title: Media, Staurosporine, replicate 5

city: Faro

first: Matthias

last: Futschik

address: Campus de Gambelas

country: Portugal

institute: Universidade do Algarve

description:
small RNA
Gene expression data from supernatant of neurons incubated with staurosporine, replicate 5

hyb_protocol: The labeled RNA sample was then added to a hybridization mixture and hybridized to Affymetrix GeneChip miRNA microarrays at 48°C for 16 hrs, washed and stained accordingly to the manufacturer’s protocol (Hybridization Wash and Stain Kit, Affymetrix Inc., Santa Clara, CA, USA)

scan_protocol: Arrays were scanned with a GeneChip scanner 3000 G7 (Affymetrix).

data_processing: Microarray data  were processed using the robust multi-array average (RMA) method on the R/Bioconductor platform using default parameter (i.e. quantile normalisation and RMA background correction).  For annotation,  the Bioconductor package pd.mirna.4.0 was used.

source_name: Supernatant of primary cultures of cortical neurons generated from forebrains of embryonic (E) 17.5 mice and incubated with 1 µM staurosporine  for 8 h.

label_protocol: For miRNA expression analysis small RNA was biotin labeled using the FlashTag™ HSR Biotin RNA labeling kit for Affymetrix miRNA arrays (Genisphere LLC., Hatfield, PA, USA), according to manufacturer's protocol and detected by fluorescent emission. The labeling kit using a two-step process that does not require any purification prior to array hybridization. Small RNA was subjected a tailing reaction followed by ligation of the biotinylated template to the target RNA.

growth_protocol: Primary cultures of cortical neurons were generated from forebrains of embryonic (E) 17.5 mice, and seeded into a 24-well plate at a density of 5x105 cells/well and incubated for 3 d at 37˚C in humidified air with 5% (v/v) CO2, before starting the experiment.

extract_protocol: miRNA extraction from conditioned medium and cortical neurons was performed as previously described using organic extraction followed by mirVana™ isolation kit (Thermo Fisher Scientific #AM1560, Waltham, MA, USA) application. 1 ml of cell-conditioned medium was used for organic total RNA extraction. 2x106 cells grown on a 6-well plate were used for organic extraction from neurons. Cells were lysed prior to organic extraction.

treatment_protocol: Staurosporine (Merck #S6942, Kenilworth, NJ, USA) was added to Neurobasal Medium (Gibco #21103-049, Thermo Fisher Scientific, Waltham, MA, USA) to reach a final concentration of 1 M. Whole medium from primary neuron cell cultures was removed and replaced by staurosporine-containing medium. Primary neuron cultures were incubated with staurosporine for 8 h. Control samples were  incubated with DMSO (0.1%) as solvent for 8 h.

value: Supernatent of primary cultures of cortical neurons

value: staurosporine


title: 3dpwP2_F3_S260

status: Public on Nov 29 2021

type: SRA

city: New York

first: Kevin Andrew

middle: Uy

last: Gonzales

state: NY

address: 1230 York Avenue

country: USA

institute: The Rockefeller University

library_source: genomic

data_processing:
Sequencing reads for scRNA-seq libraries were aligned to the mouse reference genome, combined with sequences for ERCC spike-ins as artificial chromosomes, using STAR (version 2.5.2a) with default parameters for paired-end reads.
Transcript expressions were calculated using the Salmon quantification software (version 0.14.1)
Gene expression levels as TPMs and counts were obtained using Tximport (version 1.12.3). TPMs were transformed to log2(TPM + 1).
Count and TPM matrices were filtered by removing cells with <1500 genes detected per cell and genes expressed in <5% of the cell population.
Genome_build: mouse release M23 (GRCm38.p6)
Supplementary_files_format_and_content: Count matrix file
Supplementary_files_format_and_content: TPM matrix file

molecule: polyA RNA

organism: Mus musculus

source_name: YFP+ keratinocytes

extract_protocol:
Skin were trypsinized to extract basal stem cells, which were then FACS-sorted with a 100-μm nozzle into 96 well PCR plates (Bio-Rad) containing 2μl of lysis buffer [0.2% Triton X-100, 2U/μl RNaseOUT (Thermo Scientific), 0.25μM oligo-dT30VN primer and 1:8,000,000 diluted ERCC spike-in RNAs (Ambion)].
Briefly, after sorting, plates were briefly centrifuged, snap-frozen in liquid nitrogen and stored at −80°C. Plates were then thawed on ice and incubated for 3 min at 72°C to lyse cells. Reverse transcription (4U/μl Maxima H- transcriptase), template switching reaction and PCR pre-amplification (15 cycles) were performed according to the protocol. PCR product was cleaned up using 0.8X AMPure XP beads (Beckman Coulter) and the quality and quantity of cDNA libraries were measured by Agilent 2200 TapeStation and Qubit Florometer (Thermal Fisher Scientific). To exclude empty wells and low-quality libraries, the cDNA libraries were assessed by qPCR with a primer pair for the housekeeping gene Gapdh (Table S2). Samples showing high Ct value (> 35 cycles) or no PCR amplification were discarded. 50-100pg of each cDNA library was used for generating Illumina sequencing library using a Nextera XT DNA library preparation kits (Illumina). After the final PCR amplification, samples were pooled and cleaned by 0.9X AMPure XP beads.

tag: tissue

value: skin

tag: strain

value: CD1 x C57BL/6J cross

tag: genotype

tag: treatment

value: partial-thickness wounded

tag: timepoint (days post-wound)


title: Media, DMSO, replicate 4

type: RNA

description:
small RNA
Gene expression data from supernatant of neurons incubated with DMSO, replicate 4

label: biotin

molecule: total RNA

source_name: Supernatent of primary cultures of cortical neurons generated from forebrains of embryonic (E) 17.5 mice and incubated with DMSO (0.1%) as solvent control for 8 h.

value: DMSO control


title: Media, Staurosporine, replicate 3

description:
small RNA
Gene expression data from supernatant of neurons incubated with staurosporine, replicate 3 (Sample was removed from further analysis due to insufficient results obtained by quality control (i.e. inspection of signal density plot and principal component analysis.)


title: Media, DMSO, replicate 5

description:
small RNA
Gene expression data from supernatant of neurons incubated with DMSO, replicate 5


title: Media, DMSO, replicate 2

description:
small RNA
Gene expression data from supernatent of neurons incubated with DMSO, replicate 2


title: B61

city: Harbin

first: Yingwei

last: Xue

address: 150, Haping St, Nangang District

department: Department of Gastrointestinal Oncology

country: China

institute: Harbin Medical University Cancer Hospital

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then reads count mapped to this gene.
Genome_build: Hisat2 v2.0.5
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: paired normal gastric tissue

extract_protocol:
①RNA degradation and contamination was monitored on 1% agarose gels.② RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). ③ RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5 min at 95 °Cbefore PCR. Then PCR was performed with Phusion High -Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: paired normal gastric tissue

tag: tumor stage

value: IIIC

tag: age

tag: gender

value: male


title: Media, Staurosporine, replicate 2

description:
small RNA
Gene expression data from supernatant of neurons incubated with staurosporine, replicate 2


title: B65

value: IIIB


title: 3dpwP2_F2_S184


title: Media, DMSO, replicate 3

description:
small RNA
Gene expression data from supernatant of neurons incubated with DMSO, replicate 3


title: Media, Staurosporine, replicate 4

description:
small RNA
Gene expression data from supernatant of neurons incubated with staurosporine, replicate 4


title: 3dpwP2_F4_S261


title: 3dpwP2_F11_S268


title: Neurons, DMSO, replicate 5

description:
small RNA
Gene expression data from neurons incubated with DMSO, replicate 5

source_name: Primary cultures of cortical neurons that were generated from forebrains of embryonic (E) 17.5 mice and incubated with DMSO (0.1%) as solvent control for 8 h.

value: Primary cultures of cortical neurons


title: B60


title: Media, Staurosporine, replicate 1

description:
small RNA
Gene expression data from supernatant of neurons incubated with staurosporine, replicate 1


title: 3dpwP2_F10_S267


title: B58


title: 3dpwP2_F1_S183


title: Neurons, DMSO, replicate 4

description:
small RNA
Gene expression data from neurons incubated with DMSO, replicate 4

source_name: Primary cultures of cortical neurons were generated from forebrains of embryonic (E) 17.5 mice and incubated with DMSO (0.1%) as solvent control for 8 h.


title: Media, DMSO, replicate 1

description:
small RNA
Gene expression data from supernatant of neurons incubated with DMSO, replicate 1


title: Neurons, Staurosporine, replicate 3

description:
small RNA
Gene expression data from neurons incubated with staurosporine, replicate 3

source_name: Primary cultures of cortical neurons were generated from forebrains of embryonic (E) 17.5 mice and incubated with 1 µM staurosporine  for 8 h.


title: Neurons, DMSO, replicate 3

description:
small RNA
Gene expression data from neurons incubated with DMSO, replicate 3


title: B57


title: Neurons, Staurosporine, replicate 4

description:
small RNA
Gene expression data from neurons incubated with staurosporine, replicate 4


title: 3dpwP2_E9_S180


title: B59


title: 3dpwP2_E8_S179


title: Neurons, Staurosporine, replicate 5

description:
small RNA
Gene expression data from neurons incubated with staurosporine, replicate 5


title: B55

value: female


title: Neurons, Staurosporine, replicate 2

description:
small RNA
Gene expression data from neurons incubated with staurosporine, replicate 2


title: Neurons, DMSO, replicate 2

description:
small RNA
Gene expression data from neurons incubated with DMSO, replicate 2


title: B56


title: 3dpwP2_E6_S177


title: Neurons, Staurosporine, replicate 1

description:
small RNA
Gene expression data from neurons incubated with staurosporine, replicate 1


title: 3dpwP2_E3_S175


title: 3dpwP2_E7_S178


title: B54


title: B52


title: B51


title: B53


title: 3dpwP2_E2_S174


title: Neurons, DMSO, replicate 1

description:
small RNA
Gene expression data from neurons incubated with DMSO, replicate 1


title: 3dpwP2_E4_S176


title: B49


title: 3dpwP2_E10_S181


title: B48


title: 3dpwP2_E11_S182


title: B50


title: 3dpwP2_D9_S171


title: 3dpwP2_D8_S170


title: B47


title: genomic DNA from anal sample I_145

type: genomic

city: Tampa

first: Kieran

last: Smalley

state: Fl

address: 12902 USF Magnolia Drive,

institute: Moffitt cancer Center

hyb_protocol: Genome-wide methylation was interrogated using the Infinium HumanMethylation450K BeadChip (HM450) following the manufacturer’s specifications

scan_protocol: chips were scanned on a single HiScanSQ System (Illumina Inc.)

