 7.9, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP40, 0.25% TritonX-100 and 1x PIC) and rotated for 10 min at 4°C. The released nuclei were washed (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA and 1x PIC) for 5 min at 4°C, and the nuclear pellet resuspended in 1 ml sonication buffer (10mM Tris-HCl pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine and 1xPIC). For RNAPII ChIP, 5x107 mESCs were resuspended in PBS and mixed with 4x106 HEK293T cells. Cells were crosslinked for 10 min in 1% formaldehyde. Reactions were quenched by addition of 150 mM glycine, and the crosslinked cells resuspended in FA-lysis buffer for 10 min (50mM HEPES pH 7.9, 150mM NaCl, 2mM EDTA, 0.5mM EGTA, 0.5% NP40, 0.1% sodium deoxycholate, 0.1% SDS, 10mM NaF, 1mM AEBSF, 1xPIC(Roche)).  For H3, H3K36me2, KDM2A/B or RNAPII ChIP, chromatin was sonicated using a BioRuptor Pico sonicator (Diagenode), shearing genomic DNA to approximately 0.5 kb. Sonicated chromatin was diluted 10-fold in ChIP dilution buffer (1% TritonX-100, 1mM EDTA, 20mM TrisHCl pH 8, 150mM NaCl and 1x PIC) for H3, H3K36me2 or KDM2A/B ChIP, or in FA-lysis buffer for RNAPII ChIP. Chromatin was pre-cleared for 1 hour with either protein A agarose beads (Repligen, for H3, H3K36me2 or RNAPII ChIP) or protein A magnetic Dynabeads (Invitrogen, for KDM2A/B ChIP) blocked with 1 mg/ml BSA and 1 mg/ml yeast tRNA. For each ChIP reaction, 150 ?g chromatin (KDM2A/B), 300 ?g chromatin (RNAPII) or chromatin corresponding to 1x105 cells (H3 or H3K36me2 ChIP) was incubated overnight with the appropriate antibody: anti-H3 (in house, 15 ?l), anti-H3K36me2 (in house, 15 ?l), anti-KDM2A (in house, 2.4 ?l), anti-KDM2B (in house, 2 ?l), anti-Rbp1-NTD (CST D8L4Y, 15 ?l), anti-Rbp1-CTD-Ser5P (CST D9N5I, 12.5 ?l), anti-Rbp1-CTD-Ser2P (CST E1Z3G, 12.5 ?l). Antibody-bound chromatin was isolated using blocked protein A agarose (H3, H3K63me2 or RNAPII ChIP) or magnetic beads (KDM2A/B ChIP) for 2 hours at 4°C. For H3, H3K36me2 or KDM2A/B ChIP, washes were performed with low salt buffer (0.1% SDS, 1% TritonX-100, 2mM EDTA, 20mM Tris-HCl pH 8, 150mM NaCl), high salt buffer (0.1% SDS, 1% TritonX-100, 2mM EDTA, 20mM TrisHCl pH 8, 500mM NaCl), LiCl buffer (250mM LiCl, 1% NP40, 1% sodium deoxycholate, 1mM EDTA, 10mM TrisHCl pH 8) and two washes with TE buffer (10mM Tris-HCl pH 8, 1mM EDTA). For RNAPII ChIP, washes were performed with FA-Lysis buffer, FA-Lysis buffer containing 500mM NaCl, DOC buffer (250mM LiCl, 0.5% NP40, 0.5% sodium deoxycholate, 2mM EDTA, 10mM Tris-HCl pH 8) and two washes with TE buffer. ChIP DNA was eluted in elution buffer (1% SDS, 100mM NaHCO3) and crosslinks reversed overnight at 65°C with 200mM NaCl and 2 ?l RNase A (Sigma). A matched input sample (corresponding to 10% of original ChIP reaction) was treated identically. The following day, samples were treated with 20 ?g/ml Proteinase K (Sigma) for 2 hours at 45°C and purified using the ChIP DNA Clean and Concentrator Kit (Zymo Research). For H2AK119ub1 and H3K27me3 native ChIP-seq, 5 x 107 mouse ESCs were resuspended in 1ml RSB (10mM Tris-HCl pH 8.0, 10mM NaCl, 3mM MgCl2, 5mM N-ethylmaleimide (NEM)), then lysed by addition of 28 ml RSB containing 0.1% NP40. The released nuclei were washed in RSC buffer (RSB supplemented with 0.25M sucrose and 3mM CaCl2), then resuspended in 1 ml RSC buffer containing  10mM NEM and 1xPIC(Roche). Each sample was then incubated with 150 units of MNase (Fermentas) at 37°C for 5 min, then 4 mM EDTA was added to halt MNase digestion. Following centrifugation at 5000 rpm for 5 min at 4°C, the supernatant (S1) was retained. The pellet was resuspended in 300 µl nucleosome release buffer (10mM Tris-HCl pH 7.5, 10mM NaCl, 0.2mM EDTA, 10mM NEM, 1xPIC), incubated at 4°C for 1 h, then passed five times through a 27G needle using a 1 ml syringe. After centrifugation at 5000 rpm for 5 min at 4°C, the second supernatant (S2) was combined with S1. A small aliquot of S1/S2 DNA was purified and visualized on a 1.5% agarose gel to confirm digestion to predominantly mono-nucleosomes. S1/S2 was diluted 10-fold in native ChIP incubation buffer (70mM NaCl, 10mM Tris-HCl pH 7.5, 2mM MgCl2, 2mM EDTA, 0.1% TritonX-100, 10mM NEM, 1xPIC). For each ChIP reaction, 1 ml of diluted nucleosomes was incubated overnight at 4°C with 5 ?l of anti-H2AK119ub1 (CST D27C4) or anti-H3K27me3 (in-house). Antibody-bound nucleosomes were isolated by incubation for 1 hour at 4°C with protein A agarose beads, which were pre-blocked overnight in native ChIP incubation buffer supplemented with 1 mg/ml BSA and 1 mg/ml yeast tRNA. The beads were then washed four times with native wash buffer (20mM Tris-HCl pH 7.5, 2mM EDTA, 125mM NaCl, 0.1% TritonX-100) and once with TE buffer. ChIP DNA was eluted using 100 ul of elution buffer (1% SDS, 0.1 M NaHCO3), then purified using the ChIP DNA Clean and Concentrator Kit (Zymo Research). DNA from a matched input sample (corresponding to 10% of original ChIP reaction) was also purified.

treatment_protocol: mESC lines were treated with 800 nM 4-hydroxytamoxifen (Sigma) for 96 hours to induce KDM2 long isoform knockout (Kdm2a/b-JmjCfl/fl) or ZF-CxxC domain deletion (Kdm2a/b-CXXCfl/fl).

tag: tissue

value: embryonic stem cells

tag: genotype

tag: spike in cells

value: human HEK293T cells

tag: replicate

tag: treatment

value: untreated

tag: chip antibody


title: CE-Ghs13-32

type: RNA

city: University Park

first: Vivek

last: Kapur

state: PA

address: 205 Wartik Lab

department: Animal Science

country: USA

institute: Pennsylvania State University

description:
Raw Data Technical Replicate 1: 214
Raw Data Technical Replicate 2: 215
Raw Data Technical Replicate 3: 216

data_processing:
The Ct given in the non-normalized matrix is the average of three technical replicates for each sample.
Normalization of the data was performed by using the average of 4 housekeeping genes: ACTB, GADPH, RPL4, and HMBS
Target genes were normalized to housekeeping genes and the average of the three technical replicates was the value used for further analysis (delta Ct)
The target genes of the expermiental were compared to that of the controls (delta delta Ct)
The fold change expression between the target and the controls was determined by 2^-delta delta Ct

label: FAM-MGB

molecule: total RNA

organism: Gallus gallus

source_name: Experimental

label_protocol: PCR assays were performed using the custom made OpenArray plates with the Taqman Assays available through Thermo Fisher Scientific

extract_protocol: Total RNA was extracted with RNeasy Plus Mini Kit

tag: developmental stage

value: 21 days of embryonic development

tag: breed

value: Leghorn

tag: subline

tag: infection

value: NDV

value: lung


title: KDM2B_CXXCfl_UNT_nucRNA_rep3

library_source: transcriptomic

source_name: Mouse embryonic stem cells with Drosophila SG4 cell spike-in, untreated, nuclear RNA-seq

growth_protocol: Mouse embryonic stem cells were cultured on gelatine-coated dishes at 37oC and 5% CO2 in Dulbecco’s Modified Eagle Medium (Life Technologies) supplemented with 15% fetal bovine serum (Labtech), 2mM L-glutamine (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), 1x non-essential amino acids (Life Technologies), 1x penicillin-streptomycin (Life Technologies), and 10 ng/ml leukemia-inhibitory factor. Drosophila S2 (SG4) cells were grown adhesively at 25oC in Schneider’s Drosophila Medium (Life Technologies), supplemented with 1x penicillin-streptomycin (Life Technologies) and 10% heat-inactivated fetal bovine serum (Labtech).

treatment_protocol: mESC lines were treated with 800 nM 4-hydroxytamoxifen (Sigma) for 96 hours to induce KDM2 long isoform knockout (Kdm2a/b-JmjCfl/fl) or ZF-CxxC domain deletion (Kdm2a/b-CXXCfl/fl, Kdm2a-CXXCfl/fl, Kdm2b-CXXCfl/fl).

value: Drosophila SG4


title: CE-Ghs13-31

description:
Raw Data Technical Replicate 1: 211
Raw Data Technical Replicate 2: 212
Raw Data Technical Replicate 3: 213


title: KDM2B_CXXCfl_UNT_nucRNA_rep2


title: KDM2B_CXXCfl_TAM_nucRNA_rep2

value: tamoxifen


title: CE-Ghs13-30

description:
Raw Data Technical Replicate 1: 208
Raw Data Technical Replicate 2: 209
Raw Data Technical Replicate 3: 210


title: KDM2B_CXXCfl_TAM_nucRNA_rep1


title: CE-Ghs13-29

description:
Raw Data Technical Replicate 1: 205
Raw Data Technical Replicate 2: 206
Raw Data Technical Replicate 3: 207


title: CE-Ghs13-28

description:
Raw Data Technical Replicate 1: 202
Raw Data Technical Replicate 2: 203
Raw Data Technical Replicate 3: 204


title: KDM2A_CXXCfl_TAM_nucRNA_rep3


title: KDM2A_CXXCfl_TAM_nucRNA_rep2


title: CE-Ghs13-27

description:
Raw Data Technical Replicate 1: 199
Raw Data Technical Replicate 2: 200
Raw Data Technical Replicate 3: 201


title: KDM2B_CXXCfl_UNT_nucRNA_rep1


title: CE-Ghs13-24

description:
Raw Data Technical Replicate 1: 190
Raw Data Technical Replicate 2: 191
Raw Data Technical Replicate 3: 192


title: KDM2A_CXXCfl_TAM_nucRNA_rep1


title: CE-Ghs13-23

description:
Raw Data Technical Replicate 1: 187
Raw Data Technical Replicate 2: 188
Raw Data Technical Replicate 3: 189


title: KDM2A_CXXCfl_UNT_nucRNA_rep2


title: CE-Ghs13-22

description:
Raw Data Technical Replicate 1: 184
Raw Data Technical Replicate 2: 185
Raw Data Technical Replicate 3: 186


title: CE-Ghs13-21

description:
Raw Data Technical Replicate 1: 181
Raw Data Technical Replicate 2: 182
Raw Data Technical Replicate 3: 183


title: Tox∆Ex5 Tim3 -ve P14 T-cells_Day 8

city: memphis

first: yiping

last: fan

state: tn

address: 262 Danny Thomas Place

institute: st jude children's hospital

data_processing:
Basecalling was performed using Illumina RealTimeAnalysis software
FASTQ sequences adapter trimmed (trimglore) and mapped to the mm10 genome by BSMAP
CpGs were extracted by the methratio.py in the BSMAP package
Genome_build: mm10
Supplementary_files_format_and_content: methylation ratio are in bed formats that contains methylation ratio for each CpG

extract_protocol:
DNA was extracted followed by bisulfite treatment for library prepration
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA Methylation Kit (Part# EGMK81312). Briefly, Bisulfite converted DNA was annealed with random hexamer with tagging sequence. DNA copy was synthesized using TruSeq DNA Methyl Polymerase. Then Exonuclease I was used to digest excess random primer.  The 3’ ends of the strands are then selectively tagged with a second specific sequence tag to generate di-tagged DNA using DNA polymerase. The di-tagged DNA with known sequence tags at both ends was cleaned up by the AMPureXP Beads. The dsDNA library was generated by PCR amplification with Illumina primers for 10 cycles and library fragments of ~350 bp (insert plus adaptor and PCR primer sequences). The library was purified by the AMPureXP Beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq 2500 following the manufacturer's protocols.

