title: DNAseq: OsO4 treated 4sT rep3

city: Vienna

first: Michael

last: Mitter

address: Dr.-Bohr-Gasse 3

country: Austria

institute: IMBA

description: gDNA extracted from asynchronously grown cells in the presence of 2 mM 4sT for 5 days and treated with OsO4

data_processing:
Library strategy: DNA-seq
Basecalling software: Illumina RTA
Hi-C samples were preprocessed using a custom nextflow pipeline (https://github.com/gerlichlab/scshic_pipeline). Briefly, bcl2 files were first demultiplexed using bcl2tofastq. Then, fastq files were aligned to hg19 with HeLa SNPs using bwa, aligning read pairs independently. Then, pairsam files were constructed using pairtools (https://github.com/mirnylab/pairtools), followed by sorting and deduplicating. Then, reads were split into cis sister and trans sister contacts based on the presence of signature mutations using pairtools select: A read was assigned to the Watson strand if it contained two or more A-to-G mutations and no T-to-C mutations. Similarly, if a read contained two or more T-to-C mutations, but no A-to-G mutations it was assigned to the Crick strand. Then, contacts were classified as cis sister contacts if (after correcting for the opposite read-strandedness of Illumina sequencing of the two mates) both mates mapped to the same strand. Conversely, contacts were classified as trans sister contacts if the two mates mapped to opposing strands. Then, cooler (https://github.com/mirnylab/cooler) was used to construct .cool files. For DNAseq samples,  a custom python script was used to count the number of each point mutation type.
Genome_build: hg19
Supplementary_files_format_and_content: cooler derived .cool files (Mirny lab) containing Hi-C matrices for usage with HiGlass and the cooler ecosystem for Hi-C. For DNAseq data, tables (csv) are provided that indicate the number of each point mutation type, mapping quality and average Phred-score of every sequencing read.
Supplementary_files_format_and_content: cool files were generated using cooler (https://github.com/mirnylab/cooler) using standard parameters. Separate cooler files are provided for all contacts, cis-sister contacts and trans-sister contacts. Csv files were generated using a custom python script to count different point mutation types.

source_name: cervical carcinoma

growth_protocol: For Hi-C synchronization, HeLa Kyoto cells were seeded into 25 cm2 flasks and grown for 3 h, then supplemented with 2 mM Thymidine (Sigma). Cells were released 16 h later by washing 2 times with prewarmed WT medium. 8 h later, cells were supplemented with 3 µg/ml aphidicolin (Sigma) and 2 mM 4sT. Cells were released 16 h later by washing 2 times with PBS and addition of medium containing 2 mM 4sT. For Sororin-AID experiments, 500 µM Indole-3-acetic acid (Sigma) was added 1 h prior to S-phase release. For S-phase release experiments, samples were taken at the indicated time-points. For synchronization to G2 and prometaphase, after 4 h release, 9 µg RO-3306 (Sigma) or 200 ng/ml nocodazole (Sigma) were added respectively. For NIPBL-AID experiments, 500 µM Indole-3-acetic acid (Sigma) was added 8 h after released. Samples were processed 16 h later. Cells were harvested by washing with PBS, followed by trypsinisation and resuspension in WT medium. Cells were then spun down, washed again with PBS, followed by fixation for 4 min in 1 % formaldehyde (Sigma). Cell pellets were stored at -20 °C or processed immediately. For DNAseq evaluation of 4sT mediated increase of mutation rate, cells were seeded into a 6-well plate and supplemented either with H20 or 2 mM 4sT for 5 days before harvesting.

extract_protocol:
For Hi-C, fixed cells were permeabilized using ice-cold Hi-C lysis buffer (10 mM TRIS-HCl pH 8 [Sigma], 10 mM NaCl [Sigma], 0.2 % Nonidet P-40 substitute [Sigma], 1x Complete EDTA-free Protease inhibitor [Roche]) for 30 min at 4 °C. Then, cells were spun down (2500 x g for 5 min), supernatant was discarded, and digestion mix was added (375 U DpnII [NEB] in 1x DpnII buffer [NEB]) and cells incubated for 16 h at 37 °C under rotation. Then, cells were spun down, supernatant was discarded and fill-in mix was added (38 µM Biotin-14-dATP [Thermo Fisher Scientific], 38 µM dCTP, dGTP and dCTP [Thermo Fisher Scientific], 50 U Klenow Polymerase [NEB], 1x NEB 2 buffer) and cells incubated for 1 h at 37 °C under rotation. Then, cells were spun down again, and ligation mix was added (1x T4 DNA ligase buffer [Thermo Fisher Scientific], 0.1 % Triton X-100 [Sigma], 100 µg/ml BSA [Sigma], 50 U T4 DNA ligase [Thermo Fisher Scientific]) and incubated at RT for 4 h. Then, cells were spun down, resuspended in 200 µl PBS and gDNA was purified using the DNeasy Blood and Tissue kit (Quiagen). DNA was transferred to a Covaris microTUBE (Covaris) and sheared on a Covaris S2 instrument (Duty cycle 10 %, Intensity 5.0, Cycles/burst 200) for 25 s. Double size selection was performed by employing AMPure XP beads (Beckman Coulter) first at 0.8-fold sample volume according to the standard protocol, followed by transfer of the supernatant and bead application at 0.12-fold sample volume. The resulting DNA was bound to Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher Scientific) in Biotin binding buffer (5 mM Tris-HCl pH 7.5 [Sigma], 0.5 mM EDTA [AppliChem], 1 M NaCl [Merck]) for 1 h at RT. Beads were then washed 2x in Tween wash buffer (5 mM Tris-HCl [Sigma], 0.5 mM EDTA [AppliChem], 1 M NaCl [Merck], 0.05 % Tween-20 [Sigma]) and 1x in H2O. For DNAseq, Cells were harvested by trypsinization, spun down at 1100 x g for 1 min and the supernatant was discarded. Then, cells were spun down, resuspended in 200 µl PBS and gDNA was purified using the DNeasy Blood and Tissue kit (Quiagen). DNA was transferred to Covaris microTUBE (Covaris) and sheared on a Covaris S2 instrument (Duty cycle 10 %, Intensity 5.0, Cycles/burst 200) for 25 s. Double size selection was performed by employing AMPure XP beads (Beckman Coulter) first at 0.8-fold sample volume according to the standard protocol, followed by transfer of the supernatant and bead application at 0.12-fold sample volume.
For Hi-C samples, beads with bound biotinylated DNA were resuspended in H2O and library preparation was performed using the NEBNext Ultra II DNA library prep kit for Illumina [NEB] according to the standard protocol. After this, beads were washed 4x using Tween wash buffer and DNA was eluted using 95 % formamide (Sigma), 10 mM EDTA (AppliChem) at 65 °C for 2 min. DNA was then precipitated using 80 % EtOH (Sigma), washed with 75 % EtOH and resuspended in H2O. Then, 4sT was converted to methyl-cytosine using OsO4 / NH4Cl, followed by qPCR according the NEBUltra Ultra II DNA library prep kit for Illumina [NEB]. The finished libraries were purified using AMPure XP beads (Beckman Coulter) at 0.9x sample volume following the standard protocol. For DNAseq samples, DNA library preparation was performed using the NEBNext Ultra II DNA library prep kit for Illumina [NEB] according to the standard protocol. The unamplified libraries were then treated using OsO4  and amplified according the NEBNext Ultra II DNA library prep kit for Illumina [NEB]. The finished libraries were purified using AMPure XP beads (Beckman Coulter) at 0.9x sample volume following the standard protocol.

treatment_protocol: HeLa cells were either untreated or treated with auxin to deplete target proteins as per the growth protocol.

value: HeLa Kyoto

tag: diesease state

value: cervical carcinoma


title: OSKM-D209N-D3-ATACseq-rep2

status: Public on Jun 12 2020

type: SRA

city: Guangzhou

first: Yaoyi

last: Li

state: Guangdong province

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island

country: China

institute: Guangzhou National Laboratory

description: ATAC

library_source: genomic

data_processing:
Illumina Casava software used for basecalling.
Reads were aligned to the mm10 genome using bowtie2 version 2.3.2.
Read coverage normalized to 1 x sequencing depth (also known as Reads Per Genomic Content (RPGC))
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: bigwig, bed peaks

molecule: genomic DNA

organism: Mus musculus

source_name: OSKM-reprogramming cells, overexpression of RNase H1(D209N)

growth_protocol: mES cells and iPS cells were cultured in DMEM/High Glucose medium (Hyclone) supplemented with β-mercaptoethanol (10 mM), sodium pyruvate (10 mM), non-essential amino acids (10 mM), GlutaMAX (10 mM), 15% FBS (Gibco), 1000 U/ml leukemia inhibitory factor (LIF), and 1 μM MEK inhibitor PD0325901 and 3 μM GSK3 inhibitor CHIR99021. MEF cells were cultured in 10% FBS medium supplemented with non-essential amino acids (10 mM) and GlutaMAX (10 mM).

extract_protocol:
For ssDRIP-seq, nucleic were isolated from cells, followed by SDS/proteinase K treatment at 37°C overnight. Genome DNA was extracted by the phenol-chloroform method and precipitated with isopropanol. DNA fragmentation was performed overnight using endonucleases (MboI, MseI, AluI, DdeI), and the negative control was treated with RNase H (New England Biolabs) overnight. Briefly, 3.5 ug of DNA was bound with 10 ug of S9.6 antibody in 1 X binding buffer (10 mM NaPO4 pH 7, 140 mM NaCl, 0.05% Triton X-100) overnight at 4˚C. 50 μl Protein G sepharose beads were added for 4 hours. Bound beads were washed 4 times in binding buffer and elution was performed in elution buffer (50 mM Tris pH 8, 10 mM EDTA, Proteinase K) for 45 min at 55˚C. DNA was purified and sonicated to 150 bp fragments. For RNA-seq, Total RNAs were extracted with TRIzol. For quantitative PCR, cDNAs were synthesized with ReverTra Ace (Toyobo) and oligo dT (Takara), and then analyzed by qPCR with SYBR green mixture (Genstar) and performed on a CFX Real-Time System (Bio-Rad). For ATAC-seq, a total of 50,000 cells were washed once with cold PBS and resuspended in 50 μl lysis buffer. The suspension of nuclei was then centrifuged at 500 g at 4˚C for 10 min, followed by the addition of 50 μl transposition reaction mix (10 μl TD buffer, 5 μl Tn5 transposase and 35 μl nuclease-free H2O). DNA was purified using a MinElute Kit (QIAGEN). For CLIP-seq, mES cells were irradiated at 400 mJ/cm2 with 254 nm UV light. The crosslinked cells were lysed and 15 μg of anti-DDX5 antibody was applied to pull down protein-RNA complexes. After micrococcal nuclease treatment and 3’ DNA adaptor ligation, the immunoprecipitated complexes were fractionated on a 4-12% NuPAGE Bis-Tris gel and transferred onto a nitrocellulose membrane. The DDX5-specific smear bands were excised with scalpels and treated with proteinase K (Thermo Fisher Scientific) prior to the extraction of respective RNA by using phenol and chloroform.
For ssDRIP-seq, the first adapter was ligated to the 3’ end of the ssDNA using Adaptase (Swift Biosciences) via a highly efficient, proprietary reaction that only tails 3’ ends of ssDNA and ligates the first truncated adapter to 3’ ends simultaneously. This method avoids the bias inherent in random primer-based methods, as it ligates adapters in a sequence-independent manner. The extension step was performed using the primer paired to the first adapter, followed by a ligation reaction to add the second truncated adapter to the 5’ ends. An indexing PCR step was performed to add the indexed sequence, and the library was amplified. For RNA-seq, RNA sequencing libraries were constructed using the VAHTS mRNA-seq V3 Library Prep Kit for Illumina (Vazyme). For ATAC-seq, ATAC-seq libraries were first subjected to 5 cycles of pre-amplification. To determine the suitable number of cycles required for the second round of PCR, the library was assessed by quantitative PCR as described, and the library was then PCR amplified for the appropriate number of cycles. Libraries were purified with AMPure XP beads. For CLIP-seq, A 5’ RNA linker was then added to the isolated RNA and reverse transcribed by superscript reverse transcriptase III (Life Technologies, 18080-051). The cDNA strands are PCR-amplified to produce libraries for deep sequencing. L3-IR800-biotin DNA adaptor: 5’OH -ATC TCG TAT GCC GTC TTC TGC TTG TAA AAA AAA AAA A/iAzideN/A AAA AAA AAA AA/3Bio/-3’, 5’ RNA linker: 5’-(OH) rArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU(rN)(rN) (rN)rU(OH) -3’.

