title: U2OS cells - HighMYC_rep2_4C

city: Singapore

first: Melissa

middle: Jane

last: Fullwood

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

description: U2OS_merge_C_COM.trimmed_experiment.interactions.txt

data_processing:
Library strategy: 4C-Seq
Hi-C: SIQHiC libraries include human and mouse DNA. Paired reads were separated and mapped as single reads using BWA-MEM to an artificial reference genome combining hg19 human and mm10 mouse genome sequences. After mapping, reads were paired together again and split into 2 files. Paired reads both mapping to human chromosomes were placed together as Human-Human paired reads (H-H), while paired reads both mapping to mouse chromosomes were placed together as Mouse-Mouse paired reads (M-M). Ambiguous read pairs that separately mapped to different species are discarded. H-H and M-M reads were processed using Juicer separately, filtering out duplicates, intra-fragment reads and reads with MAPQ < 30 to generate .hic matrix files for each species. H-H reads of biological replicates were also merged and processed in the same way to generate .hic matrix files for downstream analyses.
RNA-seq: Reads were aligned to the hg19 reference genome using kallisto. UCSC RefSeq transcript expression was calculated as transcripts per million (TPM) using kallisto.
ChIP-seq: ChIP-seq libraries were mapped to the hg19 genome using BWA-MEM version 0.7.5a-r405 using default settings. PCR duplicates were removed using samtools version 1.7 and reads falling within the ENCODE consensus blacklisted regions were removed using BEDTools version 2.26.0. ChIP-seq signals were visualized using deepTools version 3.2.1 (bamCompare --normalizeUsing RPKM --operation subtract -bs 1). Bam files of biological replicates were merged before calling ChIP-seq peaks using MACS2 version 2.1.2
4C-seq: 4C-seq libraries were mapped to the hg19 genome using BWA-MEM version 0.7.5a-r405 using default settings and processed using the r3Cseq pipeline.
Genome_build: hg19
Supplementary_files_format_and_content: Hi-C chromatin interactions matrix output from Juicer provided as .hic files
RNA Seq transcript per million output from kallisto at the transcript level provided as .tsv files. Fields show 1. transcript RefSeq id, 2. length, 3. effective length, 4. estimated counts, 5. transcripts per million
ChIP-Seq signficant peaks output from MACS2 provided as narrowPeak files.
4C-seq significant interactions output from r3Cseq provided as txt files. Fields show 1. chromosome, 2. start position, 3. end position, 4. number of reads, 5. reads per million, 6. p.value, 7. q.value, 8. nearest genes

source_name: U2OS human cells

extract_protocol:
40 million cells were cross-linked in PBS supplemented with 1% formaldehyde at room temperature for 10 minutes, followed by quenching with 0.25M glycine for 5 minutes. Cells were washed thrice with PBS supplemented with 1mM phenylmethylsulfonyl fluoride (Sigma Aldrich). Nuclei were isolated by lysing cells in 4C Lysis Buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 5mM EDTA, 0.5% Igepal CA-630) at 4℃ for 10 minutes, followed by homogenization using a dounce homogenizer (Wheaton) (100 strokes using Pestle B). Nuclei were permeabilized at 37℃ with the addition of 0.3% SDS for 1 hour, followed by 2% Triton-X 100 for 1 hour. Primary enzyme digestion with HindIII-HF (NEB) was done at 37℃ for 18h, before proximity ligation in dilute conditions with T4 DNA Ligase (Thermo Scientific) at 16℃ overnight. Crosslinking was reversed with the addition of 55µg/ml Proteinase K (Ambion) at 65℃ for 4 hours and 37℃ overnight, and treated with RNAse A at 37℃ for 1 hour. DNA was purified using phenol/chloroform extraction followed by ethanol precipitation to yield the 3C library. Secondary enzyme digestion with DpnII (NEB) was done on the 3C library at 37℃ overnight, followed by proximity ligation and de-crosslinking as described above.
4C libraries were generated for each viewpoint through nested inverse-PCR using Phusion DNA Polymerase (Thermo Scientific). DNA fragments between 200 and 1000bp were isolated from the 4C libraries by gel excision after running the 4C libraries on a 4-20% gradient TBE gel (Thermo Scientific). The gel slices were shredded and macerated in Tris EDTA buffer at 37℃ overnight and DNA was precipitated using ethanol. The 4C libraries were multiplexed and single-end 1 x 150bp sequencing was performed on the Illumina MiSeq.

treatment_protocol: Cells were treated with 1ug/ml doxycycline for 30h.

tag: doxycyline treatment

tag: restriction enzyme

value: HindIII; DpnII

value: Not Applicable


title: B6x129-ATAC-90m-B3

status: Public on Jan 17 2022

type: SRA

city: Los Angeles

first: Marty

middle: G

last: Yang

state: CA

address: 615 Charles E Young Dr S

department: Biological Chemistry

country: USA

institute: University of California, Los Angeles

library_source: genomic

data_processing:
Reads were trimmed with the paired-end option and with SLIDINGWINDOW:5:30 using Trimmomatic (Bolger et al., 2014).
Paired-end reads that survived trimming were re-paired using the bbmap utility (Bushnell 2014). Both unpaired and paired reads were concurrently mapped to the C57BL/6J and appropriate pseudogenome with bowtie2 using default parameters (Langmead and Salzberg, 2012).
Mapped reads were converted to .bam format with samtools view (Li et al., 2009) using the following options -h -b -F 3844 -q 10 and sorted by coordinate. Reads initially mapped to each pseudogenome were converted back to C57BL/6J coordinates by running Lapels (Huang et al., 2014).
For visualization purposes, mapped reads in .bam format were also converted to .bed format and unique reads were retained (with sort -k1,1 -k2,2n -k3,3n -u) and extended by 150 bp with bedtools slop -l 0 -r 150.
All samples were normalized to a depth of 10 million reads and read coverage was calculated by bedtools genomeCoverageBed. The output .bedgraph file was then converted with UCSC’s bedGraphtobigWig utility and all tracks displayed were visualized with the UCSC Genome Browser (GRCm38/mm10).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files of histograms normalized to 10 million mapped and in silico extended reads.

molecule: genomic DNA

organism: Mus musculus

source_name: Primary mouse embryonic fibroblasts

growth_protocol: Mouse embryonic fibroblasts (MEFs) were grown in DMEM with 10% CCS.

extract_protocol:
MEFs from 6-well dish were washed twice in 1 mL cold PBS and pelleted each time by spinning at 300 g for 5 min at 4oC. 50,000 MEFs were resuspended in 50 uL cold ATAC lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40 0.1% Tween 20, 0.01% digitonin) and incubated for 3 min on ice.  Lysed cells were washed once in 1 mL ATAC wash buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20) by gently inverting the tube 3 times and pelleted by spinning at 500 g for 10 min at 4oC.
Pelleted nuclei were resuspended in 50 uL transposition mix (25 uL 2x TD Buffer (Illumina (San Diego, CA, USA) 20034197), 2.5 uL TDE1 transposase (Illumina 20034197), 0.5 uL 10% Tween 20, 0.5% 1% digitonin, 16.5 uL PBS, 5 uL NF-H2O) and incubated for 30 min at 37oC with a Thermomixer set to 1,000 rpm. Samples were purified with MinElute PCR Purification Kit (QIAGEN 28004) per manufacturer’s instructions and eluted in 13 uL NF-H2O. Libraries were amplified by adding the following to 10 uL purified DNA: 2.5 uL 25 uM Ad1 universal primer, 2.5 uL 25 uM Ad2.* indexing primer, 25 uL NEBNext Hi-Fi 2x PCR Master Mix (NEB (Ipswich, MA, USA) M0541S), 10 uL NF-H2O. After an initial 5 PCR cycles, libraries were quantified by qPCR by adding the following to 5 uL partially amplified DNA: 0.5 uL 25 uM Ad1 universal primer, 0.5 uL 25 uM Ad2.* indexing primer, 5 uL NEBNext Hi-Fi 2x PCR Master Mix, 0.15 uL 1x SYBR Green I (Thermo Fisher S7563), 3.85 uL NF-H2O. All primer sequences referenced are described in Buenrostro et al., 2015. The number of additional PCR cycles required for amplifying remaining libraries was determined by number of qPCR cycles needed to reach 1/3 of the maximum SYBR green signal. Libraries were purified with AMPure XP beads (0.5x volume; Beckman Coulter (Indianapolis, IN, USA) A63881) and the supernatant was retained to remove large fragments. Primer dimers were removed by a subsequent cleanup with AMPure XP beads (1.3x initial volume) and libraries were eluted in 20 uL NF-H2O. Libraries were sequenced on an Illumina NextSeq 500 with 40 bp paired-end reads.

treatment_protocol: MEFs were starved for 26 hours in DMEM with 0.5% CCS and serum stimulated for the indicated times at a final concentration of 15% CCS.

tag: cell type

value: Primary mouse embryonic fibroblasts

tag: strain

value: C57BL/6J x 129S1/SvImJ F1 hybrid

tag: age

tag: genotype

value: wild-type

tag: treatment

value: 90m stimulation with 15% CCS MEF media

tag: passage

tag: experiment

value: ATAC-seq


title: U2OS cells - HighMYC_rep1_4C

organism: Homo sapiens

tag: cell line

tag: chip antibody


title: WT clone A6

city: Milan

first: Monah

last: Abou Alezz

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

data_processing:
Library strategy: DNA-seq
Trimming of reads with Trim Galore
Alignment of reads with BWA mem
Sorting and conversion to bam with picard SortSam
Indexing with samtools index
Base quality recalibration with GATK BaseRecalibrator, ApplyBQSR and BaseRecalibrator modules
Variant call and filtering with GATK Mutect2 and FilterMutectCalls modules
Genome_build: GRCh38
Supplementary_files_format_and_content: Variant call from GATK pipeline containing TP53 variants

source_name: induced pluripotent stem cells

growth_protocol: iPSCs were kept in colture with All iPSCs were maintained on mitomycin-C-treated MEF in iPSCsM (DMEM/F12  enriched with 20% Knock-out serum replacement, non essential amino acids, Sodium Pyruvate, and 10 ng/ml of FGF2. And then detached with accutase, collected and resuspended in 1 ml iPSC medium in the presence of 10 μM of the Rho kinase inhibitor Y-27632. Cells where then plated on 0.1% gelatin-coated wells for 1 hour to allow MEF to attach. Floating iPSCs were then collected and plated in iPSC medium in the presence of 10 μM of the Rho kinase inhibitor Y-27632 on matrigel-coated dishes. When iPSCs reached 50-70% confluence, cells were detached with 1ml accutase and collected for DNA exptraction.

extract_protocol:
DNeasy Blood & Tissue Kit or QIAamp DNA Micro Kit (QIAGEN)
Libraries were prepared using the ArcherDX VariantPlex p53 Panel for Targeted NGS

value: iPSCs

tag: knock-out technology

value: CRISPR-CAS9 engineered knock-out

tag: iPSc generation

value: Lentiviral vetor reprogrammed iPCs


title: Ashby_sir3D-EcoGII

city: Berkeley

first: Molly

last: Brothers

address: UC Berkeley 440 Barker Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

description: mat∆::HphMX, sir3∆::ECOGII-NatMX

data_processing:
Reads were basecalled and demultiplexed using guppy and guppy_barcoder. Read IDs were extracted using a custom python script and used to demultiplex fast5 files.
Reads were basecalled (including modified bases) and aligned to the SacCer3 genome (modified to include mat∆) using Megalodon and the all-context model (https://github.com/nanoporetech/rerio, res_dna_r941_min_modbases-all-context_v001.cfg) with the options --mod-motif “Y A 0”, --files_out “basecalls mod_mappings per_read_mods” and --read-ids-filename “barcodeXX_readIDs.txt” (the file that contained the extracted list of readIDs for a given barcode).
Data from the .db file were aggregated using Megalodon "megalodon_extras aggregate run".
Genome_build: SacCer3 (modified)
Supplementary_files_format_and_content: All experiments include a .bed file (bedMethyl format) aggregated using Megalodon (https://github.com/nanoporetech/megalodon "megalodon_extras aggregate run"). Experiments where single reads were analyzed include a .db file (SQLite database) generated using Megalodon. These .db files can be converted to .txt files using Megalodon "megalodon_extras per_read_text modified_bases".