tag: cell type

value: P14 T-cells

value: ToxKO

value: LCMV infection

tag: time

value: day 8

tag: sorted into

value: Tim-3- T-cells


title: CE-Ghs13-20

description:
Raw Data Technical Replicate 1: 178
Raw Data Technical Replicate 2: 179
Raw Data Technical Replicate 3: 180


title: Tox∆Ex5 Tim3 +ve P14 T-cells_Day 8

value: Tim-3+ T-cells


title: CE-Ghs13-37

description:
Raw Data Technical Replicate 1: 229
Raw Data Technical Replicate 2: 230
Raw Data Technical Replicate 3: 231


title: WT Tim3 -ve P14 T-cells_Day 8

value: WT


title: KDM2A_CXXCfl_UNT_nucRNA_rep3


title: WT Tim3 +ve P14 T-cells_Day 8


title: Testis_Recovery_4

city: Bergen

first: Diego

last: Crespo

address: Nordnesgaten 50

department: Reproduction and Developmental Biology

country: Norway

institute: Institute of Marine Research

data_processing:
Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite (v0.10.1; default parameters)
Reads were aligned to the zebrafish genome using TopHat v2.0.5 (standard parameters for single-end reads)
Data were filtered using SAMtools (v0.1.18)
The read counts were extracted using the Python package HTSeq
Differential expression analysis was performed using the R/Bioconductor package DESeq
Genome_build: Zv9
Supplementary_files_format_and_content: Tab-delimited text files include gene ID and raw counts for each sample

organism: Danio rerio

source_name: Testis

extract_protocol:
Total RNA was isolated from testis tissue using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio-analyzer 2100 total RNA Nano series II chip (Agilent)
Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 (Illumina, Inc.) according to the manufacturer’s instructions

tag: age

value: Adult

value: Wild type

value: Testis


title: Testis_Recovery_5


title: CE-Ghs13-19

description:
Raw Data Technical Replicate 1: 175
Raw Data Technical Replicate 2: 176
Raw Data Technical Replicate 3: 177


title: KDM2AB_CXXCfl_TAM_nucRNA_r4

value: embryonic stem cells


title: CE-Ghs13-18

description:
Raw Data Technical Replicate 1: 172
Raw Data Technical Replicate 2: 173
Raw Data Technical Replicate 3: 174

value: 21 days of embryonic development


title: Testis_Recovery_3


title: Testis_Recovery_2


title: KDM2AB_CXXCfl_TAM_nucRNA_r3


title: CE-Ghs13-25

description:
Raw Data Technical Replicate 1: 193
Raw Data Technical Replicate 2: 194
Raw Data Technical Replicate 3: 195

value: Leghorn


title: Testis_Depletion_5


title: Testis_Recovery_1


title: CE-Ghs13-17

description:
Raw Data Technical Replicate 1: 169
Raw Data Technical Replicate 2: 170
Raw Data Technical Replicate 3: 171

value: NDV


title: KDM2AB_CXXCfl_TAM_nucRNA_r2


title: CE-Ghs13-16

description:
Raw Data Technical Replicate 1: 166
Raw Data Technical Replicate 2: 167
Raw Data Technical Replicate 3: 168

value: lung


title: Testis_Depletion_4


title: KDM2AB_CXXCfl_TAM_nucRNA_r1

value: Drosophila SG4


title: KDM2A_CXXCfl_UNT_nucRNA_rep1

value: untreated


title: Testis_Depletion_3


title: KDM2AB_CXXCfl_UNT_nucRNA_rep3


title: Testis_Depletion_2


title: CE-Ghs13-15

description:
Raw Data Technical Replicate 1: 163
Raw Data Technical Replicate 2: 164
Raw Data Technical Replicate 3: 165


title: KDM2AB_CXXCfl_UNT_nucRNA_rep4


title: CE-Ghs13-13

description:
Raw Data Technical Replicate 1: 157
Raw Data Technical Replicate 2: 158
Raw Data Technical Replicate 3: 159


title: CE-Ghs13-14

description:
Raw Data Technical Replicate 1: 160
Raw Data Technical Replicate 2: 161
Raw Data Technical Replicate 3: 162


title: Testis_Depletion_1


title: Testis_Control_5


title: KDM2AB_CXXCfl_UNT_nucRNA_rep1


title: p21null_Doxo_4534

city: New Orleans

first: James

middle: G

last: Jackson

state: LA

address: 1430 Tulane

institute: Tulane

description: p21 null

data_processing:
RSEM
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression matrix (TPMs)

source_name: MMTV-Wnt1 mammary tumor

growth_protocol: In vivo spontaneous mouse mammary tumors in MMTV-Wnt1 mice, either p53 null, p21 null, or wild type for Trp53 and Cdkn1a

extract_protocol:
Rna was extracted from snap frozen, pulverized tumor tissue using Trizol reagent
Trp53 WT tumors: Illumina TruSeq® Stranded Total RNA; Trp53null tumors: Illumina TruSeq RNA Library Preparation Kit v2; Cdkn1a null tumors: Illumina TruSeq RNA Library Preparation Kit v2

treatment_protocol: Untreated or 4mg/kg Doxorubicin IP daily for 5 consecutive days, harvested 24 hours after final injection

value: mammary tumor

tag: strain

value: p21 null

value: doxorubicin


title: p21null_Doxo_4577

description: p21 null


title: p21null_Doxo_4533

description: p21 null


title: p21null_Doxo_4439

description: p21 null


title: p21null_Doxo_4439i

description: p21 null


title: CE-Ghs13-26

description:
Raw Data Technical Replicate 1: 196
Raw Data Technical Replicate 2: 197
Raw Data Technical Replicate 3: 198


title: p21null_Doxo_4380

description: p21 null


title: CE-Ghs13-11

description:
Raw Data Technical Replicate 1: 151
Raw Data Technical Replicate 2: 152
Raw Data Technical Replicate 3: 153


title: Testis_Control_4


title: CE-Ghs13-12

description:
Raw Data Technical Replicate 1: 154
Raw Data Technical Replicate 2: 155
Raw Data Technical Replicate 3: 156


title: Testis_Control_3


title: p21null_Doxo_4183

description: p21 null


title: CE-Ghs13-10

description:
Raw Data Technical Replicate 1: 148
Raw Data Technical Replicate 2: 149
Raw Data Technical Replicate 3: 150

source_name: Control

value: Control


title: p21null_Doxo_4168

description: p21 null


title: KDM2AB_JmjCfl_TAM_nucRNA_rep2

value: tamoxifen


title: KDM2AB_JmjCfl_TAM_nucRNA_rep3


title: Testis_Control_2


title: p21null_Doxo_4132

description: p21 null


title: CE-Ghs13-9

description:
Raw Data Technical Replicate 1: 145
Raw Data Technical Replicate 2: 146
Raw Data Technical Replicate 3: 147


title: Testis_Control_1


title: KDM2AB_JmjCfl_TAM_nucRNA_rep1


title: Mouse_kidney_FTO

city: Guangzhou

first: Zhang

last: Zhang

state: Guangdong

address: Xingangxi Roda 135#

country: China

institute: Sun Yat-sen University

data_processing:
Library strategy: Aim-seq
The raw reads were filtered adaptors by cutadapt with at least 15 bp remaining length of paired-end reads. The clean reads were mapped to the reference genome (hg19) using Hisat2.
Reads with ACA/TGT motif internal or at the end were used to identify transcriptome-wide candidate m6A sites.
The RNAfold program of ViennaRNA package was used to predict intramolecular secondary structure of each read which supported the candidate sites, and sites with the high pairing probability were discarded.
The FTO demethylation treatment was negative control. Only the sites with at least 10% methylation ratio decrease in FTO treatment were retained as m6A sites.
Genome_build: hg19,mm10,rn6
Supplementary_files_format_and_content: text format with the information of chromosome number, site loction, strand, #reads with internal ACA in MazF, #reads sum in MazF,#reads with internal ACA in FTO, #reads sum in FTO, in one or more replicates

molecule: polyA RNA

source_name: Mouse kidney tissue

growth_protocol: Human HEK293T cell line was cultured with DMEM (Corning) supplemented with 10% (v/v) FBS (Gibco) at 37℃ in the presence of 5% CO2, and tested to be negative for mycoplasma contamination.

extract_protocol:
Total RNA from HEK293T cells was extracted using Trizol reagent (Thermo Fisher Scientific) and the mRNA was purified using Dynabeads mRNA Purification Kit (Thermo Fisher Scientific, Cat. No. 61006). The mRNA of human tissues (brain, liver and kidney), mouse tissues (brain, liver, heart, testis and kidney) and rat tissues (brain, liver and kidney) were purchased from Takara Bio.
mRNA samples were heated to denature and digested into fragments by MazF (Takara) at 37℃ for 30 min. The fragmented mRNA was purified and end-repaired using T4 polynucleotide kinase at 37℃ for 30 min. The sample was purified for small RNA library construction.
Parallel samples demethylated by FTO in advance were as the negative controls. The FTO treatment was in 20 ul of reaction mixture containing 100-200 ng mRNA, 2.5 ug FTO demethylase, 283 μM of (NH4)2Fe(SO4)2·6H2O, 300 μM of α-KG, 2 mM of L-ascorbic acid, 20 U RNase inhibitor and 50 mM of Tris·HCl buffer (pH 7.5). After incubating at room temperature for 3h, the reaction was stopped by adding 40 mM EDTA.
Small RNA library construction protocol

value: kidney

value: FTO-MazF


title: p21null_Doxo_4093

description: p21 null


title: CE-Ghs13-8

description:
Raw Data Technical Replicate 1: 142
Raw Data Technical Replicate 2: 143
Raw Data Technical Replicate 3: 144


title: CE-Ghs13-7

description:
Raw Data Technical Replicate 1: 139
Raw Data Technical Replicate 2: 140
Raw Data Technical Replicate 3: 141


title: KDM2AB_CXXCfl_UNT_nucRNA_rep2


title: p21null_Untreated_4539

description: p21 null


title: Mouse_testis_FTO

source_name: Mouse testis tissue

value: testis


title: Mouse_testis_MazF

value: MazF


title: p21null_Untreated_4555

description: p21 null


title: p21null_Untreated_4383

description: p21 null


title: p21null_Untreated_4536

description: p21 null


title: CE-Ghs13-3

description:
Raw Data Technical Replicate 1: 127
Raw Data Technical Replicate 2: 128
Raw Data Technical Replicate 3: 129


title: CE-Ghs13-4

description:
Raw Data Technical Replicate 1: 130
Raw Data Technical Replicate 2: 131
Raw Data Technical Replicate 3: 132


title: KDM2AB_JmjCfl_UNT_nucRNA_rep1


title: Mouse_heart_FTO

source_name: Mouse heart tissue

value: heart


title: p21null_Untreated_4116i

description: p21 null


title: Mouse_heart_MazF


title: CE-Ghs13-5

description:
Raw Data Technical Replicate 1: 133
Raw Data Technical Replicate 2: 134
Raw Data Technical Replicate 3: 135


title: KDM2AB_JmjCfl_UNT_nucRNA_rep3

value: embryonic stem cells


title: p21null_Untreated_4116

description: p21 null


title: CE-Ghs13-2

description:
Raw Data Technical Replicate 1: 124
Raw Data Technical Replicate 2: 125
Raw Data Technical Replicate 3: 126

value: 21 days of embryonic development


title: CE-Ghs13-6

description:
Raw Data Technical Replicate 1: 136
Raw Data Technical Replicate 2: 137
Raw Data Technical Replicate 3: 138

value: Leghorn


title: Mouse_liver_FTO

source_name: Mouse liver tissue

value: liver


title: Sample 6 Post-training

city: Chieti

first: Rosa

last: Mancinelli

address: via dei Vestini

country: Italy

institute: university of Chieti

description:
Test
SAMPLE 12

data_processing:
We tested 4 candidate housekeeping genes (18S, GUSB, ACTB, GAPDH), however for the normalization we used the housekeeping gene GAPDH. Data were processed using SDS version 2.0; Applied  Biosystems) for data collection and analysis.  Target gene signals normalized to housekeeping gene; 2^-ΔΔCt, where ΔΔCt=[(Ct target (unknown sample)−Ct endogenous control (unknown sample))]−[(Ct target (reference sample)−Ct endogenous control (reference sample))].
Fold Change worksheet reports test/control (post-training/pre-training) ratios.