data_processing: Raw IDAT files were processed, background corrected and normalized using control probes in R using the minfi bioconductor package

label: Cy3, Cy5

molecule: genomic DNA

source_name: anal sample I_145

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using QIAamp DNA extraction kit (QIAGEN, Valencia, CA)

tag: sample type


title: genomic DNA from anal sample T_062

source_name: anal sample T_062

value: Tumor


title: genomic DNA from anal sample T_675

source_name: anal sample T_675


title: genomic DNA from anal sample I_552

source_name: anal sample I_552


title: genomic DNA from anal sample T_002

source_name: anal sample T_002


title: genomic DNA from anal sample I_103

source_name: anal sample I_103


title: genomic DNA from anal sample N_523

source_name: anal sample N_523

value: Normal


title: 3dpwP2_D7_S169


title: genomic DNA from anal sample T_681

source_name: anal sample T_681


title: genomic DNA from anal sample T_608

source_name: anal sample T_608


title: genomic DNA from anal sample T_475

source_name: anal sample T_475


title: genomic DNA from anal sample T_673

source_name: anal sample T_673


title: 3dpwP2_D6_S168

source_name: YFP+ keratinocytes


title: genomic DNA from anal sample T_629

source_name: anal sample T_629


title: genomic DNA from anal sample T_147

source_name: anal sample T_147


title: genomic DNA from anal sample N_539

source_name: anal sample N_539


title: genomic DNA from anal sample T_671

source_name: anal sample T_671


title: genomic DNA from anal sample T_651

source_name: anal sample T_651


title: B46

source_name: paired normal gastric tissue


title: genomic DNA from anal sample I_232

source_name: anal sample I_232


title: B45


title: genomic DNA from anal sample N_164

source_name: anal sample N_164


title: genomic DNA from anal sample N_339

source_name: anal sample N_339


title: genomic DNA from anal sample T_103

source_name: anal sample T_103


title: genomic DNA from anal sample T_655

source_name: anal sample T_655


title: genomic DNA from anal sample T_665

source_name: anal sample T_665


title: B43


title: B44


title: 3dpwP2_D5_S167


title: genomic DNA from anal sample T_646

source_name: anal sample T_646


title: B42


title: genomic DNA from anal sample T_667

source_name: anal sample T_667


title: genomic DNA from anal sample T_659

source_name: anal sample T_659


title: B40


title: 3dpwP2_D11_S173


title: genomic DNA from anal sample T_628

source_name: anal sample T_628


title: B41


title: 3dpwP2_D10_S172

source_name: YFP+ keratinocytes


title: B39


title: genomic DNA from anal sample T_600

source_name: anal sample T_600


title: 3dpwP2_C9_S162


title: genomic DNA from anal sample T_619

source_name: anal sample T_619


title: 3dpwP2_C8_S161


title: 3dpwP2_C7_S160


title: B37

source_name: gastric tumor

value: gastric tumor


title: 3dpwP2_D2_S165


title: B38


title: genomic DNA from anal sample T_595

source_name: anal sample T_595


title: genomic DNA from anal sample T_618

source_name: anal sample T_618


title: B36


title: genomic DNA from anal sample N_475

source_name: anal sample N_475


title: 3dpwP2_C6_S159


title: 3dpwP2_C5_S158


title: B34


title: genomic DNA from anal sample T_592

source_name: anal sample T_592


title: 3dpwP2_C4_S157


title: genomic DNA from anal sample T_614

source_name: anal sample T_614


title: B33


title: B35


title: genomic DNA from anal sample T_255

source_name: anal sample T_255


title: 3dpwP2_C3_S156


title: genomic DNA from anal sample N_608

source_name: anal sample N_608


title: B32


title: genomic DNA from anal sample T_291

source_name: anal sample T_291


title: 3dpwP2_C2_S155


title: genomic DNA from anal sample T_583

source_name: anal sample T_583


title: genomic DNA from anal sample T_279

source_name: anal sample T_279


title: genomic DNA from anal sample T_247

source_name: anal sample T_247


title: genomic DNA from anal sample T_609

source_name: anal sample T_609


title: genomic DNA from anal sample T_232

source_name: anal sample T_232


title: genomic DNA from anal sample T_258

source_name: anal sample T_258


title: 3dpwP2_D4_S166

source_name: YFP+ keratinocytes


title: B30


title: genomic DNA from anal sample T_270

source_name: anal sample T_270


title: genomic DNA from anal sample T_272

source_name: anal sample T_272


title: 3dpwP2_C11_S164


title: 3dpwP2_C10_S163


title: genomic DNA from anal sample T_198

source_name: anal sample T_198


title: B29

source_name: gastric tumor


title: genomic DNA from anal sample T_265

source_name: anal sample T_265


title: 3dpwP2_B9_S152


title: B28


title: 3dpwP2_B8_S151


title: B27


title: genomic DNA from anal sample T_193

source_name: anal sample T_193


title: 3dpwP2_B7_S150


title: genomic DNA from anal sample T_217

source_name: anal sample T_217


title: genomic DNA from anal sample T_237

source_name: anal sample T_237


title: genomic DNA from anal sample T_231

source_name: anal sample T_231


title: genomic DNA from anal sample T_575

source_name: anal sample T_575


title: B26


title: HT29-SNAIL1-HA 4F5 144h 2

city: Freiburg

first: Antoine

last: Devisme

address: Breisacherstr. 153

country: Germany

institute: Institute of Medical Bioinformatics and Systems Medicine

description:
X4F5_144h_2
replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All arrays were normalized together using the quantile normalization algorithm without background subtraction using the R Bioconductor beadarray package

label: Biotin

source_name: HT29-SNAIL1-HA, 4F5 clone Dox, 144h

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: HT29-ctrl cells and HT29-Snail1-HA clones were cultivated at 37 °C and 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% (v/v) FCS, 0.01 M HEPES/KOH, 1x MEM non-essential amino acids solution and 1x Penicillin/Streptomycin.

extract_protocol: Total RNA was extracted using the PeqGOLD total RNA kit (#732–2871, Peqlab/VWR Life Science, Bruchsal, Germany) according to manufacturer's instructions.

treatment_protocol: Cells were treated with 1 µg/ml-1 doxycycline as indicated. If necessary media were refreshed after 48 h.

tag: cell line

value: Colorectal cancer cell line HT29

tag: clone

value: HT29-Snail1-HA clone 4F5

value: Dox

tag: time


title: 3dpwP2_B6_S149


title: genomic DNA from anal sample T_197

source_name: anal sample T_197


title: genomic DNA from anal sample T_244

source_name: anal sample T_244


title: B25


title: 3dpwP2_B5_S148


title: genomic DNA from anal sample T_182

source_name: anal sample T_182


title: 3dpwP2_B4_S147


title: B24


title: 3dpwP2_B3_S146


title: B23


title: genomic DNA from anal sample T_215

source_name: anal sample T_215


title: genomic DNA from anal sample T_221

source_name: anal sample T_221


title: HT29-SNAIL1-HA 4F5 24h 2

description:
X4F5_24h_2
replicate 2

source_name: HT29-SNAIL1-HA, 4F5 clone Dox, 24 h


title: B22


title: 3dpwP2_B11_S154

source_name: YFP+ keratinocytes


title: HT29-SNAIL1-HA 4F5 24h 1

description:
X4F5_24h_1
replicate 1


title: B31


title: HT29-SNAIL1-HA 4F5 72h 2

description:
X4F5_72h_2
replicate 2

source_name: HT29-SNAIL1-HA, 4F5 clone Dox, 72 h


title: B21


title: HT29-SNAIL1-HA 4F5 144h 1

description:
X4F5_144h_1
replicate 1


title: 3dpwP2_B10_S153


title: genomic DNA from anal sample T_220

source_name: anal sample T_220


title: HT29-SNAIL1-HA 3C2 144h 2

description:
X3C2_144h_2
replicate 2

source_name: HT29-SNAIL1-HA, 3C2 clone Dox, 144h

value: HT29-Snail1-HA clone3C2


title: B20

source_name: gastric tumor


title: 3dpwP1_G12_S250

value: skin


title: HT29-SNAIL1-HA 4F5 0h 2

description:
X4F5_0h_2
replicate 2

source_name: HT29-SNAIL1-HA, 4F5 clone Dox, 0 h

value: control

value: 0 h


title: B19


title: 3dpwP1_C11_S213

value: CD1 x C57BL/6J cross

value: partial-thickness wounded


title: genomic DNA from anal sample T_169

source_name: anal sample T_169


title: B18


title: B17

value: IIIC


title: 3dpwP1_B1_S194


title: B16


title: genomic DNA from anal sample T_135

source_name: anal sample T_135


title: genomic DNA from anal sample T_139

source_name: anal sample T_139


title: 3dpwP1_A11_S193


title: HT29-SNAIL1-HA 3C2 72h 2

description:
X3C2_72h_2
replicate 2

source_name: HT29-SNAIL1-HA, 3C2 clone Dox, 72 h


title: HT29-SNAIL1-HA 3C2 72h 1

description:
X3C2_72h_1
replicate 1


title: HT29-SNAIL1-HA 3C2 144h 1

description:
X3C2_144h_1
replicate 1


title: genomic DNA from anal sample T_160

source_name: anal sample T_160


title: 2mo_YFPp_1_F_H2_S75


title: genomic DNA from anal sample T_167

source_name: anal sample T_167


title: genomic DNA from anal sample T_164

source_name: anal sample T_164


title: genomic DNA from anal sample T_205

source_name: anal sample T_205


title: HT29-SNAIL1-HA 3C2 24h 2

description:
X3C2_24h_2
replicate 2

source_name: HT29-SNAIL1-HA, 3C2 clone Dox, 24 h


title: genomic DNA from anal sample T_138

source_name: anal sample T_138


title: B15

value: male


title: 2mo_YFPp_1_F_G6_S74


title: HT29-SNAIL1-HA 3C2 24h 1

description:
X3C2_24h_1
replicate 1


title: B14

value: IIIB


title: 2mo_YFPp_1_F_G5_S73


title: B13


title: genomic DNA from anal sample T_145

source_name: anal sample T_145


title: genomic DNA from anal sample T_149

source_name: anal sample T_149


title: 2mo_YFPp_1_F_G2_S72

source_name: YFP+ keratinocytes


title: B12


title: 2mo_YFPp_1_F_F9_S70


title: B11


title: HT29-SNAIL1-HA 4F5 0h 1

description:
X4F5_0h_1
replicate 1


title: HT29 control 144h 2

description:
EV_144h_2
replicate 2

source_name: HT29 control, Dox, 144h

value: HT29 control


title: 2mo_YFPp_1_F_F7_S69


title: HT29-SNAIL1-HA 3C2 0h 2

description:
X3C2_0h_2
replicate 2

source_name: HT29-SNAIL1-HA, 3C2 clone Dox, 0 h


title: HT29-SNAIL1-HA 3C2 0h 1

description:
X3C2_0h_1
replicate 1


title: genomic DNA from anal sample T_190

source_name: anal sample T_190


title: genomic DNA from anal sample T_112

source_name: anal sample T_112


title: 2mo_YFPp_1_F_F3_S68


title: B10

source_name: gastric tumor


title: genomic DNA from anal sample T_156

source_name: anal sample T_156


title: HT29 control 144h 1

description:
EV_144h_1
replicate 1


title: HT29 control 72h 2

description:
EV_72h_2
replicate 2

source_name: HT29 control, Dox, 72 h


title: 2mo_YFPp_1_F_F2_S67


title: genomic DNA from anal sample T_128

source_name: anal sample T_128


title: genomic DNA from anal sample T_126

source_name: anal sample T_126


title: B9


title: B8

value: female


title: 2mo_YFPp_1_F_F12_S71


title: B7


title: genomic DNA from anal sample T_105

source_name: anal sample T_105

value: Tumor


title: genomic DNA from anal sample T_047

source_name: anal sample T_047


title: 2mo_YFPp_1_F_F1_S66


title: HT29 control 72h 1

description:
EV_72h_1
replicate 1


title: HT29 control 24h 2

description:
EV_24h_2
replicate 2

source_name: HT29 control, Dox, 24 h


title: 2mo_YFPp_1_F_E5_S63


title: B6


title: 2mo_YFPp_1_F_E3_S62


title: B5


title: B4


title: HT29 control 24h 1

description:
EV_24h_1
replicate 1


title: KD_N6amt1_AOM_DSS_tumour replicate5

first: Christopher

last: Berlin

address: Hugstetter Straße 55

institute: University Hospital Freiburg

description:
CountsTable_AOM_DSS_tumour.txt
KD_N6amt1_AOM_DSS_tumour_5

data_processing:
We aligned these reads to the mm10build of the mouse genome using STAR
The aligned reads were counted with the homer software (analyzeRNA) and edgeR
Genome_build: mm10, hg19
Supplementary_files_format_and_content: The processed data file are text files that include the overall read count for a specific transcript (indicated by the NM accession number)

source_name: KD_N6amt1_AOM_DSS_tumour replicate5

extract_protocol: RNA samples were sequenced by the standard Illumina protocol to create raw sequence files (.fastq files).