treatment_protocol: 10,000 MEFs at passage 2 were plated in a 12-well plate and then infected twice with retroviral stocks generated with Plat-E cells. 3 volumes of OSK supernatants and 1/4 volume of M transcription factor were mixed with 1 volume of fresh MEF medium containing polybrene at a final concentration of 8 μg/ml. The infection efficiency was tested by MEFs transduced with virus of pMXs-EGFP. pMXs-RNaseH1 and RNaseH1(D209N) were also transfected into OG2-MEFs by retrovirus generated from PlatE cells. For infecting OG2-MEFs, the medium of OG2-MEFs was replaced with 2.125 mL of infection mixture per well in a 12-well plate. Infected cells were cultured with iCD1 medium or mESC medium containing Vitamin C (Sigma; 50 μg/ml) post infection and renewed daily.

tag: cell type

value: reprogramming cell

tag: the day of reprogramming


title: KO-F-6hr-4

city: hershey

first: Nithyananda

last: Thorenoor

state: PA

address: 500 University Drive

department: Pediatrics

country: USA

institute: Penn State University College of Medicine

description:
6hrs_MvsF_deseq2_KO
sample name:
G305_JF3_S47_R1_001

library_source: transcriptomic

data_processing:
Illumina CASAVA pipeline (released version 1.8, Illumina) was used to obtain de-multiplexed sequencing reads (fastq files) passed the default purify filter.  These were further subjected to QuantSeq data analysis pipeline on a Bluebee genomics analysis platform (Bluebee, Cambridge, MA).  The differentially expressed genes (DEG) between males and females were identified by using edgeR test method and TCC v1.14.0 R package.  The DEG are selected based on their fold change and their P-value (P < 0.05) for further analyses.  We chose genes for further analysis based on their P-value (P < 0.05) and their expression levels (≥ 2 fold change) in AM cells from K. pneumoniae infected mice.  The fold differences for the identified genes between males and females were determined by dividing a specific individual male gene value by the corresponding specific female gene value and vice versa for the same gene.
The DEG are selected based on their fold change and their P-value (P < 0.05) for further analyses.  We chose genes for further analysis based on their P-value (P < 0.05) and their expression levels (≥ 2 fold change) in AM cells from K. pneumoniae infected mice.  The fold differences for the identified genes between males and females were determined by dividing a specific individual male gene value by the corresponding specific female gene value and vice versa for the same gene.
Supplementary_files_format_and_content: Matrix- excel sheet

molecule: total RNA

source_name: Female mouse exposed K.penumoniae-Alveolar Macrophage (AM) cells

extract_protocol:
AM cells were isoalated from Broncho alveolar lavage, QuantSeq 3' mRNA-Seq Library Prep Kit FWD from Illumina (Lexogen, Vienna, Austria) was used to generate mRNA-Seq libraries as per manufacturer’s recommendation, followed by deep sequencing on an Illumina HiSeq-2500 as per the manufacturer’s instructions.
The synthesis of the second cDNA strand is performed by random priming, in a manner that DNA polymerase is efficiently stopped when reaching the next hybridized random primer, so only the fragment closest to the 3′ end gets captured for later indexed adapter ligation and PCR amplification.  The processed libraries were assessed for fragment size distribution and quantity using a BioAnalyzer High Sensitivity DNA kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 (Illumina) and run for 50 cycles using a single-read recipe (TrueSeq SBS kit v3, Illumina) according to the manufacturer's instructions.  Illumina CASAVA pipeline (released version 1.8, Illumina) was used to obtain de-multiplexed sequencing reads (fastq files) passed the default purify filter.  These were further subjected to QuantSeq data analysis pipeline on a Bluebee genomics analysis platform (Bluebee, Cambridge, MA).  The differentially expressed genes (DEG) between males and females were identified by using edgeR test method and TCC v1.14.0 R package.  The DEG are selected based on their fold change and their P-value (P < 0.05) for further analyses.  We chose genes for further analysis based on their P-value (P < 0.05) and their expression levels (≥ 2 fold change) in AM cells from K. pneumoniae infected mice.  The fold differences for the identified genes between males and females were determined by dividing a specific individual male gene value by the corresponding specific female gene value and vice versa for the same gene.

treatment_protocol: Humanized transgenic (hTG) mice that carried SP-A1 (6A2, 6A4), SP-A2 (1A0, 1A3) variant,  as well as SP-A knockout (KO) mice were used in this study.  They were 12 weeks old.  hTG mice were generated on the C57BL/6J SP-A (KO) background. The animals were exposed  to K. peumoniae for 6hrs.  A group of 4 animals (males, females) were exposed and alveolar macrophages (AM) were isolated after 6 h of recovery.

tag: exposure time

value: 6 hours

tag: Sex

value: Female

tag: strain

value: Alveolar Macrophage (AM) cells

tag: genotype

value: SP-A-Knockout (KO)


title: Ddx5 PAR-CLIP-ES-rep1

description: CLIP

source_name: mES

value: mES


title: DNAseq: OsO4 treated 4sT rep2

organism: Homo sapiens


title: PB-73_Hp

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.5.4b, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Mus Musculus, UCSC, mm10
Supplementary_files_format_and_content: tad-delimited, raw counts

source_name: Hippocampus

growth_protocol: Mice were kept in a conventional hygienic grade facility and sacrificed at the indicated time point.

extract_protocol:
RNA was extracted from snap frozen brain areas (both hemispheres for hippocampus) using the RNeasy Plus Universal Kit (QIAGEN), following manufacturer’s instructions.
TruSeq RNA stranded protocol

tag: age of inoculation

value: 6 weeks

tag: type of inoculation

value: intracerebral

value: PrP present

tag: date of sacrifice

value: 16 wpi

tag: treatment

value: RML6 prions

tag: tissue

value: Hippocampus

tag: cohort

value: main cohort


title: OSKM-D209N-D3-ATACseq-rep1

description: ATAC


title: DNAseq: OsO4 treated 4sT rep1


title: OSKM-FLAG-D3-ATACseq-rep2

description: ATAC

source_name: OSKM-reprogramming cells, overexpression of Flag


title: PB-80_Hp

value: non-infectious brain homogenate


title: KO-F-6hr-2

description:
6hrs_MvsF_deseq2_KO
sample name:
G305_JF1_S45_R1_001


title: OKM-Day9-RNAseq-rep1

description: mRNA

source_name: OKM-reprogramming cells


title: KO-F-6hr-1

description:
24hrs_MvsF_deseq2-SP-A2(1A0)
sample name:
JFRm74


title: DNAseq: untreated 4sT rep2

description: gDNA extracted from asynchronously grown cells in the presence of 2 mM 4sT for 5 days


title: OKM-Day9-RNAseq-rep2

description: mRNA


title: PB-59_Hp

value: 14 wpi


title: KO-F-6hr-3

description:
6hrs_MvsF_deseq2_KO
sample name:
G305_JF2_S46_R1_001


title: PB-79_Hp


title: DNAseq: untreated 4sT rep3

value: HeLa Kyoto


title: OSKM-Day9-RNAseq-rep2

description: mRNA

source_name: OSKM-reprogramming cells


title: PB-78_Hp


title: OSKM-Day9-RNAseq-rep1

description: mRNA


title: DNAseq: untreated 4sT rep1

value: cervical carcinoma


title: DNAseq: OsO4 treated control rep4

description: gDNA extracted from asynchronously grown control cells and treated with OsO4. Same flowcell as modified samples.


title: SP-A2(1A0)-F-24hr-5

description:
24hrs_MvsF_deseq2-SP-A2(1A0)
sample name:
JFRm60

value: 24 hours


title: SP-A2(1A0)-F-24hr-4

description:
24hrs_MvsF_deseq2-SP-A2(1A0)
sample name:
JFRm59


title: PB-58_Hp


title: SP-A2(1A0)-F-24hr-3

description:
24hrs_MvsF_deseq2-SP-A2(1A0)
sample name:
JFRm71


title: PB-57_Hp


title: DNAseq: OsO4 treated control rep2

description: gDNA extracted from asynchronously grown control cells and treated with OsO4. Same flowcell as unmodified samples.


title: DNAseq: OsO4 treated control rep3


title: genomic DNA from tamoxifen-resistanct MCF-7

type: genomic

city: Goyang

first: Dawoon

last: Jeong

address: 32 Dongguk-ro, Ilsan Dong-gu

department: Life Science

country: South Korea

institute: Dongguk University

description:
breast cancer
SAMPLE 2

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina procedures using Illumina iScan scanner

data_processing: GenomeStudio V2011 – Methylation Module,  R 2.15.1

label: bead chip

source_name: Mammary Gland; Breast

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from MCF-7 and Tam-R MCF-7 using ZR Dyet DNA/RNA kit (Zymo research) according to standard instructions

tag: cell line

value: tamoxifen-resistanct MCF-7

value: breast epithelial

tag: gender

value: female

tag: disease

value: adenocarcinoma


title: PB-64_Hp


title: DNAseq: OsO4 treated control rep1


title: OSKM-Day6-RNAseq-rep2

description: mRNA

value: reprogramming cell


title: SP-A2(1A0)-F-24hr-2

description:
24hrs_MvsF_deseq2-SP-A2(1A0)
sample name:
JFRm78

value: Female

value: Alveolar Macrophage (AM) cells


title: genomic DNA from parental MCF-7

description:
breast cancer
SAMPLE 1

value: parental MCF-7


title: OSKM-Day6-RNAseq-rep1

description: mRNA


title: PB-63_Hp

value: 6 weeks

value: intracerebral

value: PrP present


title: SP-A2(1A0)-M-24hr-5

description:
24hrs_MvsF_deseq2-SP-A2(1A0)
sample name:
JFRm67

source_name: Male mouse exposed K.penumoniae-Alveolar Macrophage (AM) cells

value: Male


title: OSKM-Day3-RNAseq-rep1

description: mRNA


title: SP-A2(1A0)-M-24hr-3

description:
24hrs_MvsF_deseq2-SP-A2(1A0)
sample name:
JFRm77


title: SP-A2(1A0)-F-24hr-1

description:
24hrs_MvsF_deseq2-SP-A2(1A0)
sample name:
JFRm58


title: SP-A2(1A0)-M-24hr-4

description:
24hrs_MvsF_deseq2-SP-A2(1A0)
sample name:
JFRm76


title: amniotic fluid P5575

city: Fuzhou

first: Hailong

last: Huang

state: Fujian

address: No.18 Daoshan Road, Gulou District

institute: Fujian Maternity and Child Health Hospital

description: Hybridized to CytoScan 750K

hyb_protocol: DNA was processed as follows. Restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer`s instructions.

scan_protocol: The arrays were then washed using Affymetrix Fluidics Stations, and scanned using the GeneChip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Command Console (AGCC version 4.0.0.1567). Data processing and analysis (CEL file generation, smoothing and segmentation) were used Chromosome Analysis Suite (version 3.3).
Copy number variation status (CNV)

label: Biotin

source_name: amniotic fluid fetal cells

label_protocol: As per manufacturer (Affymetrix).

extract_protocol: Genomic DNA of fetal cells in amniotic fluid was extracted with using the QIAamp DNA extraction kit (Qiagen, Dusseldorf, Germany)