organism: Saccharomyces cerevisiae

growth_protocol: Yeast were cultured at 30°C in YPD unless otherwise noted under "conditions" for each experiment/sample.

extract_protocol:
DNA was extracted using the Zymo YeaStar genomic DNA Kit (Genesee Scientific, Cat #11-323). DNA was sheared to 15-25kb using a Covaris gTUBE and then concentrated and purified using 1X v/v SPRI Select beads (Beckman-Coulter B23317).
Oxford Nanopore Ligation Sequencing Kit (SQK-LSK109) with Native Barcode Expansion (EXP-NBD104).

tag: condition

value: Cycling in YPD


title: RNaseH2B clone19


title: Trex1 KO clone 13


title: U2OS cells - LowMYC_rep2_4C

description: U2OS_merge_C-_COM.trimmed_experiment.interactions.txt

treatment_protocol: Cells were treated with vehicle control (H2O) for 30h.


title: B6x129-ATAC-0m-B1

value: starved with 0.5% CCS MEF media


title: U2OS cells - LowMYC_rep1_4C


title: Raja_SIR4-EcoGII

description: mat∆::HphMX, SIR4-ECOGII-NatMX

value: mat<delta>::HphMX, SIR4-ECOGII-NatMX


title: B6xSPRET-RNA-20m-B2

library_source: transcriptomic

data_processing:
Reads were mapped with STAR 2.7.3 (Dobin et al., 2013) with the following options to enable WASP filtering of allele-specific reads: --outSAMattributes NH HI AS nM vG vA --waspOutputMode SAMtag.
Genome-specific reads were extracted and converted into .bam format with samtools view -h -b -F 3844 -q 10.
The featureCounts command from Subread (Liao et al., 2013) was used to quantify the number of allele-specific reads per genome that overlapped each mm10 Refseq gene bodies.
Genome_build: mm10
Supplementary_files_format_and_content: Text file with allele-specific read counts at Refseq-annotated gene bodies.

molecule: total RNA

extract_protocol:
MEFs from 15 cm dish were washed once in 15 mL cold PBS and pelleted by spinning at 300 g for 5 min at 4oC. Cell pellet was resuspended in 200 uL cold cytoplasmic lysis buffer (10 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.15% NP-40) and rotated for 5 min at 4oC. Lysate was layered on top of 500 uL cold sucrose buffer (10 mM Tris-HCl pH 7.5, 150 mM NaCl, 24% sucrose (w/v)) and centrifuged at 16,000 g for 10 min at 4oC. These steps were repeated once more to achieve higher purity in nucleoplasmic fraction. Pelleted nuclei were resuspended in 200 uL glycerol buffer (20 mM Tris-HCl pH 7.9, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol, 0.85 mM DTT) and an equal volume of cold nuclear lysis buffer was added (20 mM HEPES pH 7.5, 7.5 mM MgCl2, 0.2 mM EDTA, 300 mM NaCl, 1 M urea, 1% NP-40, 1 mM DTT). Tubes were gently vortexed twice for 2 sec, incubated for 1 min on ice, and centrifuged at 18,000 g for 2 min at 4oC. These steps were repeated once more to achieve higher purity in chromatin fraction. The remaining chromatin pellet was resuspended in 50 uL cold PBS and vortexed briefly. 500 uL of TRIzol (Thermo Fisher 15596026) was added to the pellet and vortexed for several minutes until fully resuspended.
Chromatin-associated RNA was isolated with RNeasy Mini Kit (QIAGEN 74104) per manufacturer’s instructions and libraries were generated from 250 ng starting material with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs E7765). Libraries were sequenced on an Illumina NextSeq 500 with 150 bp paired-end reads.

value: C57BL/6J x SPRET/EiJ F1 hybrid

value: 20m stimulation with 15% CCS MEF media

tag: cellular fraction

value: chromatin

value: Chromatin-associated RNA-seq

tag: fraction

value: chromatin-associated RNA


title: B6xSPRET-RNA-90m-B2


title: B6xSPRET-RNA-20m-B1


title: B6xSPRET-RNA-0m-B2


title: siRAD51_rep2

city: Paris

first: Ludovic

last: Deriano

address: 25-28 Rue du Docteur Roux

department: Immunology

country: France

institute: Institut Pasteur

description:
processed data file:
siRAD51_combined_Mosaic_reads.txt

data_processing:
Library strategy: HTGTS
Sequencing reads in FASTQ files were parallel decoded and adaptor sequence trimmed out by US-utility tool
Paired-end reads with less than 20-nucleotide bait sequence at the 5’ end of read 1 were filtered out. The remaining paired-end reads were merged by a FLASH tool with a minimum of 10 bp overlap
The merged reads were mapped to the human hg38 reference genome combined with plasmid sequence using BWA
Identification of different types of joins, including germlines, deletions, multiple copies and insertions were fulfilled by custome Perl scripts developed in-house
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text files contain all filtered mosaic reads with junctions including the following information: sequence ID; pieces of junctions; prey chromosome (including human chromosome, pCOH-CD4-reporter, IsceI_plasmid), prey junction coordinate (Junction), prey mapping cigar (length of mapped read)

source_name: fibroblasts cells

growth_protocol: 50,000 cells were seeded in 6-well plates (day 0).24h later (d1), siRNA transfection was performed with 20nmol  siRNA against 53BP1 and/or RAD51. On d3 cells are transfected for I-SceI expression. After 3 days of culture (then on d6) cells are collected for analysis

extract_protocol:
Genomic DNA was extracted with proteinase K digestion overnight and phenol/chloroforme extraction.
Briefly, DNA was purified and sonicated (Bioruptor, Diagenode) into 500–1,000 bp fragments. LAM-PCR was performed using bait primer coupled with biotin, 1U Phusion polymerase (Thermo Scientific) and the following cycles: 1x (98 °C for 120 s); 80x (95 °C for 30 s; 58 °C for 30 s; 72 °C for 90 s); and 1x (72 °C for 360 s). Biotinylated PCR fragments were incubated with MyOne streptavidin C1 beads (Invitrogen) and rotated for 4 h in 1 M NaCl and 5 mM EDTA buffer at room temperature. After washes with B&W buffer (1 M NaCl; 5 mM Tris-HCl, 0.5 mM EDTA), on-bead ligation was performed using 2.5 mM bridge adaptor, 1 mM hexamine cobalt chloride (Sigma), 15 U T4 DNA ligase (Promega), 15% PEG-8000 (Sigma) and the following cycles: 25 °C for 1 h; 22°C for 2 h; and 16°C O/N. After washing three times with B&W buffer (1 M NaCl, 5 mM Tris-HCl (pH 7.4) and 0.5 mM EDTA (pH 8.0)), the on-bead ligated products were subjected to nested PCR using Phusion polymerase, locus-specific and adaptor primers and the following cycles: 1x (95 °C for 300 s); 15x (95 °C for 60 s; 72 °C 60 s); and 1x (72 °C 600 s). Blocking digestion was then performed with I-SceI for 1 h to remove uncut germline DNA. After purification using a Qiagen column, recovered DNA was PCR-amplified using Illumina primers, Phusion polymerase and the following cycles: 1x (95°C for 180 s); 10x (95°C for 30 s; 60°C for 30 s; 72°C for 60 s); and 1x (72°C for 360 s). The tagged PCR products were size-selected for DNA fragments between 500–1000 bp on a 1% agarose gel and purified using a Qiagen column before loading onto an Illumina Miseq machine for paired-end 2X250 bp sequencing.

treatment_protocol: siRNA transfection was performed with 20 nmol of each siRNA and Interferin (Polyplus), and plasmid transfection with 1 µg I-SceI expression plasmid and JetPEI (Polyplus)

value: derived from SV40-transformed GM639 human fibroblasts


title: B6xAJ-ATAC-0m-B1

value: Primary mouse embryonic fibroblasts

value: C57BL/6J x A/J F1 hybrid


title: B6xSPRET-RNA-0m-B1

value: wild-type


title: siRAD51_si53BP1_rep1

description:
processed data file:
si53BP1_siRAD51_combined_Mosaic_reads.txt


title: B6xPWK-RNA-90m-B2

value: C57BL/6J x PWK/PhJ F1 hybrid

value: 90m stimulation with 15% CCS MEF media


title: si53BP1_rep2

description:
processed data file:
si53BP1_combined_Mosaic_reads.txt


title: Control_rep2

description:
processed data file:
CT_combined_Mosaic_reads.txt

value: Control


title: B6xSPRET-RNA-90m-B1


title: B6xPWK-RNA-90m-B1


title: siRAD51_si53BP1_rep2


title: Control_rep1


title: siRAD51_rep1


title: B6xPWK-RNA-20m-B2


title: B6xPWK-RNA-20m-B1


title: B6xMOLF-RNA-90m-B2

value: C57BL/6J x MOLF/EiJ F1 hybrid


title: B6xPWK-RNA-0m-B1


title: B6xMOLF-RNA-90m-B1


title: Patient 9 IN_009

type: RNA

city: Nanjing

first: Yan

last: Dai

address: No. 300, Guangzhou Road, Gulou District

department: Department of Infectious Diseases

country: China

institute: the First Affiliated Hospital of Nanjing Medical University

description:
IN_009
The intensity of green signal is calculated after background subtraction and four replicated spots of each probe on the same slide have been averaged.

hyb_protocol: The Hy3™-labeled samples were mixed with the hybridization buffer, denatured for 2 min at 95°C, and placed on ice for 2 min. Then, the samples were hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization System (Hybridization System-Nimblegen Systems, Inc., Madison, WI, USA).

scan_protocol: The slides were scanned using a GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA, USA). The microarray scanning image was read using GenePix Pro 6.0 (Axon, Foster City, CA, USA) and the signal values of the probes were extracted.

data_processing: The signal values of the probes were extracted. The same probes were selected to use the median value. Probes with values ≥ 30.0 in all samples were retained. Median normalization was performed over the entire microarray. Differentially-expressed probes were screened. Differential expression of miRNAs between the two samples (with repeats) was screened using the fold change and the P value. Differential expression of miRNAs between two samples (without repeats) was screened using the fold change.

source_name: Tibia

label_protocol: According to the manufacturer's instructions, miRNA labelling was carried out using the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, part of Qiagen, Cat#208032-A). We used a labeling enzyme to label miRNAs with the Hy3™ fluorophore.

extract_protocol: Total RNA was extracted from bone tissue using the TRIzol method (Invitrogen, Grand Island, NY, USA) according to the manufacturer's instructions and purified using an RNeasy Mini Kit (Qiagen, Valencia, CA, USA). The concentration of the purified RNA was measured using a NanoDrop ND-1000 (Thermo Scientific, Wilmington, DE, USA). The A260/A280 ratio was close to 2.0 indicating the high purity of the extracted RNA. Gel electrophoresis was used to detect the integration of the extracted RNA.

tag: tissue

value: Bone (Tibia)

tag: group

value: Infected nonunion

tag: gender

value: Female

value: 82 years


title: Patient 7 IN_007

description:
IN_007
The intensity of green signal is calculated after background subtraction and four replicated spots of each probe on the same slide have been averaged.

source_name: Tibial shaft

value: Bone (tibial shaft)

value: 34 years


title: Patient 8 IN_008

description:
IN_008
The intensity of green signal is calculated after background subtraction and four replicated spots of each probe on the same slide have been averaged.

value: Male

value: 54 years


title: B6x129-ATAC-0m-B2

tag: cell type

value: C57BL/6J x 129S1/SvImJ F1 hybrid

value: starved with 0.5% CCS MEF media

value: ATAC-seq


title: Patient 6 IN_006

description:
IN_006
The intensity of green signal is calculated after background subtraction and four replicated spots of each probe on the same slide have been averaged.