tag: differentiation stage

value: colorectal tumour from AOM/DSS-treated KMT9aIEC-KO

value: Vil1-CreERT2 xKmt9afl/fl


title: HT29-SNAIL1-HA 4F5 72h 1

description:
X4F5_72h_1
replicate 1

source_name: HT29-SNAIL1-HA, 4F5 clone Dox, 72 h

value: Colorectal cancer cell line HT29


title: KD_N6amt1_AOM_DSS_tumour replicate4

description:
CountsTable_AOM_DSS_tumour.txt
KD_N6amt1_AOM_DSS_tumour_4

source_name: KD_N6amt1_AOM_DSS_tumour replicate4


title: genomic DNA from anal sample T_037

source_name: anal sample T_037


title: 2mo_YFPp_1_F_E2_S61

source_name: YFP+ keratinocytes


title: B3

value: gastric tumor


title: B2


title: KD_N6amt1_AOM_DSS_tumour replicate2

description:
CountsTable_AOM_DSS_tumour.txt
KD_N6amt1_AOM_DSS_tumour_2

source_name: KD_N6amt1_AOM_DSS_tumour replicate2


title: HT29 control 0h 2

description:
EV_0h_2
replicate 2

source_name: HT29 control, Dox, 0 h


title: B1


title: 2mo_YFPp_1_F_E11_S64


title: HT29 control 0h 1

description:
EV_0h_1
replicate 1


title: genomic DNA from anal sample T_174

source_name: anal sample T_174


title: KD_N6amt1_AOM_DSS_tumour replicate3

description:
CountsTable_AOM_DSS_tumour.txt
KD_N6amt1_AOM_DSS_tumour_3

source_name: KD_N6amt1_AOM_DSS_tumour replicate3


title: 2mo_YFPp_1_F_D7_S58


title: CT_AOM_DSS_tumour replicate4

description:
CountsTable_AOM_DSS_tumour.txt
CT_AOM_DSS_tumour_4

source_name: CT_AOM_DSS_tumour replicate4

value: colorectal tumour from AOM/DSS-treated KMT9aIEC-WT


title: genomic DNA from anal sample T_033

source_name: anal sample T_033


title: KD_N6amt1_AOM_DSS_tumour replicate1

description:
CountsTable_AOM_DSS_tumour.txt
KD_N6amt1_AOM_DSS_tumour_1

source_name: KD_N6amt1_AOM_DSS_tumour replicate1


title: 2mo_YFPp_1_F_D6_S57


title: 2mo_YFPp_1_F_D9_S59


title: CT_AOM_DSS_tumour replicate3

description:
CountsTable_AOM_DSS_tumour.txt
CT_AOM_DSS_tumour_3

source_name: CT_AOM_DSS_tumour replicate3


title: Cancer Cell PC-3M-1E8 [Pca-3]

city: Peking

first: wang

middle: li

last: yong

state: Peking

address: No 10 xi tou tiao, you an gate

department: medical school

institute: Capital Medical University

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual

scan_protocol: Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm. Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing:
Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).
Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.

source_name: Cancer Cell PC-3M-1E8

label_protocol: After having passed RNA quantity measurement using the NanoDrop 1000, the samples were labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit and hybridized on the miRCURY™ LNA Array (v.18.0)

extract_protocol: Total RNA was harvested using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions.

tag: cell type

value: prostate epithelial cells


title: Normal Cell RWPE-1 [Pca-1]

source_name: Normal Cell RWPE-1


title: genomic DNA from anal sample T_059

source_name: anal sample T_059


title: CT_AOM_DSS_tumour replicate2

description:
CountsTable_AOM_DSS_tumour.txt
CT_AOM_DSS_tumour_2

source_name: CT_AOM_DSS_tumour replicate2


title: genomic DNA from anal sample T_003

source_name: anal sample T_003


title: genomic DNA from anal sample T_574

source_name: anal sample T_574


title: genomic DNA from anal sample T_556

source_name: anal sample T_556


title: 2mo_YFPp_1_F_D10_S60

value: skin


title: CT_AOM_DSS_tumour replicate1

description:
CountsTable_AOM_DSS_tumour.txt
CT_AOM_DSS_tumour_1

source_name: CT_AOM_DSS_tumour replicate1


title: genomic DNA from anal sample T_554

source_name: anal sample T_554


title: 2mo_YFPp_1_F_D4_S56

source_name: YFP+ keratinocytes


title: 2mo_YFPp_1_F_D3_S55


title: 2mo_YFPp_1_F_D2_S54


title: genomic DNA from anal sample T_012

source_name: anal sample T_012


title: genomic DNA from anal sample T_553

source_name: anal sample T_553


title: genomic DNA from anal sample T_566

source_name: anal sample T_566


title: Colon_1_KO replicate1

description:
CountsTable_Colon.txt
Colon_1_KO

source_name: Colon_1_KO replicate1

value: Benign epithelial colon cells from KMT9aIEC-KO


title: genomic DNA from anal sample T_565

source_name: anal sample T_565


title: Colon_2_KO replicate2

description:
CountsTable_Colon.txt
Colon_2_KO

source_name: Colon_2_KO replicate2


title: 2mo_YFPp_1_F_D1_S53


title: Colon_2_CT replicate2

description:
CountsTable_Colon.txt
Colon_2_CT

source_name: Colon_2_CT replicate2

value: Benign epithelial colon cells from KMT9aIEC-WT


title: 2mo_YFPp_1_F_C8_S52

value: CD1 x C57BL/6J cross


title: 2mo_YFPp_1_F_C3_S50

value: partial-thickness wounded


title: genomic DNA from anal sample T_080

source_name: anal sample T_080


title: Colon_3_CT replicate3

description:
CountsTable_Colon.txt
Colon_3_CT

source_name: Colon_3_CT replicate3


title: genomic DNA from anal sample N_103

source_name: anal sample N_103

value: Normal


title: 2mo_YFPp_1_F_E12_S65


title: genomic DNA from anal sample T_071

source_name: anal sample T_071


title: 2mo_YFPp_1_F_C2_S49


title: Colon_1_CT replicate1

description:
CountsTable_Colon.txt
Colon_1_CT

source_name: Colon_1_CT replicate1


title: APKK_s3_replicate3

description: processed data file: CountsTable_APK_APKK.txt

source_name: Cre-expressing adenovirus transdusced organoids from Apcfl/fl p53fl/fl KrasG12D/+ Kmt9αfl/fl mice

value: Cre-expressing adenovirus transdusced organoids from Apcfl/fl p53fl/fl KrasG12D/+ Kmt9alphafl/fl mice

value: ApcKO/ p53KO/KrasG12D/KMT9alphaKO


title: genomic DNA from anal sample T_552

source_name: anal sample T_552


title: APKK_s2_replicate2


title: genomic DNA from anal sample N_583

source_name: anal sample N_583


title: 2mo_YFPp_1_F_C1_S48


title: 2mo_YFPp_1_F_B8_S47


title: Cancer Cell PC-3M-2B4 [Pca-2]

source_name: Cancer Cell PC-3M-2B4


title: Colon_3_KO replicate3

description:
CountsTable_Colon.txt
Colon_3_KO

source_name: Colon_3_KO replicate3


title: APKK_s1_replicate1


title: genomic DNA from anal sample T_539

source_name: anal sample T_539


title: genomic DNA from anal sample T_550

source_name: anal sample T_550


title: 2mo_YFPp_1_F_A5_S46

source_name: YFP+ keratinocytes


title: CT_AOM_DSS_tumour replicate5

description:
CountsTable_AOM_DSS_tumour.txt
CT_AOM_DSS_tumour_5

source_name: CT_AOM_DSS_tumour replicate5


title: APK_s3_replicate2

source_name: Cre-expressing adenovirus transdusced organoids from Apcfl/fl p53fl/fl KrasG12D/+ Kmt9α+/+ mice

value: Cre-expressing adenovirus transdusced organoids from Apcfl/fl p53fl/fl KrasG12D/+ Kmt9alpha+/+ mice


title: APK_s2_replicate2


title: 2mo_YFPp_1_F_A3_S45


title: APK_s1_replicate1


title: 1dpw_H5_S144


title: AOMDSS_tumour_organoids_clone13_TAM treated biological replicate 3

data_processing:
We aligned these reads to the mm10build of the mouse genome using STAR
The aligned reads were counted with the homer software (analyzeRNA) and edgeR
Genome_build: mm10
Supplementary_files_format_and_content: The processed data file are text files that include the overall read count for a specific transcript (indicated by the NM accession number)

value: Epithelial organoids from AOM/DSS tumours

tag: passages


title: 1dpw_H9_S145


title: genomic DNA from anal sample T_533

source_name: anal sample T_533

value: Tumor


title: genomic DNA from anal sample T_558

source_name: anal sample T_558


title: AOMDSS_tumour_organoids_clone13_TAM  treated biological replicate 2


title: AOMDSS_tumour_organoids_clone13_control replicate 3


title: AOMDSS_tumour_organoids_clone13_TAM  treated biological replicate 1


title: 1dpw_G7_S140


title: 1dpw_G8_S141


title: 1dpw_G6_S139


title: genomic DNA from anal sample T_518

source_name: anal sample T_518


title: genomic DNA from anal sample N_592

source_name: anal sample N_592


title: 1dpw_G5_S138


title: AOMDSS_tumour_organoids_clone13_control replicate 2


title: 2mo_YFPp_1_F_C6_S51


title: genomic DNA from anal sample T_528

source_name: anal sample T_528


title: AOMDSS_tumour_organoids_clone13_control replicate 1


title: HEC108_ki047

city: Suita

first: Atsushi

last: Kumanogoh

state: Osaka

address: 2-2 Yamadaoka

country: Japan

institute: Osaka University

data_processing:
miCIP-Seq data were processed as described previously (DOI: 10.1007/978-1-4939-6807-7_5.) with some modifications. The adaptor sequence was removed by cutadapt. The reads were demultiplexed using the barcodes in the RT primers used in library construction by pyBarcodeFilter.py of the pyCRAC suite (version 1.2.2.2). PCR duplicates were collapsed by pyFastqDuplicateRemover.py. We transformed the header in the forward read file with the “awk” command to be compatible with downstream CIMS analysis of CTK package (version 1.1.2). We then created a CIMS-compatible header for the reverse reads and reverse-complemented the reads using match_barcodes_and_reverse_complement.pl. After concatenating the forward reads and the modified reverse reads, we mapped the reads to hg19 by Burrows-Wheeler Aligner (version 0.7.17). We then called m6A sites with the CIMS pipeline as shown in the online CTK documentation (https://zhanglab.c2b2.columbia.edu/index.php/CTK_Documentation). Briefly, we parsed the SAM files with parseAlignment.pl, removed tags from rRNAs with tagoverlap.pl, collapsed PCR duplicates with tag2collapse.pl, and obtained the mutations in the unique tags with joinWrapper.py. We then filtered C to T transitions with the awk command as described previously (Grozhik et al., 2017). Finally, we evaluated the reproducibility of mutations by permutation with CIMS.pl. From the provided .bed files, we called and annotated m6A sites with kmer.annotate.cims.sh. The sequence logo adjacent to m6A was generated with the meme command using the -w 5 option.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files were created by kmer.annotate.cims.sh and contains miCLIP-m6A site.