label: FAM

organism: Homo sapiens

source_name: Trained Vastus lateralis muscle

label_protocol: PCR assays were performed using custom TaqMan low density array cards (Thermo Fisher scientific) preloaded with 48 selected genes related to the following pathways: myogenesis, apoptosis, protein anabolism/catabolism and antioxidant enzymes to quantitate their gene expression in human skeletal muscle following the Manufacturer’s instructions. Reverse transcription was performed from 1 µg of total RNA using High Capacity cDNA Reverse Transcription Kit with RNase Inhibitor (Applied Biosystems, Thermo Fisher Scientific), according to the manufacturer’s protocol. The expression analysis using TaqMan low density array (Applied Biosystems-MDS Sciex, Toronto, ON, Canada) was performed on one hundred nanograms cDNA for each sample. Then, 48 µl nuclease-free water and 50 µl 2 x TaqMan Universal PCR Master Mix (Applied Biosystems) were added for the real-time PCR measurements. This mixture was divided over sample-loading ports of the TaqMan low density arrays. The arrays were centrifuged twice (2 min, 331 x g at RT). Quantitative real-time PCR were performed (Applied Biosystems Prism 7900HT Sequence Detection System) with 45 cycles at 95 °C for 15 seconds and 60 °C for 60 seconds.

extract_protocol: Total RNA was purified using TRIZOL Reagent (Invitrogen, Thermo Fisher Scientific), according to the manufacturer’s protocol.

treatment_protocol: Once muscle biopsies were obtained before and after the training protocol, samples of about 10 mg were collected in RNA Later (#AM7020, Ambion, Milan, Italy) and stored at -80°C until used to perform RT-PCR analysis.

value: Vastus lateralis muscle


title: Sample 6 Pre-training

description:
Control
SAMPLE 11

source_name: Non-trained Vastus lateralis muscle


title: CE-Ghs6-40

description:
Raw Data Technical Replicate 1: 118
Raw Data Technical Replicate 2: 119
Raw Data Technical Replicate 3: 120

value: NDV

value: lung


title: Sample 5 Post-training

description:
Test
SAMPLE 10


title: CE-Ghs13-1

description:
Raw Data Technical Replicate 1: 121
Raw Data Technical Replicate 2: 122
Raw Data Technical Replicate 3: 123


title: Mouse_kidney_MazF


title: KDM2AB_JmjCfl_UNT_nucRNA_rep2

value: Drosophila SG4

value: untreated


title: p53null_Doxo_2769

description: p53 null

value: mammary tumor

value: p53 null

value: doxorubicin


title: Sample 4 Post-training

description:
Test
SAMPLE 8


title: p53null_Doxo_2771

description: p53 null


title: CE-Ghs6-39

description:
Raw Data Technical Replicate 1: 115
Raw Data Technical Replicate 2: 116
Raw Data Technical Replicate 3: 117


title: p53null_Doxo_2688

description: p53 null


title: p53null_Doxo_2551rc

description: p53 null


title: Mouse_brain_MazF

source_name: Mouse brain tissue

value: brain


title: CE-Ghs6-37

description:
Raw Data Technical Replicate 1: 109
Raw Data Technical Replicate 2: 110
Raw Data Technical Replicate 3: 111


title: Sample 3 Post-training

description:
Test
SAMPLE 6


title: Sample 3 Pre-training

description:
Control
SAMPLE 5


title: p53null_Doxo_2551

description: p53 null


title: Mouse_liver_MazF


title: CE-Ghs6-36

description:
Raw Data Technical Replicate 1: 106
Raw Data Technical Replicate 2: 107
Raw Data Technical Replicate 3: 108


title: p53null_Doxo_2237

description: p53 null


title: Stim D10 rep2

city: Louisville

first: Tamer

middle: M

last: Mohamed

state: KY

address: 580 S. Preston St., Baxter II Bldg., Room 122

department: Cardiology

institute: University of Louisville

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Sscrofa11
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Sus scrofa

source_name: Heart

extract_protocol:
Heart slices were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Yorkshire

value: Heart

value: 3 months

value: WT


title: Stim D10 rep1


title: CE-Ghs6-35

description:
Raw Data Technical Replicate 1: 103
Raw Data Technical Replicate 2: 104
Raw Data Technical Replicate 3: 105


title: Stim D10 rep3


title: p53null_Untreated_881

description: p53 null


title: Mouse_brain_FTO

value: FTO-MazF


title: CE-Ghs6-34

description:
Raw Data Technical Replicate 1: 100
Raw Data Technical Replicate 2: 101
Raw Data Technical Replicate 3: 102

value: 21 days of embryonic development


title: Sample 2 Post-training

description:
Test
SAMPLE 4


title: Stim D6 rep3


title: Sample 2 Pre-training

description:
Control
SAMPLE 3


title: Sample 4 Pre-training

description:
Control
SAMPLE 7


title: Sample 5 Pre-training

description:
Control
SAMPLE 9


title: Stim D6 rep2


title: Stim D6 rep1


title: 87944_I15_3

city: Cologne

first: David

last: Vilchez

state: NRW

address: Joseph Stelzmann Strasse, 26

country: Germany

institute: CECAD - Cluster of Excellence

data_processing:
Illumina Casava software used for basecalling
Sequenced reads mapped to Caenorhabditis Elegans
Fragment Per Kilobase of exon per Million (FPKM) were calculated using a Cufflinks
Genome_build: Caenorhabditis Elegans (Ensembl 87)
Supplementary_files_format_and_content: tab-delimited file include FPKM values for each Sample

organism: Caenorhabditis elegans

source_name: iff-1 RNAi-treated worms at 15  C

growth_protocol: C. elegans strains were grown and maintained on standard nematode growth media (NGM) seeded with E. coli (OP50) until they reach adulthood. Then they were shifted to 15C or 20C and to the control empty vector RNAi bacteria or iff-1 RNAi bacteria.

extract_protocol:
Total RNA was extracted using RNAbee (Tel-Test Inc.).
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit. Library preparation started with 1 µg total RNA. After selection (using poly-T oligo-attached magnetic beads), mRNA was purified and fragmented using divalent cations under elevated temperature. The RNA fragments underwent reverse transcription using random primers followed by second strand cDNA synthesis with DNA Polymerase I and RNase H. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified (20 µl template, 14 PCR cycles) to create the final cDNA libraries. After library validation and quantification (Agilent 2100 Bioanalyzer), equimolar amounts of library were pooled. The pool was quantified by using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System. The pool was sequenced on an Illumina HiSeq 4000 sequencer with a paired- end (2 × 75bp) protocol.

treatment_protocol: Worms were treated with  iff-1 RNAi orempty vector (EV) RNAi from adulthood. Worms were shifted to  20°C or  15°C from adulthood. Worms were grown in the aforementioned conditions during 6 days and then the germ line was extruded. Day 6-adult C. elegans were washed with EBT buffer (1X egg buffer, 0.2 %Tween 20, 20 mM Sodium Azid) and decapitated to extract germ line. Extruded germ lines were collected.

value: germ line

value: iff-1 RNAi

tag: growth temperature

value: 15 degrees Celsius


title: 87942_I15_2


title: p53null_Untreated_2119

description: p53 null


title: Stim D2 rep2


title: p53null_Untreated_2493ra

description: p53 null


title: p53null_Untreated_2493

description: p53 null


title: CE-Ghs6-32

description:
Raw Data Technical Replicate 1: 94
Raw Data Technical Replicate 2: 95
Raw Data Technical Replicate 3: 96

value: Leghorn

value: NDV


title: p53null_Untreated_1556i

description: p53 null


title: Stim D2 rep1


title: CE-Ghs6-30

description:
Raw Data Technical Replicate 1: 88
Raw Data Technical Replicate 2: 89
Raw Data Technical Replicate 3: 90

value: lung


title: 87940_I15_1


title: CE-Ghs6-33

description:
Raw Data Technical Replicate 1: 97
Raw Data Technical Replicate 2: 98
Raw Data Technical Replicate 3: 99


title: 87938_C20_3

source_name: Empty vector (EV) RNAi-treated worms at 20  C

value: empty vector control

value: 20 degrees Celsius


title: p53null_Untreated_1556

description: p53 null

value: mammary tumor

value: p53 null

value: untreated


title: Sample 1 Pre-training

description:
Control
SAMPLE 1

value: Vastus lateralis muscle


title: D0 rep3

value: Yorkshire

value: Heart


title: CE-Ghs6-29

description:
Raw Data Technical Replicate 1: 85
Raw Data Technical Replicate 2: 86
Raw Data Technical Replicate 3: 87


title: D0 rep2

value: 3 months

value: WT


title: p53WT_Doxo_978

description: wild-type

value: wild-type

value: doxorubicin


title: 87936_C20_2

value: germ line


title: CE-Ghs6-28

description:
Raw Data Technical Replicate 1: 82
Raw Data Technical Replicate 2: 83
Raw Data Technical Replicate 3: 84

value: 21 days of embryonic development


title: CE-Ghs6-31

description:
Raw Data Technical Replicate 1: 91
Raw Data Technical Replicate 2: 92
Raw Data Technical Replicate 3: 93

value: Leghorn


title: CE-Ghs6-27

description:
Raw Data Technical Replicate 1: 79
Raw Data Technical Replicate 2: 80
Raw Data Technical Replicate 3: 81

value: NDV


title: 87934_C20_1


title: p53WT_Doxo_1475la

description: wild-type


title: D0 rep1


title: 87932_C15_3

source_name: Empty vector (EV) RNAi-treated worms at 15  C

value: 15 degrees Celsius


title: CE-Ghs6-26

description:
Raw Data Technical Replicate 1: 76
Raw Data Technical Replicate 2: 77
Raw Data Technical Replicate 3: 78

value: lung


title: Sample 1 Post-training

description:
Test
SAMPLE 2


title: p53WT_Doxo_1127

description: wild-type


title: 87928_C15_1

value: empty vector control


title: CE-Ghs6-24

description:
Raw Data Technical Replicate 1: 70
Raw Data Technical Replicate 2: 71
Raw Data Technical Replicate 3: 72


title: CE-Ghs6-23

description:
Raw Data Technical Replicate 1: 67
Raw Data Technical Replicate 2: 68
Raw Data Technical Replicate 3: 69


title: p53WT_Doxo_1475

description: wild-type

value: mammary tumor


title: 87930_C15_2


title: p53WT_Untreated_998

description: wild-type


title: p53WT_Doxo_1188

description: wild-type


title: ChIP-seq-scLMNA_III-3-MT

city: Stanford

first: Lei

last: Tian

state: CA

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

description:
Parental line III-3
processed data file: PT3MT_EDD_SCLMNA_vs_Input_peaks.bed

data_processing:
AQUAS pipeline from the Kundaje lab at Stanford University (https://github.com/kundajelab/chip-seq-pipeline2).
Duplicate reads were removed: MarkDuplicates from Picard Tools (v2.17.3).
LMNA data were analyzed: Enriched Domain Detector (v1.0) with an 11 Kb bin size, gap penalty of 5, and FDR significance threshold of 0.05.
LAD gain, loss, and intersection were found: bedtools (v2.27.1).
Genome_build: human reference genome hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig and bed

source_name: iPSC-CMs

growth_protocol: iPSC lines were maintained in chemically defined medium Essential 8 (E8 medium) (Life Technologies) on Matrigel-coated (BD Bioscience, San Jose, CA) plates at 37°C with 5% (vol/vol) CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and LMNA-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using The Ion Proton™ System protocols.