value: 50 years


title: si53BP1_rep1

value: derived from SV40-transformed GM639 human fibroblasts


title: B6xMOLF-RNA-20m-B2

value: Primary mouse embryonic fibroblasts

tag: strain

value: wild-type

value: 20m stimulation with 15% CCS MEF media

value: chromatin

value: Chromatin-associated RNA-seq

value: chromatin-associated RNA


title: B6xMOLF-RNA-20m-B1

value: C57BL/6J x MOLF/EiJ F1 hybrid

tag: age


title: B6xMOLF-RNA-0m-B2

tag: genotype


title: B6xMOLF-RNA-0m-B1

tag: treatment


title: B6xCAST-RNA-90m-B2

value: C57BL/6J x CAST/EiJ F1 hybrid

value: 90m stimulation with 15% CCS MEF media

tag: passage


title: B6xCAST-RNA-90m-B1

tag: experiment


title: GF101_seedling

city: Manhattan

first: Eduard

last: Akhunov

state: Kansas

address: 1712 Claflin Road

department: Plant Pathology

institute: Kansas State University

description: TPM was estimated using Kallisto

data_processing:
All high confidence (HC) and low confidence (LC) gene models from the IWGSC RefSeq v. 1.0, as well as de novo assembled transcripts were combined for estimating the TPM values using Kallisto (v. 0.4.6.0). Gene models with expression standard deviation > 0.5 and expressed (TPM > 0.5) in at least 2 samples have been used in our analyses. This set of genes included 52,511 HC gene model, 29,226 LC gene model and 13,861 de novo assembled transcripts.
Supplementary_files_format_and_content: The TPM values for all expressed HC and LC gene models are provided as an expression data matrix. The file format is gzipped text.

organism: Triticum aestivum

source_name: seedling

extract_protocol: A panel of diverse 400 wheat lines was selected based on the geographic distribution and genetic diversity, and available from the USDA National Small Grains Collection. Total RNA was isolated from 2-week seedlings of 204 lines with each line grown in three biological replicates. Ground tissues from three biological replicates were combined in equal amounts before RNA isolation using RNeasy Plant mini kit. RNA-seq libraries were prepared with TruSeq™ RNA Sample Prep Kit (Illumina) using the Beckman’s Biomek® FXP Laboratory Automation Workstation. Up to eight barcoded RNA-seq libraries were pooled per lane of NextSeq2000 flow cell to generate 2 x 100 bp reads.

value: two week seedling

value: leaf

tag: line


title: B6xCAST-RNA-20m-B2


title: GF100_seedling

description: TPM was estimated using Kallisto


title: GF102_seedling

description: TPM was estimated using Kallisto


title: GF104_seedling

description: TPM was estimated using Kallisto


title: Patient 5 IN_005

description:
IN_005
The intensity of green signal is calculated after background subtraction and four replicated spots of each probe on the same slide have been averaged.

value: Bone (Tibia)

value: Infected nonunion

value: Male

value: 51 years


title: Patient 4 IN_004

description:
IN_004
The intensity of green signal is calculated after background subtraction and four replicated spots of each probe on the same slide have been averaged.

value: Closed fracture

value: Female

value: 71 years


title: Patient 3 IN_003

description:
IN_003
The intensity of green signal is calculated after background subtraction and four replicated spots of each probe on the same slide have been averaged.

value: Bone (tibial shaft)

value: 60 years


title: B6xCAST-RNA-20m-B1

value: Primary mouse embryonic fibroblasts

value: wild-type

value: 20m stimulation with 15% CCS MEF media

value: chromatin


title: B6xCAST-RNA-0m-B1

value: C57BL/6J x CAST/EiJ F1 hybrid

value: starved with 0.5% CCS MEF media

value: Chromatin-associated RNA-seq

value: chromatin-associated RNA


title: B6xPWK-RNA-0m-B2

value: C57BL/6J x PWK/PhJ F1 hybrid


title: GF107_seedling

description: TPM was estimated using Kallisto

value: two week seedling

value: leaf


title: Patient 1 IN_001

description:
IN_001
The intensity of green signal is calculated after background subtraction and four replicated spots of each probe on the same slide have been averaged.

value: Bone (Tibia)

value: Male

value: 45 years


title: Patient 2 IN_002

description:
IN_002
The intensity of green signal is calculated after background subtraction and four replicated spots of each probe on the same slide have been averaged.

value: Closed fracture

value: 37 years


title: B6-H3K27ac-HiChIP-90m-B2

data_processing:
Library strategy: Hi-ChIP
H3K27ac Hi-ChIP reads were aligned with HiC-Pro (Servant et al., 2015) using an MboI-digested mm10 genome as the reference genome.
Significant H3K27ac loops were determined by running hichipper (Lareau and Aryee, 2018), inputting 1kb windows centered on all previously identified distal active enhancers from C57BL/6J MEFs (Vierbuchen et al., 2017) as possible loop anchors.
Only loops that were supported by at least 10 paired-end tags per replicate and had a p-value < 1e-4 from hichipper were retained from each timepoint (0m and 90m). We generated tracks for visualization by retaining the midpoint of all significant loops.
Genome_build: mm10
Supplementary_files_format_and_content: Text file with significant loop anchors from H3K27ac Hi-ChIP and associated number of paired-end tags per biological replicate.

extract_protocol:
Media was aspirated from MEFs and 2 mL or 15 mL crosslinking buffer (10 mM HEPES pH 7.5, 100 mM NaCl, 1 mM EDTA, 1 mM EGTA) with 1% formaldehyde was added for 6-well or 15 cm dishes respectively. Cells were crosslinked by shaking gently for 10 min at room temperature. Crosslinking was quenched by adding glycine to a final concentration of 125mM and incubating for 5 min at room temperature while shaking. Cells were washed once in 2 mL or 15 mL PBS for 6-well or 15 cm dishes respectively. Cells were scraped and collected in 1 mL or 5 mL cold PBS for 6-well or 15 cm dishes respectively and pelleted by spinning at 1,000 g for 5 min at 4oC.
Hi-ChIP was performed as previously described in (Mumbach et al., 2017) with the following modifications. 15 uL of MboI restriction enzyme (New England Biolabs R0147) was used for digesting chromatin from 15 million MEFs. Sonication was performed with a Covaris M220 with the following settings: duty cycle = 5, PIP = 70, cycles/burst = 200, and time = 8 min. 75 uL of Protein A Dynabeads (Thermo Fisher 10008D) was used for IP and 1 ug of anti-H3K27ac (Abcam ab4927) antibody was used per sample to typically yield 12.5 ng DNA. Accordingly, 0.6725 uL transposase enzyme (Nextera 20034197) was used to insert adapters and libraries were amplified for 8 PCR cycles.

value: 90m stimulation with 15% CCS MEF media

tag: chip antibody

value: Abcam ab4927

value: Hi-ChIP


title: B6-H3K27ac-HiChIP-90m-B3

value: Primary mouse embryonic fibroblasts

value: wild-type


title: B6-H3K27ac-HiChIP-90m-B1


title: GF11_seedling

description: TPM was estimated using Kallisto


title: GF115_seedling

description: TPM was estimated using Kallisto


title: B6-H3K27ac-HiChIP-0m-B3


title: GF119_seedling

description: TPM was estimated using Kallisto


title: B6-H3K27ac-HiChIP-0m-B1


title: GF12_seedling

description: TPM was estimated using Kallisto


title: B6-H3K27ac-HiChIP-0m-B2


title: GF121_seedling

description: TPM was estimated using Kallisto


title: B6xNOD-H3K27ac-90m-B4

data_processing:
Library strategy: CUT&RUN
Reads were trimmed with the paired-end option and with SLIDINGWINDOW:5:30 using Trimmomatic (Bolger et al., 2014).
Paired-end reads that survived trimming were re-paired using the bbmap utility (Bushnell 2014). Both unpaired and paired reads were concurrently mapped to the C57BL/6J and appropriate pseudogenome with bowtie2 using default parameters (Langmead and Salzberg, 2012).
Mapped reads were converted to .bam format with samtools view (Li et al., 2009) using the following options -h -b -F 3844 -q 10 and sorted by coordinate. Reads initially mapped to each pseudogenome were converted back to C57BL/6J coordinates by running Lapels (Huang et al., 2014).
For visualization purposes, mapped reads in .bam format were also converted to .bed format and unique reads were retained (with sort -k1,1 -k2,2n -k3,3n -u) and extended by 150 bp with bedtools slop -l 0 -r 150.
All samples were normalized to a depth of 10 million reads and read coverage was calculated by bedtools genomeCoverageBed. The output .bedgraph file was then converted with UCSC’s bedGraphtobigWig utility and all tracks displayed were visualized with the UCSC Genome Browser (GRCm38/mm10).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files of histograms normalized to 10 million mapped and in silico extended reads.

extract_protocol:
Media was aspirated from MEFs and 2 mL or 15 mL crosslinking buffer (10 mM HEPES pH 7.5, 100 mM NaCl, 1 mM EDTA, 1 mM EGTA) with 1% formaldehyde was added for 6-well or 15 cm dishes respectively. Cells were crosslinked by shaking gently for 10 min at room temperature. Crosslinking was quenched by adding glycine to a final concentration of 125mM and incubating for 5 min at room temperature while shaking. Cells were washed once in 2 mL or 15 mL PBS for 6-well or 15 cm dishes respectively. Cells were scraped and collected in 1 mL or 5 mL cold PBS for 6-well or 15 cm dishes respectively and pelleted by spinning at 1,000 g for 5 min at 4oC. Crosslinked MEFs per protocol above from 6-well dish were washed once in 2 mL PBS and collected in 1 mL cold NE1 buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM MgCl2, 1 mM DTT, 0.1% Triton X-100, Roche Protease Inhibitor Cocktail (Millipore (Burlington, MA, USA) 11873580001)). Cells were permeabilized to isolate nuclei by rotating for 10 min at 4oC. Nuclei were pelleted by spinning at 500 g for 5 min at 4oC and resuspended in 1 mL cold CUT&RUN wash buffer (20 mM HEPES pH 7.5, 0.2% Tween-20, 150 mM NaCl, 0.1% BSA, 0.5 mM spermidine, 10 mM sodium butyrate, Roche Protease Inhibitor Cocktail). 10 uL concanavalin-coated bead slurry (Bangs Laboratories (Fishers, IN, USA) BP531) per sample was washed twice in 1.5 mL CUT&RUN binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM CaCl2, 20 mM MnCl2) and resuspended in a final volume of 10 uL CUT&RUN binding buffer per sample. After adding 10 uL bead slurry to each sample, tubes were inverted 10 times and incubated for 10 min at room temperature to bind nuclei. Beads were separated from wash buffer by placing on magnet for >30 sec and were resuspended in 50 uL antibody buffer (0.1% Triton X-100, 2 mM EDTA, diluted in CUT&RUN wash buffer). Antibodies (in-house anti-Fos, anti-H3K27ac (Abcam ab4927), or rabbit IgG (Cell Signaling Technology (Danvers, MA, USA) 2729S)) were added at 1:50 dilution and samples were incubated overnight at 4oC. Beads were washed once in 1 mL Triton-wash buffer (0.1% Triton X-100, diluted in CUT&RUN wash buffer) and resuspended in 50 uL antibody buffer. Protein-A MNase (Skene and Henikoff, 2017) was added to a final concentration of 700 ng/mL and samples were incubated for 1 hr at 4oC.  Beads were washed twice in 1 mL Triton-wash buffer and resuspended in 100 uL Triton-wash buffer. 2 uL 100 mM CaCl2 was added per sample to activate the MNase and each sample incubated on ice for 30 min. 100 uL 2x STOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.1% Triton X-100, 50 ug/mL RNase A (Sigma Aldrich R6513), 2 pg/mL yeast spike-in DNA (provided by S. Henikoff)) was added and samples were incubated for 20 min at 37oC to release CUT&RUN fragments from nuclei. Samples were placed on magnet and supernatant transferred to a new tube along with 2 uL 10% SDS and 2 uL 20 mg/mL proteinase K (New England Biolabs P8107). Samples were incubated overnight at 65oC to reverse crosslinks. DNA was extracted with 1 volume of 25:24:1 phenol-chloroform-isoamyl alcohol and precipitated in 2.5 volumes of 100% ethanol with 2 uL glycogen (Sigma Aldrich 10901393001). Pellet was washed once in 1 mL 100% ethanol and dissolved in 40 uL 10 mM Tris-HCl pH 8.5.
Libraries were prepared as described in (Skene and Henikoff, 2017) with two subsequent AMPure XP bead cleanups (1.1x volume) to fully remove contaminating adapter dimers from libraries. Libraries were sequenced on an Illumina NextSeq 500 with 40 bp paired-end reads.