value: amniotic fluid fetal cell

tag: diagnosis


title: amniotic fluid P3583

description: Hybridized to CytoScan 750K


title: amniotic fluid P4637

description: Hybridized to CytoScan 750K


title: OSKM-Day3-RNAseq-rep2

description: mRNA


title: OSKM-FLAG-D7-RNAseq-rep1

description: mRNA


title: amniotic fluid P6557

description: Hybridized to CytoScan 750K


title: OSKM-FLAG-D7-RNAseq-rep2

description: mRNA


title: PB-43_Hp

value: 12 wpi

value: RML6 prions

value: Hippocampus

value: main cohort


title: SP-A2(1A0)-M-24hr-2

description:
24hrs_MvsF_deseq2-SP-A2(1A0)
sample name:
JFRm70

value: 24 hours


title: amniotic fluid P245

description: Hybridized to CytoScan 750K


title: PB-41_Hp


title: amniotic fluid P86

description: Hybridized to CytoScan 750K


title: OSKM-FLAG-D3-RNAseq-rep1

description: mRNA


title: SP-A2(1A0)-M-24hr-1

description:
18hrs_MvsF_deseq2_SP-A2(1A0)
sample name:
JFRm54


title: PB-48_Hp

value: non-infectious brain homogenate


title: OSKM-FLAG-D1-RNAseq-rep2

description: mRNA


title: PB-47_Hp


title: PB-62_Hp

value: 14 wpi


title: amniotic fluid E2860

description: Hybridized to CytoScan 750K

value: 1q21.1duplication syndrome


title: PB-42_Hp


title: OSKM-FLAG-D1-RNAseq-rep1

description: mRNA

value: reprogramming cell


title: SP-A2(1A0)-F-18hr-3

description:
18hrs_MvsF_deseq2_SP-A2(1A0)
sample name:
JFRm51

value: 18 hours

value: Female


title: PB-46_Hp


title: amniotic fluid E1960

description: Hybridized to CytoScan 750K


title: OSKM-FLAG-D3-RNAseq-rep2

description: mRNA


title: amniotic fluid B16

description: Hybridized to CytoScan 750K

value: Prader-willi syndrome


title: OSKM-RNaseH1-D7-RNAseq-rep2

description: mRNA

source_name: OSKM-reprogramming cells, overexpression of RNase H1


title: SP-A2(1A0)-F-18hr-1

description:
18hrs_MvsF_deseq2_SP-A2(1A0)
sample name:
JFRm50

value: Alveolar Macrophage (AM) cells


title: PB-27_Hp

value: 6 weeks

value: intracerebral

value: 8 wpi


title: OSKM-RNaseH1-D3-RNAseq-rep2

description: mRNA


title: PB-25_Hp

value: PrP present


title: SP-A2(1A0)-M-18hr-3

description:
18hrs_MvsF_deseq2_SP-A2(1A0)
sample name:
JFRm48

value: Male


title: OSKM-RNaseH1-D7-RNAseq-rep1

description: mRNA


title: SP-A2(1A0)-M-18hr-2

description:
18hrs_MvsF_deseq2_SP-A2(1A0)
sample name:
JFRm49


title: OSKM-RNaseH1-D3-RNAseq-rep1

description: mRNA


title: PB-26_Hp

value: RML6 prions


title: amniotic fluid G6960

description: Hybridized to CytoScan 750K

value: amniotic fluid fetal cell


title: PB-32_Hp

value: Hippocampus

value: main cohort


title: OSKM-RNaseH1-D1-RNAseq-rep2

description: mRNA


title: PB-31_Hp

value: non-infectious brain homogenate


title: SP-A2(1A0)-F-6hr-4

description:
6hrs_MvsF_deseq2_SP-A2(1A0)
sample name:
JFRm46

value: 6 hours


title: OSKM-RNaseH1-D1-RNAseq-rep1

description: mRNA


title: PB-30_Hp


title: SP-A2(1A0)-F-18hr-2

description:
18hrs_MvsF_deseq2_SP-A2(1A0)
sample name:
JFRm52


title: SP-A2(1A0)-F-6hr-2

description:
6hrs_MvsF_deseq2_SP-A2(1A0)
sample name:
JFRm65


title: SP-A2(1A0)-F-6hr-1

description:
6hrs_MvsF_deseq2_SP-A2(1A0)
sample name:
JFRm64


title: PB-10_Hp

value: 4 wpi


title: PB-11_Hp


title: OSKM-D209N-D3-RNAseq-rep2

description: mRNA

value: reprogramming cell


title: PB-9_Hp


title: OSKM-D209N-D3-RNAseq-rep1

description: mRNA


title: OSKM-D209N-D7-RNAseq-rep1

description: mRNA


title: SP-A2(1A0)-M-6hr-3

description:
6hrs_MvsF_deseq2_SP-A2(1A0)
sample name:
JFRm41


title: PB-16_Hp


title: OSKM-D209N-D7-RNAseq-rep2

description: mRNA


title: OSKM-D209N-D1-RNAseq-rep2

description: mRNA


title: SP-A2(1A0)-F-6hr-3

description:
6hrs_MvsF_deseq2_SP-A2(1A0)
sample name:
JFRm63


title: SP-A2(1A0)-M-6hr-4

description:
6hrs_MvsF_deseq2_SP-A2(1A0)
sample name:
JFRm42


title: SP-A2(1A0)-M-6hr-2

description:
6hrs_MvsF_deseq2_SP-A2(1A0)
sample name:
JFRm40


title: PB-15_Hp


title: PB-14_Hp


title: Wntlow lung epithelial cell from experiment ID#9

type: RNA

city: Columbus

first: Yan

last: Hu

state: OH

address: 575 Children’s Crossroad, RB3 6th Floor WB6271

institute: Nationwide Children's Hospital

description: Gene expression data from Wnt low mouse lung epithelial cells

hyb_protocol: Processed samples were hybridized to a Clariom™ D arrays in the GeneChip® Hybridization Oven 645 with rotation at 60 rpm for 16 hr at 45°C. The arrays were washed and stained using FS450_0002 protocol.

scan_protocol: Gene chips were scanned with an Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Signal Space Transformation-Robust-Multi-chip Analysis (SST-RMA) algorithm.

label: biotin

source_name: FACS sorted mouse lung epithelial cells with low Wnt activity

label_protocol: The cRNA was converted to biotinylated sense-strand DNA hybridization targets for unbiased coverage of the transcriptome, according to the GeneChip™ WT Pico Reagent Kit User Guide.

extract_protocol: RNA samples were prepared with RNeasy Micro kit (Qiagen 74004, Germantown, US). The integrity of extracted RNA was analyzed using an Agilent Tapestation 2200 and the RNA integrity numbers are all well above 8. Transcriptional microarray assay was done at the University of Colorado Denver Genomics and Microarray Core facility. Following the manufacturer’s protocol, 8 ng of starting total RNA was converted to cDNA with the Affymetrix GeneChip® WT Pico Kit.

treatment_protocol: Lungs with trachea and bronchi from TCF/Lef:H2B/GFP mice were digested with dispase for 45min followed by filtering with 70um and 40um cell strainers, repectively, to generate single cells suspension. Endothelial cells and blood cells were removed using anti-CD31 and anti-CD45 MACS meganetic beans. Then lung epithelial cells were selceted with anti-EpCAM MACS beads followed by staining with anti-EpCAM-APC and DAPI for FACS sorting. The DAPI-EpCAM+GFPneg/low/high cells were collected, respectively for RNA extraction. Each sample were pooled from 3-4 animals.

tag: age

value: 8-12 weeks old

value: Distal Lungs

tag: wnt reporter

value: GFPlow


title: Wntnegative lung epithelial cell from experiment ID#9

description: Gene expression data from Wnt negative mouse lung epithelial cells

source_name: FACS sorted mouse lung epithelial cells with negative Wnt activity

value: GFPneg


title: Macaque5.2

city: Ann Arbor

first: Qianyi

last: Ma

state: MI

address: 1141 E Catherine St

department: Human Genetics

institute: University of Michigan

data_processing:
Two paired-end fastq files were converted to one query-sorted bam file using Picard tools v2.6.0 and samtools v1.2.
Sequence reads were tagged with cell and molecular barcodes, filtered for low base quality in cell or molecular barcodes, trimmed for starting sequence and polyA tail using Drop-seq tools v1.12.
The barcode-tagged, filtered and trimmed bam file is converted back to fastq file using Picard tools v2.6.0.
Alignment was performed using Star v2.5.2b.
Aligned reads were tagged with gene exons and cleaned for bead synthesis errors using Drop-seq tools v1.12.
Gene expressoin matrix was generated using Drop-seq tools v1.12.
For mixed-species samples, spike-in mouse cells were separated from other species based on gene expression data and removed from the unaligned fastq file.
Genome_build: GRCh37, Mmul_8.0.1, GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw UMI counts for each cell (column) and each gene (row)

organism: Macaca mulatta

source_name: Adult Testis

extract_protocol:
Briefly, cells, barcoded microparticle beads and lysis buffer were co-flown into a microfluidic device and captured in nanoliter sized droplets. After droplet collection and breakage, the beads were washed, and cDNA synthesis occurred on the bead. Excess oligos were removed by exonuclease I digestion. cDNA amplification was done from a pool of 2,000 bead. Individual PCRs were purified and pooled for library generation.
A total of 600 pg of amplified cDNA was used for a Nextera XT library preparation (Illumina).

value: Testis

value: 5.9 years

tag: source name for spike-in

tag: organism for spike-in


title: OSKM-iPSC-RNAseq-rep2

description: mRNA

source_name: iPS

tag: cell type

value: iPS


title: Wnthigh lung epithelial cell from experiment ID#8

description: Gene expression data from Wnt high mouse lung epithelial cells

source_name: FACS sorted mouse lung epithelial cells with high Wnt activity

tag: strain

value: GFPhigh


title: Wntlow lung epithelial cell from experiment ID#8


title: Wntnegative lung epithelial cell from experiment ID#7


title: Wntnegative lung epithelial cell from experiment ID#8


title: Wntlow lung epithelial cell from experiment ID#7


title: Wnthigh lung epithelial cell from experiment ID#7


title: Wnthigh lung epithelial cell from experiment ID#9


title: Atg5KO_IFNg_RepC

city: St. Louis

first: Anthony

last: Orvedahl

state: Missouri

address: 425 S. Euclid Ave

institute: Washington University School of Medicine

data_processing:
demultiplexed using fastq-multx (v1.3.0) allowing 2 mismatches
sequence quality was assessed using FastQC (v0.11.2)
Trimming for poly-T sequences and quality was performed with bbduk (BBmap package) using quality score of 20 and minlen of 25. For read pairs where reads from poly-T end failed trimming threshold, the read mate that passed trimming criteria was analyzed as a single-end read
Read mapping was performed with STAR (v20201) to the GRCm38 genome with the following options: --outFilterMultimapNmax 15 --outFilterMismatchNmax 6.
Reads were quantified using HTSeq (v0.6.1) with default parameters.
Counts for mate pairs were analyzed as paired-end, and those for which a mate was analyzed as single end were combined in final counts file for differential expression. Annotations for which there were no reads in any sample were removed.
Differential expression was assessed using DESeq2 (v1.10.1) in the R software package (v3.2.3). An adjusted p-value < 0.1 was considered significant. Analyses and pathway comparisons were performed on normalized read counts.
Genome_build: GRCm38

molecule: polyA RNA

source_name: BV2 microglial cell line

growth_protocol: Grown in DMEM with 10% FBS, 1% Hepes

extract_protocol:
Cell pellets were gently lysed in 100 μL buffer RLN (per Qiagen RY25 protocol: 50 mM Tris-Cl (pH 8.0), 140 mM NaCl, 1.5 mM MgCl2, 0.5% (v/v) Nonidet P-40 Substitute (USB)) per 8 × 105 cells for 10 min on ice, and then centrifuged briefly at 16k rcf to remove nuclei and incompletely lysed cells. Total RNA from cytosolic lysates was extracted with 1 mL TRI reagent (Sigma) per 200 μl lysate with isopropanol precipitation per manufacturer’s instructions. Each biological replicate for library construction was generated independently.
One μg of total purified RNA from cytoplasmic fractions was enriched for poly-A-containing transcripts using Dynabeads mRNA DIRECT Purification kit (Life Technologies). mRNA was fragmented thermo-chemically in RT buffer (Agilent) in the presence of custom barcoded oligo-dT primer/adapters (IDT) at 94 C for exactly 4.5 min and immediately eluted from beads. Primers were allowed to anneal to transcripts at room temperature and cDNA was generated using AffinityScript Reverse Transcriptase (Agilent). Samples were normalized and pooled by relative levels of mActB transcripts. RNA from cDNA hybrids was degraded with 1M NaOH at 70 °C for 12 min and neutralized with 0.5 M acetic acid. 3’ barcodes were removed by Agencourt AMPure XP beads (Beckman Coulter). Following ligation of a pre-adenylated 5’ adapter (IDT) using Thermostable T4 ligase (NEB), and barcode cleanup, fragments were amplified using 12 cycles of enrichment with Fusion High-Fidelity Master Mix (NEB) with primers compatible with Illumina sequencing. Library quantity and quality was confirmed using High Sensitivity D1000 ScreenTape on a 2200 TapeStation (Agilent).

treatment_protocol: Media ("untreated") or 1 U/mL IFNγ ("IFNg") for 24 hours prior to RNA extraction.

