title: Ctrl_retina_5

city: Biberach an der Riß

first: Kolja

last: Becker

address: Birkendorfer Str. 65

department: Global Computational Biology and Digital Sciences

institute: Boehringer Ingelheim Pharma GmbH & Co. KG

data_processing:
Generation of genomic indices and read alignment was carried out via STAR  (version 2.5.2b).
Quantification on gene level was performed using FeatureCounts (version 1.5.1) and RSEM (version 1.3.0), while discarding multimapping reads.
Assembly: GRCm38.96  (+AAV sequences)

source_name: Retina cells

growth_protocol: C57BL/6J mice were purchased from Charles River (Sulzfeld, Germany). 6–8-week-old male mice were used for the AAV study.  Mice were housed in individually ventilated cages in groups of 2-5, constant temperature and a 12-hour light/dark cycle. Mice had ad libitum access to standard rodent chow and water. Animal experiments were performed in accordance with the German animal welfare act, the guidelines of the Federation of the European Laboratory Animal Science Association (FELASA), the ARRIVE guidelines and were reviewed and approved by the local authorities.

extract_protocol:
Flash frozen dissected retina and eye cup tissues (n=72) were homogenized in 700 µL Qiazol (Qiagen) using a Precellys Evolution homogenizer (Bertin Technologies). Retina samples were homogenized by ceramic beads (MPbio, 6913-500) and eye cup samples by metal beads (Bertin Technologies, 15987602). Total RNA was extracted using the miRNeasy Micro Kit (Qiagen, 217084) according to the manufacturer’s tissue protocol including on-column DNase treatment (Qiagen, 79254). Total RNA samples (36 eye cup, 36 retina) were quantitatively and qualitatively assessed using the fluorescence-based Broad Range Quant-iT RNA Assay Kit (Thermo Fisher Scientific) and the Standard Sensitivity RNA Analysis DNF-471 Kit on a 96-channel Fragment Analyzer (Agilent), respectively.
Retina- and eye cup-derived RNA samples were normalized on the MicroLab STAR automated liquid platform (Hamilton). Total RNA input of 250ng was used for library construction with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina #E7760, together with the NEBNext Poly(A) mRNA Magnetic Isolation Module #E7490 upstream and the NEBNext Multiplex Oligos for Illumina #E7600 downstream (all New England Biolabs). The only deviation from the manufacturer’s protocol was the use of Ampure XP beads (Beckman Coulter) for double-stranded cDNA purification, instead of the recommended SPRIselect Beads. The index PCR was performed with 12 cycles, while the final library was eluted in 35µL. mRNA libraries were then quantified by the High Sensitivity dsDNA Quanti-iT Assay Kit (ThermoFisher) on a Synergy HTX (BioTek). Library molarity averaged at 149nM. mRNA libraries were also assessed for size distribution (smear analysis of 360bp average) and adapter dimer presence (<0.5%) by the High Sensitivity Small Fragment DNF-477 Kit on a 96-channel Fragment Analyzer (Agilent). All 70 sequencing libraries were then normalized on the MicroLab STAR (Hamilton), pooled and spiked in with PhiX Control v3 (Illumina). The library pool was subsequently clustered on an S4 Flow Cell and sequenced on a NovaSeq 6000 Sequencing System (Illumina) with dual index, paired-end reads at 2 x 100 bp length.

treatment_protocol: Plasmids with the ubiquitous CAG promoter were generated encoding for three human, codon optimized transgenes (VEGF-A 165, TNF-α and IL-6) that have a V5-tag sequence at the 3’ end of the gene were generated previously (Weigelt et al., 2021).The AAV-stuffer control construct includes a non-coding sequence from the 3’ UTR of the UBE3A gene and has been described elsewhere (Strobel 2015). AAVs used in this study were packaged into the ShH10 capsid (Klimczak 2009). Mice were intravitreally injected with the different AAVs under isoflurane anesthesia and after local anesthetic eye drops were applied (Novesin®, OmniVision). Both eyes of 6 mice per group were injected with either 1x108 viral genomes (VG)/eye (low dose) or 1x109 VG/eye (high dose) in 1 µL AAV buffer.