value: C57BL/6J x NOD/ShiLtJ F1 hybrid

tag: cut&run antibody

value: Abcam ab4729

value: CUT&RUN


title: GF110_seedling

description: TPM was estimated using Kallisto


title: B6xCAST-RNA-0m-B2

value: C57BL/6J x CAST/EiJ F1 hybrid

value: starved with 0.5% CCS MEF media

value: chromatin

value: Chromatin-associated RNA-seq

value: chromatin-associated RNA


title: GF123_seedling

description: TPM was estimated using Kallisto

value: two week seedling

value: leaf


title: GF103_seedling

description: TPM was estimated using Kallisto


title: B6xNOD-H3K27ac-90m-B2


title: B6xNOD-H3K27ac-90m-B1


title: GF106_seedling

description: TPM was estimated using Kallisto


title: GF124_seedling

description: TPM was estimated using Kallisto


title: GF125_seedling

description: TPM was estimated using Kallisto


title: B6xNOD-H3K27ac-0m-B3


title: GF117_seedling

description: TPM was estimated using Kallisto


title: GF120_seedling

description: TPM was estimated using Kallisto


title: GF128_seedling

description: TPM was estimated using Kallisto


title: GF127_seedling

description: TPM was estimated using Kallisto


title: GF13_seedling

description: TPM was estimated using Kallisto


title: B6xNOD-H3K27ac-0m-B1


title: B6xNOD-Fos-90m-B4

value: In-house generated Fos 1096AE


title: GF138_seedling

description: TPM was estimated using Kallisto


title: B6xNOD-Fos-90m-B3


title: GF14_seedling

description: TPM was estimated using Kallisto


title: GF15_seedling

description: TPM was estimated using Kallisto


title: B6xNOD-Fos-90m-B1


title: B6xNOD-Fos-0m-B2


title: GF154_seedling

description: TPM was estimated using Kallisto


title: B6xDBA-H3K27ac-90m-B4

value: C57BL/6J x DBA/2J F1 hybrid


title: B6xNOD-H3K27ac-90m-B3

value: 90m stimulation with 15% CCS MEF media


title: B6xNOD-H3K27ac-0m-B4


title: B6xDBA-H3K27ac-90m-B2


title: GF152_seedling

description: TPM was estimated using Kallisto


title: B6xNOD-Fos-0m-B1


title: B6xDBA-H3K27ac-90m-B1


title: B6xDBA-H3K27ac-90m-B3


title: B6xNOD-H3K27ac-0m-B2


title: B6xDBA-H3K27ac-0m-B4


title: GF168_seedling

description: TPM was estimated using Kallisto


title: GF175_seedling

description: TPM was estimated using Kallisto


title: GF170_seedling

description: TPM was estimated using Kallisto


title: GF184_seedling

description: TPM was estimated using Kallisto


title: GF180_seedling

description: TPM was estimated using Kallisto


title: GF157_seedling

description: TPM was estimated using Kallisto


title: GF186_seedling

description: TPM was estimated using Kallisto


title: B6xDBA-H3K27ac-0m-B2


title: B6xDBA-H3K27ac-0m-B3


title: GF188_seedling

description: TPM was estimated using Kallisto


title: SKMEL-1206_noab_rep2

city: New York

first: Joshua

middle: M

last: Weiss

state: NY

address: 417 E 68th St

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

description:
No antibody replicate 2
Table_AllPeaks_HOXA13_H3K27ac_normCounts_Annotated.txt

data_processing:
Library strategy: Cut&Run
Reads were trimmed and filtered for quality (q=15) and adapter content using version 0.4.5 of TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore).
Reads were aligned to human assembly hg38 with version 2.3.4.1 of bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) and duplicates were collapsed to one read using MarkDuplicates in version 2.16.0 of Picard Tools.
CUT&RUN target enrichment was assessed using MACS2 (https://github.com/taoliu/MACS) with FDR=0.1 and fold change of 2 over the matched IgG control background.
Depth-normalized read density profiles were created using the BEDTools suite (http://bedtools.readthedocs.io).
A global peak atlas was created by first removing blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/hg38.blacklist.bed.gz) then merging all overlapping peaks.
Peak-gene associations were created by assigning peaks using linear genomic distance to transcription start sites. Motif signatures were obtained using Homer v4.5 (http://homer.ucsd.edu).
Pathway analysis of enriched peaks (from MACS2) was performed using Cistrome-GO with the following parameters: peak number to use: all, half-decay distance: automatic, FDR cutoff: 0.2.
Genome_build: hg38
Supplementary_files_format_and_content: txt file containing normalize peaks scores for HOXA13 and H3K27ac binding, normalized to IgG.

source_name: Human acral melanoma cell line

growth_protocol: Cells were grown in standard conditions of RPMI with 20% FBS and 1X penicillin/streptomycin/glutamine.

extract_protocol:
We performed Cut&Run for the melanoma cell lines SKME-1088, SKMEL-1766, and SKME-1206. For Cut&Run we used 100’000 cells per condition and it was performed as described in Skene et al., Nat Protocol, 2018. We used antibodies against HOXA13 (Invitrogen, #PA5-76440, 1:100), H3K27ac (Active Motiv, #39034, 1:100), IgG (abcam, #ab6709, 1:100) and we added a “no antibody” condition as additional negative control. In brief, 100’000 melanoma cells were collected per condition. Cells were harvested and bound to concanavalin A-coated magnetic beads after 8min incubation at RT on a rotator. Cell membranes were permeabilized with digitonin and the different antibodies were incubated overnight at 4°C on a rotator. Beads were washed and incubated with pA-MN. Ca2+-induced digestion occurred on ice for 30min and stopped by chelation. DNA was isolated using an extraction method with phenol and chloroform as described in Skene et al., Nat Protoc, 2018.
KAPA HTP using manufacturers recommendations

tag: disease

value: Melanoma

tag: tag

tag: antibody

value: No antibody


title: B6xDBA-H3K27ac-0m-B1

value: Primary mouse embryonic fibroblasts


title: B6xDBA-Fos-90m-B4

value: wild-type


title: B6xNOD-Fos-0m-B3

value: C57BL/6J x NOD/ShiLtJ F1 hybrid


title: GF151_seedling

description: TPM was estimated using Kallisto


title: SKMEL-1206_noab_rep1

description:
No antibody replicate 1
Table_AllPeaks_HOXA13_H3K27ac_normCounts_Annotated.txt


title: GF19_seedling

description: TPM was estimated using Kallisto


title: B6xDBA-Fos-90m-B3


title: SKMEL-1206_IgG_rep2

description:
IgG replicate 2
Table_AllPeaks_HOXA13_H3K27ac_normCounts_Annotated.txt

value: IgG


title: B6xDBA-Fos-90m-B2

value: CUT&RUN


title: GF201_seedling

description: TPM was estimated using Kallisto


title: GF202_seedling

description: TPM was estimated using Kallisto


title: GF196_seedling

description: TPM was estimated using Kallisto


title: GF197_seedling

description: TPM was estimated using Kallisto


title: SKMEL-1206_IgG_rep1

description:
IgG replicate 1
Table_AllPeaks_HOXA13_H3K27ac_normCounts_Annotated.txt


title: GF204_seedling

description: TPM was estimated using Kallisto


title: B6xDBA-Fos-90m-B1


title: SKMEL-1206_HOXA13_rep2

description:
HOXA13 replicate 2
Table_AllPeaks_HOXA13_H3K27ac_normCounts_Annotated.txt


title: GF208_seedling

description: TPM was estimated using Kallisto


title: GF207_seedling

description: TPM was estimated using Kallisto


title: GF21_seedling

description: TPM was estimated using Kallisto


title: B6xDBA-Fos-0m-B2


title: SKMEL-1206_HOXA13_rep1

description:
HOXA13 replicate 1
Table_AllPeaks_HOXA13_H3K27ac_normCounts_Annotated.txt


title: GF205_seedling

description: TPM was estimated using Kallisto


title: GF189_seedling

description: TPM was estimated using Kallisto


title: B6xDBA-Fos-0m-B3


title: B6xBALB-H3K27ac-90m-B3

value: C57BL/6J x BALB/cJ F1 hybrid

value: Abcam ab4729


title: GF213_seedling

description: TPM was estimated using Kallisto


title: SKMEL-1206_H3K27ac_rep2

description:
H3K27ac replicate 2
Table_AllPeaks_HOXA13_H3K27ac_normCounts_Annotated.txt


title: SKMEL-1206_H3K27ac_rep1

description:
H3K27ac replicate 1
Table_AllPeaks_HOXA13_H3K27ac_normCounts_Annotated.txt


title: GF215_seedling

description: TPM was estimated using Kallisto


title: GF224_seedling

description: TPM was estimated using Kallisto


title: GF190_seedling

description: TPM was estimated using Kallisto


title: SKMEL-1176_noab_rep2

value: BRAF V600E


title: B6xBALB-H3K27ac-90m-B2


title: GF225_seedling

description: TPM was estimated using Kallisto


title: B6xBALB-H3K27ac-90m-B1


title: GF226_seedling

description: TPM was estimated using Kallisto


title: SKMEL-1176_noab_rep1


title: GF23_seedling

description: TPM was estimated using Kallisto


title: GF228_seedling

description: TPM was estimated using Kallisto


title: GF231_seedling

description: TPM was estimated using Kallisto


title: GF230_seedling

description: TPM was estimated using Kallisto


title: B6xBALB-H3K27ac-0m-B2

value: starved with 0.5% CCS MEF media


title: B6xBALB-H3K27ac-0m-B3


title: SKMEL-1176_IgG_rep2


title: GF234_seedling

description: TPM was estimated using Kallisto


title: SKMEL-1176_HOXA13_rep2


title: B6xBALB-Fos-90m-B3


title: GF238_seedling

description: TPM was estimated using Kallisto


title: GF235_seedling

description: TPM was estimated using Kallisto


title: B6xBALB-H3K27ac-0m-B1


title: GF247_seedling

description: TPM was estimated using Kallisto


title: GF24_seedling

description: TPM was estimated using Kallisto


title: SKMEL-1176_H3K27ac_rep2


title: SKMEL-1176_HOXA13_rep1


title: GF221_seedling

description: TPM was estimated using Kallisto


title: B6xBALB-Fos-90m-B2


title: SKMEL-1176_H3K27ac_rep1


title: evoHLn Gd rep 2

first: Nathan

last: Good

address: 111 Koshland Hall

department: Plant and Microbial Biology

institute: UC-Berkeley

data_processing:
HISAT2 to align reads
StringTie v2.1.5 to assemble and quantify transcripts
DeSeq v1.20.0 for differential expression analysis
Genome_build: ASM2268v1
Supplementary_files_format_and_content: gene counts for every gene and every sample, and FPKM values for each sample

organism: Methylorubrum extorquens AM1

source_name: bacterial cells

growth_protocol: Cultures were grown in MP minimal medium with 50 mM methanol as the growth substrate and 2 μM lanthanide (chloride salt) were indicated.