treatment_protocol: iPSCs were grown to 90% confluence and subsequently differentiated into beating cardiomyocytes, using a small-molecule-based monolayer method described previously. Ten days after cardiac differentiation, iPSC-CM monolayers were purified using RPMI-1640 without glucose (Life Technologies) with B27 supplement (Life Technologies). Non-glucose culture medium was changed every 2 days. After 5 days, iPSC-CMs were reseeded onto Matrigel-coated plates in a culture medium containing glucose.

value: iPSC-CMs

tag: day post-differentiation

value: day 40

tag: genotype/variation

value: LMNA WT/MT

value: Lamin A/C (Santa Cruz Biotechnology sc-376248)


title: CE-Ghs6-25

description:
Raw Data Technical Replicate 1: 73
Raw Data Technical Replicate 2: 74
Raw Data Technical Replicate 3: 75

source_name: Experimental

tag: tissue


title: CE-Ghs6-22

description:
Raw Data Technical Replicate 1: 64
Raw Data Technical Replicate 2: 65
Raw Data Technical Replicate 3: 66


title: p53WT_Doxo_824

description: wild-type

tag: genotype


title: CE-Ghs6-21

description:
Raw Data Technical Replicate 1: 61
Raw Data Technical Replicate 2: 62
Raw Data Technical Replicate 3: 63


title: p53WT_Untreated_713

description: wild-type

value: untreated


title: CE-Ghs6-19

description:
Raw Data Technical Replicate 1: 55
Raw Data Technical Replicate 2: 56
Raw Data Technical Replicate 3: 57


title: p53WT_Untreated_620

description: wild-type


title: ChIP-seq-H3K27me3_III-3-MT

description:
Parental line III-3
processed data file: H3K27_PT3MT.paired.PE2SE.nodup.tagAlign_x_Input_2_R1.paired.PE2SE.nodup.tagAlign.fc.signal.bw

value: H3K27me3 (Active Motif 39155)


title: ChIP-seq-scLMNA_III-3-WT

description:
Isogenic line to III-3 to correct LMNA mutation
processed data file: PT3WT_EDD_SCLMNA_vs_Input_peaks.bed

value: LMNA WT/Corr-WT


title: ChIP-seq-H3K27me3_III-3-WT

description:
Isogenic line to III-3 to correct LMNA mutation
processed data file: H3K27_PT3WT.paired.PE2SE.nodup.tagAlign_x_Input_1_R1.paired.PE2SE.nodup.tagAlign.fc.signal.bw


title: CE-Ghs6-18

description:
Raw Data Technical Replicate 1: 52
Raw Data Technical Replicate 2: 53
Raw Data Technical Replicate 3: 54


title: p53WT_Untreated_996

description: wild-type

value: wild-type


title: ChIP-seq-H3K4me3_III-3-WT

description:
Isogenic line to III-3 to correct LMNA mutation
processed data file: H3K4_PT3WT.paired.PE2SE.nodup.tagAlign_x_Input_1_R1.paired.PE2SE.nodup.tagAlign.fc.signal.bw

value: H3K4me3 (Active Motif 39159)


title: ChIP-seq-H3K4me3_III-3-MT

description:
Parental line III-3
processed data file: H3K4_PT3MT.paired.PE2SE.nodup.tagAlign_x_Input_2_R1.paired.PE2SE.nodup.tagAlign.fc.signal.bw


title: ChIP-seq-abLMNA_III-3-MT

description:
Parental line III-3
processed data file: PT3MT_EDD_abLMNA_vs_Input_peaks.bed

value: Lamin A/C (Abcam ab8984)


title: ChIP-seq-abLMNA_III-3-WT

description:
Isogenic line to III-3 to correct LMNA mutation
processed data file: PT3WT_EDD_abLMNA_vs_Input_peaks.bed


title: p53WT_Untreated_1198

description: wild-type


title: CE-Ghs6-16

description:
Raw Data Technical Replicate 1: 46
Raw Data Technical Replicate 2: 47
Raw Data Technical Replicate 3: 48

value: 21 days of embryonic development


title: CE-Ghs6-17

description:
Raw Data Technical Replicate 1: 49
Raw Data Technical Replicate 2: 50
Raw Data Technical Replicate 3: 51

value: Leghorn


title: ChIP-seq-Input_III-3-MT

description: Parental line III-3


title: CE-Ghs6-20

description:
Raw Data Technical Replicate 1: 58
Raw Data Technical Replicate 2: 59
Raw Data Technical Replicate 3: 60

value: NDV


title: CE-Ghs6-15

description:
Raw Data Technical Replicate 1: 43
Raw Data Technical Replicate 2: 44
Raw Data Technical Replicate 3: 45


title: p53WT_Untreated_1178

description: wild-type


title: epididymal adipose_4

city: Singapore

first: Roger

last: Foo

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Paired-end reads were aligned to hg19 and mm9 genomes using Tophat2 (v2.2.0.12) with default parameters. Gene expression analysis was performed using Cufflinks2 (v2.2.1).
Genome_build: hg19 or mm9
Supplementary_files_format_and_content: bed file with chromosomal coordinates and count (5th column) of back-spliced junctions for circRNAs.

source_name: Tissue

extract_protocol:
Ribosome-depleted RNA from 3 biological replicates of human visceral (omental) and subcutaneous adipose, as well as mouse epididymal and inguinal adipose, was extracted using Trizol (Life Technologies) and purified using RNeasy kit (Qiagen).
Replicates from the same tissue type were pooled into one sample for library preparation (4 samples in total), processed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) and sequenced on the Illumina HiSeq2000 platform.

value: epididymal adipose


title: epididymal adipose_2


title: CE-Ghs6-14

description:
Raw Data Technical Replicate 1: 40
Raw Data Technical Replicate 2: 41
Raw Data Technical Replicate 3: 42

value: lung


title: epididymal adipose_1


title: ChIP-seq-Input_III-3-WT

description: Isogenic line to III-3 to correct LMNA mutation


title: ATAC-seq_III-3-MT, rep2

description:
Parental line III-3
ATAC-seq Replicate #2
processed data file: PT3MT_ATAC_USPD16084652_HJ35WBBXX_L8_1.trim.PE2SE.nodup.tn5_pooled.pf.fc.signal.bigwig

data_processing:
ATAC-seq reads were mapped to hg19 genome: bowtie 2
Following QC to remove duplicate reads, average read intensities were calculated: deepTools and R/Bioconductor (v.3.2.1).
Genome_build: human reference genome hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig

extract_protocol:
The samples were extracted as described in previous protocol (Buenrostro J et al. Nat Methods 10: 1213-1218).
ATAC-seq libraries were prepared for sequencing using TruSeq Library Prep Kit (Illumina).


title: inguinal adipose_4

value: inguina adipose


title: CE-Ghs6-13

description:
Raw Data Technical Replicate 1: 37
Raw Data Technical Replicate 2: 38
Raw Data Technical Replicate 3: 39


title: CE-Ghs6-12

description:
Raw Data Technical Replicate 1: 34
Raw Data Technical Replicate 2: 35
Raw Data Technical Replicate 3: 36


title: ATAC-seq_III-3-MT, rep1

description:
Parental line III-3
ATAC-seq Replicate #1
processed data file: PT3MT_ATAC_USPD16084652_HJ35WBBXX_L8_1.trim.PE2SE.nodup.tn5_pooled.pf.fc.signal.bigwig


title: epididymal adipose_3


title: ATAC-seq_III-3-WT, rep2

description:
Isogenic line to III-3 to correct LMNA mutation
ATAC-seq Replicate #2
processed data file: PT3WT_ATAC_USPD16084651_HJ35WBBXX_L8_1.trim.PE2SE.nodup.tn5_pooled.pf.fc.signal.bigwig


title: ATAC-seq_III-3-WT, rep1

description:
Isogenic line to III-3 to correct LMNA mutation
ATAC-seq Replicate #1
processed data file: PT3WT_ATAC_USPD16084651_HJ35WBBXX_L8_1.trim.PE2SE.nodup.tn5_pooled.pf.fc.signal.bigwig


title: CE-Ghs6-11

description:
Raw Data Technical Replicate 1: 31
Raw Data Technical Replicate 2: 32
Raw Data Technical Replicate 3: 33


title: inguinal adipose_3


title: CE-Ghs6-38

description:
Raw Data Technical Replicate 1: 112
Raw Data Technical Replicate 2: 113
Raw Data Technical Replicate 3: 114


title: CE-Ghs6-9

description:
Raw Data Technical Replicate 1: 25
Raw Data Technical Replicate 2: 26
Raw Data Technical Replicate 3: 27

value: Control


title: RNA-seq_IV-1-MT, rep2

description:
Isogenic line of IV-1 to insert LMNA mutation (heterozygous line)
RNA-seq Replicate #2

data_processing:
Base quality of raw reads: FastQC 0.11.4
Aligned the reads to the human reference genome (hg19): STAR 2.5.1b
Calculating fragments per kilobase per million aligned reads (FPKM): Cufflinks 2.2.1
Genome_build: human reference genome hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig

extract_protocol:
iPSC-CMs were detached from cell culture plates and RNA was extracted using a microRNeasy kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: iPSC-CMs

value: LMNAT WT/Ins-MT


title: CE-Ghs6-10

description:
Raw Data Technical Replicate 1: 28
Raw Data Technical Replicate 2: 29
Raw Data Technical Replicate 3: 30


title: CE-Ghs6-8

description:
Raw Data Technical Replicate 1: 22
Raw Data Technical Replicate 2: 23
Raw Data Technical Replicate 3: 24


title: RNA-seq_IV-1-WT, rep2

description:
Parental line IV-1
RNA-seq Replicate #2

value: day 40

value: LMNA WT/WT


title: CE-Ghs6-7

description:
Raw Data Technical Replicate 1: 19
Raw Data Technical Replicate 2: 20
Raw Data Technical Replicate 3: 21


title: HM450_VAT_E023_1

type: genomic

city: Darlinghurst

first: Stephen

last: Bradford

state: NSW

address: 384 Victoria St

country: Australia

institute: Garvan Institute of Medical Research

description: Visceral Adipose

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Briefly normalization was performed using the dasen method from wateRmelon {Pidsley, 2013 #515}. Some probes were excluded from the analysis. In particular these were, the union of probes on the sex chromosomes (n = 11,648), probes targeting CpGs located two or fewer nucleotides from a known single nucleotide polymorphism (SNP) with a minor allele frequency >0.05 (n = 29,476), and known cross-hybridizing probes (n = 30,969) published by Chen et al {Chen, 2013 #518}. Probes were also excluded if they failed quality control metrics in one or more samples, based on a detection P value >0.05.Probe M-values were used to detect differentially methylated probes via Limma {Ritchie, 2015 #460}.

label: Cy5 and Cy3

source_name: VAT

label_protocol: Standard Illumina Protocol

extract_protocol: SA and VA samples - In brief, freshly isolated VAT and SAT samples were weighed and minced with surgical scissors. For each gram of minced tissue, 1.25 mg/mL of Collagenase I (Sigma Aldrich, CAT#C6885-1G) was added to 2 mL of HEPES buffer containing 7.9 g/L NaCl, 323 mg/L CaCl2.2H2O, 308 mg/L MgSO4.7H2O, 154.3 mg/L Na2HPO4 (anhydrous), 5 mL/L of 1M Hepes (Sigma Aldrich), 450 mg/L D-glucose, pH 7.2 – 7.4, 20 g/L BSA. The tissue was incubated for 30-45 minutes at 37ºC before being diluted 1:9 with additional HEPES buffer. The mixture was passed through a 250 micron mesh before being centrifuged at 300 rcf for 6 minutes at room temperature. The top lipid layer was removed and the adipocytes collected for snap-freezing in liquid nitrogen.; VATsamples - Snap frozen in liquid Nirtogen; PBL - 10 mL blood was collected into K2EDTA vacutainers. Following centrifugation at 1,300 rcf for 10 minutes at room temperature, the top plasma layer was removed and the buffy coat layer collected. Cells were washed three times, with vigorous resuspension, in 10 mL Tris-EDTA buffer (100 mM Tris-HCl, 0.1 mM EDTA), with pellets collected after centrifugation at 10,000 rcf for 10 minutes. The final pellet was resuspended in 500 µL of buffer and stored at -80ºC. DNA was extracted: SAVA - using proteinase K digestion and phenol chloroform extraction; VAT - DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen, Cat#69504); PBL - DNA was extracted from PBL sample types following the Gentra Puregene Blood Cell Kit (Qiagen, Cat#158445).