value: murine microglial cells

tag: genotype/variation

value: Atg5 KO

tag: barcode

value: TCCTTGGT


title: OSKM-iPSC-RNAseq-rep1

description: mRNA


title: Atg5KO_IFNg_RepB

value: AAGTAGAG


title: Macaque5.1


title: OSKM-D209N-D1-RNAseq-rep1

description: mRNA

source_name: OSKM-reprogramming cells, overexpression of RNase H1(D209N)

tag: the day of reprogramming


title: Macaque4.2

value: 13 years


title: SP-A2(1A0)-M-6hr-1

description:
6hrs_MvsF_deseq2_SP-A2(1A0)
sample name:
JFRm39

tag: exposure time

tag: Sex

value: Male

value: Alveolar Macrophage (AM) cells

tag: genotype


title: Atg5KO_IFNg_RepA

value: TTGAGCCT


title: OSKM-D5-RNAseq-rep2

description: mRNA

value: reprogramming cell


title: OSKM-D7-RNAseq-rep1

description: mRNA


title: OSKM-D7-RNAseq-rep2

description: mRNA


title: Atg5KO_untreated_RepC

value: CAGCAAGG


title: Wntnegative lung epithelial cell from experiment ID#5

value: 8-12 weeks old

tag: tissue

value: Distal Lungs


title: Wntnegative lung epithelial cell from experiment ID#3

value: GFPneg


title: Wntlow lung epithelial cell from experiment ID#5

value: GFPlow


title: Macaque3.2

value: Testis

value: 7.3 years


title: Atg5KO_untreated_RepB

tag: cell line

value: AACTTGAC


title: Atg5KO_untreated_RepA

value: murine microglial cells

value: GCACATCT


title: Macaque3.1


title: Macaque4.1


title: OSKM-D5-RNAseq-rep1

description: mRNA


title: Macaque2

value: 9.3 years


title: WT_IFNg_RepC

value: Wild Type

value: CCAGAGCT


title: OSKM-D3-RNAseq-rep2

description: mRNA


title: Macaque1.2

description: mixed-species samples

value: ≥ 4 years

value: NIH3T3 cell line

value: Mus musculus


title: WT_IFNg_RepB

value: GTATAACA


title: Macaque1.1


title: OSKM-D3-RNAseq-rep1

description: mRNA

value: reprogramming cell


title: OSKM-D1-RNAseq-rep2

description: mRNA


title: WT_IFNg_RepA

value: ACACGATC


title: OSKM-D1-RNAseq-rep1

description: mRNA


title: OSKM-D0-RNAseq-rep2

description: mRNA


title: 202756030055: Earlytransition_DNMT3L_KD2

city: London

first: Hemalvi

last: Patani

address: Charterhouse Square

country: United Kingdom

institute: Barts Cancer Institute

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

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

label: Cy5 and Cy3

source_name: H9-NK2 hESCs

label_protocol: Cy5 and Cy3 Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using PureLink® Genomic DNA extraction kit from Thermo Fisher Scientific following manufacturer's instructions

tag: gender

value: Female

value: H9-NK2 hESCs


title: Wntnegative lung epithelial cell from experiment ID#4

value: 8-12 weeks old

value: Distal Lungs

value: GFPneg


title: 202756030055: Earlytransition_DNMT3L_KD1


title: OSKM-D0-RNAseq-rep1

description: mRNA


title: Wntlow lung epithelial cell from experiment ID#3

value: GFPlow


title: Wntlow lung epithelial cell from experiment ID#4


title: Wnthigh lung epithelial cell from experiment ID#2

value: GFPhigh


title: Wnthigh lung epithelial cell from experiment ID#5


title: WT_untreated_RepB

value: murine microglial cells

value: AGTTGCTT


title: UVB irradiated melanocyte-derived exosomes 3

city: Hangzhou

first: Zeren

last: Shen

address: No. 79 Qingchun Road

institute: The First Affiliated Hospital, School of Medicine, Zhejiang University

description: Exosomal microRNAs

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Clean reads were obtained after remove of low quality reads and removing reads with 5' linker sequence, reads without 3' linker sequence, reads without the insert tag, reads with poly (A), and reads shorter than 17 nt.
Total clean reads were mapped to the human reference genome using the bowtie aligner.
miRDeep2 was used to identify known mature miRNA based on miRBase21 (www.miRBase.org) and predict novel miRNA. Databases of Rfam12.1 (www.rfam.xfam.org) and pirnabank (www.pirnabank.ibab.ac.in) were used to identify rRNA, tRNA, snRNA, snoRNA and piRNA
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM/COUNT values for each Sample
Supplementary_files_format_and_content: Processed data file. Differentially expressed miRNAs in UVB irradiated melanocyte-derived exosomes (UVBM-exo) and non-irradiated melanocyte-derived exosomes (Mexo).xlsx

growth_protocol: Adult human epidermal melanocytes were grown in Melanocyte Medium, which contained melanocyte growth factors (Sciencell #2201), at 37 °C and 5% CO2.

extract_protocol:
Melanocyte derived exosomes were isolated using differential centrifugation. Exosomal RNA was extracted by HiPure Liquid miRNA Kit/HiPure Serum/Plasma miRNA Kit (Megan, China).
50 ng exosomal RNA of each samples were used to prepare small RNA libraries by NEBNext® Multiplex Small RNA Library Prep Set for Illumina (NEB, USA) according to manufacturer’s instructions.

treatment_protocol: The melanocytes were irradiated with UVB at doses of 30 mJ/cm2 or 60 mJ/cm2 once at a 24-h interval for three consecutive days and then cultivated for 3 days.

value: Adult human epidermal melanocytes

value: HEM-a

tag: treatment

value: UVB-irradiated


title: UVB irradiated melanocyte-derived exosomes 2

description: Exosomal microRNAs


title: UVB irradiated melanocyte-derived exosomes 1

description: Exosomal microRNAs


title: Wnthigh lung epithelial cell from experiment ID#4


title: WT_untreated_RepA

value: Wild Type

value: AGCAATTC


title: Non-irradiated melanocyte-derived exosomes 3

description: Exosomal microRNAs

value: untreated


title: 202756030055: Earlytransition_DNMT3B_KD2


title: 202756030055: Earlytransition_DNMT3B_KD1


title: 202756030055: Earlytransition_DNMT3A_KD2


title: Non-irradiated melanocyte-derived exosomes 2

description: Exosomal microRNAs


title: OSKM-D9-DRIPseq

description: DNA:RNA hybird

data_processing:
Library strategy: DRIP-seq
Illumina Casava software used for basecalling.
Reads were aligned to the mm10 genome using bowtie2 version 2.3.2.
Read coverage normalized to 1 x sequencing depth (also known as Reads Per Genomic Content (RPGC))
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: bigwig, bed peaks

source_name: OSKM-Reprogramming cells

value: reprogramming cell


title: WT_untreated_RepC

value: GTCGCCTT


title: RNaseHtreat-DRIPseq-rep2

description: DNA:RNA hybird

source_name: Reprogramming cells, RNase H-treated


title: Non-irradiated melanocyte-derived exosomes 1

description: Exosomal microRNAs


title: OmniATAC-seq_MM029_R2_BL

city: Leuven

first: Stein

last: Aerts

address: O&N4 Herestraat 49 PO Box 602

country: Belgium

institute: KU Leuven

data_processing:
Data processing of human melanoma baseline OmniATAC-seq samples: Paired-end reads were mapped to the human genome (hg19-Gencode v18) using bowtie2 (v2.2.6). Mapped reads were sorted using SAMtools (v1.8) and duplicates were removed using Picard MarkDuplicates (v1.134). Reads were filtered by removing chromosomal reads and filtering for Q>30 using SAMtools. Bam files of technical replicates of the same cell line were merged at this point using samtools merge. Peaks were called using MACS2 (v2.1.2) callpeak using the parameters -q 0.05, --nomodel, --call-summits, --shift -75 --keep-dup all and --extsize 150 per sample. Chromosomal peaks, blacklisted regions (ENCODE) and peaks overlapping with alternative chromosomes were removed. Summits were extended by 250bp up- and downstream using slopBed (bedtools; v2.28.0), providing human chromosome sizes. Peaks were normalised for the library size using a custom script and overlapping peaks were filtered using the peak score by keeping the peak with the highest score. For visualisation in IGV, normalised bigWigs were made by bamCoverage (Deeptools, v3.3.1), using as parameters --normalizeUsing None, -bl EncodeBlackListedRegions --effectiveGenomeSize 2913022398 and as scaling parameter (-scaleFactor) 1/(RIP/1E6), where the RIP stands for the number of reads in peaks.
Data processing of non-human (Omni)ATAC-seq samples, and of human SOX10 and TFAP2A knock-down OmniATAC-seq data: Adapter sequences were trimmed from the fastq files using fastq-mcf (as part of eautils; v1.05) and the read quality was checked using FastQC (v0.11.8). Reads were mapped using STAR (v2.5.1b) (for the zebrafish samples paired-end reads were mapped) to the genome which were downloaded from UCSC (http://hgdownload.cse.ucsc.edu/goldenPath/) (for human: hg19-Gencode v18; for dog: canFam3; for horse: equCab2; for pig: susScr11; for mouse: mm10; for zebrafish: danRer10) and by applying the parameters --alignIntronMax 1 and --aslignIntronMin 2. Mapped reads were filtered for quality using SAMtools (v1.2) view with parameter –q4, sorted with SAMtools sort and indexed using SAMtools index. Peaks were called using MACS2 (v2.1.2) callpeak using the parameters -q 0.05, --nomodel, --call-summits, --shift -75 --keep-dup all and with the genome size for the correct species in --g, and this for each sample per species separately. Summits were extended by 250bp up- and downstream using slopBed (bedtools; v2.28.0), providing the chromosome sizes for the specific species. Per sample, peaks were normalised for the library size using a custom script and overlapping peaks were filtered using the peak score (keeping the highest scoring peak). Normalised bedGraphs were produced by genomeCoverageBed (as part of bedtools; v2.28.0) using as scaling parameter (-scale) 1E6/(number of non-chromosomal mapping reads). BedGraphs were converted to bigWigs by the bedtools suit functions bedSort to sort the bedGraphs, followed by bedGraphToBigWig to create the bigWigs, which were used in IGV for visualisation.
Genome_build: For human: hg19-Gencode v18; for dog: canFam3; for horse: equCab2; for pig: susScr11; for mouse: mm10; for zebrafish: danRer10.
Supplementary_files_format_and_content: bigWig files represent the coverage of the ATAC-seq signal.

source_name: Melanoma cell line

growth_protocol: Cells were cultured at 37°C with 5% CO2 and were maintained in Ham's F10 nutrient mix (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS; Invitrogen) and 100 µg ml-1 penicillin/streptomycin (Thermo Fisher Scientific).

extract_protocol:
Cells were washed, trypsinised, spun down at 1000 RPM for 5 min, medium was removed and the cells were resuspended in 1 mL medium. Cells were counted and experiments were only continued when a viability of above 90% was observed. 50,000 cells were used per sample. OmniATAC-seq was performed as described previously in Corces et al., 2017; and ATAC-seq as described in Buenrostro et al., 2015.
Library prep was performed as described before in Corces et al., 2017 for OmniATAC-seq samplas; and as in Buenrostro et al., 2013 for ATAC-seq samples.

treatment_protocol: For the knock-down data: SOX10, TFAP2A and the control knockdown was performed in MM001 using respectively a SMARTpool of four siRNAs against, respectively, SOX10 (SMARTpool: ON-TARGETplus SOX10 siRNA, number L017192-00-0005, Dharmacon), TFAP2A (SMARTpool: ON-TARGETplus TFAP2A siRNA, number L-006348-02-0005, Dharmacon) and a negative control pool (ON-TARGETplus non-targeting pool, number D-001810-10-05, Dharmacon) at a concentration of 20 nM for SOX10-KD, and 40 nM for TFAP2A-KD and the control using as medium Opti-MEM (Thermo Fisher Scientific) and omitting antibiotics. The cells were incubated for 72 h before processing.

tag: tissue type

value: Cutaneous melanoma

tag: condition

value: Baseline


title: RNaseHtreat-DRIPseq-rep1

description: DNA:RNA hybird


title: 202756030055: Earlytransition_DNMT3A_KD1

value: Female

value: H9-NK2 hESCs


title: siM2

city: hefei

first: Xiaolin

last: Wang

address: anhui,hefei,huangshan road 443

institute: USTC

description: KD.txt.gz

data_processing:
For circular RNA (circRNA) prediction, we identified the candidates with find_circ (Memczak et al., 2013) and the junction reads were calculated as Transcripts Per Kilobase Million (TPM). A criterion of P value ≤0.05, TPM ≥0.1 and |log2(fold change)| ≥1 among four pairs of samples was used to identify differentially expressed circRNAs.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: AGS cells

extract_protocol:
The clinical samples were cut into small pieces and homogenized in TRizol reagent (Life Technologies) by homogenizer. Total RNA was extracted by using TRizol reagent according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina or BGISEQ protocols

value: AGS

value: Treated with sihnRNPM-2


title: siM1

description: KD.txt.gz

value: Treated with sihnRNPM-1


title: PBMC/Biopsy CD2 rest

city: Oxford

first: Dominik

last: Trzupek

address: Roosevelt Drive

department: Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre

institute: University of Oxford

description: Data was generated using the BD Rhapsody targeted single-cell RNA-sequencing system (BD Biosciences). CD45+ cells were flow sorted from either cryopreserved peripheral blood mononuclear cells (PBMCs) or paired duodenal biopsies collected from two paediatric coeliac disease patients with active disease undergoing routine endoscopies. Sorted cells from each sample type and donor were labelled with oligo-conjugated barcode antibodies (BD) to identify donor and material type (blood or duodenal biopsy).  Single-cell suspensions from each donors  – containing equal proportions of blood-derived and biopsy-derived cells – were then pooled and stained with oligo-conjugated antibodies against 68 cell-surface markers (AbSeq) and loaded on a microplate (BD Rhapsody cartridge) according to manufacturer’s instructions.

data_processing:
For AbSeq1 RNA reads were aligned using BDRhapsody_Immune_Response_Panel_hs.fasta and protein reads were aligned using AbSeq1_Panel_37plex.fasta
For AbSeq2 RNA reads were aligned using BDRhapsody_Immune_Response_Panel_hs.fasta and protein reads were aligned using AbSeq2_Panel_43plex.fasta
For AbSeq3 RNA reads were aligned using BDRhapsody_Immune_Response_Panel_hs.fasta and protein reads were aligned using AbSeq3_Panel_68plex.fasta
FASTQ files were processed with BD Rhapsody Analysis Pipeline on Seven Bridges Genomics platform
Genome_build: BDRhapsody_Immune_Response_Panel_hs
Supplementary_files_format_and_content: Comma separated values with molecules per target per cell and with sample tag calls

source_name: Blood/Duodenal biopsy

extract_protocol:
Cells were lysed on the microplate and polyA-tailed mRNA and oligo-conjugated antibodies were captured by uniquely barcoded cell-capture beads. cDNA was then generated by RT from the pooled cell-capture beads.
Library preparation was performed using a pre-designed primer panel (Immune Response panel; BD) containing 399 probes targeting 397 genes, according to the manufacturer’s instructions. Protein (AbSeq) and sample barcoding libraries were also amplified in parallel and pooled for sequencing.