extract_protocol:
RNA was extracted using the Rneasy RNA extraction kit from Qiagen according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mutant strain evo-HLn

value: methanol + gadolinium growth


title: GF248_seedling

description: TPM was estimated using Kallisto

value: two week seedling

value: leaf


title: B6xBALB-Fos-90m-B1

value: In-house generated Fos 1096AE


title: GF249_seedling

description: TPM was estimated using Kallisto


title: evoHLn Gd rep 1


title: B6xBALB-Fos-0m-B3


title: SKMEL-1088_noab_rep2

source_name: Human melanoma cell line


title: SKMEL-1176_IgG_rep1


title: GF25_seedling

description: TPM was estimated using Kallisto


title: GF256_seedling

description: TPM was estimated using Kallisto


title: B6xBALB-Fos-0m-B1


title: evoHLn La rep 2

value: methanol + lanthanum growth


title: B6xBALB-Fos-0m-B2


title: GF263_seedling

description: TPM was estimated using Kallisto


title: SKMEL-1088_noab_rep1

value: Melanoma


title: evoHLn La rep 1


title: SKMEL-1088_HOXA13_rep2


title: SKMEL-1088_IgG_rep2


title: GF262_seedling

description: TPM was estimated using Kallisto


title: B6xAJ-H3K27ac-90m-B3

value: C57BL/6J x A/J F1 hybrid

value: 90m stimulation with 15% CCS MEF media


title: MDH-3 La rep 3

value: mutant strain MDH-3


title: B6xAJ-H3K27ac-90m-B1

value: Primary mouse embryonic fibroblasts

value: wild-type


title: MDH-3 La rep 1


title: B6xAJ-H3K27ac-90m-B2

value: CUT&RUN


title: SKMEL-1088_IgG_rep1

value: IgG


title: GF265_seedling

description: TPM was estimated using Kallisto


title: SKMEL-1088_H3K27ac_rep2


title: TCFL5-ChIP-seq

first: Weiya

last: Xu

state: Jiangsu

address: No. 818, Tianyuan East Road

department: State Key Laboratory of Reproductive Medicine

institute: Nanjing Medical University

data_processing:
Raw reads were filtered first to remove low-quality or adaptor sequences by SOAPnuke.
Cleaned reads were mapped to the reference genome of Mouse GRCm38/mm10 using SOAPaligner/SOAP2 (version: 2.2.5)
MACS2 (version: 2.1.2) were used to call peaks (open chromatin regions).
The different enrichment peaks from different samples was plotted by MAnorm(v1.1).
Also the gene element annotation of peak or different enrichment peak from different samples was carry out by bedtools intersect mode with overlap 50%
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: soap files were generated by SOAPaligner/SOAP2 (version: 2.2.5), representing cleaned reads mapped to the reference genome of GRCm38/mm10

source_name: testes

extract_protocol:
Lysates were clarified from sonicated testicular lysate and protein-DNA complexes were isolated with antibody.
The DNA is combined with End Repair Mix, and incubate at 20℃ for 30 min. Purify the end-repaired DNA with QIAquick PCR Purification Kit(Qiagen)，then add A-Tailing Mix, incubate at 37℃ for 30 min. Combine the purified Adenylate 3'Ends DNA, Adapter and Ligation Mix, incubate the ligation reaction at 20℃ for 15 min. Purify the Adapter-ligated DNA with the QIAquick PCR Purification Kit. Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix are performed to enrich the Adapter-ligated DNA fragments. Then the PCR products are selected (about 100-300bp, including adaptor sequence) by running a 2% agarose gel to recover the target fragments. Purify the gel with QIAquick Gel Extraction kit (QIAGEN). The final library is quantitated in two ways: Determine the average molecule length and sample integrity as well as purity using the Agilent 2100 bioanalyzer instrument (Agilent DNA 1000 Reagents) and quantify the library by real-time quantitative PCR (QPCR). The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library. Library was qualified by Qubit ssDNA kit. The sequencing will be performed with the BGISEQ-500 sequencing system, featuring combinatorial probe-anchor synthesis (cPAS) and DNA Nanoballs (DNB) technology for superior data quality (BGI-Shenzhen, China).

value: post natal day 21

value: testis

value: TCFL5(Abcam, Ab188075)


title: Input-DNA


title: GF267_seedling

description: TPM was estimated using Kallisto


title: B6xAJ-H3K27ac-0m-B3

value: starved with 0.5% CCS MEF media

value: Abcam ab4729


title: SKMEL-1088_H3K27ac_rep1

value: BRAF V600E


title: evoHLn La rep 3

value: mutant strain evo-HLn


title: B6xAJ-H3K27ac-0m-B2


title: B6xAJ-H3K27ac-0m-B1


title: GF27_seedling

description: TPM was estimated using Kallisto

value: two week seedling

value: leaf


title: Tcfl5-Heter2 [RNA-seq]

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set then expression level of gene was calculated by RSEM (v1.2.12)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: excel files include gene_id, gene_id_alias, gene_transcript_id, gene_type, gene_transcript_num, gene_start, gene_end, gene_chr, gene_strand, gene_len, gene_max_transcript_len, fpkm_Wt2

source_name: Pachytene spermatocytes_Tcfl5-Het

extract_protocol:
Pachytene spermatocytes were isolated, flash frozen on dry ice, and followed by total RNA isolation using Trizol reagent and sequencing by BGISEQ-500.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

tag: strain background

value: Adult

value: Pachytene spermatocytes


title: MDH-3 La rep 2

value: methanol + lanthanum growth


title: H9d7_WT_rep2

city: Stanford

first: Anthony

last: Oro

address: 269 Campus Drvie

department: Dermatology

institute: Stanford University

data_processing:
Tophat used for alignment.
Homer for raw counts and RPKM values
DESEQ2 used for differential expression
Genome_build: hg38
Supplementary_files_format_and_content: text file, raw counts

source_name: H9 day7

extract_protocol:
RNA was isolated using Trizol per manufacturer protocol. The aqueous phase was transferred to an Rneasy spin column for purificiation. DNA was removed with a Qiagen Dnase kit on the Rneasy column.
Libraries were consructed with the KAPA kit for PolyA enriched mRNA per manufacterer instructions.

tag: cell line

value: WT


title: B6xAJ-Fos-90m-B3

value: Primary mouse embryonic fibroblasts

value: C57BL/6J x A/J F1 hybrid

value: 90m stimulation with 15% CCS MEF media

value: In-house generated Fos 1096AE


title: Tcfl5-Heter1 [RNA-seq]

tag: tissue


title: H9d7_WT_rep1


title: GF264_seedling

description: TPM was estimated using Kallisto


title: GF276_seedling

description: TPM was estimated using Kallisto


title: B6xAJ-Fos-90m-B2

value: wild-type

value: CUT&RUN


title: Wt2 [RNA-seq]

source_name: Pachytene spermatocytes_WT

value: testis


title: SKMEL-1088_HOXA13_rep1

value: Melanoma


title: B6xAJ-Fos-0m-B3

value: starved with 0.5% CCS MEF media


title: H9d7_TFAP2C_KO_rep1

value: TFAP2A knockout


title: GF278_seedling

description: TPM was estimated using Kallisto


title: B6xAJ-Fos-0m-B2


title: H9d7_TFAP2C_KO_rep2


title: bovine satellite cells 1

city: Blacksburg

first: Honglin

last: Jiang

state: VA

address: 3130 Litton Reaves Hall

department: Animal and Poultry Sciences

institute: Virginia Polytechnic Institute and State University

data_processing:
Sequencing reads were processed and analyzed using the Cell Ranger 3.0.2 pipeline (10x Genomics).
Sequencing reads were de-multiplexed and aligned to the bovine genome and transcriptome (Bos_taurus.ARS-UCD1.2) at default parameters.
Uniquely mapped sequences from each library were used for unique molecular identifiers (UMI) counting using the cellranger count pipeline.
The output files from the cellranger counting of reads from two scRNA-seq libraries were combined using the cellranger aggr program.
Differential gene expression between cell clusters was identified using the quick and simple method sSeq and edgeR
Genome_build: Bos_taurus.ARS-UCD1.2
Supplementary_files_format_and_content: excel

organism: Bos taurus

source_name: skeletal muscle

growth_protocol: cells were cultured in growth medium consisting of DMEM and 10% FBS for a week prior to the analysis

extract_protocol:
n/a
The scRNA-seq libraries were constructed using the Chromium Single Cell 3ʹ Gel Bead-in-Emulsion (GEM), Library & Gel Bead Kit v3 (10x Genomics) and following the manufacturer’s instruction.

tag: gender

value: male

value: two-week-old

tag: breed

value: Holstein


title: bovine satellite cells 2


title: U2OS cells - HighMYC_TotalInput_rep1_ChIP

data_processing:
Hi-C: SIQHiC libraries include human and mouse DNA. Paired reads were separated and mapped as single reads using BWA-MEM to an artificial reference genome combining hg19 human and mm10 mouse genome sequences. After mapping, reads were paired together again and split into 2 files. Paired reads both mapping to human chromosomes were placed together as Human-Human paired reads (H-H), while paired reads both mapping to mouse chromosomes were placed together as Mouse-Mouse paired reads (M-M). Ambiguous read pairs that separately mapped to different species are discarded. H-H and M-M reads were processed using Juicer separately, filtering out duplicates, intra-fragment reads and reads with MAPQ < 30 to generate .hic matrix files for each species. H-H reads of biological replicates were also merged and processed in the same way to generate .hic matrix files for downstream analyses.
RNA-seq: Reads were aligned to the hg19 reference genome using kallisto. UCSC RefSeq transcript expression was calculated as transcripts per million (TPM) using kallisto.
ChIP-seq: ChIP-seq libraries were mapped to the hg19 genome using BWA-MEM version 0.7.5a-r405 using default settings. PCR duplicates were removed using samtools version 1.7 and reads falling within the ENCODE consensus blacklisted regions were removed using BEDTools version 2.26.0. ChIP-seq signals were visualized using deepTools version 3.2.1 (bamCompare --normalizeUsing RPKM --operation subtract -bs 1). Bam files of biological replicates were merged before calling ChIP-seq peaks using MACS2 version 2.1.2
4C-seq: 4C-seq libraries were mapped to the hg19 genome using BWA-MEM version 0.7.5a-r405 using default settings and processed using the r3Cseq pipeline.
Genome_build: hg19
Supplementary_files_format_and_content: Hi-C chromatin interactions matrix output from Juicer provided as .hic files
RNA Seq transcript per million output from kallisto at the transcript level provided as .tsv files. Fields show 1. transcript RefSeq id, 2. length, 3. effective length, 4. estimated counts, 5. transcripts per million
ChIP-Seq signficant peaks output from MACS2 provided as narrowPeak files.
4C-seq significant interactions output from r3Cseq provided as txt files. Fields show 1. chromosome, 2. start position, 3. end position, 4. number of reads, 5. reads per million, 6. p.value, 7. q.value, 8. nearest genes

extract_protocol:
Cells were fixed in 1% formaldehyde and sonicated using the truChIP Chromatin Shearing Kit (Covaris) on the ME220 Focused-Ultrasonicator (Covaris) according to the manufacturer’s protocol. 3.5µg of each antibody was rotated with 15µl of Dynabeads Protein G magnetic beads (Invitrogen) at 4℃ overnight and washed thrice with Beads Wash Buffer (0.1% Triton X-100 in PBS) to remove unbound antibodies. Antibody-bound beads were combined with sonicated chromatin from 5 million cells and rotated at 4℃ overnight. Beads were then washed thrice with Shearing Buffer D3 (Covaris), once with High Salt Washing Buffer (50mM HEPES pH 7.5, 350mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate, 0.1% SDS), once with Lithium Chloride Wash Buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP-40, 0.5% Sodium Deoxycholate) and once with Tris-EDTA buffer. Chromatin was eluted from the magnetic beads in 100µl elution buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) supplemented with 2µl of 0.5mg/ml RNase A (QIAGEN) at 55℃ for 2 hours. Chromatin was then decrosslinked with the addition of 2µl of 20mg/ml proteinase K (Ambion) at 55℃ for 4 hours and 37℃ overnight. For total input, chromatin from 500,000 cells were treated with RNase A and decrosslinked similarly. DNA was purified using the MinElute PCR Purification Kit (QIAGEN).
ChIP-seq libraries were prepared using the ThruPLEX DNA-seq Kit (Rubicon) and sequenced paired-end 2 x 100bp on the HiSeq 2500 (Illumina).

tag: doxycyline treatment

tag: restriction enzyme

value: Not Applicable


title: U2OS cells - HighMYC_TotalInput_rep2_ChIP


title: B6xAJ-Fos-0m-B1

tag: cell type

tag: strain

tag: age

tag: genotype


title: GF280_seedling

description: TPM was estimated using Kallisto

value: two week seedling

value: leaf

tag: line


title: B6x129-H3K27ac-90m-B3

value: C57BL/6J x 129S1/SvImJ F1 hybrid

tag: treatment

tag: passage

value: Abcam ab4729

tag: experiment


title: GF281_seedling

description: TPM was estimated using Kallisto


title: GF270_seedling

description: TPM was estimated using Kallisto


title: U2OS cells - LowMYC_TotalInput_rep1_ChIP

tag: chip antibody


title: B6x129-H3K27ac-90m-B2

value: Primary mouse embryonic fibroblasts

tag: cut&run antibody


title: GF283_seedling

description: TPM was estimated using Kallisto


title: GF282_seedling

description: TPM was estimated using Kallisto


title: U2OS cells - HighMYC_MYC rep2_ChIP

value: c-Myc (#sc-40,Santa Cruz)


title: Differentiated satellite cells.

city: Poznan

first: Karol

last: Jopek

address: Swiecicki 6

department: Department of Histology and Embryology.