tag: gender

value: Female

tag: tissue origin

value: Visceral Adipose


title: HM450_PBL_E013

description: Blood

source_name: PBL

value: Blood


title: HM450_VAT_E013

description: Visceral Adipose


title: day 6 rMEFs_small RNA-seq

city: Harbin

first: Xiaolei

address: No.59 Mucai street

institute: Northeast Agricultural University

description: Total small RNA

data_processing:
RNA-seq reads were aligned to the mouse genome (mm9) using HISAT2
small RNA-seq reads were aligned to miRBase
Expression levels were obtained using CuffLinks
Genome_build: mm9
Supplementary_files_format_and_content: csv file include FPKM values for each RNA-seq sample; xls file include counts for each small RNA-seq sample

source_name: reprogramming MEFs at day 6 post-OSKM induction

growth_protocol: For iPSCs reprogramming, MEFs from tetO-OSKM mouse within two passages were split when they reached 80–90 % confluence, placed at 5 000 cells/cm2. 2 ug/ml doxycycline was added to induce over-expression of OSKM. Reprogramming was performed in KSR medium (DMEM/F12 (Gibco) supplemented with 15 % Knockout Serum Replacement (Gibco), 2 mM L-glutamine (Gibco), 1 × Pen/Strep (Gibco) 100 uM MEM non-essential amino acids (Gibco), 100 uM b-mercaptoethanol (Gibco), and 1000 U/mL LIF (ESGRO, Millipore), 3 uM CHIR99021 (Stemgent) and 0.5 × N-2 Supplement (Gibco).

extract_protocol:
Total RNA was isolated from the cells at day 0, day 3 and day 6 post-OSKM induction and the fully reprogrammed iPSCs using Trizol RNA extraction reagent (ThermoFisher), following the manufacturer’s protocol. The concentration and purity of total RNA were assessed on Nanodrop 2000 (ThermoFisher Scientific, MA, USA), and the integrity of total RNA was evaluated with 2 % agarose gel electrophoresis and RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
The cDNA libraries of long chain RNAs (mRNA/lncRNA/circRNA) and small RNAs were generated from 10 μg and 2 μg of total RNA, respectively. rRNA was removed using Epicentre Ribo-zero rRNA Kit (Epicentre, USA). Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) and NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (#E7300L, NEB, USA), respectively.


title: HM450_VA_E027

description: Visceral Adipose

source_name: VA

value: Male


title: HM450_PBL_E018

description: Blood


title: HM450_PBL_E017

description: Blood


title: inguinal adipose_2


title: inguinal adipose_1


title: iPSCs_small RNA-seq

description: Total small RNA

source_name: fully reprogrammed iPSCs from MEFs


title: CE-Ghs6-5

description:
Raw Data Technical Replicate 1: 13
Raw Data Technical Replicate 2: 14
Raw Data Technical Replicate 3: 15

source_name: Control


title: HM450_VA_E017

description: Visceral Adipose


title: HM450_PBL_E023_1

description: Blood


title: HM450_PBL_E027

description: Blood


title: HM450_PBL_E023_2

description: Blood


title: HM450_VAT_E018

description: Visceral Adipose


title: HM450_VA_E018

description: Visceral Adipose


title: iPSCs_RNA-seq

description: Total RNA


title: HM450_VA_E023_1

description: Visceral Adipose


title: RNA-seq_IV-1-WT, rep1

description:
Parental line IV-1
RNA-seq Replicate #1


title: RNA-seq_III-3-WT, rep2

description:
Isogenic line to III-3 to correct LMNA mutation
RNA-seq Replicate #2

value: LMNA WT/Corr-WT


title: CE-Ghs6-6

description:
Raw Data Technical Replicate 1: 16
Raw Data Technical Replicate 2: 17
Raw Data Technical Replicate 3: 18


title: HM450_SA_E017

description: Subcutaneous Adipose

source_name: SA

value: Subcutaneous Adipose


title: HM450_VA_E023_2

description: Visceral Adipose


title: day 6 rMEFs_RNA-seq

description: Total RNA


title: RNA-seq_III-3-MT, rep2

description:
Parental line III-3
RNA-seq Replicate #2

value: LMNA WT/MT


title: RNA-seq_III-3-MT, rep1

description:
Parental line III-3
RNA-seq Replicate #1


title: day 3 rMEFs_small RNA-seq

description: Total small RNA

source_name: reprogramming MEFs at day 3 post-OSKM induction


title: CE-Ghs6-2

description:
Raw Data Technical Replicate 1: 4
Raw Data Technical Replicate 2: 5
Raw Data Technical Replicate 3: 6

value: 21 days of embryonic development

value: Leghorn


title: SH881_rep1

city: Shanghai

first: Faming

last: Chen

address: 320 Yue Yang Road

department: CAS-MPG Partner Institute for Computational Biology

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: strand-specific RNA sequencing

data_processing:
Read quality was checked using FastQC.
Raw sequencing reads were trimmed by quality using Trimmomatic.
Cleaned reads were mapped to the Os-Nipponbare-Reference-IRGSP-1.0 using STAR 2.5.3a with "--quantMode GeneCounts" option to report the read counts per gene.
Differentially expressed genes were determined using EBSeq with read counts as input.
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary_files_format_and_content: tab-delimited text files include read counts per gene for each Sample

organism: Oryza sativa

source_name: leaf blades of 40 d seedling

extract_protocol:
Total RNA was extracted from the fresh leaf blades of 40 d seedlings using TRIzol reagent (Invitrogen, USA).
RNA libraries were prepared following the strand-specific RNA-seq protocol of MGISEQ-2000 platform.

tag: rice line

value: recurrent parent SH881


title: D248_rep1

description: strand-specific RNA sequencing

value: early-maturing NIL D248


title: SH881_rep2

description: strand-specific RNA sequencing


title: D248_rep2

description: strand-specific RNA sequencing


title: CE-Ghs6-4

description:
Raw Data Technical Replicate 1: 10
Raw Data Technical Replicate 2: 11
Raw Data Technical Replicate 3: 12

tag: developmental stage

value: lung


title: MEFs_small RNA-seq

description: Total small RNA

source_name: embryonic fibroblasts from 13.5D fetal mice


title: day 3 rMEFs_RNA-seq

description: Total RNA


title: HM450_SA_E023_2

description: Subcutaneous Adipose


title: HM450_VA_E013

description: Visceral Adipose


title: RNA-seq_III-3-WT, rep1

description:
Isogenic line to III-3 to correct LMNA mutation
RNA-seq Replicate #1


title: HM450_SA_E018

description: Subcutaneous Adipose


title: HM450_SA_E023_1

description: Subcutaneous Adipose


title: HM450_SA_E027

description: Subcutaneous Adipose


title: Cfp1 KO_H3K4me3

status: Public on Jul 02 2019

city: Seoul

first: Chanhyeok

last: Park

address: 5, Hwarang-ro 14-gil

department: Brain Science Institute

country: South Korea

institute: KIST (Korea Institute of Science and Technology)

data_processing:
ChIP-seq raw reads were aligned to mouse mm9 genome using Bowtie2 (v2.2.9).
SAMtools (v1.2) was used for the data arrangement.
ChIP-seq peaks were called using the following MACS2 (v2.1.0) parameters: -B --nomodel -f BAM -g mm -p 1e-5.
Genome_build: mm9
Supplementary_files_format_and_content: The bedGraph files were generated using MACS2

source_name: Spermatocyte

growth_protocol: Primary mouse spermatocytes derived from C57BL/6 were were grown in culture medium (DMEM, high glucose supplemented with Penicillin/Streptomycin. MEM0NEAA, β-mercaptoethanol, 10% FBS) on 0.2% gelatin-coated culture dish. Cells were maintained in a humidified incubator equilibrated with 5% CO2 at 37°C.

extract_protocol:
testes were harvested from anesthetized C57BL/6 mice and mechanically dissociated. Seminiferous tubules were removed, minced, and incubated Krebs-Ringer bicarbonate media (EKRB) containing 0.5mg/ml collagenase at 33°C for 1 hour. After removal of extra non-germ cells, dissociated seminiferous tubules were further digested with EKRB containing 0.5mg/ml trypsin and 1µg/ml DNase I at 33°C for 15 min. After washing and centrifugation, cell pellets were resuspended in EKRB containing 1µg/ml DNase I and 0.5% (w/v) BSA. After centrifugation, cells were resuspended in EKRB/0.5% BSA and passed through a cell strainer. Spermatocytes were then isolated using a method of sedimentation velocity at unit gravity at 5°C. Cells suspended in EKRB/0.5% BSA were loaded onto a sedimentation chamber and flow was applied (10ml/min).
ChIP-Seq libraries were produced using Truseq ChIP Sample kit (Illumina) according to manufacturer’s instruction.

treatment_protocol: Testes were harvested from anesthetized C57BL/6 mice and tunica albuginea were removed. Seminiferous tubules were removed using Collagenase, DNaseI, Soybean trypsin inhibitor mixture at 37°C for 15min. After centrifugation, cells were resuspended in Collagenase, DNaseI, Soybean trypsin inhibitor and Hyaluronidase mixture and incubated at 37°C for 10min. After centrifugation, cells were maintained in culture medium in a humidified incubator equilibrated with 5% CO2 at 37°C overnight. Suspension cells were haversted and washed using PBS.

value: Spermatocyte

tag: passages

value: Primary cell(p1)

tag: chip antibody

value: H3K4me3 antibodies(39159, Active Motif, Lot#:12613005)


title: CE-Ghs6-1

description:
Raw Data Technical Replicate 1: 1
Raw Data Technical Replicate 2: 2
Raw Data Technical Replicate 3: 3

tag: breed

tag: subline

tag: infection

value: Control


title: MEFs_RNA-seq

description: Total RNA


title: SC_Input (H3K4me3)

tag: cell type


title: CE-Ghs6-3

description:
Raw Data Technical Replicate 1: 7
Raw Data Technical Replicate 2: 8
Raw Data Technical Replicate 3: 9


title: SC_H3K4me3


title: Cfp1 KO_Input (H3K4me3)


title: Multichamber Study

city: Baltimore

first: Suraj

last: Kannan

state: MD

address: 720 Rutland Avenue Ross 954

institute: Johns Hopkins University

description:
Cardiomyocytes isolated from each chamber of adult heart.
PolyA RNA
Single Cell RNA-seq

data_processing:
For the RNA-seq data generated in this manuscript, we mapped raw reads to the mouse genome GRCm38 from Ensembl concatenated with ERCC spike-in references. We mapped reads using zUMIs 2.2.35 with default settings and barcodes provided as a list. By default, zUMIs uses STAR (2.5.4b) in a two-pass mapping format, and featureCounts through Rsubread (1.28.1) to tabulate counts and UMI tables.
Genome_build: GRCm38_r92
Supplementary_files_format_and_content: *.csv: For each study, we provide both the 3’ reads as well as the collapsed UMIs (output from zUMIs). In addition, we provide a metadata table for each cell. All cells (including those that we subsequently filtered for our analysis) are included here, enabling other users to perform their own desired filtering.
Supplementary_files_format_and_content: multistudy_comparison.RData: We provide an R workspace containing all of the objects necessary to perform our multistudy analysis included in the manuscript.