tag: well

value: Healthy

value: Retina

tag: angiogram

tag: eye

value: OS

value: N

tag: rin

tag: replicate

value: FALSE

tag: transgene


title: iPS Gustav MIM P4 3

status: Public on Nov 11 2022

type: SRA

city: Salzburg

first: Rodolphe

last: Poupardin

address: Strubergasse 22

country: Austria

library_source: transcriptomic

data_processing:
Quality control was conducted using FASTQC (version 0.11.7 - Bioinformatics Group at the Babraham Institute).
Trimming and removal of residual adapters was done with AdapterRemova
Reads were then mapped to the Ensembl GRCh38 human genome using Tophat2
The number of mapped reads/gene (counts) was then calculated using HTseq
Genome_build: Human GRCh38
Supplementary_files_format_and_content: Normalized counts per gene

molecule: total RNA

organism: Homo sapiens

source_name: Umbilical cord blood

growth_protocol: Approval was obtained for human cell and tissue sample collection and genetic reprogramming from the Institutional Review Board (protocols 19–252, 18–243, 21–060, 19–284 and 415-E/1776/4-2014, Ethics Committee of the province of Salzburg). Adult samples were collected in accordance with the Declaration of Helsinki after written informed consent from healthy volunteers. Umbilical cord blood (UCB) samples were collected after written informed consent by the mother-to-be obtained prior to delivery of full-term pregnancies. MSCs from bone marrow (BM) and UCB were isolated and expanded under animal serum-free conditions using pooled human platelet lysate (pHPL) replacing fetal bovine serum and their purity, identity, and viability was characterized by flow cytometry . Clonogenicity and differentiation capacity was assessed. PBMC were isolated by density centrifugation from random donor buffy coats.   Induced pluripotent stem cells (iPSCs) were reprogrammed from primary MSCs (derived from BM or UCB) by non-integrative Sendai Viral vector kit (CytoTuneTM-iPS Sendai Reprogramming Kit encoding for Oct4, Sox2, KLF4 and c-Myc, Life Technologies Cat.No.A1378001) by the Harvard Stem Cell Institute (HSCI) iPS Core Facility (Cambridge, MA, USA). The reprogramming protocol was described by Fusaki and colleagues in 2009 and adapted by the HSCI. Human iPSCs were characterized by cytogenetic analysis of at least twenty G-banded metaphase cells per clone and teratoma formation.   Human iPSCs were initially transferred from mouse embryonic feeder layers to feeder-free conditions and thereafter maintained on a selected batch of Matrigel® (Corning) in mTeSRTM1 (STEMCELL Technologies) medium. When reaching a cell density appropriate for splitting, iPSCs were harvested using Gentle Cell Dissociation Reagent (STEMCELL Technologies). Viable cells were counted and seeded at a density of 5 x 104 cells per cm2 on Matrigel® in mTeSRTM1 containing 10 µM Y-27632 ROCK pathway inhibitor (Selleckchem).

extract_protocol:
RNASeq  RNA was isolated using Macherey&Nagel RNA isolation kit according to the manufacturers protocol. The quality of total RNA isolates was analyzed using the Agilent RNA 6000 Nano Kit.   Poly-(A)-selection was performed utilizing the NEBNext Poly(A)mRNA Magnetic Isolation Module (NEB) according to the manufacturer’s requirements.
mRNA libraries were prepared with the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB). All libraries were analyzed with the Agilent DNA 1000 Kit and quantified using the Qubit® dsDNA BR Assay Kit (ThermoFisher). After equimolar pooling all samples were sequenced on an Illumina HiSeq 1500 system with High Output chemistry v4 (50 cycles, single-read).

treatment_protocol: After 24 hours, the medium was changed to STEMdiff™ Mesoderm Induction Medium (STEMCELL Technologies, defined, xeno-free medium) and the medium was replaced daily for the next consecutive 4 days. On day 5, cells were harvested using TrpLETM (Gibco) and the expression of early mesoderm markers Brachyury and CD56 was determined by flow cytometric analysis. Cells were seeded in EGMTM-2 containing hydrocortisone, hFGF-B, VEGF, R3-IGF, Ascorbic Acid, hEGF (Lonza), preservative-free heparin 10 IU/mL (Biochrom), dipeptiven (1.2 mg/ml, L-glutamin – L-arginin dipeptide, clinical grade: Fresenius Kabi), 10% pHPL and 10 µM Y-27632 at a cell density of 27,000 cells/cm2 without Matrigel® coating and cultured in humidified incubators (Binder CB210) at 37°C and 5% CO2 in ambient air. Until passage five, iPS-MSCs were passaged at a density of 27,000 cells/cm2 twice per week with addition of Y-27632. For microscopical documentation EVOS XL (Thermo Fhisher Scientific) was used. Differentiations were performed with iPS reprogrammed from MSCs derived from bone marrow (4 clones) or umbilical cord blood (3 clones).