growth_protocol: The cells were cultured in Dulbecco's modified Eagle medium containing 10% fetal bovine serum (Gibco) and 1% penicillin/streptomycin (Gibco). The cells were maintained at 37°C under a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted from knock-in cells by QIAZol Lysis Reagent (79306; QIAGEN). Then, poly(A) RNA was purified by poly(A) Purist MAG Kit (AM1922, Thermo Fisher Scientific). 20 ug of poly(A) RNA was used for each replicate in this study. miCLIP libraries were prepared as previously described (PMID: 28349454).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: endometrial cancer cell

tag: rip antibody

value: anti-m6A antibody (ab151230, abcam)

tag: replicate number

tag: barcode

value: CANNN


title: 1dpw_G10_S143

tag: tissue

tag: strain


title: HEC108_ki004

tag: genotype

value: TGNNN


title: 1dpw_F9_S135

tag: treatment

tag: timepoint (days post-wound)


title: 1dpw_G9_S142


title: genomic DNA from anal sample T_502

source_name: anal sample T_502


title: AOMDSS_tumour_organoids_clone10_TAM treated biological replicate 3


title: HEC108_ki042

value: TCNNN


title: genomic DNA from anal sample T_517

source_name: anal sample T_517


title: genomic DNA from anal sample T_531

source_name: anal sample T_531


title: 1dpw_F8_S134


title: AOMDSS_tumour_organoids_clone10_TAM  treated biological replicate 2


title: AOMDSS_tumour_organoids_clone10_TAM  treated biological replicate 1


title: H1C1a-X1-cXdel7

city: Boston

first: Janet

last: Song

state: Massachusetts

address: 3 Blackfan St

institute: Boston Children's Hospital

data_processing:
Sequencing reads were trimmed for adapter sequences using cutadapt v1.8.1 and read quality was confirmed using fastqc v0.11.9.
Reads were aligned using STAR v2.7.1a with two-pass mapping to a concatenated human-chimpanzee genome (hg38 and pt6).
The number of uniquely-mapped reads (MAPQ = 255) that overlap each gene was counted with featurecounts from the subread v1.6.0 package using a curated annotation (hg38.pt6.gtf). To generate the annotations, GRCh38.94 human exon annotations from Ensembl were mapped from hg38 to pt6 using pslMap. After removing mappings where the number of bases that map is less than half of the query exon size, we retained only exons that uniquely mapped from humans to chimpanzees. We then removed genes for which exons map to opposite DNA strands, different scaffolded chromosomes, or where consecutive exons map more than 800kb apart. We further filtered out exons where more than 10% of reads from diploid or auto-tetraploid lines map to the incorrect species when mapped to the composite genome.
Genome_build: hg38 and pt6
Supplementary_files_format_and_content: Gene counts for each species are represented with the human ensembl ID in the processed files. For allo-tetraploid lines, each sample is represented twice in the associated processed file, once as human allele counts ("Hs" prefix) and once as chimpanzee allele counts ("Pt" prefix).

organism:
Pan troglodytes
Homo sapiens

source_name: induced pluripotent stem cells

growth_protocol: iPSC lines were grown in mTeSR1 or mTeSR Plus (StemCell Technologies).

extract_protocol:
RNA was isolated using the Direct-Zol RNA Miniprep kit (Zymo Research, cat #R2051) or by Genewiz.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Library Prep (Illumina) or by Genewiz and sequenced on a HiSeq 4000 (2x150bp).

treatment_protocol: iPSCs were collected using accutase and flash frozen for storage at -80C.

value: induced pluripotent stem cells


title: 1dpw_F7_S133

value: skin


title: AOMDSS_tumour_organoids_clone10_control replicate 3


title: genomic DNA from anal sample T_492

source_name: anal sample T_492


title: H1C1a-X1-cXdel5


title: genomic DNA from anal sample T_476

source_name: anal sample T_476


title: genomic DNA from anal sample T_523

source_name: anal sample T_523


title: AOMDSS_tumour_organoids_clone10_control replicate 2


title: 1dpw_F6_S132


title: H1C1a-X1-cXdel6


title: genomic DNA from anal sample T_423

source_name: anal sample T_423


title: H1C1a-X1-cXdel4


title: AOMDSS_tumour_organoids_clone7_TAM treated biological replicate 3


title: AOMDSS_tumour_organoids_clone10_control replicate 1


title: 1dpw_F5_S131


title: 1dpw_F4_S130


title: 1dpw_F11_S137


title: genomic DNA from anal sample T_471

source_name: anal sample T_471


title: 1dpw_F10_S136

source_name: YFP+ keratinocytes


title: genomic DNA from anal sample T_463

source_name: anal sample T_463


title: H1C1a-X1-cXdel1


title: H1C1a-X1-cXdel3


title: AOMDSS_tumour_organoids_clone7_TAM  treated biological replicate 2


title: H1C1a-X1-cXdel2


title: AOMDSS_tumour_organoids_clone7_TAM  treated biological replicate 1


title: 1dpw_E9_S128


title: genomic DNA from anal sample T_410

source_name: anal sample T_410


title: H1C1a-X1-hXdel8


title: AOMDSS_tumour_organoids_clone7_control replicate 3


title: genomic DNA from anal sample T_412

source_name: anal sample T_412


title: 1dpw_E8_S127


title: genomic DNA from anal sample T_409

source_name: anal sample T_409


title: genomic DNA from anal sample T_465

source_name: anal sample T_465


title: H1C1a-X1-hXdel7


title: AOMDSS_tumour_organoids_clone7_control replicate 2


title: 1dpw_E7_S126


title: H1C1a-X1-hXdel6


title: genomic DNA from anal sample T_457

source_name: anal sample T_457


title: 1dpw_E6_S125


title: AOMDSS_tumour_organoids_clone7_control replicate 1


title: AOMDSS_tumour_organoids_clone3_TAM treated biological replicate 3


title: 1dpw_E5_S124


title: H1C1a-X1-hXdel5


title: AOMDSS_tumour_organoids_clone3_TAM  treated biological replicate 2


title: 1dpw_E4_S123


title: AOMDSS_tumour_organoids_clone3_TAM  treated biological replicate 1


title: H1C1a-X1-hXdel3


title: genomic DNA from anal sample T_458

source_name: anal sample T_458


title: 1dpw_E3_S122


title: genomic DNA from anal sample T_401

source_name: anal sample T_401


title: H1C1a-X1-hXdel2


title: AOMDSS_tumour_organoids_clone3_control replicate 3


title: 1dpw_E10_S129


title: genomic DNA from anal sample T_395

source_name: anal sample T_395


title: H1C1a-X1-hXdel1


title: H1C1a-X1-hXdel4


title: 1dpw_E1_S121


title: AOMDSS_tumour_organoids_clone3_control replicate 2


title: genomic DNA from anal sample T_367

source_name: anal sample T_367


title: genomic DNA from anal sample T_394

source_name: anal sample T_394


title: 1dpw_D9_S119


title: H1C1a-X1-cX1

source_name: induced pluripotent stem cells


title: genomic DNA from anal sample T_436

source_name: anal sample T_436


title: H1C1a-X1-hX6


title: 1dpw_D8_S118


title: H4K12me1_AOMDSS_Clone3

data_processing:
ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie2
peak finding algorithm MACS
Genome_build: mm10
Supplementary_files_format_and_content: The processed data are wiggle and bed files. The wig files include the read data mapped to the mm10 genome. The bed files contain the peaks that were obtained when normalizing the reads of the ChIP-Seq to the Input.

extract_protocol:
Metzger, E., et al. Phosphorylation of histone H3 at threonine 11 establishes a novel chromatin mark for transcriptional regulation. Nat Cell Biol 10, 53-60 (2008).
Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using STAR

treatment_protocol: AOM/DSS tumour organoids were maintained in DMEM/F12 medium supplemented with 10mmol/L HEPES, 1x Glutamax, 1xN2, 1xB27, 1mmol/L N-Acc, 50ng/ml murine EGF and treated with 1µM tamoxifen and vehicle

value: AOM/DSS tumour organoids

tag: chip antibody


title: KMT9b_AOMDSS_Clone3

value: anti-KMT9Beta, #28358, lot 20062017, Schule Lab


title: AOMDSS_tumour_organoids_clone3_control replicate 1


title: 1dpw_D7_S117

value: CD1 x C57BL/6J cross


title: H1C1a-X1-hX4


title: H1C1a-X1-hX5


title: KMT9a_AOMDSS_Clone3

value: anti-KMT9alpha, #27630, lot 20062017, Schule Lab


title: genomic DNA from anal sample T_354

source_name: anal sample T_354


title: genomic DNA from anal sample T_375

source_name: anal sample T_375


title: H1C1a-X1-hX3


title: genomic DNA from anal sample T_359

source_name: anal sample T_359


title: genomic DNA from anal sample T_447

source_name: anal sample T_447


title: genomic DNA from anal sample T_353

source_name: anal sample T_353


title: H1C1a-X1-hX2


title: genomic DNA from anal sample T_382

source_name: anal sample T_382


title: 1dpw_D4_S114

source_name: YFP+ keratinocytes

value: partial-thickness wounded


title: 1dpw_D5_S115


title: Input_AOMDSS_Clone3


title: genomic DNA from anal sample T_324

source_name: anal sample T_324


title: genomic DNA from anal sample T_370

source_name: anal sample T_370


title: 1dpw_D3_S113


title: H1C1a-X1-S


title: H1C1a-X1


title: 1dpw_D10_S120


title: 1dpw_D2_S112


title: 1dpw_D6_S116


title: H2C2j


title: 1dpw_C9_S109


title: H1C1a-X1-hX1


title: H2C2i


title: Bap1 loss-of-function partial hepatectomy, age 6 months, biological rep3

first: Anirban

last: Maitra

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

description: partial hepatectomy with tumors, pooled litter

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Hybridize 16 hours at 45° to Affymetrix Mouse Transcriptome Array 1.0 ST. Wash and stain using Affymetrix proprietary reagents in the GeneChip Fluidics Station 450 (FS450).

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The CEL files were pre-processed and normalized using the Robust Multichip Average (RMA) algorithm implemented in oligo package within R

source_name: homozygous knockout, BhomoKA, liver

label_protocol: Samples were enzymatically fragmented and biotinylated according to manufacturer’s standard protocol (Affymetrix)

growth_protocol: Mouse liver tumors from mice of variable ages demonstrating signs of disease

extract_protocol: Mouse genotype was determined via PCR on tail clippings obtained at 7-10 days of age.  Mice demonstrating one or more signs of disease were euthanized and immediately underwent necropsy. All tissue samples were snap frozen in liquid N2. RNA was extracted from samples using RNeasy Mini kit (Quigen).  cDNA synthesis and amplification was performed using the WT Plus assay (Affymetrix).

treatment_protocol: not applicable

tag: age

value: 6 months

value: liver


title: 1dpw_C8_S108


title: genomic DNA from anal sample T_349

source_name: anal sample T_349

tag: sample type


title: genomic DNA from anal sample T_348

source_name: anal sample T_348


title: genomic DNA from anal sample T_339

source_name: anal sample T_339


title: Bap1 loss-of-function partial hepatectomy, age 6 months, biological rep2


title: wild-type, partial hepatectomy, age 11 months, biological rep3

source_name: wild-type, KA, liver

value: wild-type

value: 11 months


title: genomic DNA from anal sample T_345

source_name: anal sample T_345

value: Tumor


title: 1dpw_C7_S107


title: genomic DNA from anal sample T_330

source_name: anal sample T_330


title: wild-type, partial hepatectomy, age 8 months, biological rep3

value: 8 months


title: wild-type, partial hepatectomy, age 16 months, biological rep1

value: 16 months


title: H2C2g

source_name: induced pluripotent stem cells

tag: cell line


title: genomic DNA from anal sample T_302

source_name: anal sample T_302


title: genomic DNA from anal sample T_295

source_name: anal sample T_295


title: 1dpw_C6_S106


title: genomic DNA from anal sample T_303

source_name: anal sample T_303


title: Seedlings, Wild type treated with DTT_replicate 3

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Gene expression data from 17 day old wild type seedlings grown supplemented with 2 mmM DTT

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of Aragene-1_0-type from Affymetrix. A Custom CDF Version 16 with TAIR-ID based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

organism: Arabidopsis thaliana

source_name: WT seedling grown on MS medium

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: RNA was extracted from 17-day-old wild-type (Col-0) and naa20-1 (SALK_027687) seedlings grown on 1xMS medium under short day conditions (100 µE, 8.5h light,).

extract_protocol: RNA was extracted with the peqGOLD Total RNA Kit (Peqlab, Germany) according to the manufacturers protocol.

treatment_protocol: Seedlings of the same developmental stage (2 days) were transferred to 1xMS medium supplemented with or without 2 mM DTT and grown for 15 more days under short day conditions (Percival). Whole seedlings were harvested (three pools per sample combining min. 10 seedlings each) 17 days post stratification and total RNA was extracted for microarray analysis.