source_name: Adult Cardiomyocytes

extract_protocol:
Langendorff perfusion was performed based on established literature protocols using collagenase and protease. We used a horizontal (i.e. non-hanging) Langendorff apparatus with a chamber filled with perfusion buffer. To perform isolation, we first performed isofluorane anaesthesia on non-heparinized mice. Mice were observed until clearly anaesthetized and unresponsive to toe pinch, and subsequently euthanized by cervical dislocation. The heart was then rapidly excised from the chest and cannulated to the Langendorff apparatus. We flowed digestion buffer for 9 minutes at 1.5 mL/min. Subsequently, the ventricle was excised and minced. We filtered isolated cells through a 100 µM screen to eliminate large tissue chunks, spun down at 800 RPM for 1 minute (Eppendorf centrifuge 5702), and resuspended cells in 10 mL Tyrode’s buffer.
We performed scRNA-seq using the established SCRB-seq protocol. Cells were sorted into 96-well plates composed of RNase-free water plus 1:500 Phusion HF Buffer (New England Biolabs) and 1:250 RNaseOUT RNase inhibitor(Life Technologies). Plates were placed on dry ice immediately after sorting and stored at -80C until ready for sequencing. For preparing sequencing libraries, we performed proteinase K treatment followed by RNA desiccation to reduce the reaction volume (50C for 15 minutes with plate seal on, followed by 95C for 10 minutes with plate seal removed). RNA was subsequently reverse transcribed using a custom template-switching primer as well as a barcoded adapter primer (see below). The customized SCRB-seq barcode primers contain a unique 6 base pair cell-specific barcode as well as a 10 base pair unique molecular identifier (UMI). Transcribed products were pooled and concentrated, with unincorporated barcode primers subsequently digested using Exonuclease I treatment (37C for 30 minutes, followed by 80C for 20 minutes to inactivate the enzyme). cDNA was PCR-amplified using Terra PCR Direct Polymerase (Takara Bio), performing 17 cycles of amplification. Final libraries were prepared using 1ng of cDNA per library with the Nextera XT kit (Illumina) using a custom P5 primer as previously described. Pooled libraries were sequenced on two high-output lanes of the Illumina NextSeq500 with 16 base pair barcode read (barcode + UMI) and 8 base pair i7 index read, and 66-92 base pair cDNA read design. The live/fixed study, which was performed first, utilized a 66 base pair read, which was sufficient for gene expression analysis and comparisons. However, we observed that with shorter read lengths, we obtained large counts of pseudogenes, many of which had significant sequence homology with mitochondrial genes. This likely implied mismapping due to short read length. Thus, for further studies (including the multi-chamber study presenting in the manuscript), we used the longer read length of 92 base pairs, which we found completely eliminated mapping to pseudogenes.

tag: strain/background

value: Wild type

value: Cardiomyocyte

tag: heart chambers

value: Multiple

tag: age

value: Adult

tag: ethanol fixation


title: Live/Fixed Study

description:
Ventricular cardiomyocytes isolated either before or after ethanol fixation.
PolyA RNA
Single Cell RNA-seq

treatment_protocol: For ethanol fixation, we used the following protocol: we first pelleted isolated CMs and resuspended in 200 µL of cold phosphate buffered saline (PBS). We then added 800 µL of -20C 100% ethanol drop by drop with gentle stirring to prevent clumping of cells. We performed experiments shortly after fixation, though we found that we could store cells up to two weeks at -20C without observing significant degradation of cell structure.

tag: genotype/variation

value: Ventricles

value: pre- and post-fixation


title: Mdb pilot 2

city: Pamplona

first: Marisol

last: Aymerich

state: Navarra

address: CIMA Universidad de Navarra, Avda. Pío XII, 55

country: Spain

institute: University of Navarra

data_processing:
Verification of sample quality with FastQC software
Alignment of reads to the mouse genome (GRCm38) with STAR 2.5.3a (Dobin et al, 2013)
Gene expression quantification using read counts of exonic gene regions with featureCounts v1.6.0(Liao et al, 2014)
Gene annotation reference with Gencode M17 (Harrow et al, 2012)
Statistical analysis of differential expression with R/Bioconductor (Gentleman et al, 2004)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw count values summarized by "featureCounts v1.6.0" for each gene

source_name: Acute isolated microglial cells

growth_protocol: Normal animal housing conditions

extract_protocol:
Animals were transcardialy perfussed with ice-cold PBS 1X and brains were rapidly dissected. Tissue was incubated with 2 mg/mL of papain (Worthington) and then filtered through 70 um cell strainer. Then samples were centrifuged at 300g for 15 min and pellets were resuspended in 25% Percoll in PBS. Samples were centrifuged for 10 min at 1000g. Microglial cells were sorted using CD11b MicroBeads (Miltenyi Biotec) using the AutoMACS Pro Separator (Miltenyi) following manufacturer's instructions. CD11b+ cells were resuspended in Lysis buffer from the Dynabeads mRNA Purification Kit (Ambion). PolyA RNA was extracted using Dynabeads mRNA Purification Kit (Ambion) following manufacturer's intructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Untreated

tag: strain

value: 3 months


title: Str pilot 1


title: Mdb pilot 1


title: Str 1


title: Str pilot 2


title: Str 3


title: Str 2


title: Mdb 1


title: Mdb 3


title: Mdb 2


title: Wild-type, replicate 3, Ly6C Low macrophages on Day 4 after muscle injury.

city: Debrecen

first: Halasz

last: Laszlo

address: Egyetem tér 1

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

data_processing:
Raw ATAC-seq sequencing reads were aligned to the mouse reference genome (mm10) with BWA using default parameters.
Reads with mapping quality less then 10 (MAPQ<10) and duplicated reads are discarded. Furthermore, reads falling into blacklisted regions are also discarded.
To minimize technical variablity across samples we performed upper-quartile normalization using custom scripts. For this, we first generated read number normalized bedgraph files with HOMER and calculated the read distributions for the distal consensus (promoter associated peaks are not considered) ATAC-seq summits.
For each sample, we calculated the top 10% value and divided all values with this normalization factor.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files (bedgraph) contains the upper-quartile (UQ) normalized coverage of the samples.

extract_protocol:
Fascia of the injured TA muscle was removed. Muscles were dissociated in RPMI containing 0.2% collagenase B (Roche Diagnostics GmbH) at 37°C for 1 hour and filtered through a 100 µm and a 40 µm filter. CD45+ cells were isolated using magnetic sorting (Miltenyi Biotec). For FACS, macrophages were treated with Fcγ receptor blocking antibodies and with 10% normal rat serum: normal mouse serum 1:1 mix, then stained with a combination of PE-conjugated anti-Ly6C antibody (HK1.4, eBioscience), APC-conjugated F4/80 antibody (BM8, eBioscience) and FITC-conjugated Ly6G antibody (1A8, Biolegend). Ly6Chigh F4/80low macrophages, Ly6Clow F4/80high macrophages and Ly6Ghigh Ly6Cmed F4/80- neutrophils were quantified. In each experiment, compared samples were processed in parallel to minimize experimental variation. Cells were analyzed on a BD FACSAria III sorter and data analysis was performed using BD FACSDIVA and FlowJo V10 software.
ATAC-seq was carried out as described earlier with minor modification (Buenrostro J.D. et al. 2013). 20 000 cells were sorted in ice-cold PBS. Nuclei were isolated with ATAC-Lysis Buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL) and were used for tagmentation using Nextera DNA Library Preparation Kit (Illumina) from 2-3 biological replicates. After tagmentation DNA was purified with MinElute PCR Purification Kit (Qiagen). Tagmented DNA was amplified with Kapa Hifi Hot Start Kit (Kapa Biosystems) using 9 PCR cycles. Amplified libraries were purified again with MinElute PCR Purification Kit. Fragment distribution of libraries was assessed with Agilent Bioanalyzer and libraries were sequenced on a HiSeq 2500 platform.

value: Muscle infiltrating macrophages

tag: time

value: Day 4 after muscle injury


title: Wild-type, replicate 2, Ly6C Low macrophages on Day 4 after muscle injury.


title: HM450_SA_E013

description: Subcutaneous Adipose

tag: gender

value: Female

value: Subcutaneous Adipose


title: Wild-type, replicate 1, Ly6C Low macrophages on Day 4 after muscle injury.


title: Wild-type, replicate 1, Ly6C Low macrophages on Day 2 after muscle injury.

value: Day 2 after muscle injury


title: Wild-type, replicate 2, Ly6C High macrophages on Day 4 after muscle injury.


title: Wild-type, replicate 2, Ly6C Low macrophages on Day 2 after muscle injury.


title: Wild-type, replicate 1, Ly6C High macrophages on Day 4 after muscle injury.


title: Wild-type, replicate 2, Ly6C High macrophages on Day 1 after muscle injury.

value: Day 1 after muscle injury


title: Wild-type, replicate 2, Ly6C High macrophages on Day 2 after muscle injury.


title: Wild-type, replicate 1, Ly6C High macrophages on Day 1 after muscle injury.


title: NEO51 [Patient_51_T4]

city: Carrington Crescent

first: Andrew

middle: H

last: Sims

state: Edinburgh

address: Systems Medicine Building

department: Institute of Genetics and Molecular Medicine

institute: University of Edinburgh

description:
Patient_51_T4
processed data file: Processed_data.txt

data_processing:
All pre-processing was accomplished in fastQC for base calling, alignment, and quality control of the FASTQ files.
Expression analysis of the resultant relative expression matrix was carried out in R using limma, DEseq and edgeR packages.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Processed_data.txt: Tab-delimited text file includes raw read counts.

source_name: Breast Tissue

extract_protocol:
RNA extraction was performed via Ribo0-RNAseq performed with Life Sciences Ion AmpliSeq™ Transcriptome Human Gene Expression Kit.
Libraries were constructed according to the Ion AmpliSeq Library Kit 2.0 instructions.

tag: patient identifier

tag: tissue

value: Breast

tag: grade

tag: histology

value: NST

value: Negative

tag: t

tag: n

tag: m

value: MX

tag: biopsy time


title: NEO8 [Patient_8_T2]

description:
Patient_8_T2
processed data file: Processed_data.txt

value: Ductal NST with basal phenotype


title: NEO8 [Patient_8_T1]

description:
Patient_8_T1
processed data file: Processed_data.txt


title: NEO8 [Patient_8_T4]

description:
Patient_8_T4
processed data file: Processed_data.txt


title: NEO51 [Patient_51_T3]

description:
Patient_51_T3
processed data file: Processed_data.txt


title: NEO51 [Patient_51_T1]

description:
Patient_51_T1
processed data file: Processed_data.txt


title: NEO50 [Patient_50_T3]

description:
Patient_50_T3
processed data file: Processed_data.txt


title: NEO50 [Patient_50_T1]

description:
Patient_50_T1
processed data file: Processed_data.txt


title: NEO5 [Patient_5_T2]

description:
Patient_5_T2
processed data file: Processed_data.txt

value: PCR


title: NEO49 [Patient_49_T4]

description:
Patient_49_T4
processed data file: Processed_data.txt

value: NST with basal phenotype


title: NEO49 [Patient_49_T1]

description:
Patient_49_T1
processed data file: Processed_data.txt


title: NEO49 [Patient_49_T3]

description:
Patient_49_T3
processed data file: Processed_data.txt


title: NEO48 [Patient_48_T3]

description:
Patient_48_T3
processed data file: Processed_data.txt

value: Pleomorphic Lobular

value: Positive


title: NEO48 [Patient_48_T4]

description:
Patient_48_T4
processed data file: Processed_data.txt


title: NEO48 [Patient_48_T1]

description:
Patient_48_T1
processed data file: Processed_data.txt


title: NEO47 [Patient_47_T3]

description:
Patient_47_T3
processed data file: Processed_data.txt

value: Apocrine


title: NEO47 [Patient_47_T1]

description:
Patient_47_T1
processed data file: Processed_data.txt


title: NEO46 [Patient_46_T4]

description:
Patient_46_T4
processed data file: Processed_data.txt


title: NEO47 [Patient_47_T4]

description:
Patient_47_T4
processed data file: Processed_data.txt


title: NEO46 [Patient_46_T1]

description:
Patient_46_T1
processed data file: Processed_data.txt


title: NEO5 [Patient_5_T1]

description:
Patient_5_T1
processed data file: Processed_data.txt


title: NEO45 [Patient_45_T1]

description:
Patient_45_T1
processed data file: Processed_data.txt


title: NEO43 [Patient_43_T4]

description:
Patient_43_T4
processed data file: Processed_data.txt

value: Lobular


title: NEO43 [Patient_43_T3]