tag: cell line

tag: cell type

value: induced Pluripotent stem cells

tag: treatment

value: Mesoderm Induction Medium


title: OO-12h5

city: Liběchov

first: Matej

last: Murín

state: Central Bohemia

address: Rumburská, 89

department: Laboratory of Developmental Biology

country: Czech Republic

institute: Institute of Animal Physiology and Genetics CAS

data_processing:
Reads with lengths less than 15 nt were discarded.
Expression analysis was done using the Differential Expression in Two Groups tool in CLC Genomics Workbench v. 22.0 according to a negative binomial Generalized Linear Model function.
Data were normalized (counts per million mapped reads) and filtered (cpm > 0.5, at least two samples from each group of replicates) and expression values of read count and CPM were calculated for all of the genes.
For the normalization of data, the trimmed mean of M-values normalization method was used.
Assembly: SScrofa11.1
Supplementary files format and content: Expression Browser processed data DESeq2.xlsx; Complete list of genes after data processing and comparison of different cultivation times among themselves.

organism: Sus scrofa

source_name: oocyte

extract_protocol:
Total RNA was isolated from denuded oocytes from 4 experimental groups (each of three replicates) using an AllPRep DNA/RNA Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
RNA libraries were prepared using SMARTer Stranded Total RNA - v2 Kit Pico Input Mammalian (Takara Bio, Japan) according to SMARTer Stranded Total RNA - v2 kit Pico Input Mammalian protocol. After PCR amplification (15 cycles), RNA libraries were purified. Their quantity and quality were assessed using the Agilent DNA High Sensitivity Chip and Bioanalyzer 2100 instrument. Fragment length distribution was evaluated using the Agilent 2100 Expert software. After the quantification, libraries were pooled in equimolar ratios according to the quality and concentration measurements, denatured, diluted to final loading concentration (275 pM) and subsequently sequenced in NovaSeq 6000 S4 flow cell (Illumina, San Diego, CA, USA) to reach 100 M pair-end reads per sample.

value: oocyte


title: Ctrl_retina_3

country: Germany

organism: Mus musculus

tag: disease

tag: tissue

value: OD

tag: strain


title: iPS Gustav MIM P4 2


title: Patient_10_NK

city: Cambridge

first: Ce

last: Gao

state: MA

address: 400 Technology Square

country: USA

institute: Ragon Institute of MGH, MIT and Harvard

data_processing:
FASTQ files were obtained by Illumina bcl2fastq2.
STAR and RSEM were used to align to GRCh38 and to calculate the raw counts for genes, respectively.
Assembly: GRCh38
Supplementary files format and content: raw counts and TPM in csv

source_name: peripheral blood

extract_protocol:
Total RNA was extracted from the 7 cell populations using a commercial PicoPure RNA Isolation Kit
RNA-Seq libraries were generated as described in a previous study. Briefly, whole transcriptome amplification (WTA) and tagmentation-based library preparation was performed using SMART-seq2, followed by sequencing with a 75-cycle kit on a NextSeq 500 instrument (Illumina, CA). The quantification of transcript abundance was conducted using RSEM software (v1.2.22) supported by the STAR aligner software (STAR_2.4.2a). The raw reads were aligned to the Hg38 human genome database and the ZIKV sequence (ZIKV strain PRVABC59, GenBank: KU501215.1).