tag: age [years]

value: male

tag: disease

value: Coeliac disease

tag: individual

value: Flow sorted CD45+ cells isolated from blood/duodenal biopsy

tag: experimental condition

value: unstimulated


title: siGCirc2

description: KD.txt.gz

tag: cell type

value: Treated with sicircURI1-2


title: 202756030055: Earlytransition_NS_control_2


title: 202756030055: Earlytransition_NS_control_1


title: OSKM-FLAG-D7-DRIPseq-rep1

description: DNA:RNA hybird

source_name: OSKM-reprogramming cells, overexpression of Flag


title: OKM-D9-DRIPseq

description: DNA:RNA hybird

source_name: OKM-Reprogramming cells


title: PBMC T1D1/HC1 stim

description: Data was generated using the BD Rhapsody targeted single-cell RNA-sequencing system (BD Biosciences). Three subsets of CD4+ T cells were flow sorted from cryopreserved peripheral blood mononuclear cells (PBMCs). Namely: (i) CD127+ CD25-; (ii) CD127low CD25-; and (iii) CD127low CD25+. Sorted cells from each subset were labelled with oligo-conjugated barcode antibodies (BD) to identify sorting gate.  Single-cell suspensions from each donor – containing equal proportions of each sorted T-cell subset – were then pooled and stained with oligo-conjugated antibodies agaist surface expressed markers (AbSeq) and loaded on a microplate (BD Rhapsody cartridge) according to manufacturer’s instructions.

source_name: Blood

treatment_protocol: In vitro stimulation (90 min) with PMA and Ionomycin

value: male/male

value: Type 1 diabetes/Healthy donor

value: Flow sorted CD4+ T cells from PBMCs

value: stimulated


title: OSKM-FLAG-D3-DRIPseq-rep2

description: DNA:RNA hybird

value: reprogramming cell


title: PBMC SLE1 stim

value: female

value: Systemic lupus erythematosus


title: 202242420201: Latetransition_DNMT3B_KD1

value: Female


title: 202242420201: Latetransition_DNMT3A_KD2

value: H9-NK2 hESCs


title: OSKM-FLAG-D3-DRIPseq-rep1

description: DNA:RNA hybird


title: PBMC T1D1/HC1 rest


title: 202242420201: Primed_DNMT3B_KD1


title: OSKM-FLAG-D1-DRIPseq-rep2

description: DNA:RNA hybird


title: NC

description: KD.txt.gz

value: AGS

value: Negative Control


title: OSKM-FLAG-D7-DRIPseq-rep2

description: DNA:RNA hybird


title: siGCirc1

description: KD.txt.gz

value: Treated with sicircURI1-1


title: Thymus5 CD34+

city: Los Angeles

first: chintan

last: parekh

state: CA

address: 4650 sunset blvd, mail stop 54, mail stop 54

institute: CHLA

data_processing:
Conversion of fastq to UMI counts
Conversion of fastq to HTseq counts
Cellranger (10x genomics, thymuses 1, 2, 3, and 7), BD™ Precise WTA Analysis v2.0 (thymus 6, Seven Bridges Genomics, RSEC adjusted UMI counts), or Indrops (https://github.com/indrops/indrops) (thymuses 4, 5) pipelines. For thymus 1, the data from libraries from CD34+ cells and CD34- cells (n=2 libraries) was aggregated using the cellranger aggr function with normalize=mapped (the two libraries were normalized for sequencing depth) to generate a combined gene expression matrix for CD34+ and CD34- cells. The combined matrix was split to provide expression data for each cell type (CD34+ or CD34-)  as a separate file.  The indrops v3 library analysis pipeline was used for thymus 4, where FASTQ files generated from basecall files are demultiplexed to generate single composite filtered fastq files that include cell and UMI barcodes  in the read headers and are filtered to only include reads with the correct barcode structure that survive trimommatic trimming and a low complexity filter. The composite FASTQ file for thymus 4 is deposited in the NCBI SRA and can seve as the input data for the indrops analysis pipeline at  the "Identify abundant barcodes" step (https://github.com/indrops/).The indrops v2 library analysis pipeline was used for thymus 5. We excluded barcodes with reads <1000 and reads <10000 for thymus 4 and thymus 5 respectively. Default values were used for all other parameters in the indrops analysis pipeline. The refdata-cellranger-GRCh38  (thymuses 1,2,3,and 7) , GRCh38.85.gtf (thymuses 4,5), and the  gencode.v19.annotation.gtf (thymus 6), and transcriptome annotation files were used.
To analyze high-throughput RNA-Seq data, we used the web-based Galaxy platform (https://usegalaxy.org/). The reads were first trimmed to remove adapter sequences  (Nextera paired-ended adapter sequences) using Trimmomatic (Galaxy version 0.38.0). TopHat (Galaxy version 2.1.1) was used to align trimmed reads to a pseudoatosomal region masked GRCh38 version of the human genome (GCA_000001405.15_GRCh38_no_alt_analysis_set.fna, http://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/analysisSet/). Gene counts were computed by running HTseq (Galaxy version 0.9.1) against the gencode.v31.annotation.gff3.gz annotation file (https://www.gencodegenes.org/human/release_31.html) on BAM files that had first been sorted using Samtools (Galaxy version 2.0.3). Default parameters were used for Trimmomatic (Bolger et al., 2014), TopHat (Kim et al., 2013) and HT-Seq (Anders et al., 2015) with the following exceptions: minimum quality of Trimmomatic operation = 2 for Trimmomatic, mean inner distance between mate pairs = 0 for TopHat (since the fragment size for these libraries tends to be short relative to the read length we used  (150 bases paired end reads)), and mode = Intersection (nonempty) and ID attribute = gene_name for HT-seq.
Genome_build: hg38 for all thymuses except Thymus 6 ( hg19)

source_name: CD34+ thymic progenitor cells

extract_protocol:
Single cells were captured into barcoded hydrogels using the 10X (Thymuses 1, 2, 3, and 7) or Indrops (Thymuses 4, 5) microfluidics platforms. For thymus 6, single cells were index sorted into a 96 well plate (two 96 well plates, 1 cell/ well) containing RNA extraction buffer (BD Precise WTA Single Cell Kit (BD Genomics, PN 634100, 96 well plates). Cell type information based on FACS for thymus 6 is provided as a csv file. Cell barcodes used for sequencing are provided as csv files for plate 1 (S1) and plate 2 (S2). RNA was extracted from FACS sorted CD34+CD7+CD1a-CD19-CD4-CD8-CD123+ cells for thymuses 8 (367 cells)  and 9 (600 cells) using the Arcturus picopure kit  and then used for making bulk RNA-Seq libraries.
Single cell RNA-Seq libraries were prepared using the 10x Genomics Chromium Single Cell v2 kit (thymus 1), the 10x Genomics Chromium Single Cell v3.2 kit (thymuses 2,3,and 7), the Indrops protocol (Zilionis et al, Nature Protocols, 2017) (thymuses  4,5), or the BD Precise WTA Single Cell Kit (BD Genomics, PN 634100, thymus 6) . The indrops v3 and v2 protocols were used for Thymus 4 and thymus 5 respectively.Bulk RNA-Seq libraries (thymuses 8 and 9) were prepaered by extracting RNA using the Arcturus picopure RNA extraction kit followed by  libraray preparation using the The Smart-Seq V4 ultralow input RNA-Seq kit (Clontech) .
Illumina Hiseq (Thymuses 1,3,7,8,and 9; 150 base pair paired end) or Nextseq500 (thymuses 2,4-6). The Nextseq high output (150 cycles,  thymus 2),  mid output kit (150 cycles,  thymus 6) , or high output  (75 cycles, thymuses 4 and 5) kits were used. For thymus 2, the cycles were distributed as read 1 (96 bases) and read 2 (28 bases). For thymus 4, cycles were distributed as read 1 (61 cycles, biological read), read 2 (8 cycles, first half of the gel barcode), read 3  (8 cycles, library index ), and  read 4 (14 cycles, the second half of the gel barcode, the UMI and a fraction of the polyA tail) (indrops v3). For thymus 5 cycles were distributed as read 1 (37 cycles, biological read), read 2 (51 cycles, metadata read),  and index read (6 cycles, library index) (indrops v2). For thymus 6 the cycles were distributed as read 1 (50 cycles) and read 2 (100 cycles).

value: Thymus

tag: donor sex

tag: donor age

value: 2 years


title: SP-A2(1A0)-F-18hr-4

description:
18hrs_MvsF_deseq2_SP-A2(1A0)
sample name:
JFRm53

source_name: Female mouse exposed K.penumoniae-Alveolar Macrophage (AM) cells

value: 18 hours

tag: strain

value: Alveolar Macrophage (AM) cells


title: Thymus6 CD34+

value: male

value: 4 days


title: OSKM-FLAG-D1-DRIPseq-rep1

description: DNA:RNA hybird

tag: the day of reprogramming


title: PBMC SLE1 rest

tag: Sex

value: unstimulated


title: Thymus4 CD34+

value: 13 days


title: PBMC/Biopsy CD1 rest

value: Coeliac disease

value: Flow sorted CD45+ cells isolated from blood/duodenal biopsy


title: 202242420201: Primed_DNMT3A_KD2


title: 202242420201: Latetransition_DNMT3A_KD1


title: Thymus 9 CD123+

source_name: CD34+CD7+CD123+ thymic cells

value: female

value: 3 years


title: SP-A2(1A0)-M-18hr-1

description:
18hrs_MvsF_deseq2_SP-A2(1A0)
sample name:
JFRm66

source_name: Male mouse exposed K.penumoniae-Alveolar Macrophage (AM) cells

tag: exposure time

value: Male

tag: genotype


title: 202242420201: Latetransition_NS_control

value: Female

tag: tissue

value: H9-NK2 hESCs


title: genomic DNA from tamoxifen-resistant MCF-7_850K

description:
breast cancer
SAMPLE 2

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Methylatioin Module v1.9.0) and R 3.0.2

source_name: Mammary Gland; Breast

tag: cell line

value: tamoxifen-resistant MCF-7

value: breast epithelial

tag: gender

value: adenocarcinoma


title: Thymus 8 CD123+

value: Thymus

value: 10 days


title: Thymus2 CD34+

value: 23 months


title: OSKM-RNaseH1-D7-DRIPseq-rep1

description: DNA:RNA hybird

source_name: OSKM-reprogramming cells, overexpression of RNase H1

value: reprogramming cell


title: genomic DNA from parental MCF-7_850K

description:
breast cancer
SAMPLE 1

value: parental MCF-7


title: Thymus7 CD8SP

source_name: CD8 single positive thymic cells

value: 5 years


title: T47D cells, siPRMT1 T6H replicate 3

city: LYON 3EME ARRONDISSEMENT

first: Lucie

last: Malbeteau

address: 28 rue Laennec

department: Cancer Cell Plasticity

country: France

institute: Cancer Research Center of Lyon

data_processing:
All libraries were mapped on the hg19 version of the human genome using Bowtie2 (Galaxy Version 2.3.2.2).
Count tables were prepared using HTSeq-count (Galaxy Version 0.9.1).
Differential gene expression analysis was performed with DESeq2 using the following a fold change cutoff when indicated and false discovery rate adjusted p-value ≤ 0.01.
Expression > 40 million reads per sample
Genome_build: hg19
Supplementary_files_format_and_content: comma separated file (csv) containing log2 fold change and adjpvalue for the comparisons made in the columns and each row representing a gene; tabular files containing gene counts

growth_protocol: Cells were maintained in RPMI 1640 medium containing L-Glutamine, 5mg Insulin, 5% PS and 10% fetal bovine serum at 37°C and 5% CO2

extract_protocol:
Total RNA was extracted using TRIzol (Thermo Scientific) and 3 biological replicates for each condition were performed.
cDNA libraries were prepared using the SENSE mRNA-Seq Library Prep Kit V2 (Lexogen, Vienna Austria). Quality of the cDNA was assessed and RT-qPCR was performed for selected PR target genes as quality control. Standard illumina protocols were used to construct the library for sequencing.

treatment_protocol: T47D cells depleted for PRMT1 using siRNA were incubated with 10 nM of Progesterone (R5020) or equivalent volume of vehicle ethanol for 6 h.