description:
Patient_43_T3
processed data file: Processed_data.txt


title: NEO43 [Patient_43_T1]

description:
Patient_43_T1
processed data file: Processed_data.txt


title: NEO42 [Patient_42_T1]

description:
Patient_42_T1
processed data file: Processed_data.txt


title: NEO45 [Patient_45_T4]

description:
Patient_45_T4
processed data file: Processed_data.txt


title: NEO46 [Patient_46_T3]

description:
Patient_46_T3
processed data file: Processed_data.txt


title: NEO39 [Patient_39_T1]

description:
Patient_39_T1
processed data file: Processed_data.txt


title: NEO36 [Patient_36_T3]

description:
Patient_36_T3
processed data file: Processed_data.txt

value: TX


title: NEO36 [Patient_36_T1]

description:
Patient_36_T1
processed data file: Processed_data.txt


title: NEO34 [Patient_34_T4]

description:
Patient_34_T4
processed data file: Processed_data.txt


title: NEO42 [Patient_42_T4]

description:
Patient_42_T4
processed data file: Processed_data.txt


title: NEO34 [Patient_34_T1]

description:
Patient_34_T1
processed data file: Processed_data.txt


title: NEO33 [Patient_33_T4]

description:
Patient_33_T4
processed data file: Processed_data.txt


title: NEO34 [Patient_34_T3]

description:
Patient_34_T3
processed data file: Processed_data.txt


title: NEO39 [Patient_39_T4]

description:
Patient_39_T4
processed data file: Processed_data.txt


title: NEO30 [Patient_30_T3]

description:
Patient_30_T3
processed data file: Processed_data.txt


title: NEO30 [Patient_30_T1]

description:
Patient_30_T1
processed data file: Processed_data.txt


title: NEO33 [Patient_33_T1]

description:
Patient_33_T1
processed data file: Processed_data.txt


title: NEO3 [Patient_3_T3]

description:
Patient_3_T3
processed data file: Processed_data.txt


title: NEO3 [Patient_3_T1]

description:
Patient_3_T1
processed data file: Processed_data.txt


title: NEO3 [Patient_3_T4]

description:
Patient_3_T4
processed data file: Processed_data.txt


title: NEO33 [Patient_33_T3]

description:
Patient_33_T3
processed data file: Processed_data.txt


title: NEO45 [Patient_45_T3]

description:
Patient_45_T3
processed data file: Processed_data.txt


title: NEO27 [Patient_27_T1]

description:
Patient_27_T1
processed data file: Processed_data.txt


title: NEO29 [Patient_29_T1]

description:
Patient_29_T1
processed data file: Processed_data.txt


title: NEO29 [Patient_29_T3]

description:
Patient_29_T3
processed data file: Processed_data.txt


title: NEO26 [Patient_26_T3]

description:
Patient_26_T3
processed data file: Processed_data.txt

value: Tis


title: NEO26 [Patient_26_T1]

description:
Patient_26_T1
processed data file: Processed_data.txt


title: NEO27 [Patient_27_T4]

description:
Patient_27_T4
processed data file: Processed_data.txt


title: NEO26 [Patient_26_T4]

description:
Patient_26_T4
processed data file: Processed_data.txt


title: NEO24 [Patient_24_T4]

description:
Patient_24_T4
processed data file: Processed_data.txt


title: NEO23 [Patient_23_T3]

description:
Patient_23_T3
processed data file: Processed_data.txt


title: NEO24 [Patient_24_T1]

description:
Patient_24_T1
processed data file: Processed_data.txt


title: NEO22 [Patient_22_T4]

description:
Patient_22_T4
processed data file: Processed_data.txt


title: RNA-seq_IV-1-MT, rep1

description:
Isogenic line of IV-1 to insert LMNA mutation (heterozygous line)
RNA-seq Replicate #1

source_name: iPSC-CMs

tag: cell type

value: iPSC-CMs

tag: day post-differentiation

value: day 40

value: LMNAT WT/Ins-MT


title: NEO22 [Patient_22_T3]

description:
Patient_22_T3
processed data file: Processed_data.txt


title: NEO23 [Patient_23_T1]

description:
Patient_23_T1
processed data file: Processed_data.txt


title: NEO22 [Patient_22_T2]

description:
Patient_22_T2
processed data file: Processed_data.txt


title: NEO23 [Patient_23_T2]

description:
Patient_23_T2
processed data file: Processed_data.txt


title: NEO22 [Patient_22_T1]

description:
Patient_22_T1
processed data file: Processed_data.txt


title: NEO21 [Patient_21_T4]

description:
Patient_21_T4
processed data file: Processed_data.txt


title: NEO21 [Patient_21_T2]

description:
Patient_21_T2
processed data file: Processed_data.txt


title: NEO21 [Patient_21_T3]

description:
Patient_21_T3
processed data file: Processed_data.txt


title: NEO27 [Patient_27_T3]

description:
Patient_27_T3
processed data file: Processed_data.txt


title: NEO21 [Patient_21_T1]

description:
Patient_21_T1
processed data file: Processed_data.txt


title: NEO20 [Patient_20_T1]

description:
Patient_20_T1
processed data file: Processed_data.txt


title: NEO19 [Patient_19_T1]

description:
Patient_19_T1
processed data file: Processed_data.txt


title: NEO19 [Patient_19_T4]

description:
Patient_19_T4
processed data file: Processed_data.txt


title: NEO18 [Patient_18_T2]

description:
Patient_18_T2
processed data file: Processed_data.txt

value: Ductal NST


title: NEO17 [Patient_17_T4]

description:
Patient_17_T4
processed data file: Processed_data.txt

value: Breast


title: NEO17 [Patient_17_T3]

description:
Patient_17_T3
processed data file: Processed_data.txt

value: NST


title: NEO16 [Patient_16_T2]

description:
Patient_16_T2
processed data file: Processed_data.txt

value: Negative


title: NEO17 [Patient_17_T1]

description:
Patient_17_T1
processed data file: Processed_data.txt

value: MX


title: NEO17 [Patient_17_T2]

description:
Patient_17_T2
processed data file: Processed_data.txt


title: NEO16 [Patient_16_T1]

description:
Patient_16_T1
processed data file: Processed_data.txt


title: NEO15 [Patient_15_T4]

description:
Patient_15_T4
processed data file: Processed_data.txt


title: NEO18 [Patient_18_T4]

description:
Patient_18_T4
processed data file: Processed_data.txt


title: NEO15 [Patient_15_T1]

description:
Patient_15_T1
processed data file: Processed_data.txt


title: NEO15 [Patient_15_T3]

description:
Patient_15_T3
processed data file: Processed_data.txt


title: NEO15 [Patient_15_T2]

description:
Patient_15_T2
processed data file: Processed_data.txt


title: NEO14 [Patient_14_T1]

description:
Patient_14_T1
processed data file: Processed_data.txt


title: NEO14 [Patient_14_T2]

description:
Patient_14_T2
processed data file: Processed_data.txt


title: NEO13 [Patient_13_T1]

description:
Patient_13_T1
processed data file: Processed_data.txt


title: NEO12 [Patient_12_T4]

description:
Patient_12_T4
processed data file: Processed_data.txt


title: NEO11 [Patient_11_T4]

description:
Patient_11_T4
processed data file: Processed_data.txt

value: Ductal NST with basal phenotype


title: NEO11 [Patient_11_T1]

description:
Patient_11_T1
processed data file: Processed_data.txt


title: NEO11 [Patient_11_T3]

description:
Patient_11_T3
processed data file: Processed_data.txt


title: NEO18 [Patient_18_T1]

description:
Patient_18_T1
processed data file: Processed_data.txt


title: NEO16 [Patient_16_T4]

description:
Patient_16_T4
processed data file: Processed_data.txt


title: postOSKM shSETD2-3 rep2

city: Istanbul

last: Onder

address: Rumelifeneri Yolu Sariyer

department: School of Medicine

country: Turkey

institute: Koc University

data_processing:
a soft adapter trimming was applied to low quality ends of all samples with using cutadapt with - -quality-cutoff=5. The trimmed fastqs were aligned to human genome GRCh37.75 using TopHat2 with default parameters only adding --library-type=fr-unstranded --num-threads=8 –no-mixed –no-coverage-search. Tophat-recondition is used to restore correct and restore unmapped reads with default parameters. Samtools is used to merge the two BAM files.
Raw read counts are generated using feautureCounts with -s 0 parameter.
Genome_build: GRCh37.75
Supplementary_files_format_and_content: Tab delimeted text files with raw counts for all samples.

source_name: Fibroblast cells

growth_protocol: dH1f cells were seeded to 6 well tissue culture plates with DMEM supplemented with 10% FBS and 1% pen/Strep at 100.000 cell/well density and incubated for 24 hr until cells were fully attached.

extract_protocol:
High quality total RNA was extracted from samples using Directzol RNA miniprep Kit (Zymogen R2050) and eluted in RNAse free water.
Library preparation was performed at Udo Opperman's Laboratory in Botnar Research Centre (UK). Library preparation was performed with  NEBNext Ultra RNA library prep kit for Illumina (NEB E7770). Libraries were sequenced on NexSeq 500 platform (Illumina)  with paired-end run of 2x75 reads. Fastqs were aligned using TopHat2 with default options. Differentially expressed genes between shCntrl and shSETD2 samples were  quantified using DESeq2 tool. To determine statistically significant differences in gene sets among control and SETD2 knock-down samples,  Gene Set Enrichment Analysis (GSEA) was performed with GSEA software using Molecular Signature Database (MSigDB).

treatment_protocol: preOSKM cells were infected with shRNAs targeting SETD2 for 2 times and puromycin selected. postOSKM cells were prepared from preOSKM cells and infected with OSKM overexpression viruses and cells were collected 6 days postOSKM infection.

tag: passages

tag: genotype

value: wild type


title: postOSKM shSETD2-3 rep1


title: postOSKM shSETD2-1 rep1


title: postOSKM shCntrl rep2


title: postOSKM shSETD2-1 rep3


title: postOSKM shSETD2-1 rep2


title: postOSKM shSETD2-3 rep3


title: preOSKM shSETD2-3 rep3


title: postOSKM shCntrl rep3


title: preOSKM shSETD2-3 rep1


title: preOSKM shSETD2-1 rep1


title: preOSKM shSETD2-1 rep3


title: postOSKM shCntrl rep1


title: preOSKM shCntrl rep3


title: NEO13 [Patient_13_T3]

description:
Patient_13_T3
processed data file: Processed_data.txt


title: preOSKM shCntrl rep2


title: NEO12 [Patient_12_T1]

description:
Patient_12_T1
processed data file: Processed_data.txt


title: HFF, Myr1_2

first: Adit

last: Naor

address: 300 Pasteur Drive Stanford, D305 Fairchild Building

institute: Stanford

data_processing:
Illumina Nextseq 500 model instrument was used for sequencing, Sequenced reads were trimmed for adaptor sequence.
Raw reads were uploaded onto the CLC Genomics Workbench 8.0 (Qiagen) platform for independent alignments against the human genomes (Ensembl.org/ hg19) and Toxoplasma Type I GT1 strain (ToxoDB-24, GT1 genome)
Supplementary_files_format_and_content: tab-delimited text files include number of reads value for each Sample

source_name: Human foreskin fibroblast - tissue culture

growth_protocol: HFFs were serum-starved for 24 hours before infection by growth in DMEM containing 0.5% serum. They were then infected with the indicated line of tachyzoites at an MOI of 5, for  6hours. Multiplex sequencing libraries were generated with RNA Sample Prep Kit (Illumina) according to manufacturer’s instructions and pooled for a single high-throughput sequencing run using the Illumina NextSeq platform (Illumina Nextseq 500 model instrument)at thethe Stanford University Functional Genomic Facility (SFGF).