value: peripheral blood

value: NK

tag: phenotype

value: nM


title: OO-12h3


title: Ctrl_retina_4


title: OO-28h4


title: iPS Cornelius MIM P4 3


title: Patient_10_mDC

value: mDC


title: iPS Gustav MIM P4 1


title: Patient_11_B

value: B

value: HD


title: Ctrl_retina_6


title: OO-0h4


title: Patient_10_CD8


title: OO-0h3


title: Ctrl_retina_1


title: OO-0h2


title: Ctrl_RPE_6

source_name: RPE cells

value: RPE

tag: comment

value: Failed R QC, but included

value: TRUE


title: Patient_10_CD4


title: iPS Cornelius MIM P4 1


title: Patient_10_B


title: iPS Gustav MIM Tag 5 P0 3


title: Patient_10_Monocytes

value: Monocytes


title: iPS Gustav MIM Tag 5 P0 2


title: OO-12h1


title: Patient_09_pDC

value: pDC


title: h1_endo_R3

city: Kannapolis

first: Tzung-Fu

last: Hsieh

state: NC

address: Tzung-Fu Hsieh, 600 Laureate Way

department: Plant and Microbial Biology

institute: North Carolina State University

data_processing:
For RNA-seq, adapter trimming was performed using the fastp program. For allele-specific transcriptome analysis, adapter-trimmed sequencing reads were mapped to the Col-0 and Ler cDNA scaffold using custom scripts and pipeline (https://zilbermanlab.net/tools/). Reads were assigned to Col-0 or Ler sudogenomes based on the SNPs detected between the two ecotypes. Each gene received Col-0 and Ler scores, which represented the number of reads aligned to the corresponding ecotype. These numbers were used to calculate the maternal transcript proportion for each gene. For endosperm and embryo transcriptomes, adapter-trimmed sequencing reads were aligned to TAIR10 using the Salmon aligner version 1.9.0 and quantified by the Salmon quant program and normalized by transcripts per million (TPM). DESeq2 was used to identify differentially expressed genes.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text file of normalized count matrix

organism: Arabidopsis thaliana

source_name: endosperm

growth_protocol: Long day condition (16 hours light, 8 hours dark) at 23 °C

extract_protocol:
Embryos and endosperms were collected 8 days after cross and total RNA was extracted using RNAeasy kit (Qiagen) plus in-column DNase digestion.
Illumina cDNA libraries were constructed with the Ovation RNA-seq System V2 (NuGen Technologies) per manufacturer’s instruction.

treatment_protocol: Crosses were performed between h1 triple mutant h1.1-1 h1.2-2 h1.3-1 and wild type Ler. Crosses between Col-0 and Ler were used as the control.

value: endosperm

tag: genotype

value: h1 triple mutant x Ler


title: h1_emb_R3

source_name: embryo

value: embryo


title: Ctrl_RPE_4

value: Healthy

value: OS

value: N

value: FALSE


title: Patient_09_NK

value: peripheral blood

value: NK


title: iPS Gustav MIM Tag 5 P0 1

value: induced Pluripotent stem cells

value: Mesoderm Induction Medium


title: Ctrl_RPE_3

value: OD


title: wt_endo_R3

value: wt Col x Ler


title: Ctrl_retina_2

value: Retina


title: iPS Cornelius MIM P4 2


title: Patient_09_Monocytes

value: nM


title: Ctrl_RPE_2

value: RPE


title: iPS Cornelius MIM Tag 5 P0 2


title: iPS Cornelius MIM Tag 5 P0 3


title: Ctrl_RPE_1


title: wt_emb_R3


title: h1_endo_R2


title: Patient_09_mDC

value: mDC


title: Patient_09_CD8


title: AAVvegf_low_retina_6

value: Retinopathy

value: Y

value: hVEGF


title: Ctrl_RPE_5

value: Healthy

value: Failed R QC, but included

value: TRUE


title: AAVvegf_low_retina_5

value: FALSE


title: iPS Cornelius MIM Tag 5 P0 1


title: iPS Gustav 3


title: h1_emb_R2

value: embryo

value: h1 triple mutant x Ler


title: Patient_09_CD4

value: peripheral blood


title: wt_endo_R2

value: endosperm


title: Patient_09_B

value: B


title: iPS Gustav 2

value: induced Pluripotent stem cells


title: h1_endo_R1


title: iPS Gustav 1


title: Patient_08_pDC

value: pDC


title: h1_emb_R1


title: AAVvegf_low_retina_3

value: Retina

value: OD


title: iPS Cornelius 3


title: Patient_08_NK

value: NK

value: nM


title: wt_endo_R1

value: wt Col x Ler


title: iPS Cornelius 2


title: Patient_08_Monocytes

value: Monocytes


title: Patient_12_mDC

value: mDC

value: vS


title: AAVvegf_low_retina_1

value: Retinopathy

value: Y

value: hVEGF


title: wt_emb_R1

value: embryo


title: AAVvegf_low_retina_2

value: FALSE

value: TRUE


title: iPS Cornelius 1


title: Patient_08_mDC

value: peripheral blood


title: h1xLer endo rep3

library_source: genomic

data_processing:
We used Perl scripts to convert all the Cs in the ‘forward’ reads to Ts, and all the Gs in the ‘reverse’ reads to As. The converted reads were then aligned to the equivalently converted TAIR10 reference genome, allowing up to two mismatches per read.
We use Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp window for each sequence context (CG, CHG, CHH).
Assembly: TAIR10
Supplementary files format and content: gff