value: Breast Cancer cells

tag: sirna

value: depleted for PRMT1

tag: treatment


title: OSKM-RNaseH1-D3-DRIPseq-rep2

description: DNA:RNA hybird


title: Thymus7 CD4SP

source_name: CD4 single positive thymic cells


title: T47D cells, siPRMT1 T6H replicate 2


title: 202242420201: Primed_DNMT3A_KD1

source_name: H9-NK2 hESCs


title: OSKM-RNaseH1-D3-DRIPseq-rep1

description: DNA:RNA hybird


title: 202242420201: Primed_NS_control


title: T47D cells, siPRMT1 T6H replicate 1


title: Thymus7CD34-

source_name: CD34- thymic cells


title: OSKM-RNaseH1-D1-DRIPseq-rep2

description: DNA:RNA hybird


title: OSKM-RNaseH1-D7-DRIPseq-rep2

description: DNA:RNA hybird


title: 201465930035: hESC_latetransition_noPKCi_c


title: T47D cells, siPRMT1 T0 replicate 3

value: Ethanol 6h


title: Thymus3 CD34-

value: male

value: 9 days


title: 201465930035: hESC_latetransition_noPKCi_b


title: T47D cells, siPRMT1 T0 replicate 2


title: Thymus3 CD34+


title: OSKM-RNaseH1-D1-DRIPseq-rep1

description: DNA:RNA hybird


title: 201465930035: hESC_latetransition_noPKCi_a


title: OSKM-D209N-D7-DRIPseq-rep2

description: DNA:RNA hybird

source_name: OSKM-reprogramming cells, overexpression of RNase H1(D209N)


title: T47D cells, siCT T6H replicate 3

value: siControl

value: control


title: 201465930035: hESC_naive_c

value: Female

value: H9-NK2 hESCs


title: 201465930035: hESC_naive_b


title: T47D cells, siPRMT1 T0 replicate 1


title: Sample_48_RL_R1446C_gRNA2_KDAC001_Repl1_Input_ChIPseq

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to hg19 using STAR with default parameters
FPKM were obtained using Rsubread
ChIP-seq reads were aligned to hg19 using BWA with default parameters
Peaks were called using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq: MACS2 peaks
Supplementary_files_format_and_content: RNA-seq: FPKM

source_name: RL cell line

extract_protocol:
RNA-seq libraries were prepared using the Illumina TruSeq stranded mRNA sample kits, respectively, according to the manufacturer
ChIP-seq ws performed using H3K27Ac antibodies (Active Motif; catalog No. 39133).  ChIPseq libraries were prepared using  KAPA Hyper Prep Kits (Roche) and TruSeq adaptors according to the manufacturer

value: RL

value: Transfected with CRISPR gRNAs inducing CREBBP point mutation


title: T47D cells, siCT T6H replicate 1


title: 201465930035: hESC_latetransition_PKCi_c


title: T47D cells, siCT T6H replicate 2


title: T47D cells, siCT T0 replicate 3


title: OSKM-D209N-D7-DRIPseq-rep1

description: DNA:RNA hybird


title: 201465930014: hESC_latetransition_PKCi_b


title: OSKM-D209N-D3-DRIPseq-rep1

description: DNA:RNA hybird


title: Sample_47_RL_R1446C_gRNA2_KDAC001_Repl1_H3K27Ac_ChIPseq


title: Sample_45_RL_R1446C_gRNA2_KDAC005_Repl2_H3K27Ac_ChIPseq


title: OSKM-D209N-D1-DRIPseq-rep1

description: DNA:RNA hybird


title: T47D cells, siCT T0 replicate 2


title: OSKM-D209N-D3-DRIPseq-rep2

description: DNA:RNA hybird


title: OSKM-iPSC-DRIPseq-rep2

description: DNA:RNA hybird

source_name: iPS

value: iPS


title: T47D cells, siCT T0 replicate 1


title: 201465930014: hESC_latetransition_PKCi_a


title: Sample_44_RL_R1446C_gRNA2_KDAC005_Repl1_Input_ChIPseq


title: Sample_49_RL_R1446C_gRNA2_KDAC001_Repl2_H3K27Ac_ChIPseq


title: Sample_43_RL_R1446C_gRNA2_KDAC005_Repl1_H3K27Ac_ChIPseq


title: OSKM-iPSC-DRIPseq-rep1

description: DNA:RNA hybird


title: 201465930014: hESC_earlytransition_b


title: OSKM-D7-DRIPseq-rep2

description: DNA:RNA hybird

source_name: OSKM-reprogramming cells


title: 201465930014: hESC_earlytransition_a


title: 201465930035: hESC_naive_a


title: OSKM-D209N-D1-DRIPseq-rep2

description: DNA:RNA hybird


title: Sample_41_RL_R1446C_gRNA1_KDAC001_Repl2_H3K27Ac_ChIPseq


title: Sample_46_RL_R1446C_gRNA2_KDAC005_Repl2_Input_ChIPseq


title: Sample_40_RL_R1446C_gRNA1_KDAC001_Repl1_Input_ChIPseq


title: 201465930014: hESC_primed_c


title: 201465930014: hESC_primed_b


title: 201465930014: hESC_primed_a


title: Sample_39_RL_R1446C_gRNA1_KDAC001_Repl1_H3K27Ac_ChIPseq


title: 200863770004: hESC_naive_b


title: OSKM-D3-DRIPseq-rep2

description: DNA:RNA hybird


title: 200863770004: hESC_naive_a


title: Sample_38_RL_R1446C_gRNA1_KDAC005_Repl2_Input_ChIPseq


title: Sample_37_RL_R1446C_gRNA1_KDAC005_Repl2_H3K27Ac_ChIPseq


title: OSKM-D3-DRIPseq-rep1

description: DNA:RNA hybird


title: Sample_36_RL_R1446C_gRNA1_KDAC005_Repl1_Input_ChIPseq


title: OSKM-D5-DRIPseq-rep1

description: DNA:RNA hybird


title: Sample_42_RL_R1446C_gRNA1_KDAC001_Repl2_Input_ChIPseq


title: 200863770004: hESC_latetransition_b


title: 200863770004: hESC_latetransition_a


title: OSKM-D1-DRIPseq-rep1

description: DNA:RNA hybird


title: Sample_35_RL_R1446C_gRNA1_KDAC005_Repl1_H3K27Ac_ChIPseq


title: OSKM-D7-DRIPseq-rep1

description: DNA:RNA hybird


title: 200863770004: hESC_earlytransition_b


title: Sample_34_RL_R1446C_gRNA2_KDAC005_Repl2_RNAseq


title: OSKM-D0-DRIPseq-rep1

description: DNA:RNA hybird


title: OSKM-D5-DRIPseq-rep2

description: DNA:RNA hybird


title: PBK-28-Hc

source_name: Hippocampus

extract_protocol:
RNA was extracted from snap frozen brain areas (both hemispheres for hippocampus) using the RNeasy Plus Universal Kit (QIAGEN), following manufacturer’s instructions.
TruSeq RNA stranded protocol, 76-151 bp paired end

tag: age of inoculation

value: 6 weeks

tag: type of inoculation

value: intracerebral

value: PrP knockout

tag: date of sacrifice

value: 8 wpi

value: non-infectious brain homogenate

value: Hippocampus


title: Sample_33_RL_R1446C_gRNA2_KDAC005_Repl1_RNAseq


title: 200863770004: hESC_earlytransition_a


title: OSKM-D1-DRIPseq-rep2

description: DNA:RNA hybird

extract_protocol:
For ssDRIP-seq, nucleic were isolated from cells, followed by SDS/proteinase K treatment at 37°C overnight. Genome DNA was extracted by the phenol-chloroform method and precipitated with isopropanol. DNA fragmentation was performed overnight using endonucleases (MboI, MseI, AluI, DdeI), and the negative control was treated with RNase H (New England Biolabs) overnight. Briefly, 3.5 ug of DNA was bound with 10 ug of S9.6 antibody in 1 X binding buffer (10 mM NaPO4 pH 7, 140 mM NaCl, 0.05% Triton X-100) overnight at 4˚C. 50 μl Protein G sepharose beads were added for 4 hours. Bound beads were washed 4 times in binding buffer and elution was performed in elution buffer (50 mM Tris pH 8, 10 mM EDTA, Proteinase K) for 45 min at 55˚C. DNA was purified and sonicated to 150 bp fragments. For RNA-seq, Total RNAs were extracted with TRIzol. For quantitative PCR, cDNAs were synthesized with ReverTra Ace (Toyobo) and oligo dT (Takara), and then analyzed by qPCR with SYBR green mixture (Genstar) and performed on a CFX Real-Time System (Bio-Rad). For ATAC-seq, a total of 50,000 cells were washed once with cold PBS and resuspended in 50 μl lysis buffer. The suspension of nuclei was then centrifuged at 500 g at 4˚C for 10 min, followed by the addition of 50 μl transposition reaction mix (10 μl TD buffer, 5 μl Tn5 transposase and 35 μl nuclease-free H2O). DNA was purified using a MinElute Kit (QIAGEN). For CLIP-seq, mES cells were irradiated at 400 mJ/cm2 with 254 nm UV light. The crosslinked cells were lysed and 15 μg of anti-DDX5 antibody was applied to pull down protein-RNA complexes. After micrococcal nuclease treatment and 3’ DNA adaptor ligation, the immunoprecipitated complexes were fractionated on a 4-12% NuPAGE Bis-Tris gel and transferred onto a nitrocellulose membrane. The DDX5-specific smear bands were excised with scalpels and treated with proteinase K (Thermo Fisher Scientific) prior to the extraction of respective RNA by using phenol and chloroform.
For ssDRIP-seq, the first adapter was ligated to the 3’ end of the ssDNA using Adaptase (Swift Biosciences) via a highly efficient, proprietary reaction that only tails 3’ ends of ssDNA and ligates the first truncated adapter to 3’ ends simultaneously. This method avoids the bias inherent in random primer-based methods, as it ligates adapters in a sequence-independent manner. The extension step was performed using the primer paired to the first adapter, followed by a ligation reaction to add the second truncated adapter to the 5’ ends. An indexing PCR step was performed to add the indexed sequence, and the library was amplified. For RNA-seq, RNA sequencing libraries were constructed using the VAHTS mRNA-seq V3 Library Prep Kit for Illumina (Vazyme). For ATAC-seq, ATAC-seq libraries were first subjected to 5 cycles of pre-amplification. To determine the suitable number of cycles required for the second round of PCR, the library was assessed by quantitative PCR as described, and the library was then PCR amplified for the appropriate number of cycles. Libraries were purified with AMPure XP beads. For CLIP-seq, A 5’ RNA linker was then added to the isolated RNA and reverse transcribed by superscript reverse transcriptase III (Life Technologies, 18080-051). The cDNA strands are PCR-amplified to produce libraries for deep sequencing. L3-IR800-biotin DNA adaptor: 5’OH -ATC TCG TAT GCC GTC TTC TGC TTG TAA AAA AAA AAA A/iAzideN/A AAA AAA AAA AA/3Bio/-3’, 5’ RNA linker: 5’-(OH) rArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU(rN)(rN) (rN)rU(OH) -3’.

value: reprogramming cell


title: 200863770004: hESC_primed_b


title: 200863770004: hESC_primed_a


title: PBK-26-Hc


title: PBK-27-Hc


title: PBK-24-Hc

value: RML6 prions


title: Sample_50_RL_R1446C_gRNA2_KDAC001_Repl2_Input_ChIPseq


title: Sample_30_RL_R1446C_gRNA1_KDAC001_Repl2_RNAseq


title: Sample_29_RL_R1446C_gRNA1_KDAC001_Repl1_RNAseq


title: Sample_28_RL_R1446C_gRNA1_KDAC005_Repl2_RNAseq


title: OSKM-D0-DRIPseq-rep2

description: DNA:RNA hybird


title: PBK-22-Hc


title: Sample_26_RL_WT_gRNA2_KDAC001_Repl2_RNAseq

value: Transfected with control CRISPR gRNAs


title: Sample_27_RL_R1446C_gRNA1_KDAC005_Repl1_RNAseq


title: Sample_25_RL_WT_gRNA2_KDAC001_Repl1_RNAseq


title: Sample_32_RL_R1446C_gRNA2_KDAC005_Repl2_RNAseq


title: Sample_31_RL_R1446C_gRNA2_KDAC005_Repl1_RNAseq


title: Sample_24_RL_WT_gRNA2_KDAC005_Repl2_RNAseq


title: Sample_23_RL_WT_gRNA2_KDAC005_Repl1_RNAseq


title: PBK-23-Hc


title: Sample_22_RL_WT_gRNA1_KDAC001_Repl2_RNAseq


title: LA5

city: Herston

first: Susanna

last: Ng

state: QLD

address: 300 Herston Road

department: Immunology

country: Australia

institute: QIMR Berghofer Medical Research Institute

description:
replicate 5
9255008019_E

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Initial processing performed using GenomeStudio v1.6.0 (Illumina) to generate Sample_Probe_Profile.txt. Quality control was assessed using the Lumi package, run on R.