country: Poland

institute: Poznan University of Medical Sciences

data_processing:
Demultiplexing of the sequencing reads was carried out using Illumina bcl2fastq (2.20), leading to the obtaining of FASTQ files.
Then adapters were trimmed with Skewer (version 0.2.2).
Trimmed raw reads were aligned to the turkey reference genome (Meleagris_gallopavio. Turkey 2.01) with relevant GTF file downloaded from Ensembl database. Alignment was carried out using STAR (version 2.5.2b) software.
NOISeq R-package was used for quality control and quantitative analysis of count data [17] where count values were normalized to RPKM (Reads Per Kilobase Million), applied for the calculation of the essential parameters for the differences in expression between the compared groups.
Genome_build: melGal5
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

organism: Meleagris gallopavo

source_name: Satellite cells.

growth_protocol: Satellite cells were isolated from breast muscle (Pectroralis thoracicus) of new born turkeys cultured for two weeks as undifferentiated. A complex characterisation of the isolated cell population was already described in previous works of the co-authors [11,12]. At the end of two weeks cells were divided to three different groups including undifferentiated, differentiated (identified through a downregulation of self-renewal genes and no telomerase activity, as described in a previous article of our group [11])  and suspended. Which means that some cells were kept to grow as undifferentiated (undifferentiated group) and cultured as adherent, some cells were fused to form myotubes (differentiated group) as the adherent culture and some cells were cultured as suspension (suspended group). Therefore, briefly satellite cells were isolated from 1 days old turkeys using sterile forceps and scissors, mechanically disassociated with sterile forceps and incubated for 30 min in warm (37³C) 0.17% Trypsin+0.085% collagenase solution in Hank's balanced salt, for satellite cell liberation. Subsequently, the tissue was washed twice with turkey plating medium (TPM), which consisted of 89% Dulbecco's Modified Eagle's medium (DMEM), 10% horse serum (Gibco, Grand Island, NY), and 1% penicillin streptomycin fungizone (Gibco). The tissue was resuspended in TPM, triturated through a Pasteur pipette followed by an 18-gauge needle, the cell concentration was estimated using a hemocytometer, and the cells for adherent cultures cells were plated on 0.1% gelatin-coated 100-mm cell culture dishes at a concentration of cells per dish. After a 24-h attachment period, TPM was replaced with turkey growth medium (TGRM), which consisted of 84% McCoy's 5A, 15% chicken serum (Gibco), and 1% penicillin streptomycin fungizone. Satellite cells were cultured for two weeks before growth media were replaced with differentiating media DMEM-4% Horse Serum. Moreover, additional cells were washed with PBS, detached through incubation in EDTA at 37˚C for 5 min, and directly incoculated to an Erlenmeyer flasks containing Mcoy’s 5A and 15% Chicken Serum to culture growing cells as suspension under rotation at 110 rpm. All of the groups were cultured for several passages until they were viable and continuously growing. Suspended cells were cultured for three months, after which RNA isolation was performed . Then, all groups were subjected to RNA isolation and RNA sequencing with bioinformatics evaluations to compare viability and self-renewal ability of different groups. Adherent undifferentiated group was compared to adherent differentiated group, as well as cells cultured in suspension.

extract_protocol:
Cells from one confluent T75 flask for each sample were digested in 500 µl of trizol and incubated at room temperature for 5 minutes. In the next step, 100 µl of chloroform was added and the sample was shaken by vortex for 1 minutes and incubated for 5 minutes. The resulting mix was centrifuged at 12000 rcf for 20 minutes. The upper aqueous phase was transferred to a new vial on ice and cooled isopropanol (isopropyl alcohol) in the equal amount was added, vortexed and incubated on ice for 30 minutes. The vial was centrifuged in a refrigerated centrifuge for 20 minutes. When the RNA pellet was visible supernatants were removed and in order to remove isopropanol it was washed twice with 75% ethanol. Ethanol was removed and the pellet was dried in room temperature for 30 minutes. Afterwards, the dried pellet was dissolved in 25 µl DEPC water and kept in -80 ° C.
The NanoDrop ND2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA USA) was used to assess RNA quantity and purity.  Five hundred nanograms of total RNA from each sample were submitted to the North Carolina State University Genomics Research Laboratory for library preparation and sequencing on the Illumina NovoSeq 6000 (Illumina Inc, San Diego CA, USA). Each sample generated 35-40 million sequence reads.

treatment_protocol: No treatment.

value: Muscle- Pectroralis thoracicus.

value: Satellite cells.

tag: type of culture

value: Differentiated cells.


title: B6x129-H3K27ac-0m-B3

value: wild-type

value: CUT&RUN


title: Adherent satellite cells.

value: Adherent cells.


title: Wt1 [RNA-seq]

tag: strain background

value: Adult

value: testis

value: Pachytene spermatocytes


title: GF277_seedling

description: TPM was estimated using Kallisto

tag: tissue


title: U2OS cells - HighMYC_MYC rep1_ChIP

tag: cell line


title: B6x129-H3K27ac-90m-B1

value: 90m stimulation with 15% CCS MEF media


title: Suspended satellite cells.

value: Suspended cells.


title: GF285_seedling

description: TPM was estimated using Kallisto

value: two week seedling


title: B6x129-H3K27ac-0m-B2

value: starved with 0.5% CCS MEF media


title: U2OS cells - LowMYC_MYC rep2_ChIP

value: Not Applicable


title: GF279_seedling

description: TPM was estimated using Kallisto

value: leaf


title: GF287_seedling

description: TPM was estimated using Kallisto


title: B6x129-H3K27ac-0m-B1

value: Primary mouse embryonic fibroblasts

value: C57BL/6J x 129S1/SvImJ F1 hybrid

value: Abcam ab4729


title: U2OS cells - LowMYC_MYC rep1_ChIP

value: c-Myc (#sc-40,Santa Cruz)


title: GF289_seedling

description: TPM was estimated using Kallisto


title: GF29_seedling

description: TPM was estimated using Kallisto


title: U2OS cells - LowMYC_TotalInput_rep2_ChIP


title: U2OS cells - HighMYC_H3K27ac rep2_ChIP

value: H3K27ac (#ab4729,abcam)


title: B6x129-Fos-90m-B2

value: wild-type

value: In-house generated Fos 1096AE


title: U2OS cells - HighMYC_H3K27ac rep1_ChIP


title: B6x129-Fos-90m-B1

value: CUT&RUN


title: B6x129-Fos-0m-B2


title: GF294_seedling

description: TPM was estimated using Kallisto


title: U2OS cells - LowMYC_H3K27ac rep1_ChIP


title: GF295_seedling

description: TPM was estimated using Kallisto


title: GF293_seedling

description: TPM was estimated using Kallisto


title: B6x129-Fos-0m-B1


title: B6-IgG-90m-B1

value: Cell Signaling Technology 2729S


title: GF296_seedling

description: TPM was estimated using Kallisto


title: B6x129-Fos-90m-B3


title: GF297_seedling

description: TPM was estimated using Kallisto


title: B6-IgG-0m-B1


title: U2OS cells - LowMYC_rep2_RNA

extract_protocol:
Total RNA was extracted from U2OS cells with or without doxycycline induction in duplicate, using the RNeasy Mini Kit (QIAGEN)
Ribosomal RNA depletion and library preparation was performed using the TruSeq Stranded Total RNA LT Kit (Illumina) according to the manufacturer’s protocol. Paired-end 2 x 100bp sequencing was performed on the Illumina HiSeq 2501

value: Arima (multi-enzyme)


title: GF299_seedling

description: TPM was estimated using Kallisto


title: U2OS cells - LowMYC_H3K27ac rep2_ChIP


title: XFN

description: Acral melanoma model fin microenvironment

data_processing:
Data was processed using R version 4.0.4 and Seurat version 4.0.3 (Hao, Hao et al., 2021). Each of the four reactions were processed separately before merging into a single object.
Cells with fewer than 200 unique genes were filtered out.
Expression data was normalized with SCTransform (Hafemeister and Satija, 2019).
Principal component analysis (Joliffe, 1986) and UMAP dimensionality reduction (McInnes, 2018) were performed using default parameters, with 15 principal components used for UMAP calculations.
Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell-type marker genes as done previously (Baron et al., 2020; Hunter, Moncada et al., 2021).
Genome_build: GRCz10
Supplementary_files_format_and_content: csv file containing counts from all 4 samples
Supplementary_files_format_and_content: Cell ranger output

organism: Danio rerio

source_name: Zebrafish fins

extract_protocol:
Droplet-based scRNA-seq was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 (10X Genomics) and Chromium Single Cell 3’ Chip G (10X Genomics). Approximately 10,000 cells were encapsulated per each of the four reactions.
GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles, i5 10 cycles, i7 10 cycles, Read2 90 cycles. Sequencing depth was approximately 40,000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 (10X Genomics).
scRNA-seq (10X genomics)

tag: model

value: Acral melanoma model (Caspers with MiniCoopR-eGFP, mitfa:hsCRKL, mitfa:hsGAB2, mitfa:hsTERT, mitfa:Cas9-mCherry;U6-nf1a-gRNA, mitfa:Cas9-mCherry;U6-nf1b-gRNA)

value: Fin

value: GFP-


title: U2OS cells - HighMYC_rep2_RNA

source_name: U2OS human cells

extract_protocol:
Total RNA was extracted from U2OS cells with or without doxycycline induction in duplicate, using the RNeasy Mini Kit (QIAGEN)
Ribosomal RNA depletion and library preparation was performed using the TruSeq Stranded Total RNA LT Kit (Illumina) according to the manufacturer’s protocol. Paired-end 2 x 100bp sequencing was performed on the Illumina HiSeq 2503

tag: doxycyline treatment


title: time_180min_3

city: Tampere

first: Andre

middle: Sanches

last: Ribeiro

state: Pirkanmaa

address: Address:Arvo Ylpön katu 34

country: Finland

institute: Tampere University

data_processing:
RNA sequencing reads were trimmed to remove possible adapter sequences and nucleotides with poor quality with Trimmomatic v.0.36
Trimmed reads were then mapped to the reference genome, E. coli MG1655 (NC_000913.3), using the STAR aligner v.2.5.2b, which outputs BAM files
featureCounts from the Rsubread R package (v.1.34.7) was used to calculate unique gene hit counts. Gene hit counts was then used for the subsequent differential expression analysis. Genes with less than 5 counts in more than 3 samples, and genes whose mean counts are less than 10 were removed from further analysis.
We used the DESeq2 R package (v.1.24.0) to compare gene expression between groups of samples and calculate p-values and log2 of fold changes (LFC) using Wald tests (function nbinomWaldTest).
P-values were adjusted for multiple hypotheses testing (Benjamini–Hochberg, BH procedure)
Genome_build: Escherichia coli str. K-12 substr. MG1655 (NC_000913.3)
Supplementary_files_format_and_content: tab-delimited .csv file containing raw counts
Supplementary_files_format_and_content: tab-delimited .csv file containing DESeq normalized raw counts
Supplementary_files_format_and_content: tab-delimited .csv file containing TPM normalized raw counts
Supplementary_files_format_and_content: tab-delimited .csv file containing results from differential expression analysis

organism: Escherichia coli

growth_protocol: From glycerol stocks (at - 80 ºC), cells were streaked on lysogeny broth (LB) agar plates and kept at 37 ºC overnight. Next, a single colony was picked and inoculated into fresh LB medium and kept at 30 ºC overnight, with aeration at 250 rpm. Next, these cultures were diluted to optical density (O.D600) of 0.05 in fresh LB medium and incubated at 37 ºC with a 250 rpm agitation. RNA-seq was performed over time at (0, 20,80 and 180 min).