value: WT

value: seedlings

value: DTT


title: H2C2f

value: induced pluripotent stem cells


title: 1dpw_C5_S105

value: skin


title: H2C2e


title: Seedlings, Wild type treated with DTT_replicate 2


title: H2C2h


title: 1dpw_C4_S104


title: 1dpw_C3_S103


title: genomic DNA from anal sample I_215

source_name: anal sample I_215


title: genomic DNA from anal sample I_667

source_name: anal sample I_667


title: H2C2c


title: 1dpw_C11_S111

source_name: YFP+ keratinocytes


title: Seedlings, Wild type treated with DTT_replicate 1


title: H2C2d


title: Seedlings, naa20-1 treated with DTT_replicate 3

description: Gene expression data from 17 day old naa20-1 mutant seedlings grown supplemented with 2 mmM DTT

source_name: naa20-1 mutant seedling grown on MS medium


title: Seedlings, naa20-1 treated with DTT_replicate 2


title: genomic DNA from anal sample I_608

source_name: anal sample I_608


title: 7S-3: Spt7m in YP+Sucrose, replicate3

city: Wuhan

first: Junhua

last: Huang

state: Hubei

address: NO. 368, Youyi Ave., Wuchang District

department: School of Life Sciences

institute: Hubei University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using Cutadapt software v1.16 with parameters -q 20 -m 20, and masked for low-complexity or low-quality sequence, then mapped to whole genome (NCBI GCF000146045.2 R64) using hisat 2 v2.1.0  with parameters -p 10 --rna-strandness R.
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using StringTie v1.3.3b with parameters -B -e -p 8.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: The wild type Saccharomyces cerevisiae strain (BY4741), the Ada3 acetylation mutant (Ada3-3KR), Gcn5 bromodomain mutant (Gcn5m) and Spt7 bromodomain mutant (Spt7m) were cultured in 5mL YPD media (1% yeast extract, 2% peptone, and 2% Glucose) at 28℃ in 300rpm shaker.

extract_protocol:
The yeast cells were collected, 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 according to Illumina's instructions accompanying the Illumina TruseqTM RNA sample prep Kit.

treatment_protocol: The yeast cell cultures (OD600=0.7) were respectively transferred to YP media with Glucose or Sucrose, treated for 30 min.

value: Spt7 Bromodomain mutant (Spt7m)

tag: culture

value: treated in YP media supplemented with 2% Sucrose for 30 minutes


title: H2C2a


title: genomic DNA from anal sample I_160

source_name: anal sample I_160


title: 7S-2: Spt7m in YP+Sucrose, replicate2


title: genomic DNA from anal sample I_595

source_name: anal sample I_595


title: H1C1l


title: 7S-1: Spt7m in YP+Sucrose, replicate1


title: 1dpw_C10_S110

value: CD1 x C57BL/6J cross


title: Seedlings, naa20-1 treated with DTT_replicate 1


title: genomic DNA from anal sample I_135

source_name: anal sample I_135


title: genomic DNA from anal sample I_475

source_name: anal sample I_475


title: 7G-3: Spt7m in YP+Glucose, replicate3

value: in YP media supplymented with 2% Glucose for 30 minutes


title: 1dpw_B9_S100

value: partial-thickness wounded


title: 1dpw_B8_S99


title: 1dpw_B7_S98


title: H1C1k


title: H1C1j


title: Bap1 loss-of-function partial hepatectomy, age 7 months, biological rep1

source_name: homozygous knockout, BhomoKA, liver

value: 7 months


title: genomic DNA from anal sample I_423

source_name: anal sample I_423


title: 7G-2: Spt7m in YP+Glucose, replicate2


title: 1dpw_B6_S97


title: H1C1i

source_name: induced pluripotent stem cells


title: 7G-1: Spt7m in YP+Glucose, replicate1


title: 1dpw_B5_S96


title: 5S-3: Gcn5m in YP+Sucrose, replicate3

value: Gcn5 Bromodomain mutant (Gcn5m)


title: H1C1h


title: 1dpw_B3_S95


title: H1C1g


title: 5S-2: Gcn5m in YP+Sucrose, replicate2


title: 1dpw_B11_S102


title: H2C2b


title: genomic DNA from cervical sample C3_06

hyb_protocol: standard Illumina protocol

data_processing: IDAT files were processed, background corrected and normalized using control probes in R using the minfi bioconductor package.

label: Cy5, Cy3

source_name: cervical sample C3_06

label_protocol: standard Illumina protocol


title: H1C1f


title: 1dpw_B10_S101


title: genomic DNA from anal sample I_353

source_name: anal sample I_353


title: genomic DNA from cervical sample N_10

source_name: cervical sample N_10

value: Normal


title: 1dpw_B1_S94


title: 5S-1: Gcn5m in YP+Sucrose, replicate1


title: H1C1e


title: genomic DNA from cervical sample C3_08

source_name: cervical sample C3_08


title: 5G-3: Gcn5m in YP+Glucose, replicate3


title: H1C1c


title: H1C1d


title: 1dpw_A9_S92


title: genomic DNA from cervical sample C3_09

source_name: cervical sample C3_09


title: genomic DNA from cervical sample N_08

source_name: cervical sample N_08


title: 5G-1: Gcn5m in YP+Glucose, replicate1


title: 5G-2: Gcn5m in YP+Glucose, replicate2


title: genomic DNA from cervical sample C3_07

source_name: cervical sample C3_07


title: 1dpw_A7_S91

source_name: YFP+ keratinocytes


title: genomic DNA from cervical sample C3_05

source_name: cervical sample C3_05


title: genomic DNA from cervical sample T_07

source_name: cervical sample T_07


title: WT_S3: WT in YP+Sucrose, replicate3

source_name: whole cell

value: wild type


title: 1dpw_A6_S90


title: 1dpw_A4_S89


title: CHO_HDAC4_5kb_5d_nodox_H3K9me3

city: Stanford

first: Sarah

last: Lensch

state: CA

address: 443 Via Ortega

department: Bioengineering

institute: Stanford University

data_processing:
library strategy: CUT&RUN
Make genome file with appropriate reporter appended to end of genome file
Align reads to genome with Bowtie 2 version 2.3.4.1 with command 'bowtie2 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 -x {reference genome} -p 8 -1 {first mate of pair} -2 {second mate of pair} -S {output SAM file name}'
Convert SAM files to BAM files and subsequently sort and index BAM files with Samtools version 1.7
Quantify and mark duplicates with Picard version 11.0.7 with command 'java -jar {picard tool} MarkDuplicates -I {input sorted BAM file} -O {output deduplicated BAM file} -M {output metrics file} --REMOVE_DUPLICATES true'
Subtract duplicate reads and remove reads from regions where alignment is ambigous (ie non-unique reporter element sequences)
Normalize by reads per million with bamCoverage version 3.3.1 with command 'bamCoverage --bam {input deduplicated BAM file} -o {output bedgraph file} --outFileFormat bedgraph --extendReads --centerReads --binSize 10 --normalizeUsing CPM'
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files

organism: Cricetulus griseus

source_name: Chinese hamster ovarian cell line (CHO-K1)

growth_protocol: Cells were cultured at 37°C in a humidified incubator (Panasonic MCO-230AICUVL) with 5% CO2. CHO-K1 cells were grown in Alpha MEM Earle’s Salts media with 10% Tet Approved FBS (Takara Bio 631367, Lots # A16039 & #17033) and 1X Penicillin/Streptomycin/L-glutamine (Gibco 10378016). CHO-K1 cells were passaged by rinsing with Dulbecco's Phosphate-Buffered Saline (DPBS, Gibco 14190250), and incubating at room temperature with 0.25% Trypsin (Gibco, 25200056). K562 cells were grown in RPMI 1640 medium (Gibco, 11875119) with 10% Tet Approved FBS (Takara Bio 631367, Lot #17033) and 1X Penicillin/Streptomycin/L-glutamine (Gibco 10378016).

extract_protocol:
CUT&RUN for the K562 KRAB and CHO-K1 KRAB cell lines was performed according to the third version of the published protocol on protocols.io. For each antibody condition, 250,000 K562 or CHO-K1 cells were harvested and incubated with 10uL of activated Concanavalin A beads. Cells were permeabilized with 0.05% digitonin and incubated at room temperature for two hours with a 1:100 dilution of one of the following antibodies: guinea pig anti-rabbit IgG H&L chain (Antibodies-Online; Cat. No.: ABIN101961); rabbit anti-H3ac (Active Motif; Cat. No.: 39139); rabbit anti-H3K4me3 (Active Motif; Cat. No.: 39159); rabbit anti-H3K9me3 (Abcam; Cat. No.: ab8898). Unbound antibody was washed out, and cells were incubated with 140ng/mL of a protein A and micrococcal nuclease fusion (pA-MNase; generously provided by the Henikoff lab). Unbound pA-MNase was washed out, and cells were resuspended in a low-salt buffer. Tubes were placed in a thermal block chilled to 0°C, and 10mM CaCl2 was added to trigger DNA cleavage by pA-MNase. After 5 minutes, the reaction was stopped by chelating calcium ions with the addition of 20mM EGTA, and tubes were incubated at 37°C for 30 minutes under physiological salt conditions to promote diffusion of fragmented chromatin into the supernatant. Fragmented chromatin in the supernatant was collected and purified using the DNA Clean & Concentrator-5 kit (Zymo; Cat. No.: D4004). CUT&RUN for the CHO-K1 HDAC4 cell lines was performed using the EpiCypher CUTANA ChIC/CUT&RUN Kit (Cat. No.: 14-1048) according to the User Manual Version 2.0 with the following conditions: an input of 500,000 CHO-K1 cells per antibody condition; a final digitonin concentration of 0.01%; an overnight antibody incubation at 4°C with 1:100 dilutions of the anti-H3Kac and anti-H3K9me3 antibodies described above along with a 1:50 dilution of rabbit anti-H3K27me3 (Cell Signaling Technologies, Cat. No: 9733S); and DNA purification with the provided spin columns.
Dual-indexed sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs; Cat. No.: E7645L) with 12-14 cycles of PCR, and size selection was performed with either Agencourt AMPure XP (Beckman Coulter; Cat. No.: A63880) or SPRIselect (Beckman Coulter; Cat. No.: B23318) magnetic beads. Library concentrations were quantified with the Qubit 1X dsDNA HS Assay Kit (Invitrogen; Cat. No.: Q33231), and library fragment sizes were assessed with the High Sensitivity D1000 ScreenTape (Agilent; Cat. No.: 5067-5584) and High Sensitivity D1000 Reagent (Agilent; Cat. No.: 5067-5585) on an Agilent 4200 TapeStation System. Libraries were pooled for genome-wide sequencing.

treatment_protocol: Cells were treated with 1000 ng/mL doxycyline (dox) (Tocris Bioscience, 4090) for 5 days during which fresh dox diluted from frozen aliquots was added to the media before each cell passage every 2-3 days.

tag: reporter

value: 5kb spacer

tag: chromatin regulator

value: no dox

tag: timepoint

value: 5 days

tag: antibody

value: H3K9me3 (Abcam; Cat. No.:ab8898)


title: genomic DNA from cervical sample T_10

source_name: cervical sample T_10

value: Tumor


title: WT_G3: WT in YP+Glucose, replicate3


title: CHO_HDAC4_5kb_5d_dox_H3K27me3

value: dox (1000 ng/mL)

value: H3K27me3 (Cell Signaling Technologies, Cat. No:9733S)


title: H1C1a

tag: cell type

value: induced pluripotent stem cells


title: WT_S2: WT in YP+Sucrose, replicate2


title: D80_EpdSC_1

data_processing:
75bp paired-end reads were aligned to mm10 using Bowtie with the parameters –X 2000 and –m 1.
Duplicates were removed using Picard.
Peaks were called using MACS2 (2.1.1.20160309) with the parameter –keep-dup all to let MACS skip the filtering and keep all the sequencing tags.
Peaks with a score per million (SPM) < 9 were considered insignificant and removed
Reads were normalized based on the total number of reads in significant peaks in each sample using the genomecov function in bedtools (v2.29.2)
Genome_build: mm10
Supplementary_files_format_and_content: peak bed files
Supplementary_files_format_and_content: bigwig files

source_name: epidermal stem cells

extract_protocol:
Skin were trypsinized to extract basal stem cells, which were then FACS-sorted to isolate populations of interest.
Freshly sorted cells (15K-100K) were pelleted and incubated with cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). After removing lysis buffer, samples were immediately subjected to a transposition reaction at 37°C for 30 min with 2-10μl TnD transposase enzyme (Illumina Nextera DNA Preparation Kit). Transposed DNA was purified using QIAGEN MiniElute PCR purification kit and PCR amplified with 10-15 cycles.