source_name: CD4+ T cells

label_protocol: Biotinylated cRNA

extract_protocol: CD4+ T cells were sorted into buffer RLT and homogenised in QIAshredder (QIAGEN) columns prior to RNA extraction using the Rneasy Mini Kit (QIAGEN) according to manufacturer's instructions.

tag: organ

value: liver

tag: status

value: infected (day 56)


title: Sample_21_RL_WT_gRNA1_KDAC001_Repl1_RNAseq


title: Sample_20_RL_WT_gRNA1_KDAC005_Repl2_RNAseq


title: Bipolar depression5 BD-05

city: nanjing

first: yu

last: chen

address: 264, Guangzhou Road

department: Department of Psychiatry

institute: The Affiliated Brain Hospital of Nanjing Medical University

description: Gene expression data of plasma from patients with bipolar depression

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 48C on GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: bipolar depression

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)

extract_protocol: Extraction of plasma，then total RNA was extracted using a miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

value: plasma

tag: diagnosis

value: bipolar depression


title: Bipolar depression6 BD-06


title: Bipolar depression7 BD-07


title: LA4

description:
replicate 4
9255008067_C


title: LA3

description:
replicate 3
9255008083_E


title: LA1

description:
replicate 1
9255008083_C


title: Bipolar depression3 BD-03


title: LN4

description:
replicate 3
9255008083_D

value: naïve


title: Sample_19_RL_WT_gRNA1_KDAC005_Repl1_RNAseq

value: RL


title: Bipolar depression4 BD-04


title: Bipolar depression1 BD-01


title: Bipolar depression2 BD-02


title: Sample_18_RL_R1446C_gRNA2_RNAseq

value: Transfected with CRISPR gRNAs inducing CREBBP point mutation


title: LN3

description:
replicate 2
9255008067_A


title: Unipolar depression7 UD-07

description: Gene expression data of plasma from patients with unipolar depression

source_name: unipolar depression

value: unipolar depression


title: LA2

description:
replicate 2
9255008019_C


title: Unipolar depression6 UD-06


title: Sample_17_RL_R1446C_gRNA1_RNAseq


title: SA5

description:
replicate 5
9255008088_A

value: spleen


title: LN1

description:
replicate 1
9255008019_B


title: Unipolar depression5 UD-05


title: SA4

description:
replicate 4
9255008083_A


title: Sample_16_RL_CREBBPKO_gRNA2_RNAseq

value: Transfected with CRISPR gRNAs inducing CREBBP frameshift mutation


title: SA3

description:
replicate 3
9255008019_D


title: LN5

description:
replicate 4
9255008067_F


title: Unipolar depression4 UD-04


title: Sample_15_RL_CREBBPKO_gRNA1_RNAseq


title: SA2

description:
replicate 2
9255008067_B


title: Unipolar depression3 UD-03


title: Sample_14_RL_WT_gRNA2_RNAseq


title: SA1

description:
replicate 1
9255008083_B


title: Sample_12_RL_R1446C_gRNA2_Input_ChIPseq


title: SN5

description:
replicate 5
9255008019_A


title: Sample_13_RL_WT_gRNA1_RNAseq


title: Sample_11_RL_R1446C_gRNA2_H3K27Ac_ChIPseq


title: Unipolar depression1 UD-01


title: 201465930014: hESC_earlytransition_c

value: Female

value: H9-NK2 hESCs


title: Day 1 adults, H02_AWK43.g2

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

data_processing:
Aligned to C. Elegans ce11 using STAR spliced read aligner
Count read using HT-seq and using ce11  as reference
Normalization (TMM), quantitation (logCPM), and differential expression analysis using edgeR and limma voom.
Genome_build: ce11
Supplementary_files_format_and_content: logCPM values

organism: Caenorhabditis elegans

growth_protocol: Synchronized day 1 adulthood from egg lay

extract_protocol:
Qiagen miRNeasy kit (Qiagen #217004)
Illumina TruSeq Stranded Total RNA

treatment_protocol: No additional treatment

tag: age

value: day 1 adults

tag: group

value: AWK43 pgrn-1(-); granulin 2(+)


title: Sample_10_RL_R1446C_gRNA1_Input_ChIPseq


title: Sample_9_RL_R1446C_gRNA1_H3K27Ac_ChIPseq


title: Healthy control 6 HC-06

description: Gene expression data of plasma from healthy controls

source_name: healthy control

value: healthy control


title: Unipolar depression2 UD-02


title: SN4

description:
replicate 4
9255008019_F

tag: strain


title: Sample_8_RL_CREBBPKO_gRNA2_Input_ChIPseq


title: Day 1 adults, G02_AWK43.g2


title: Naive_c

data_processing:
Sequencing reads were mapped to GRCh38 using hisat2 (v2.1.0)
Data were processed using FeatureCounts (Subread, v. 1.6.3) to count over exons and the R package EdgeR was used to generate counts per million (CPM) for each gene.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file include CPM values for each Sample

extract_protocol:
RNA was extracted as above, before mRNA was isolated from 500 ng of total RNA using mRNA DIRECT (Thermo Fisher Scientific) and fragmented with RNA fragmentation reagent (Thermo Fisher Scientific). First strand cDNA synthesis was performed with SuperScript III First-Strand Synthesis System and 3 μg/μl random hexamers (Thermo Fisher Scientific) followed by second strand synthesis with DNA polymerase I and RNase H.
After purification, the double stranded cDNA was ligated to in house designed adapters (based on TruSeq Indexed adapters (Illumina)) using NEBNext Ultra II (NEB) followed by 15 cycles of amplification and library purification.

tag: cell type

value: Human embryonic stem cells

tag: source gender

tag: cell status

value: Naïve


title: Healthy control 5 HC-05

tag: tissue


title: Healthy control 4 HC-04


title: SN1

description:
replicate 1
9255008067_E


title: Day 1 adults, G01_CF3050


title: Sample_7_RL_CREBBPKO_gRNA2_H3K27Ac_ChIPseq

tag: cell line

tag: genotype


title: SN3

description:
replicate 3
9255008067_D


title: SN2

description:
replicate 2
9255008083_F


title: Healthy control 1 HC-01


title: Naive_b


title: Adult-Cortex

city: Shinjuku

first: Sho

last: Yoshimatsu

state: Tokyo

address: 35 Shinanomachi

department: Physiology

country: Japan

institute: Keio University School of Medicine

data_processing:
Data of RNA-seq (fastq file format) were quality-checked, and low-quality reads (score < 30), adapter sequences, and overrepresented sequences such as poly-A chain were trimmed using the Trim Galore! (ver.0.4.0).
The remaining reads were mapped to the Callithrix jacchus genome (cj3.2.1.86) using the STAR (ver.2.5.3a), and the output file (BAM file format) were summarized using the featureCounts (1.5.2).
Genome_build: cj3.2.1.86
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Callithrix jacchus

source_name: Cortex

growth_protocol: See the citation

extract_protocol:
RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: See the citation

value: Cortex


title: Sample_6_RL_CREBBPKO_gRNA1_Input_ChIPseq


title: Day 1 adults, F02_AWK43.g2


title: Day 1 adults, F01_CF3050


title: Naive_a


title: Late_transition_c


title: Day 1 adults, H01_CF3050


title: No40-EBmethod-differentiated-Day72

source_name: ESC-derived neural differentiated cells

value: ESC-derived neural differentiated cells


title: Healthy control 2 HC-02

value: plasma


title: Healthy control 3 HC-03


title: Day 1 adults, E02_AWK43.g2


title: Sample_4_RL_WT_gRNA2_Input_ChIPseq

value: Transfected with control CRISPR gRNAs


title: Late_transition_b


title: Late_transition_a


title: Sample_2_RL_WT_gRNA1_Input_ChIPseq


title: Day 1 adults, E01_CF3050


title: Sample_3_RL_WT_gRNA2_H3K27Ac_ChIPseq


title: Day 1 adults, D03_AWK107.g3

value: AWK107 pgrn-1(-); granulin 3(+)


title: Day 1 adults, D01_WT

value: WT

value: N2 wildtype


title: No40-ES-P63

source_name: Embryonic stem cells

value: Embryonic stem cells


title: Early_transition_1W_c


title: Early_transition_1W_b


title: Sample_1_RL_WT_gRNA1_H3K27Ac_ChIPseq

value: RL


title: No20_ES_P45


title: scRNA-seq_R133C CO

city: Montréal

first: Yoshiaki

last: Tanaka

state: Québec

address: 5415 boul. l'Assomption

department: Medicine

country: Canada

institute: Centre de Recherche l'Hôpital Maisonneuve-Rosemont, Université de Montréal

description: Gene expression in hCO

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned to hg19 human genome by Cellranger (v2.1.0).
All libraries were merged by aggr function of Cellranger.
Genome_build: hg19
Supplementary_files_format_and_content: Read count matrix was formated by mtx. Barcodes and genes were provided by tsv format.
Supplementary_files_format_and_content: Please note that mtx format is composed of header line, comment line, matrix size and each nonzero entry. header and comment line starts with %. matrix size represents the number of row, columns and entries. Entry line represents the index of row and column and data value. The column was ordered with WT MGE +JQ1, R133C MGE +JQ1, WT MGE, R133C MGE, WT CO +JQ1, R133C CO +JQ1, WT CO and R133C CO."

source_name: human cortex organoids

growth_protocol: ESCs were cultured on Matrigel coated cell culture dish with mTeSR1 media. hMGEOs and hCOs were cultured in each established condition.

extract_protocol: Chromium™ Single Cell 3’ Reagent Kits

tag: tissue/cell type

value: cortex organoids


title: Early_transition_1W_a

value: Female


title: Day 1 adults, D02_AWK33.g1

value: AWK33 pgrn-1(-); granulin 1(+)


title: scRNA-seq_WT CO

description: Gene expression in hCO

tag: treatment


title: DSY127_ES_P17


title: Early_transition_72h_c


title: scRNA-seq_R133C CO JQ1+

description: Gene expression in hCO


title: No20-ES-P45


title: Day 1 adults, C02_AWK33.g1

value: day 1 adults


title: Day 1 adults, C01_WT


title: DSY127-ES-P17


title: scRNA-seq_WT CO JQ1+

description: Gene expression in hCO


title: Day 1 adults, B03_AWK107.g3


title: Early_transition_72h_b


title: scRNA-seq_R133C MGE

description: Gene expression in hMGEO

source_name: human MGE organoids

value: medial ganglionic eminence (MGE) organoids


title: Early_transition_72h_a


title: Primed_c

value: Primed


title: E01F_Fibroblast_P1

source_name: Fibroblasts

value: Fibroblasts


title: paraGC5

description: GC-circRNA.txt.gz

source_name: GC

value: paratumor


title: paraGC4

description: GC-circRNA.txt.gz


title: paraGC3

description: GC-circRNA.txt.gz


title: scRNA-seq_R133C MGE JQ1+

description: Gene expression in hMGEO


title: Primed_b

value: Human embryonic stem cells


title: Day 1 adults, C03_AWK107.g3


title: Primed_a


title: scRNA-seq_WT MGE JQ1+

description: Gene expression in hMGEO


title: paraGC2

description: GC-circRNA.txt.gz


title: Day 1 adults, A03_AWK107.g3


title: paraGC1

description: GC-circRNA.txt.gz


title: Chromatin accessibility R133C KCl+ JQ1+

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned to hg19 human genome by Bowtie2 (v2.3.0)
Peaks were called by HOMER (v4.10.1)
Genome_build: hg19
Supplementary_files_format_and_content: Bed format

source_name: Chromatin accessibility R133C

growth_protocol: hESCs were differentiated into cortical interneurons as described previously (Maroof et al., 2013)

extract_protocol: ATAC-seq library was prepared as described previously (Buenrostro et al., 2013)

treatment_protocol: Membrane was depolarized with 55mM KCl. 75nM JQ1 was added to the media starting from 2 weeks of neuronal maturation.

value: in vitro differentiated interneurons (INs)

tag: genotype/variation

value: MeCP2 R133C mutant

tag: stimulation

value: KCl


title: 18_F_DSC_PBS_IS

city: La Jolla

first: Andrei

last: Chernov

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

data_processing:
The reads data were processed using BaseSpace software (Illumina)
Reads were aligned to m. musculus genome (version Mm10) using STAR aligner with default settings.
Statistical data processing and differential transcript expression was determined using the Cufflinks package (http://cufflinks.cbcb.umd.edu/).
Biological pathway analysis and comparison were performed using Ingenuity Pathway Analysis (Qiagen).
Genome_build: mm10

source_name: dorsal spinal cord

growth_protocol: Adult female and male C57BL6/J mice (n = 6/group) were obtained from Jackson Labs and housed in a temperature-controlled room (∼22 °C), on a 12-h light/dark cycle with free access to food and water. The procedure and testing were conducted during the light cycle.