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen).
RNA-seq libraries were constructed according to the Illumina's protocol.
Library strategy established by GENEWIZ, Inc. (Leipzig, Germany) for RNA-seq

treatment_protocol: Cells from 3 independent biological replicates of MG1655 in LB medium at different time moments were treated with RNA protect bacteria reagent (Qiagen, Germany), to prevent degradation of RNA.

value: E.coli MG1655


title: GF298_seedling

description: TPM was estimated using Kallisto

value: two week seedling


title: U2OS cells - LowMYC_rep1_RNA

extract_protocol:
Total RNA was extracted from U2OS cells with or without doxycycline induction in duplicate, using the RNeasy Mini Kit (QIAGEN)
Ribosomal RNA depletion and library preparation was performed using the TruSeq Stranded Total RNA LT Kit (Illumina) according to the manufacturer’s protocol. Paired-end 2 x 100bp sequencing was performed on the Illumina HiSeq 2500

tag: restriction enzyme

value: Not Applicable


title: GF30_seedling

description: TPM was estimated using Kallisto

value: leaf


title: GF300_seedling

description: TPM was estimated using Kallisto


title: XFG

description: Acral melanoma model fin melanocytes

tag: cell type

value: GFP+


title: time_180min_1

tag: strain


title: time_80min_2


title: time_80min_1


title: Aged mouse CD4 Tconv KO2

city: Esch-sur-Alzette

first: Feng

middle: Q.

last: Hefeng

address: 29, rue Henri Koch

department: Department of Infection and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

description: Expression value derived using Expression Console software; Exon analysis summarized using PLIER

hyb_protocol: The fragmented/labeled single-strand cDNA (with hybridization controls) was hybridized to the Affymetrix Mouse Gene 2.0 ST Array at 45°C for 16h with rotation (60rpm). After the hybridization step, each of the arrays has been washed and stained on the GeneChip Fluidics Stations 450 (Affymetrix), using the GeneChip® Hybridization Wash and Stain Kit.

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 7G with GeneChip Command Console software (Affymetrix). The software generates the .CEL files containing the probe cell intensity data and enables sample and array registration, data management, instrument control as well as automatic and manual image gridding.

data_processing: The expression signal at exon level was summarized with Affymetrix PLIER algorithm with DABG and PM-GCBG options using the sketch-quantile normalization approach (Affymetrix Expression Console v1.4).The corresponding probesets were considered differentially expressed if they passed the following combinatory filters: (a) whether the change folds >= 2 between the means of DJ-1 KO and WT Tconv; (b), whether the P-value, resulted from two-tailed unpaired Student T-test, <=0.05; (c),  whether the cross-hyb type of the probeset was equal to 1; (d), whether the probeset with the highest expression level is higher than 100 (with the median ~90 of each sample); (e), for a given group (e.g. WT) with higher mean intensity value of the probeset, whether the probeset in all the replicates of the given group was detected as ‘present’ according to the default setting of the Expression Console.

label: biotin

source_name: aged DJ-1 KO mouse 2

label_protocol: Single-strand cDNA was labeled and fragmented using the WT Terminal Labeling, polyA and hyb Controls Kit.

growth_protocol: All mice were maintained in our specific-pathogen-free (SPF) animal facility and all animal experimental procedures were performed following the approval of the Animal Warfare Society (AWS) of University of Luxembourg and Luxembourg Institute of Health.

extract_protocol: Freshly sorted T cells were first lysed with RLT buffer, supplemented with 1% beta-Mercaptoethanol and RNA were extracted using RNeasy Mini Kit following the manufacturer’s instructions including the digestion of genomic DNA with DNAse I.

treatment_protocol: No treatment. The cells were sorted from the spleen of homeostatic aged mice (~45-week old) under the SPF condition.

value: CD4 Tconv

tag: Sex

value: Male

tag: age

value: ~45-week old

value: DJ-1 KO


title: Aged mouse CD4 Tconv WT1

source_name: aged WT mouse 1

tag: genotype

value: WT


title: Aged mouse CD4 Tconv WT2

source_name: aged WT mouse 2


title: GF301_seedling

description: TPM was estimated using Kallisto

extract_protocol: A panel of diverse 400 wheat lines was selected based on the geographic distribution and genetic diversity, and available from the USDA National Small Grains Collection. Total RNA was isolated from 2-week seedlings of 204 lines with each line grown in three biological replicates. Ground tissues from three biological replicates were combined in equal amounts before RNA isolation using RNeasy Plant mini kit. RNA-seq libraries were prepared with TruSeq™ RNA Sample Prep Kit (Illumina) using the Beckman’s Biomek® FXP Laboratory Automation Workstation. Up to eight barcoded RNA-seq libraries were pooled per lane of NextSeq2000 flow cell to generate 2 x 100 bp reads.

tag: line


title: GF304_seedling

description: TPM was estimated using Kallisto


title: U2OS cells - HighMYC_rep1_RNA

extract_protocol:
Total RNA was extracted from U2OS cells with or without doxycycline induction in duplicate, using the RNeasy Mini Kit (QIAGEN)
Ribosomal RNA depletion and library preparation was performed using the TruSeq Stranded Total RNA LT Kit (Illumina) according to the manufacturer’s protocol. Paired-end 2 x 100bp sequencing was performed on the Illumina HiSeq 2502


title: Aged mouse CD4 Tconv WT3

source_name: aged WT mouse 3


title: XBG

description: Acral melanoma model body melanocytes

source_name: Zebrafish body skin

value: Body


title: U2OS cells - siCTCF_rep2_HiC

description:
siCTCF_merged_inter_30.hic
siCTCF_merged_inter_30_SIQHIC.hic

data_processing:
Hi-C: SIQHiC libraries include human and mouse DNA. Paired reads were separated and mapped as single reads using BWA-MEM to an artificial reference genome combining hg19 human and mm10 mouse genome sequences. After mapping, reads were paired together again and split into 2 files. Paired reads both mapping to human chromosomes were placed together as Human-Human paired reads (H-H), while paired reads both mapping to mouse chromosomes were placed together as Mouse-Mouse paired reads (M-M). Ambiguous read pairs that separately mapped to different species are discarded. H-H and M-M reads were processed using Juicer separately, filtering out duplicates, intra-fragment reads and reads with MAPQ < 30 to generate .hic matrix files for each species. H-H reads of biological replicates were also merged and processed in the same way to generate .hic matrix files for downstream analyses.
RNA-seq: Reads were aligned to the hg19 reference genome using kallisto. UCSC RefSeq transcript expression was calculated as transcripts per million (TPM) using kallisto.
ChIP-seq: ChIP-seq libraries were mapped to the hg19 genome using BWA-MEM version 0.7.5a-r405 using default settings. PCR duplicates were removed using samtools version 1.7 and reads falling within the ENCODE consensus blacklisted regions were removed using BEDTools version 2.26.0. ChIP-seq signals were visualized using deepTools version 3.2.1 (bamCompare --normalizeUsing RPKM --operation subtract -bs 1). Bam files of biological replicates were merged before calling ChIP-seq peaks using MACS2 version 2.1.2
4C-seq: 4C-seq libraries were mapped to the hg19 genome using BWA-MEM version 0.7.5a-r405 using default settings and processed using the r3Cseq pipeline.
Genome_build: hg19
Supplementary_files_format_and_content: Hi-C chromatin interactions matrix output from Juicer provided as .hic files
Supplementary_files_format_and_content: RNA Seq transcript per million output from kallisto at the transcript level provided as .tsv files. Fields show 1. transcript RefSeq id, 2. length, 3. effective length, 4. estimated counts, 5. transcripts per million
Supplementary_files_format_and_content: ChIP-Seq signficant peaks output from MACS2 provided as narrowPeak files.
Supplementary_files_format_and_content: 4C-seq significant interactions output from r3Cseq provided as txt files. Fields show 1. chromosome, 2. start position, 3. end position, 4. number of reads, 5. reads per million, 6. p.value, 7. q.value, 8. nearest genes

organism:
Homo sapiens
Mus musculus

source_name: U2OS human cells; spike in NIH3T3

extract_protocol:
Human U2OS cells and mouse 3T3 cells were fixed with 2% formaldehyde using the Arima Hi-C Kit (Arima). 1 million fixed 3T3 mouse cells were added to each sample of 4 million human U2OS cells before subsequent steps of restriction enzyme digest, biotin end filling and ligation according to the Arima Hi-C protocol.
Libraries were prepared using the KAPA Hyper-Prep Kit (KAPA), according to manufacturers’ protocols.

treatment_protocol: Cells were treated with 1ug/ml doxycycline for 30h and transfected with CTCF siRNA for 48h.

value: U2OS; NIH3T3

tag: antibody


title: GF306_seedling

description: TPM was estimated using Kallisto

source_name: seedling


title: Aged mouse CD4 Tconv KO3

source_name: aged DJ-1 KO mouse 3


title: Aged mouse CD4 Tconv KO1

source_name: aged DJ-1 KO mouse 1


title: GF305_seedling

description: TPM was estimated using Kallisto


title: time_20min_2


title: U2OS cells - siCTCF_rep1_HiC


title: GF307_seedling

description: TPM was estimated using Kallisto


title: U2OS cells - siControl_rep2_HiC

treatment_protocol: Cells were treated with 1ug/ml doxycycline for 30h and transfected with control siRNA for 48h.


title: CD8 T cells from the sibling P1 with DJ-1-heterozygous mutation

hyb_protocol: The fragmented/labeled single-strand cDNA (with hybridization controls) was hybridized to the Affymetrix Human Gene 2.0 ST Array at 45°C for 16h with rotation (60rpm). After the hybridization step, each of the arrays has been washed and stained on the GeneChip Fluidics Stations 450 (Affymetrix), using the GeneChip® Hybridization Wash and Stain Kit.

data_processing: The expression signal at the exon level was summarized by the Affymetrix PLIER algorithm with DABG and PM-GCBG options by means of the sketch-quantile normalization approach (Affymetrix Expression Console v1.4). The corresponding probesets were considered for further analysis if they passed the combinatory filters below: (a) the change folds were >= 2 between both the two comparisons P2 versus P1 and P2 versus P3; (b) the cross-hyb type of the probeset was equal to 1; (d) the probeset with the highest expression level was higher than 100; (e) if the expression of the given probeset was higher in the patient P2, the probeset in P2 had to be detected as ‘present’ according to the default setting of the Affymetrix Expression Console; if the expression of the given probeset was lower in the patient P2, the probeset in both P1 and P3 had to be detected as ‘present’.

source_name: PBMC of P1 with DJ-1-heterozygous mutation

growth_protocol: We complied with all the relevant ethic regulations and Luxembourg CNER (Comité National d'Ethique de Recherche) has approved the PD patients related study. The family carrying the c.192G>C mutation in the DJ-1 gene has been already described elsewhere and written informed consent for all participating individuals was obtained. The three subjects are all male, 56-63-year old at the time of sampling

treatment_protocol: No treatment. Following staining and washing, the cells were sorted (BD Aria III) from PBMC of peripheral blood from the three siblings.

value: CD8 T cells

value: DJ-1-heterozygous mutation


title: XBN

description: Acral melanoma model body microenvironment

value: Acral melanoma model (Caspers with MiniCoopR-eGFP, mitfa:hsCRKL, mitfa:hsGAB2, mitfa:hsTERT, mitfa:Cas9-mCherry;U6-nf1a-gRNA, mitfa:Cas9-mCherry;U6-nf1b-gRNA)


title: time_0min_2


title: CD8 T cells from the sibling P2 with DJ-1-the homozygous c.192G>C mutation (loss-of-function)

source_name: PBMC of P2 with DJ-1 loss-of-function mutation

value: DJ-1 loss-of-function mutation


title: time_0min_3


title: GF309_seedling

description: TPM was estimated using Kallisto


title: CD8 T cells from the sibling P3 with DJ-1-heterozygous mutation

source_name: PBMC of P3 with DJ-1-heterozygous mutation


title: time_20min_1


title: U2OS cells - HighMYC_rep2_HiC

value: Arima (multi-enzyme)


title: U2OS cells - HighMYC_rep1_HiC


title: GF31_seedling

description: TPM was estimated using Kallisto


title: time_20min_3

value: E.coli MG1655


title: time_180min_2


title: I1_rep3

city: Kyoto

first: Shusaku

last: Uchida

state: Kyoto

address: 53 Kawaharamachi, Sakyo-ku

country: Japan

institute: Kyoto University

data_processing:
Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.32 tool.
The sequence reads were aligned to the mouse reference genome (mm10) using Tophat 2.0.13 (bowtie2-2.2.3), which can adequately align reads onto the location including splice sites in the genome sequence.
The aligned reads were subjected to downstream analyses using StrandNGS 2.6 software (Agilent Technologies). The read counts allocated for each gene and transcript (UCSC version 2013.3.6) were quantified using a Trimmed Mean of M-value (TMM) method.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for every gene and every sample (all data are summarized in single file)

source_name: Prefrontal cortex

extract_protocol:
Prefrontal cortex tissues were removed, flash frozen on dry ice, and RNA was extracted using Direct-zol RNA kit. SureSelect Strand-Specific RNA Library Prep for Illumina (Agilent Technology) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard protocols.