value: skin

value: unwounded


title: D80_EpdSC_3

value: CD1 x C57BL/6J cross


title: D80_EpdSC_2


title: H1C1b


title: WT_S1: WT in YP+Sucrose, replicate1

value: treated in YP media supplemented with 2% Sucrose for 30 minutes


title: 1dpw_A10_S93

value: partial-thickness wounded


title: WT_G1: WT in YP+Glucose, replicate1

value: in YP media supplymented with 2% Glucose for 30 minutes


title: CHO_HDAC4_5kb_5d_nodox_H3K27me3


title: genomic DNA from cervical sample N_09

source_name: cervical sample N_09


title: WT_G2: WT in YP+Glucose, replicate2


title: CHO_HDAC4_5kb_5d_dox_H3K9me3


title: D80_Dremel_3

source_name: wound-responsive hair follicle stem cell progeny


title: CHO_HDAC4_5kb_5d_dox_H3Kac

value: H3Kac (Active Motif; Cat. No.:39139)


title: CHO_HDAC4_5kb_5d_nodox_H3Kac


title: genomic DNA from cervical sample T_09

source_name: cervical sample T_09


title: genomic DNA from cervical sample T_06

source_name: cervical sample T_06


title: D80_Dremel_1


title: CHO_HDAC4_5kb_5d_nodox_H3K4me3

value: H3K4me3 (EpiCypher; Cat. No.:14-1048)


title: 3S-3: Ada3-3KR in  YP+Sucrose, replicate3

value: Ada3 acetylation mutant (Ada3-3KR)


title: 3S-1: Ada3-3KR in  YP+Sucrose, replicate1


title: D7_Dremel_2


title: 3S-2: Ada3-3KR in  YP+Sucrose, replicate2


title: CHO_HDAC4_5kb_5d_nodox_IgG

value: 5kb spacer

value: IgG (EpiCypher; Cat. No.:14-1048)


title: 3G-3: Ada3-3KR in  YP+Glucose, replicate3


title: genomic DNA from cervical sample C3_03

source_name: cervical sample C3_03


title: CHO_HDAC4_NS_5d_dox_H3K9me3

value: no spacer

value: 5 days


title: genomic DNA from cervical sample T_08

source_name: cervical sample T_08

value: Tumor


title: 3G-2: Ada3-3KR in  YP+Glucose, replicate2


title: genomic DNA from cervical sample C3_04

source_name: cervical sample C3_04


title: D7_Dremel_1


title: D3_Dremel_3


title: CHO_HDAC4_NS_5d_nodox_H3K9me3

value: no dox

value: H3K9me3 (Abcam; Cat. No.:ab8898)


title: 3G-1: Ada3-3KR in  YP+Glucose, replicate1


title: 9uninfected

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

institute: Max Planck Institute for Infection Biology

data_processing:
Reads were aligned against GRCm38 using STAR v2.4
Per-gene expression levels were determined by counting reads per gene using htseq-count against gene models from Ensembl, version Mus_musculus.GRCm38.76
Genome_build: GRCm38
Supplementary_files_format_and_content: htseq-count output as tab-separated text file. Columns: Ensembl gene id, read count

source_name: stomach mucosa

growth_protocol: not applicable

extract_protocol:
Stomach tissues were sorted for Myh11+ myofibroblasts (GFP) and RNA was isolated from sorted cells using Qiagen RNeasy Plus Micro Kit
cDNA was generated from total RNA using SMART-Seq® v4 Ultra® Low Input RNA Kit resulting in enrichment of polyA RNA. Libraries were generated from cDNA using Nextera XT DNA Library Preparation Kit.

treatment_protocol: 3x Myh11CreErt2/Rosa26-mTmG mice were infected with H. pylori for 2 months and 3x uninfected mice were used as a control, 2 days before sacrifizing mice were intraperitoneally injected with one dose (4mg/25g BW) of Tamoxifen to induce Myh11+ lineage.

tag: condition

value: Uninfected control


title: WS-3: WT in YP+Sucrose, replicate3

value: wild type


title: D3_Dremel_2

value: skin


title: 7infected

value: Helicobacter pylori infection


title: D80_Dremel_2

value: CD1 x C57BL/6J cross


title: genomic DNA from cervical sample T_05

source_name: cervical sample T_05


title: CHO_HDAC4_NS_5d_nodox_H3K27me3

value: H3K27me3 (Cell Signaling Technologies, Cat. No:9733S)


title: WS-2: WT in YP+Sucrose, replicate2

value: treated in YP media supplemented with 2% Sucrose for 30 minutes


title: CHO_HDAC4_NS_5d_dox_H3K27me3

value: dox (1000 ng/mL)


title: D3_Dremel_1

value: partial-thickness wounded


title: 5uninfected


title: D0_EpdSC_4

value: unwounded


title: genomic DNA from cervical sample N_06

source_name: cervical sample N_06

value: Normal


title: WS-1: WT in YP+Sucrose, replicate1


title: D0_EpdSC_3


title: WG-3: WT in YP+Glucose, replicate3

value: in YP media supplymented with 2% Glucose for 30 minutes


title: CHO_HDAC4_NS_5d_nodox_H3Kac

value: no spacer

value: H3Kac (Active Motif; Cat. No.:39139)


title: WG-2: WT in YP+Glucose, replicate2


title: genomic DNA from cervical sample C3_01

source_name: cervical sample C3_01


title: 1infected


title: genomic DNA from cervical sample C3_02

source_name: cervical sample C3_02


title: CHO_KRAB_5kb_5d_nodox_H3K9me3

value: 5kb spacer

value: KRAB

value: 5 days


title: 14uninfected

value: Uninfected control


title: 2infected


title: WG-1: WT in YP+Glucose, replicate1

value: wild type


title: D0_EpdSC_1

value: skin


title: 11infected

value: Helicobacter pylori infection


title: CHO_HDAC4_NS_5d_dox_H3Kac


title: genomic DNA from cervical sample T_04

source_name: cervical sample T_04

value: Tumor


title: genomic DNA from cervical sample N_02

source_name: cervical sample N_02


title: genomic DNA from cervical sample N_05

source_name: cervical sample N_05


title: D0_HFSC_4

source_name: hair follicle stem cells

value: CD1 x C57BL/6J cross


title: 10uninfected


title: MeDIP-Seq Tet2Rank–/–; Tet3aRank+/– osteoclasts rep2

city: Kyotanabe

first: Keizo

last: Nishikawa

state: Kyoto

address: 1-3, Tatara Miyakodani

department: Medical Life Systems

institute: Graduate School of Life and Medical Sciences

data_processing:
Sequenced reads were trimmed with Trim Galore and mapped to the mouse genome (mm10) with Bowtie2.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig

source_name: Tet2Rank–/–; Tet3aRank+/– osteoclasts

extract_protocol:
Genomic DNA was prepared from cultured cells using the GenElute Mammalian Genomic DNA Miniprep Kit (Sigma-Aldrich) according to the manufacturers’ instructions.
Genomic DNA was sonicated to 150 bp fragments with Covaris (Covaris). Methylated DNA was enriched using MEDIP Kit (Active Motif) according to manufacturer’s protocol. The illumina libraries were prepared using KAPA Hyper Prep Kit (Kapa Biosystems) and TruSeq DNA UD Indexes (Illumina) according to manufacturer’s instructions. Paired-end sequencing (100 bp x 2) was performed using HiSeq3000 (Illumina).

treatment_protocol: Bone marrow cells derived from mice were seeded and cultured in alpha-MEM with 10%FBS containing M-CSF. After 2 days, adherent cells were used as bone marrow-derived monocyte/macrophage precursor cells (BMMs). The BMMs were further cultured in the presence of RANKL and M-CSF to generate osteoclasts.

value: Bone marrow-derived osteoclasts

tag: gender

value: Male


title: D0_HFSC_3

tag: tissue


title: genomic DNA from cervical sample N_04

source_name: cervical sample N_04


title: D0_HFSC_2

tag: strain


title: CHO_KRAB_5kb_5d_dox_H3K4me3

source_name: Chinese hamster ovarian cell line (CHO-K1)

value: dox (1000 ng/mL)

value: H3K4me3 (Active Motif; Cat. No.:39159)


title: CHO_KRAB_5kb_5d_dox_H3Kac


title: CHO_KRAB_5kb_5d_dox_H3K9me3

value: H3K9me3 (Abcam; Cat. No.:ab8898)


title: CHO_KRAB_5kb_5d_nodox_H3K4me3

value: no dox


title: MeDIP-Seq Tet2Rank–/–; Tet3aRank+/– osteoclasts rep1


title: D0_HFSC_1

tag: genotype

value: unwounded


title: MeDIP-Seq Wild-type osteoclasts rep2

description: Wild-type osteoclasts rep2

source_name: Wild-type osteoclasts


title: MeDIP-Seq Wild-type osteoclasts rep1

description: Wild-type osteoclasts rep1


title: CHO_KRAB_5kb_5d_dox_IgG

tag: treatment

value: IgG (Antibodies-Online; Cat. No.:ABIN101961)


title: CHO_KRAB_5kb_5d_nodox_H3Kac

value: 5kb spacer

value: H3Kac (Active Motif; Cat. No.:39139)


title: genomic DNA from cervical sample T_03

source_name: cervical sample T_03


title: genomic DNA from cervical sample N_01

source_name: cervical sample N_01

value: Normal


title: TM-1-leaf-K4me3_rep2_clean

city: Xuzhou

first: Cen

middle: Ai

last: Zhang

state: Jiangsu

address: No.2 Kunpeng

institute: Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District

data_processing:
Raw reads of all sequencing data were trimmed using fastp (Chen et al., 2018b) based on the quality value (Q≥25) and read length (≥20 bp).
The trimmed reads ChIP-seq data were mapped to the G. hirsutum reference genome with Bowtie2 aligner (Langmead and Salzberg, 2012).
Any PCR duplicates were removed using Picard. Aligned reads with mapping quality (MapQ) less than 30 were removed using samtools (Li et al., 2009).
H3K27me3 peaks were called with ‘--broad’ parameter on (-f BAM -g 2.3e+9 --nomodel -q 0.01 --broad --broad-cutoff 0.1) and H3K4me3 peaks were called with off (-f BAM -g 2.3e+9 --nomodel -q 0.01) using the MACS2 software (Zhang et al., 2008)
Genome_build: NBI_Gossypium_hirsutum_v1.1
Supplementary_files_format_and_content: bed files were generated using MACS2, the bw files were generates using deeptools

organism: Gossypium hirsutum

growth_protocol: The allotetraploid cotton cultivar Gossypium hirsutum was used in this study. Cotton seeds were soaked in water for 24 h, then transferred to soil in pots to continue to grow in a greenhouse with 60 % humidity at 28/25°C and 16/8-h light/dark cycle. Two and three true leaves were collected from 20-old plants and ground into fine powder using liquid nitrogen

extract_protocol:
20 d-old cotton leaves were used for nuclei preparation. The nuclei were extracted using nuclei isolation buffer (NIB, pH 5.0, 1.0 M Glucose, 0.1 M citric acid, 80 mM KCl, 10 mM EDTA, adding fresh Triton X-100 to final 1% just before use). The nuclei were purified using 1x nuclei washing buffer (NWB, pH 5.0, 1 M Glucose, 0.1 M Na-citrate, adding fresh Triton X-100 to final 1% just before use). The purified nuclei were resuspended using 600 µl MNB buffer (50 % w/v Sucrose, 50 mM Tris-HCl, pH 7.5, 4 mM MgCl2, 1 mM CaCl2) for MNase digestion at 37°C for 10 min. Centrifuge the digestion mix at 13,000 rpm for 10 min at 4°C and transferred supernatant into a new 1.5 ml tube. The digested nuclei pellet was resuspended in lysis buffer (1 mM Tris-HCl, pH 7.5, 0.1 mM PMSF, 2 % v/v Complete Mini) and leave it on ice for 1 h. After centrifugation, the supernatant was transferred into the 1.5 m tube containing digested chromatin. ChIP incubation buffer was added to the digested chromatin to make 1.7 ml total. The remaining steps were followed the published procedures (Zhang et al., 2012), including antibody incubation followed by adding protein A-sepharose beads, beads washing and ChIPed DNA elution, purification of ChIPed DNA for library preparation and sequencing on Illumina platform.
The final purified DNA was used for ChIP-seq library preparation using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina purchased from NEB (Cat#: E7645S)

value: leaf

value: 20 days


title: genomic DNA from cervical sample N_03

source_name: cervical sample N_03


title: genomic DNA from cervical sample T_01

source_name: cervical sample T_01


title: genomic DNA from cervical sample N_07

source_name: cervical sample N_07


title: TM-1-leaf-Input_rep2_clean


title: TM-1-leaf-K27me3_rep2_clean


title: CHO_KRAB_5kb_5d_nodox_IgG

value: KRAB

value: 5 days


title: SMH_133_plus_OHT (Smg6-iKO)