extract_protocol:
Total RNA was extracted from mouse tissues using TRI reagent (Zymo Research) and purified using Direct-zol microRNA system (Zymo Research). The RNA purity was estimated by measuring the OD260/280 ratio using a ND-1000 spectrophotometer (Thermo Scientific). RNA integrity was determined using 2100 Bioanalyser (Agilent Technologies).
Poly(A) RNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Ribosomal RNA was depleted using NEBNext rRNA Depletion reagents (New England Biolabs). A NEBNext Ultra Directional II RNA Library Preparation Kit for Illumina (New England Biolabs) was used to obtain barcoded cDNA libraries from total RNA. Barcoded libraries were pooled and the High Output v2 kit (IlluminaO) was employed to prepare the sequencing libraries. Libraries were sequenced on a NextSeq 500 DNA sequencer (Illumina).

treatment_protocol: Under isoflurane anesthesia a single intrasciatic bolus injections of the MBP peptides (60 µg in 5 µl PBS each) or PBS carrier were performed into a nerve fascicle using a 33-gauge needle on a Hamilton syringe. In 7 days sciatic nerve segments (injection site), L5 DRG and DSC were collected for RNA-seq. All animal procedures were performed in agreement with the PHS Policy on Humane Care and Use of Laboratory Animals and the protocol approved by the Institutional Animal Care and Use Committee at the VA San Diego Healthcare System.

value: dorsal spinal cord

tag: Sex

value: female

value: PBS carrier

tag: injection site

value: intrasciatic


title: Day 1 adults, A01_WT

value: WT

value: N2 wildtype


title: 17_F_DSC_MBPS_IS

value: MBP84-104-SCR (scramble) peptide


title: GC5

description: GC-circRNA.txt.gz

value: tumor


title: Chromatin accessibility R133C KCl- JQ1+


title: 16_F_DSC_MBP_IS

value: MBP84-104-WT (wild type) peptide


title: GC4

description: GC-circRNA.txt.gz


title: Chromatin accessibility R133C KCl+JQ1-


title: 15_M_DSC_PBS_IS

value: male


title: GC3

description: GC-circRNA.txt.gz


title: Day 1 adults, B02_AWK33.g1

value: day 1 adults

value: AWK33 pgrn-1(-); granulin 1(+)


title: Day 1 adults, B01_WT


title: Chromatin accessibility R133C KCl-JQ1-


title: scRNA-seq_WT MGE

description: Gene expression in hMGEO

value: medial ganglionic eminence (MGE) organoids


title: Hi-C: NIPBL-AID + auxin G2

city: Vienna

first: Michael

last: Mitter

address: Dr.-Bohr-Gasse 3

institute: IMBA

description: scsHi-C library of cells synchronized to G2 using RO3306 and treated with auxin to deplete NIPBL; Merge of 4 replicates.All contacts, cis-sister contacta and trans-sister contacts.

data_processing:
Basecalling software: Illumina RTA
Hi-C samples were preprocessed using a custom nextflow pipeline (https://github.com/gerlichlab/scshic_pipeline). Briefly, bcl2 files were first demultiplexed using bcl2tofastq. Then, fastq files were aligned to hg19 with HeLa SNPs using bwa, aligning read pairs independently. Then, pairsam files were constructed using pairtools (https://github.com/mirnylab/pairtools), followed by sorting and deduplicating. Then, reads were split into cis sister and trans sister contacts based on the presence of signature mutations using pairtools select: A read was assigned to the Watson strand if it contained two or more A-to-G mutations and no T-to-C mutations. Similarly, if a read contained two or more T-to-C mutations, but no A-to-G mutations it was assigned to the Crick strand. Then, contacts were classified as cis sister contacts if (after correcting for the opposite read-strandedness of Illumina sequencing of the two mates) both mates mapped to the same strand. Conversely, contacts were classified as trans sister contacts if the two mates mapped to opposing strands. Then, cooler (https://github.com/mirnylab/cooler) was used to construct .cool files. For DNAseq samples,  a custom python script was used to count the number of each point mutation type.
Genome_build: hg19
Supplementary_files_format_and_content: cooler derived .cool files (Mirny lab) containing Hi-C matrices for usage with HiGlass and the cooler ecosystem for Hi-C. For DNAseq data, tables (csv) are provided that indicate the number of each point mutation type, mapping quality and average Phred-score of every sequencing read.
Supplementary_files_format_and_content: cool files were generated using cooler (https://github.com/mirnylab/cooler) using standard parameters. Separate cooler files are provided for all contacts, cis-sister contacts and trans-sister contacts. Csv files were generated using a custom python script to count different point mutation types.

source_name: cervical carcinoma

extract_protocol:
For Hi-C, fixed cells were permeabilized using ice-cold Hi-C lysis buffer (10 mM TRIS-HCl pH 8 [Sigma], 10 mM NaCl [Sigma], 0.2 % Nonidet P-40 substitute [Sigma], 1x Complete EDTA-free Protease inhibitor [Roche]) for 30 min at 4 °C. Then, cells were spun down (2500 x g for 5 min), supernatant was discarded, and digestion mix was added (375 U DpnII [NEB] in 1x DpnII buffer [NEB]) and cells incubated for 16 h at 37 °C under rotation. Then, cells were spun down, supernatant was discarded and fill-in mix was added (38 µM Biotin-14-dATP [Thermo Fisher Scientific], 38 µM dCTP, dGTP and dCTP [Thermo Fisher Scientific], 50 U Klenow Polymerase [NEB], 1x NEB 2 buffer) and cells incubated for 1 h at 37 °C under rotation. Then, cells were spun down again, and ligation mix was added (1x T4 DNA ligase buffer [Thermo Fisher Scientific], 0.1 % Triton X-100 [Sigma], 100 µg/ml BSA [Sigma], 50 U T4 DNA ligase [Thermo Fisher Scientific]) and incubated at RT for 4 h. Then, cells were spun down, resuspended in 200 µl PBS and gDNA was purified using the DNeasy Blood and Tissue kit (Quiagen). DNA was transferred to a Covaris microTUBE (Covaris) and sheared on a Covaris S2 instrument (Duty cycle 10 %, Intensity 5.0, Cycles/burst 200) for 25 s. Double size selection was performed by employing AMPure XP beads (Beckman Coulter) first at 0.8-fold sample volume according to the standard protocol, followed by transfer of the supernatant and bead application at 0.12-fold sample volume. The resulting DNA was bound to Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher Scientific) in Biotin binding buffer (5 mM Tris-HCl pH 7.5 [Sigma], 0.5 mM EDTA [AppliChem], 1 M NaCl [Merck]) for 1 h at RT. Beads were then washed 2x in Tween wash buffer (5 mM Tris-HCl [Sigma], 0.5 mM EDTA [AppliChem], 1 M NaCl [Merck], 0.05 % Tween-20 [Sigma]) and 1x in H2O. For DNAseq, Cells were harvested by trypsinization, spun down at 1100 x g for 1 min and the supernatant was discarded. Then, cells were spun down, resuspended in 200 µl PBS and gDNA was purified using the DNeasy Blood and Tissue kit (Quiagen). DNA was transferred to Covaris microTUBE (Covaris) and sheared on a Covaris S2 instrument (Duty cycle 10 %, Intensity 5.0, Cycles/burst 200) for 25 s. Double size selection was performed by employing AMPure XP beads (Beckman Coulter) first at 0.8-fold sample volume according to the standard protocol, followed by transfer of the supernatant and bead application at 0.12-fold sample volume.
For Hi-C samples, beads with bound biotinylated DNA were resuspended in H2O and library preparation was performed using the NEBNext Ultra II DNA library prep kit for Illumina [NEB] according to the standard protocol. After this, beads were washed 4x using Tween wash buffer and DNA was eluted using 95 % formamide (Sigma), 10 mM EDTA (AppliChem) at 65 °C for 2 min. DNA was then precipitated using 80 % EtOH (Sigma), washed with 75 % EtOH and resuspended in H2O. Then, 4sT was converted to methyl-cytosine using OsO4 / NH4Cl, followed by qPCR according the NEBUltra Ultra II DNA library prep kit for Illumina [NEB]. The finished libraries were purified using AMPure XP beads (Beckman Coulter) at 0.9x sample volume following the standard protocol. For DNAseq samples, DNA library preparation was performed using the NEBNext Ultra II DNA library prep kit for Illumina [NEB] according to the standard protocol. The unamplified libraries were then treated using OsO4  and amplified according the NEBNext Ultra II DNA library prep kit for Illumina [NEB]. The finished libraries were purified using AMPure XP beads (Beckman Coulter) at 0.9x sample volume following the standard protocol.

value: HeLa Kyoto

tag: diesease state

value: cervical carcinoma

value: NIPBL-depleted G2

value: auxin


title: Hi-C: Sororin-AID + auxin G2

description: scsHi-C library of cells synchronized to G2 using RO3306 and treated with auxin to deplete Sororin; Merge of 3 replicates. All contacts, cis-sister contacta and trans-sister contacts.

value: Sororin-depleted G2


title: 14_M_DSC_MBPS_IS

value: dorsal spinal cord


title: Day 1 adults, A02_AWK33.g1


title: GC2

description: GC-circRNA.txt.gz


title: Hi-C: G1 after labeling

description: scsHi-C library of cells synchronized to the subsequent G1 phase after 4sT labeling during the preceding S-Phase; Merge of 2 replicates. All contacts, cis-sister contacta and trans-sister contacts.

value: w.t. G1


title: Hi-C: Prometaphase

description: scsHi-C library of cells synchronized to Prometaphase using Nocodazole; Merge of 2 replicates. All contacts, cis-sister contacta and trans-sister contacts.

value: w.t. Prometa


title: Chromatin accessibility WT KCl+ JQ1+

source_name: Chromatin accessibility WT

value: in vitro differentiated interneurons (INs)

value: WT

value: KCl


title: 12_F_DRG_PBS_IS

source_name: dorsal root ganglia

value: dorsal root ganglia

value: female

value: PBS carrier

value: intrasciatic


title: GC1

description: GC-circRNA.txt.gz

value: tumor


title: Chromatin accessibility WT KCl+JQ1-


title: 11_F_DRG_MBPS_IS

value: MBP84-104-SCR (scramble) peptide


title: Hi-C: G2

description: scsHi-C library of cells synchronized to G2 using RO3306; Merge of 11 replicates. All contacts, cis-sister contact and trans-sister contacts.

value: HeLa Kyoto

value: w.t. G2


title: Chromatin accessibility WT KCl-JQ1-


title: Hi-C: 8h S-Phase Release

description: scsHi-C library of cells synchronized to G1 using thymidine/aphidicoline and released into S-Phase for 8h; Merge of two replicates. All contacts, cis-sister contacta and trans-sister contacts.

value: cervical carcinoma

value: w.t. S-Phase 8h


title: DMN_D22016_R1

city: Erie

middle: A

last: Campbell

address: 4205 College Drive

department: School of Science

institute: Penn State Erie

description: DMN early ecodormant tissue

data_processing:
fastq files were uploaded to the Galaxy Suite (https://usegalaxy.org) and mapped to the double haploid potato genome (Solanum tuberosum SolTub_ver3) using Tophat2-SE and differential expression of transcripts was determined using Cufflinks v2.2.1a
Genome_build: SolTub_3.0
Supplementary_files_format_and_content: genes.fpkm_tracking

organism: Solanum tuberosum

source_name: tuber meristems

growth_protocol: Tubers were treated in a 9 liter container  for two days

extract_protocol:
Tuber meristems were extracted with a microcurette and frozen in liquid N2, total RNA was isolated using a PureLink RNA Mini Kit (www.thermofisher.com) and quantified on a BioSpecNano (www.ssi.shimadzu.com)
The libraries were made with the Illumina TruSeq Stranded mRNA Kit and sequenced on the HiSeq 2500 in Rapid Mode

treatment_protocol: Tubers received either water at 22.5 ul per 9liters of head space (Control) or 22.5 ul of DMN per 9 liters of head space (treated)

value: tuber meristem

value: 1,4-dimethylnaphthalene treated

tag: dormancy status

value: early ecodormant tissue


title: DMN_D42616_R1

description: DMN clate ecodormant tissue

value: late ecodormant tissue


title: 09_M_DRG_PBS_IS

value: male


title: Hi-C: 2h S-Phase Release

description: scsHi-C library of cells synchronized to G1 using thymidine/aphidicoline and released into S-Phase for 2h; Merge of two replicates. All contacts, cis-sister contacta and trans-sister contacts.

value: w.t. S-Phase 2h


title: DMN_D43016_R1

description: DMN late ecodormant tissue


title: Hi-C: 4h S-Phase Release

description: scsHi-C library of cells synchronized to G1 using thymidine/aphidicoline and released into S-Phase for 4h; Merge of two replicates. All contacts, cis-sister contacta and trans-sister contacts.

value: w.t. S-Phase 4h


title: 13_M_DSC_MBP_IS

value: dorsal spinal cord

value: MBP84-104-WT (wild type) peptide


title: Chromatin accessibility WT KCl- JQ1+

value: in vitro differentiated interneurons (INs)

value: WT


title: DMN_D21816_R1

description: DMN early ecodormant tissue


title: 08_M_DRG_MBPS_IS

value: dorsal root ganglia

value: intrasciatic