value: Prefrontal cortex

value: BALB/c

tag: treatment

value: Duloxetine

tag: behavior

value: Non-responder


title: GF310_seedling

description: TPM was estimated using Kallisto

data_processing:
All high confidence (HC) and low confidence (LC) gene models from the IWGSC RefSeq v. 1.0, as well as de novo assembled transcripts were combined for estimating the TPM values using Kallisto (v. 0.4.6.0). Gene models with expression standard deviation > 0.5 and expressed (TPM > 0.5) in at least 2 samples have been used in our analyses. This set of genes included 52,511 HC gene model, 29,226 LC gene model and 13,861 de novo assembled transcripts.
Supplementary_files_format_and_content: The TPM values for all expressed HC and LC gene models are provided as an expression data matrix. The file format is gzipped text.

value: two week seedling

value: leaf


title: U2OS cells - siControl_rep1_HiC

value: Not Applicable


title: GF308_seedling

description: TPM was estimated using Kallisto


title: U2OS cells - LowMYC_rep2_HiC

description:
inter_30_low_merged.hic
inter_30_low_1_merged_SIQHIC.hic

tag: chip antibody


title: Cap CD2AP rep3 h9coD35 SVA-KO

city: Amsterdam

first: Frank

last: Jacobs

address: Science Park 904

department: Sammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

description:
Captured RNA
Enrichment of targeted transcripts was performed with biotinylated probes from myBaits Custom RNA-Seq following the manufacturer’s standard protocol v.5.00 (Arbor biosciences)

data_processing:
Trimming of reads: trimmomatic (0.36). ChIP:  leading and trailing bases below quality 3, cutting when average quality per base in a 4-base sliding window is below 15, and dropping reads below a length of 40. RNA: cutting when average quality per base in a 4-base sliding window is below 20, and dropping reads below a length of 30.
Mapping of reads: ChIP: bowtie2 (2.3.3.1) on NCBI hg38 analysis set (GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna) with the following settings: --end-to-end --very-sensitive -X 700 -I 50 -q --mm. Duplicates were removed using samtools (1.9) view/sort/rmdup and true multi-mapping reads were filtered out using samtools view -q 2. RNA: HISAT2 (Galaxy Version 2.1.0+galaxy5) on hg38.
Peak calling ChIP: MACS2 (version 2.2.6) callpeak -f BAM -g 2.9e9 --broad --nomodel --nolambda
Assigning reads to features: featureCounts (Galaxy Version 1.6.4+galaxy2)
Coverage tracks: ChIP: bedtools (v2.17.0) genomecov (-bga). RNA: bamCoverage (Galaxy Version 3.3.2.0.0) from the deeptools2 package.
Scaling and merging of replicates: bamCoverage (Galaxy Version 3.3.2.0.0) and wiggletools mean.
Genome_build: hg38 and hg19 (only P300 data)
Supplementary_files_format_and_content: bed.trk = MACS2 output bed file with first line specifying information for uploading to UCSC genome browser.
Supplementary_files_format_and_content: broadPeak = MACS2 output.
Supplementary_files_format_and_content: tabular = featureCounts output for RNA-seq data.
Supplementary_files_format_and_content: tsv = featureCounts output for Capture RNA-seq data.

source_name: cortical organoids day 35

growth_protocol: For cortical organoid formation, hESC colonies were grown on mouse embryonic fibroblasts in daily refreshed hESC medium (DMEM-F12 (Gibco) supplemented with 20% KnockOut Serum Replacement (Gibco), 100 U/ml penicillin/100 µg/ml streptomycin (Gibco), 2 mM GlutaMAX (Gibco), 1x MEM Non-Essential Amino Acids solution (Gibco), 100 µM 2-mercaptoethanol (Gibco)) and fresh 8 ng/ml bFGF (Sigma)). Colonies of 1-2 mm were transfered to 60 mm ultra low attachment dishes (corning) in 99% hESC medium supplemented with 1 mM sodium pyruvate (Gibco). The next day, media was replaced for differentiation media with fresh 3 µM IWR-1-Endo, 1 µM Dorsomorphin, 10 µM SB-431542 hydrate, and 1 µM Cyclopamine hydrate and changed every other day. On day 3, the dish was placed on a rocker. From day 18 onwards, organoids were cultured in Neurobasal/N2 media (Neurobasal (Gibco) supplemented with 100 U/ml penicillin/100 µg/ml streptomycin (Gibco), 2 mM GlutaMAX (Gibco), 1x N-2 supplement (Gibco)) with 1 µM Cyclopamine hydrate, and from day 24 onwards, no inhibitors were added anymore.

extract_protocol:
RNA was isolated using Trizol according to manufacturer's protocol with DNAse I treatment and cleaned-up using the RNA Clean & Concentration kit (ZYMO).
TruSeq Stranded Total RNA Library Prep kit (Illumina)

treatment_protocol: h9ESCs were transfected with the pX330-U6-Chimeric_BB-CBh-hSpCas9 plasmid containing gRNAs targeting the SVA near BCKDK, before cortical organoid formation

value: h9ESC derived cortical organoids


title: I1_rep2


title: U2OS cells - LowMYC_rep1_HiC

first: Melissa

last: Fullwood

address: 60 Nanyang Drive

institute: Nanyang Technological University


title: GF311_seedling

description: TPM was estimated using Kallisto


title: Cap CD2AP rep2 h9coD35 SVA-KO


title: I1_rep1


title: GC1_24_Tet1

city: Hefei

first: Lingling

last: Liu

state: Anhui

address: Anhui Medical University, No.81 Meishan Road, Shushan District, Hefei, Anhui, China

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Mouse spermatogenic cells(GC-1)

extract_protocol:
GC-1 cells were removed, manipulated on ice, and RNA was harvested using Trizol reagent. an Illumina TruSeq RNA Sample Preparation Kit (Cat# FC-122-1001) and 1 ug of total RNA were used to construct a sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spermatogenic cells

value: Overexpression of TET1 gene

tag: group

tag: time point


title: Cap CD2AP rep1 h9coD35 SVA-KO


title: GF312_seedling

description: TPM was estimated using Kallisto

tag: tissue


title: time_0min_1


title: H1_rep3

value: Responder


title: GC1_24_Myc

tag: cell line

value: untreated

value: control


title: H1_rep2


title: Cap EV rep3 h9coD35 SVA-KO

value: WT


title: H1_rep1


title: GF313_seedling

description: TPM was estimated using Kallisto


title: Cap EV rep1 h9coD35 SVA-KO


title: GF317_seedling

description: TPM was estimated using Kallisto


title: G1_rep3

value: Sertraline


title: GC1_36_Myc


title: GC1_36_Tet1


title: Cap EV rep2 h9coD35 SVA-KO


title: G1_rep2


title: BCKDK rep3 h9coD35 SVA-KO

data_processing:
Trimming of reads: trimmomatic (0.36). ChIP:  leading and trailing bases below quality 3, cutting when average quality per base in a 4-base sliding window is below 15, and dropping reads below a length of 40. RNA: cutting when average quality per base in a 4-base sliding window is below 20, and dropping reads below a length of 30.
Mapping of reads: ChIP: bowtie2 (2.3.3.1) on NCBI hg38 analysis set (GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna) with the following settings: --end-to-end --very-sensitive -X 700 -I 50 -q --mm. Duplicates were removed using samtools (1.9) view/sort/rmdup and true multi-mapping reads were filtered out using samtools view -q 2. RNA: HISAT2 (Galaxy Version 2.1.0+galaxy5) on hg38.
Peak calling ChIP: MACS2 (version 2.2.6) callpeak -f BAM -g 2.9e9 --broad --nomodel --nolambda
Assigning reads to features: featureCounts (Galaxy Version 1.6.4+galaxy2)
Coverage tracks: ChIP: bedtools (v2.17.0) genomecov (-bga). RNA: bamCoverage (Galaxy Version 3.3.2.0.0) from the deeptools2 package.
Scaling and merging of replicates: bamCoverage (Galaxy Version 3.3.2.0.0) and wiggletools mean.
Genome_build: hg38 and hg19 (only P300 data)
Supplementary_files_format_and_content: bed.trk = MACS2 output bed file with first line specifying information for uploading to UCSC genome browser.
Supplementary_files_format_and_content: broadPeak = MACS2 output.
Supplementary_files_format_and_content: tabular = featureCounts output for RNA-seq data.

extract_protocol:
RNA was isolated using Trizol according to manufacturer's protocol with DNAse I treatment and cleaned-up using the RNA Clean & Concentration kit (ZYMO).
TruSeq Stranded Total RNA Library Prep kit (Illumina)
RNA-seq 75bp paired end reads on a NextSeq 550 device.

value: BCKDK-SVA-KO


title: GF319_seedling

description: TPM was estimated using Kallisto


title: BCKDK rep2 h9coD35 SVA-KO


title: GF32_seedling

description: TPM was estimated using Kallisto


title: G1_rep1


title: GF320_seedling

description: TPM was estimated using Kallisto


title: BCKDK rep1 h9coD35 SVA-KO


title: GF323_seedling

description: TPM was estimated using Kallisto


title: F1_rep3


title: BIN1 rep3 h9coD35 SVA-KO

treatment_protocol: h9ESCs were transfected with the pX330-U6-Chimeric_BB-CBh-hSpCas9 plasmid containing gRNAs targeting the SVA near BIN1, before cortical organoid formation


title: time_80min_3

value: E.coli MG1655


title: F1_rep2

value: Prefrontal cortex


title: BIN1 rep1 h9coD35 SVA-KO


title: BIN1 rep2 h9coD35 SVA-KO


title: GF325_seedling

description: TPM was estimated using Kallisto


title: GF327_seedling

description: TPM was estimated using Kallisto


title: E1_rep3

value: BALB/c

value: water

value: Control


title: GF330_seedling

description: TPM was estimated using Kallisto

value: two week seedling


title: EV rep3 h9coD35 SVA-KO

treatment_protocol: h9ESCs were transfected with the pX330-U6-Chimeric_BB-CBh-hSpCas9 plasmid before cortical organoid formation


title: GF315_seedling

description: TPM was estimated using Kallisto

value: leaf


title: GF331_seedling

description: TPM was estimated using Kallisto


title: E1_rep1


title: GF332_seedling

description: TPM was estimated using Kallisto


title: EV rep2 h9coD35 SVA-KO


title: BCKDK rep3 H3K27ac h9coD35 SVA-KO

extract_protocol:
Organoids were rinsed in medium, homogonized in a 2ml Kontes Glass Co. dounce and immediately crosslinked after. Cells were lysed, chromatin was sheared to ~400bp fragments and chromatin was extracted using antibody-coated beads. DNA was purified using RNase cocktail enzyme mix, proteinase K, two phenol:chloroform (1:1) and one chloroform extractions followed by DNA precipitation in ethanol and a Zymo DNA Clean & Concentrator clean-up.
TruSeq ChIP Library Preparation Kit (Illumina) with the following modifications: DNA clean & concentrator-5 kit (Zymo research) was used instead of beads for DNA purification. Size selections were performed before and after amplification on an E-gel Safe Imager (Invitrogen) using 2% E-gel SizeSelect gels (Invitrogen). The ChIP-DNA fraction of 300-400 bp in size (including adapters) was isolated and purified.
ChIP-seq 75bp paired end reads on a NextSeq 550 device.


title: MFG3

data_processing:
md5sum to confirm files copied to server without corruption; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 (Ensemble version 81) and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample.
Genome_build: GRCz10
Supplementary_files_format_and_content: tab delimited text file for every sample with raw counts for every gene
Supplementary_files_format_and_content: table with raw counts for every gene and every sample with genes annotated

source_name: Zebrafish fins

extract_protocol:
Cells were FACS sorted into TRIZOL LS and snap-frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng, all having RIN scores > 7.
Reverse transcription and cDNA amplification were performed with SMART-Seq v4 Ultra Low Input RNA Kit (Clontech). Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration (Qubit), size distribribution (Agilent Bioanalyzer).

value: Wildtype melanocyte model (Caspers with MiniCoopR-eGFP)

tag: anatomic location

value: Fin

tag: gfp+ or gfp-

value: GFP+


title: GF335_seedling

description: TPM was estimated using Kallisto


title: MFN3

value: GFP-


title: EV rep1 h9coD35 SVA-KO

value: h9ESC derived cortical organoids


title: MBN3

value: Body


title: BCKDK rep2 H3K27ac h9coD35 SVA-KO