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2FastQ v1.8.4.
Reads were mapped to the Mus musculus genome (GRCm38 with the Ensembl genome annotation Release 92) using STAR (version 2.5.4b, parameters: --alignIntronMax 100000 --outSJfilterReads --outSAMmultNmax Unique --outFilterMismatchNoverLmax 0.04) (PMID: 23104886).
For each gene, reads that map uniquely to one genomic position were counted with FeatureCounts (version 1.5.0, multi-mapping or multi-overlapping reads were not counted, stranded mode was set to “–s 2”, Ensembl release 92 gene annotation) (PMID: 24227677).
Genome_build: GRCm38
Supplementary_files_format_and_content: txt-file with tab-separated columns (original output format of FeatureCounts)

source_name: E13.5 embryo brain

growth_protocol: After isolation, neural stem cells were plated in DMEM/F12 medium (Gibco) supplemented with 2% B-27 supplement (Invitrogen), 1X penicillin and streptomycin (Thermo Fischer Scientific), 20 ng/ml EGF and 10 ng/ml bFGF (PeproTech).

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (217004, Qiagen) following the manufacturer’s manual.
Preparation of libraries was done using Illumina‘s TruSeq Stranded Total RNA (RiboZero Gold) kit according the manufacturer‘s description.

treatment_protocol: Smg6 was deleted by adding 1 µM 4-OHT ((Z)-4-Hydroxytamoxifen, Sigma H7904) to the medium and incubation for 3 days.

value: C57BL/6 mixed with 129SV

value: Smg6 Flox/Flox; RosaCreER tg/+

value: neural stem cells from E13.5 brains


title: SMH_132_plus_OHT (Smg6-iKO)


title: SMH_128_plus_OHT (Smg6-iKO)


title: TM-1-leaf_rep3

data_processing:
Raw reads of all sequencing data were trimmed using fastp (Chen et al., 2018b) based on the quality value (Q≥25) and read length (≥20 bp).
The trimmed reads RNA-seq data were mapped to the G. hirsutum reference genome with Hisat2 (Kim et al., 2015a).
Aligned reads with mapping quality (MapQ) less than 30 were removed using samtools (Li et al., 2009).
FPKM computed from StringTie (Pertea et al., 2015) was used to measure the expression level of each gene.
Genome_build: NBI_Gossypium_hirsutum_v1.1
Supplementary_files_format_and_content: FPKM files were generated from StringTie

extract_protocol:
Total RNAs were prepared using Trizol followed by DNase I treatment and removal of majority of mRNAs with oligo(T)-conjugated magnetic beads.
The enriched mRNA was subse-  quently used for RNA-seq library preparation following the  standard protocol for preparing Illumina RNA-seq libraries.


title: TM-1-leaf_rep2


title: SMH_127_plus_OHT (Smg6-iKO)


title: SMH_131_plus_OHT (control with 4-OHT)

value: Smg6 Flox/Flox; RosaCreER +/+


title: WT_NI-3

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
Obtained reads were checked for quality and adapter contamination with fastqc.
Reads were mapped to the mm10 reference genome using the ensembl structural annotation (release 100) using the hisat2 aligner (v 2.1.0) with additional options, next to index, splice sites and reads: --avoid-pseudogene and -p 8
A count matrix was made with featurecounts (v 2.0.0) with extra options --primary and -T 8
The count matrix was processed using DESeq2 to obtain differentially expressed genes (v 1.26.0) according to the standard workflow.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: counts.txt: Counts matrix.

source_name: mouse embryonic fibroblast

growth_protocol: Cells were cultured in DMEM (Dulbecco’s modified Eagle’s medium, Gibco®, Life TechnologiesTM) supplemented with 10% FCS, 1mM sodium pyruvate, 0.1mM non-essential amino acids, 2mM L-glutamate, 0.2% β-mercapto-ethanol, 0.1mM pen/strep and 0.2% prophylactic PlasmocinTM at 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated from solvent- or Dex-stimulated MEF cells with Aurum total RNA mini kit (732‐6820; Bio‐Rad) according to the manufacturer's instructions. RNA concentration was measured and RNA quality was checked with the Agilent RNA 6000 Pico Kit (Agilent Technologies).
Library preparation and sequencing were performed according to the manufacturer’s instruction with the Illumina TruSeq library prep kit.

treatment_protocol: MEF cells were seeded in 6-well plates in supplemented DMEM. Cells were treated for 5 hours with 10 nM Dex or solvent.

value: FVB/NJ

value: GRwt/wt

value: Mouse embryonic fibroblasts

value: Vehicle


title: WT_NI-2


title: HemEC_48hr_ITR10_02

city: chongqing

first: shuang

last: chen

address: No. 1 Youyi Road, Yuzhong District

institute: the First Affiliated Hospital of Chongqing Medical University

description: Gene expression after 48hr ITR10uM treatment upon infantile hemangioma endothelial cells in vitro

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

scan_protocol: Scanned on an Agilent G2565CA scanner.

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

source_name: hemangioma endothelial cells, 48hr, ITR10uM, patient 2

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

growth_protocol: Infantile primary hemangioma endothelial cells were successfully cultured with the method of tissue block from proliferative infantile hemangioma tissues, which were then cultured in RPMI 1640 (GIBCO) containing 10% fetal bovine serum, 10ng/ml basic fibroblast growth factor, and penicillin/streptomycin/glutamine. All cells were cultured at 37°C in humidified atmosphere containing 5% CO2.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Infantile primary hemangioma endothelial cells of 2 infants treated with 10μM itraconazole for 48 hours were performed, with 0.1% DMSO as control.

value: infantile hemangioma endothelial cells

value: female

tag: agent


title: Patient23 C1D8

type: protein

city: Seoul

first: Jung Hyun

last: Jo

state: --- Select ---

address: 50-1 Yonsei-ro

country: South Korea

institute: Yonsei University Health System

description: Normalized signal is calculated from average intensity of replicate spots / median signal.

hyb_protocol: protein sample was detected with Cy3-streptavidin (GE Healthcare, Chalfont St. Giles, UK).

scan_protocol: The slide was rinsed scanned using the GenePix 4100A scanner (Axon Instrument, USA) at 10 m resolution, optimal laser power and PMT.

data_processing: Following image scanning, they were gridded and quantified with GenePix 7.0 Software (Axon Instrument, USA).

molecule: protein

source_name: Pancreatic cancer

label_protocol: 50ug of protein sample was labeled and incubated with coupling mixture on the antibody microarray slide (Fullmoon Biosystems).

extract_protocol: Protein was extracted from plasma using a protein extraction buffer (Fullmoon Biosystems, Sunnyvale, CA) and protein expression was analyzed using antibody microarray analysis (Fullmoon Biosystems) according to the manufacturer’s protocol.

value: Blood


title: Patient23 EOT


title: HemEC_48hr_ITR0_01

description: Gene expression after 48hr ITR0uM treatment upon infantile hemangioma endothelial cells in vitro

source_name: hemangioma endothelial cells, 48hr, ITR0uM, patient 1

value: DMSO


title: HemEC_48hr_ITR0_02

source_name: hemangioma endothelial cells, 48hr, ITR0uM, patient 2


title: Patient23 C1D1


title: HemEC_48hr_ITR10_01

source_name: hemangioma endothelial cells, 48hr, ITR10uM, patient 1


title: WT_NI-1


title: SMH_129_plus_OHT (control with 4-OHT)


title: WT_DEX-3

value: Dexamethasone


title: Patient22 EOT


title: TM-1-leaf-K4me3_clean

data_processing:
Raw reads of all sequencing data were trimmed using fastp (Chen et al., 2018b) based on the quality value (Q≥25) and read length (≥20 bp).
The trimmed reads ChIP-seq data were mapped to the G. hirsutum reference genome with Bowtie2 aligner (Langmead and Salzberg, 2012).
Any PCR duplicates were removed using Picard. Aligned reads with mapping quality (MapQ) less than 30 were removed using samtools (Li et al., 2009).
H3K27me3 peaks were called with ‘--broad’ parameter on (-f BAM -g 2.3e+9 --nomodel -q 0.01 --broad --broad-cutoff 0.1) and H3K4me3 peaks were called with off (-f BAM -g 2.3e+9 --nomodel -q 0.01) using the MACS2 software (Zhang et al., 2008)
Genome_build: NBI_Gossypium_hirsutum_v1.1
Supplementary_files_format_and_content: bed files were generated using MACS2

value: leaf

tag: chip antibody


title: Patient22 C1D8


title: TM-1-leaf-K27me3_clean

tag: age

value: 20 days


title: SMH_126_plus_OHT (control with 4-OHT)


title: TM-1-leaf-Iuput_clean


title: WT_DEX-2


title: SMH_125_plus_OHT (control with 4-OHT)


title: Patient22 C1D1


title: Patient21 EOT


title: SMH_133 (control)

value: no treatment


title: MON_NI-3

value: GRD+L/D+L


title: MON_NI-2


title: SMH_132 (control)

value: C57BL/6 mixed with 129SV


title: MON_NI-1


title: Urine no AKI 1

city: Birmingham

first: Matthew

middle: David

last: Cheung

state: AL

address: 1825 University Blvd

institute: University of Alabama at Birmingham School of Medicine

data_processing:
10x Genomics Cell Ranger version 6.0
Genome_build: Human genome GRCh38 with SARS-CoV-2 genome (NC_045512.2)
Supplementary_files_format_and_content: mtx

source_name: Urine

extract_protocol: All steps were performed on ice. Urine was collected as either a voided specimen or from a urinary catheter. Samples were immediately transferred to a biosafety level (BSL) 2+ laboratory for processing. Urine samples were transferred to a 50mL conical tube and centrifuged at 1000x g for 10 minutes at 4 degrees celsius. Cell pellets were washed with ice-cold PBS, filtered through a 40µm filter, and centrifuged again. Live cells were purified using the MACS Debris Removal Kit (Miltenyi Biotec) followed by the EasySep Annexin V Dead Cell Removal Kit (StemCell). Briefly, cells were resuspended in ice-cold PBS and mixed with debris removal solution. Cold PBS was overlaid on the mixture and centrifuged at 300x g for 10 minutes at 4 degrees celsius. The top two phases were aspirated and then remaining cells were washed with PBS. Cells were resuspended and mixed with Dead Cell Removal Cocktail, Biotin Selection Cocktail, then RapidSpheres before separation in an EasySep magnet. Cells were washed and resuspended in 52µL of PBS (no calcium or magnesium) + .04% BSA (Fisher Scientific) for scRNAseq processing. Purified cells were immediately processed using the Chromium 3’ Single Cell RNA sequencing kit (10X Genomics) according to the manufacturer’s instructions.