extract_protocol:
1 ml TRIzol reagent (Invitrogen) was added to each T25 and the cells were scraped. Lysates were collected into RNAse/DNAse-free Eppendorf tubes and frozen at −20 °C. Total RNA was extracted following the manufacturer’s instructions, with some modifications. Briefly: frozen samples were thawed on ice and 0.2 ml chloroform was added to TRIzol suspensions, which were then mixed by inverting 10 times, and incubated for 5 minute. Tubes were then spun at 12,000 rpm for 15 min at 4 °C. RNA in the aqueous phase was transferred into a fresh tube and 0.5 ml absolute isopropyl alcohol was added. Each tube was inverted three times and incubated at 4°C for 10 min. They were then spun at 12,000 rpm for 20 min at 4 °C. After decanting the supernatants, RNA pellets were washed with 1 ml 75% ethanol. Tubes were mixed by inverting 10 times and then spun at 12,000 rpm for 20 min at 4°C. Supernatants were removed and the RNA pellets were air-dried in open tubes for approximately 10 min. The RNA pellets were resuspended in 30 μl RNase-free DEPC-water.
Multiplex sequencing libraries were generated with RNA Sample Prep Kit (Illumina) according to manufacturer’s instructions and pooled for a single high-throughput sequencing run using the Illumina NextSeq platform (Illumina Nextseq 500 model instrument) at the Stanford University Functional Genomic Facility (SFGF).

value: foreskin fibroblast

tag: infection

value: Infected with RH∆myr1 Toxoplasma parasites

value: 6 hours post infection


title: HFF, Myr1_1


title: HFF, rop17_1

value: Infected with RH∆rop17 Toxoplasma parasites


title: HFF, rop17_2


title: HFF, RH_2

value: Infected with RH Toxoplasma parasites


title: NEO11 [Patient_11_T2]

description:
Patient_11_T2
processed data file: Processed_data.txt


title: HFF, Mock_1

value: Human foreskin fibroblast (HFF)

value: Mock-infected


title: HFF, Mock_2


title: KK cell line RNA-seq replicate 3

city: St. Petersburg

first: Alexander

last: Kanapin

address: 7/9 University Emb.

department: Institute for Translational Biomedicine

country: Russia

institute: St Petersburg Universoty

data_processing:
FASTQ files were trimmed to remove adaptors and low-quality bases with TrimGalore v0.4.3
Trimmed reads were aligned to the human reference genome (build hg19) with STAR aligner v2.5.1 with two mismatches allowed
Differential gene expression analysis was done with DESeq2 R Bioconductor package v1.16.1 using read count data provided by the aligner.
Genes were considered differentially expressed if the adjusted P-value, calculated using Benjamini-Hochberg method was less than 0.01 and the change in expression level was greater than 2-fold.
Differential splicing analysis was performed with rMATS turbo package v4.0.1.  The FDR threshold for PSI was chosen to be 0.01
Genome_build: hg19

source_name: KK U2OS stable cells

growth_protocol: U2OS inducible cell lines weregrown in Dulbecco’s modified Eagle medium supplemented with 10% (v/v) FBS, penicillin/streptomycin, 100 ug/ml G418  and 150 ug/ml hygromycin B

extract_protocol:
total RNA was extracted using TRIzol.  mRNA was subsequently enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module as per the manufacturer’s instructions
cDNA libraries were made using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®

treatment_protocol: E2F-1 protein expression was induced with 1 ug/ml doxycycline for 24h

tag: cell line

value: Osteosarcoma, epithelial

tag: ectopic e2f-1 expressed

value: HA-tagged R111/113K mutated E2F-1 (KK)

tag: conditions

value: 1ug/ml doxycycline, 24h


title: NEO20 [Patient_20_T2]

description:
Patient_20_T2
processed data file: Processed_data.txt


title: KK cell line RNA-seq replicate 2


title: WT cell line RNA-seq replicate 1

source_name: WT U2OS stable cells

value: HA-tagged wild-type E2F-1


title: WT cell line RNA-seq replicate 3


title: preOSKM shCntrl rep1


title: TSN siRNA E2F-1 RIP-seq 2

data_processing:
FASTQ files were trimmed to remove adaptors and low-quality bases with TrimGalore v0.4.3
The reads were aligned to the human genome (build hg19) by gsnap aligner v2017-04-21 with two mismatches allowed.
RIP-seq analysis was performed with RIPSeeker R package v1.18.0 with the following parameters: uniqueHit=TRUE, assignMultihits=TRUE, rerunWithDisambiguatedMultihits=TRUE, automatic bin size selection.
EnsEMBL bioMart build 75 was used for functional annotation of the RIP-seq results.
Genome_build: hg19

source_name: U2OS cells

growth_protocol: U2OS cells were grown in high glucose Dulbecco’s modified Eagle medium (+ glycine + Na-pyruvate) supplemented with 10% (v/v) FBS and penicillin/streptomycin.

extract_protocol:
Cells are lysed in RIP-lysis buffer and E2F-1 RIP is performed.  RNA is extracted using Trizol, DNAse treated, and ribodepleted using a GeneRead rDNA Depletion kit
Libraries were prepared using NEBNext Ultra Directional RNA library prep kit for Illumina

treatment_protocol: Cells treated with 25nM siRNA to p100/TSN, E2F-1, or non-targeting control for 72h

value: 25nM p100/TSN siRNA, 72h


title: R109K cell line RNA-seq replicate 2

source_name: R109K U2OS stable cells

value: HA-tagged R109K mutated E2F-1


title: NT siRNA E2F-1 RIP-seq 2

value: 25nM NT siRNA, 72h


title: R109K cell line RNA-seq replicate 1


title: E2F-1 siRNA E2F-1 RIP-seq

value: 25nM E2F-1 siRNA, 72h


title: NT siRNA E2F-1 RIP-seq 1


title: pTRE cell line RNA-seq replicate 3

source_name: pTRE U2OS stable cells

value: empty vector cell line


title: KK cell line RNA-seq replicate 1


title: TSN siRNA E2F-1 RIP-seq 1


title: 14N_rep2

city: Illkirch

first: Hinrich

last: Gronemeyer

address: 1 rue Laurent Fries

department: Functional genomics and cancer

country: France

institute: IGBMC

description:
Differential analysis using two biological replicates of tumor tissue against two biological replicates of normal tissue
DESeq2_out_14

data_processing:
Illumina Casava1.7 software used for basecalling.
QC of fastq files were performed using FASTQC, Alignment was performed using Hisat2 using human genome build hg19
Raw read counts were performed using SummarizedExperiment (R package)
Differetial expression was assessed using DEseq2 (R package)
Genome_build: hg19
Supplementary_files_format_and_content: DEseq2 output file having differential expressed genes

source_name: Prostate tissue

extract_protocol:
Total RNA was isolated from fresh frozen prostate cancer tissue along with matched normal using Trizol (Invitrogen), rRNA was removed using Ribo minus Gold kit
Strand specific total RNA libraries were prepared using Illumina guidelines

value: Normal

value: Frozen tissue

tag: replicate

value: Biological Replicate 2


title: R109K cell line RNA-seq replicate 3


title: 15T_rep1

description:
Differential analysis using two biological replicates of tumor tissue against two biological replicates of normal tissue
DESeq2_out_15

value: Tumor

value: Biological Replicate 1


title: pTRE cell line RNA-seq replicate 1


title: 15T_rep2


title: 15N_rep2


title: 14T_rep2


title: 14N_rep1


title: 15N_rep1


title: pTRE cell line RNA-seq replicate 2


title: 14T_rep1


title: 13T_rep2

description:
Differential analysis using two biological replicates of tumor tissue against two biological replicates of normal tissue
DESeq2_out_13


title: WT cell line RNA-seq replicate 2


title: 12N_rep2

description:
Differential analysis using two biological replicates of tumor tissue against two biological replicates of normal tissue
DESeq2_out_12


title: 13T_rep1


title: 12T_rep1


title: 12N_rep1


title: 11T_rep2

description:
Differential analysis using two biological replicates of tumor tissue against two biological replicates of normal tissue
DESeq2_out_11


title: 10N_rep2

description:
Differential analysis using two biological replicates of tumor tissue against two biological replicates of normal tissue
DESeq2_out_10


title: 11N_rep1


title: 10N_rep1


title: HFF, RH_1

value: foreskin fibroblast

value: Infected with RH Toxoplasma parasites

tag: time

value: 6 hours post infection


title: 10T_rep2

tag: tissue


title: 9N_rep1

description:
Differential analysis using two biological replicates of tumor tissue against two biological replicates of normal tissue
DESeq2_out_9


title: 8N_rep2

description:
Differential analysis using two biological replicates of tumor tissue against two biological replicates of normal tissue
DESeq2_out_8


title: 9N_rep2


title: 13N_rep2


title: 9T_rep1


title: 10T_rep1


title: 8T_rep1


title: 13N_rep1


title: 9T_rep2


title: 8T_rep2


title: 7T_rep2

description:
Differential analysis using two biological replicates of tumor tissue against two biological replicates of normal tissue
DESeq2_out_7


title: 8N_rep1


title: 7N_rep1


title: 7T_rep1


title: 6N_rep2

description:
Differential analysis using two biological replicates of tumor tissue against two biological replicates of normal tissue
DESeq2_out_6


title: 6T_rep2


title: 6N_rep1


title: 6T_rep1


title: 12T_rep2


title: 11T_rep1


title: 5N_rep2

description:
Differential analysis using two biological replicates of tumor tissue against two biological replicates of normal tissue
DESeq2_out_5


title: 11N_rep2


title: 4N_rep2

description:
Differential analysis using two biological replicates of tumor tissue against two biological replicates of normal tissue
DESeq2_out_4


title: 5N_rep1


title: 5T_rep2


title: 4N_rep1


title: 5T_rep1


title: 7N_rep2


title: 3T_rep1

description:
Differential analysis using two biological replicates of tumor tissue against two biological replicates of normal tissue
DESeq2_out_3


title: 4T_rep2


title: 2N_rep1

description:
Differential analysis using two biological replicates of tumor tissue against two biological replicates of normal tissue
DESeq2_out_2


title: 2N_rep2


title: 3T_rep2


title: 2T_rep2


title: 2T_rep1


title: 3N_rep1


title: 1N_rep2

description:
Differential analysis using two biological replicates of tumor tissue against two biological replicates of normal tissue
DESeq2_out_1


title: 1T_rep2


title: 4T_rep1


title: AXI rep2

city: Bologna

first: Fabrizio

last: Ferrè

address: Via Selmi 3

department: Pharmacy and Biotechnology

institute: University of Bologna

data_processing:
After adapter sequence removal, read ends were trimmed if base quality scores were lower than Q20, using Trimmomatic. After trimming, reads with the total length shorter than 25 bases, with average quality less than Q20, or with the fraction of undetermined bases >2% were discarded
Read mapping with TopHat v2.1.1 and Bowtie 2.3.4.1, default parameters
Expression estimate (FPKM units) with Cufflinks v2.1.1, default parameters
Differential expression test with CuffDiff, using human GTF from Ensembl 91, FDR-corrected p-values signifcance threshold 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: Expression estimates for all samples, FPKM units

source_name: HUVEC cells (pooled donors)_AXI

growth_protocol: Complete endothelial cell growth medium (EGM-2, Lonza) containing basal medium (EBM-2, Lonza) supplemented with endothelial cell Bullet Kit (2% BBS, hEGF-2, hVEGF, R3-IGF-1, ascorbic acid, hydrocortisone, heparin, gentamicin and amphotericin-B) (Lonza). Cells were grown at 37° C in a humidified atmosphere of 5% CO2-95% air.

extract_protocol:
Total RNA from 3 biological replicates was isolated by TRIzol  (ThermoFisher Scientific) and subjected to DNAse digestion (RQ1 DNAse, Promega). DNA-free RNA was purified by PureLink RNA (Life Technologies Carlsbad CA, USA) and 2 μg were used for sequencing analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: One hour-long pulse of Axitinib (25 μM) or Doxorubicin (5 μM), followed by  extensive washing and culturing in drug-free complete culturing medium.

value: Human Umbilical Vein Endothelial Cells (HUVEC)

value: between 2 and 4

tag: treatment

value: Axitinib (25 μM) one-hour pulse


title: AXI rep3


title: AXI rep1


title: DOXO rep3

source_name: HUVEC cells (pooled donors)_DOXO

value: Doxorubicin (5 μM) one-hour pulse


title: DOXO rep2


title: DOXO rep1


title: HUVEC rep2

source_name: HUVEC cells (pooled donors)


title: HUVEC rep3