tag: disease state

value: CTL

tag: sediment

value: urine


title: TM-1-leaf_rep1


title: SMH_128 (control)

value: Smg6 Flox/Flox; RosaCreER tg/+

value: neural stem cells from E13.5 brains


title: Patient21 C1D1


title: Urine AKI 5

value: COVID AKI


title: 9H_S9 wt_hip

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
FASTQ sequencing reads were adaptor-trimmed and quality-filtered with Trimmomatic (Bolger et al., 2014), prior to mapping to the mm10 mouse reference genome with STAR (Dobin and Gingeras, 2016).
Gene count normalization and differential gene expression havehas been done with DESeq2 (Love et al., 2014).
GeneSCF was employed for functional enrichment analysis and ontology (Subhash and Kanduri, 2016).
Low-dimensional embedding of high-dimensional data was done by t-Distributed Neighbor Embedding (t-SNE) machine learning algorithm.
Genome_build: mm10

source_name: Scn1a wt  Hippocampus

extract_protocol:
Cerebral cortex and hippocampus from 4-5- month- old mice were dissected and total RNA has been extracted with TRIzolTM reagent (ThermoFisher Scientific). Only high-quality RNA with ana RNA integrity number (RIN) of 8 or higher was used.
Library preparation and sequencing havehas been performed with the TruSeq RNA Library Preparation Kit v2 kit (Illumina) by Genewiz.

value: hippocampus


title: Urine AKI 4


title: 12H_S12 wt_hip


title: WT_DEX-1

value: FVB/NJ

value: GRwt/wt

value: Mouse embryonic fibroblasts


title: MON_DEX-2


title: MON_DEX-1


title: 11H_S11 wt_hip


title: Urine AKI 2


title: Patient6 EOT

value: Blood


title: Patient19 C1D8


title: DIM2_NI-3

value: GRL/L

value: Vehicle


title: Urine AKI 1


title: Patient19 C1D1


title: Urine no AKI 2


title: LQT1_hiPSCCM_gene expression_multiplex_untreated_antimiRCtrl_antimiR365  [scRNA-seq]

city: Munich

first: Dena

last: Esfandyari

state: Bavaria

address: Haus 607, Biedersteiner Str. 29, IPT

department: Institute of Pharmacology and Toxicology

institute: Technical University of Munich

description: single cell 3' mRNA expression library multiplexed using cell hashing technology (10x Genomics - Biolegend)

data_processing:
bcl2fastq for basecalling, fastq conversion and demultiplexing
cellranger v6.0.1 for LQT1 and v2.1.0 healthy cells for alignment, filtering, barcode counting, UMI counting, demultiplexing of HTOs
Genome_build: GRCh38, Gencode annotation v33 for LQT1 and v28 for healthy cells
Supplementary_files_format_and_content: Feature-Barcode Matrices and HTOs from cellranger (10x Genomics)

source_name: iPSC-derived cardiomyocyte

growth_protocol: the hiPSCs were maintained in Geltrex-coated plates (1 ml per 35 mm plate, 1 hour incubation at 37 °C) in E8-flex medium (2 ml per 35 mm plate, medium exchange every other day) and passaged with Versene (1 ml per 35 mm plate, incubation for 5-10 min at room temperature) when confluent. For cardiac differentiation, the cells were passaged into 12 well plates and cultured in cardio differentiation medium to reach 85-90% of confluency, the optimal cell density for starting the differentiation (d0). The differentiation carried out using Wnt signaling modulators, CHIR99021 and IWP2 (both from Merck Millipore). The yielded hiPSC-CMs were maintained in cardio culture medium and one round of metabolic selection was performed between d20-30 in order to enrich cardiomyocytes. After selection hiPSC-CMs were enzymatically dissociated (using Collagenase I and Trypsin), replated in lower densities and maintained in cardio culture medium for approximately 60 days for further maturation.

extract_protocol:
After transfection of hiPSC-CMs with mimics or antimiRs for 48 hours, the cells were washed and dissociated to single cells with collagenase II and trypsine and proceeded for single cell capture, barcoding and library preparation (10x genomics). For LQT1 hiPSC-CMs, the cells from different treatment conditions were stained with TotalSeq-A cell hashing antibodies (according to Biolegend's instructions) and were pooled together prior to single cell capture with Chromium.
Barcoding and library preparation from healthy hiPSC-CMs was done using Chromium single cell 3’ (v2, 10x Genomics). For LQT1 cells Chromium Next GEM single cell 3’ (v3.1, 10x Genomics) was used for preparation of gene expression library. The libraries from the TotalSeq-A hashtag oligonucleotides (HTO) for cell multiplexing was prepared according to Biolegend's cell hashing manual.

treatment_protocol: To elevate the intracellular level of miR-365, the cells were transfected with synthetic mimic-365. Inhibition of endogenous miR-365 was achieved by transfection of LNA-antimiR-365 (Exiqon-Qiagen). Negative control oligonucleotides with the same chemistry were used in each case (mimic-Ctrl and antimir-Ctrl, respectively). Transfection was performed using Lipofectamine RNAiMAX to  reach final concentration of 25 nM oligonucleotides. The medium was exchanged 15-24 hours after transfection and the cells were processed 48 hours post-transfection.

tag: cell/sample type

value: iPSC-derived cardiomyocyte

value: untreated, antimiR-ctrl and antimiR-365 multiplexed

value: long QT syndrome type 1


title: 22C_S22 wt_cx

source_name: Scn1a wt Cortex

value: cortex


title: D0_EpdSC_2

city: New York

first: Kevin Andrew

last: Gonzales

address: 1230 York Avenue

institute: The Rockefeller University

source_name: epidermal stem cells

value: skin

value: CD1 x C57BL/6J cross

value: unwounded


title: Patient21 C1D8


title: LQT1_hiPSCCM_TotalSeqA_HTO

description: single cell hashtag oligonucleotide (HTO) multiplexing library

tag: sample type

value: Biolegend TotalSeq-A cell hashing oligonucleotides


title: 21C_S21 wt_cx


title: Patient6 C1D8


title: SQT1_hiPSCCM_mimic365_2

data_processing:
bcl2fastq (v2.20) for basecalling, fastq conversion, adapter trimming (only for SQT1 samples) and demultiplexing
Trim Galore! (v0.4.2 in Galaxy) for adapter trimming in healthy hiPSC-CMs
RNA STAR (v2.6.0 in Galaxy) with default parameters for alignment
StringTie (v1.3.6 in Galaxy) was used for transcript assembly and quantification
DESeq2 (v2.11.40.2 in Galaxy) for differential expression analysis and normalizing the counts
Genome_build: GRCh38, Gencode annotation v34 for SQT1 and v28 for healthy cells
Supplementary_files_format_and_content: tabular raw gene counts; excel file of the normalized count generated by DESeq2, TPM and FPKM

extract_protocol:
After transfection of hiPSC-CMs with mimics or antimiRs for 48 h, the cells were washed with PBS 3 times and total RNA was isolated using peqGOLD RNAPure (VWR). The integrity and quantity of RNA was determined using Agilent Bioanalyzer 2100 or Agilent TapeStation 4200.
For healthy hiPSC-CMs, libraries were prepared from 1 µg RNA using Illumina TruSeq Stranded mRNA kit and for SQT1 hiPSC-CMs Illumina mRNA ligation kit was used for library preparation.

treatment_protocol: To elevate the intracellular level of miR-365, the cells were transfected with synthetic mimic-365. Inhibition of endogenous miR-365 was achieved by transfection of LNA-antimiR-365 (Exiqon-Qiagen). Negative control oligonucleotides with the same chemistry were used in each case (mimic-Ctrl and antimir-Ctrl, respectively). Transfection was performed using Lipofectamine RNAiMAX to  reach a final concentration of 25 nM oligonucleotides. The medium was exchanged 15-24 hours after transfection and the cells were processed 48 hours post-transfection.

value: short QT syndrome type 1


title: 24C_S24 wt_cx


title: DIM2_NI-2


title: DIM2_DEX-2

value: Dexamethasone


title: 23C_S23 wt_cx


title: DIM2_NI-1


title: 8H_S8 rec_hip

source_name: Scn1a rec Hippocampus

value: hippocampus


title: MON_DEX-3

value: FVB/NJ

value: GRD+L/D+L


title: C1C1e-2

description: diploid-and-auto-tetraploid_gene_counts.txt

data_processing:
Sequencing reads were trimmed for adapter sequences using cutadapt v1.8.1 and read quality was confirmed using fastqc v0.11.9.
Reads were aligned using STAR v2.7.1a with two-pass mapping to a concatenated human-chimpanzee genome (hg38 and pt6).
The number of uniquely-mapped reads (MAPQ = 255) that overlap each gene was counted with featurecounts from the subread v1.6.0 package using a curated annotation (hg38.pt6.gtf). To generate the annotations, GRCh38.94 human exon annotations from Ensembl were mapped from hg38 to pt6 using pslMap. After removing mappings where the number of bases that map is less than half of the query exon size, we retained only exons that uniquely mapped from humans to chimpanzees. We then removed genes for which exons map to opposite DNA strands, different scaffolded chromosomes, or where consecutive exons map more than 800kb apart. We further filtered out exons where more than 10% of reads from diploid or auto-tetraploid lines map to the incorrect species when mapped to the composite genome.
Genome_build: hg38 and pt6
Supplementary_files_format_and_content: Gene counts for each species are represented with the human ensembl ID in the processed files. For allo-tetraploid lines, each sample is represented twice in the associated processed file, once as human allele counts ("Hs" prefix) and once as chimpanzee allele counts ("Pt" prefix).

organism: Pan troglodytes

source_name: induced pluripotent stem cells

extract_protocol:
RNA was isolated using the Direct-Zol RNA Miniprep kit (Zymo Research, cat #R2051) or by Genewiz.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Library Prep (Illumina) or by Genewiz and sequenced on a HiSeq 4000 (2x150bp).

value: induced pluripotent stem cells

tag: cell line


title: SQT1_hiPSCCM_mimic365_3


title: Patient19 EOT

value: Blood


title: 7H_S7 rec_hip


title: SQT1_hiPSCCM_mimicCtrl_3

value: mimic-Ctrl


title: Patient6 C1D1


title: Patient3 EOT


title: DIM2_DEX-3

value: GRL/L

value: Mouse embryonic fibroblasts


title: 10H_S10 wt_hip


title: SQT1_hiPSCCM_mimicCtrl_2

value: iPSC-derived cardiomyocyte


title: 6H_S6 rec_hip


title: Patient3 C1D8


title: 5H_S5 rec_hip


title: C1C1d-1


title: SQT1_hiPSCCM_mimic365_1


title: DIM2_DEX-1


title: 20C_S20 rec_cx

source_name: Scn1a rec Cortex


title: Patient3 C1D1


title: DIM1_NI-2

value: GRD/D

value: Vehicle


title: C1C1e-1


title: AS-415990-LR-47252

city: Freiburg

first: Christopher

last: Berlin

address: Hugstetter Straße 55

institute: University Hospital Freiburg

description: plus TAM

data_processing:
The Cell Ranger Single Cell Software Suite 3.1 was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting
Instrument model NOVASEQ6000
Genome_build: mm10
Supplementary_files_format_and_content: mtx: count matrix in a sparse matrix format; barcodes.tsv: barcode ids for each sample; genes.tsv: gene ids for each sample

extract_protocol:
10x Chromium 3´ scRNA-seq (v2 chemistry) was performed according to the manufacturer's instructions.
10x Sequencing libraries were generated according to the manufacturer's instructions.

value: AOM/DSS tumour organoids

tag: passages


title: DIM1_DEX-1


title: C2-2

first: Janet

last: Song

address: 3 Blackfan St

institute: Boston Children's Hospital


title: DIM1_NI-1


title: AS-415988-LR-47251

description: plus TAM


title: DIM1_DEX-3


title: 2H_S2 het_hip

source_name: Scn1a het  Hippocampus


title: C1C1c-1


title: DIM1_DEX-2


title: C1C1b-1


title: 18C_S18 rec_cx

value: cortex


title: 1H_S1 het_hip


title: AS-415986-LR-47252

description: plus TAM


title: C1C1b-2


title: AS-415986-LR-47251

description: plus TAM


title: 19C_S19 rec_cx


title: C1-2


title: C1C1a-1


title: AS-415990-LR-47251

description: plus TAM


title: 17C_S17 rec_cx


title: AS-415984-LR-47252

description: plus TAM