molecule: genomic DNA

extract_protocol:
Embryos and endosperms were collected 8 days after crossing and purified through FACS. Genomic DNA was isolated from FACS-purified nuclei using CTAB method.
Bisulfite sequencing libraries were constructed using the ACCEL-NGS Methyl-Seq DNA library kit (Product Code 30024, Swift Biosciences, Ann Arbor, MI) per the manufacturer’s instruction.

value: endosperm

value: h1 triple mutant x Ler

value: bisulfite conversion


title: MSPCs UCB144 3

value: Mesenchymal stromal cells


title: Patient_08_CD8


title: AAVvegf_low_RPE_4

value: RPE

value: OS


title: MSPCs UCB144 2


title: AAVvegf_low_RPE_6

value: OD


title: h1xLer endo rep2


title: AAVvegf_low_RPE_3


title: AAVvegf_low_retina_4

value: Retina


title: MSPCs UCB144 1


title: AAVvegf_low_RPE_2


title: Patient_08_B

value: B

value: nM


title: Patient_08_CD4


title: h1xLer emb rep2


title: h1xLer emb rep3


title: AAVvegf_low_RPE_1

value: Retinopathy


title: iPS Betty MIM P8+ 3

source_name: Bone marrow

value: induced Pluripotent stem cells

value: Mesoderm Induction Medium


title: Patient_07_pDC

value: pDC

value: vS


title: Patient_07_NK

value: NK


title: h1xLer endo rep1


title: iPS Betty MIM P8+ 1


title: AAVtnfa_high_retina_6

value: Y

value: FALSE

value: hTNFa


title: seedlings, an3, rep3 (RNA-seq)

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

country: China

institute: National Institute of Biological Sciences

data_processing:
Zebracall software used for basecalling.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using hisat2.
The expression of genes were obtained with the R package edgeR.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text file include normalized reads for each sample.

source_name: Arabidopsis seedlings

growth_protocol: The Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a long day photoperiod (23°C, 16 h light/22°C, 8 h dark).

extract_protocol:
Total RNA was extracted from 12-day-old Arabidopsis seedlings with TRIzol reagent (Invitrogen).
Sequencing libraries were built for RNA-seq (the single-ended 50-bp strategy on the BGISEQ500 platform).

value: seedlings


title: h1xLer emb rep1

value: embryo

value: h1 triple mutant x Ler

value: bisulfite conversion


title: Patient_07_Monocytes

value: peripheral blood

value: Monocytes


title: Patient_07_mDC

value: mDC


title: AAVtnfa_high_retina_4

value: Retina

value: OS


title: iPS Alice MIM P8+ 3

value: induced Pluripotent stem cells


title: AAVtnfa_high_retina_5

value: Retinopathy

value: OD


title: seedlings, an3, rep2 (RNA-seq)


title: iPS Alice MIM P8+ 2

value: Mesoderm Induction Medium


title: Patient_07_CD8

value: vS


title: seedlings, an3, rep1 (RNA-seq)


title: AAVtnfa_high_retina_3

value: Y


title: AAVtnfa_high_retina_2

value: FALSE


title: iPS Alice MIM P8+ 1


title: seedlings, bcl7a/b, rep3 (RNA-seq)


title: Patient_07_B

value: B


title: Patient_07_CD4


title: iPS Betty MIM P8+ 2


title: seedlings, bcl7a/b, rep2 (RNA-seq)

value: seedlings


title: iPS Betty MIM P4 3


title: AAVtnfa_high_retina_1

value: OCT Messung nicht mÃ¶glich

value: hTNFa


title: iPS Betty MIM P4 2


title: AAVtnfa_high_RPE_6

value: RPE


title: iPS Betty MIM P4 1


title: AAVtnfa_high_RPE_5


title: seedlings, swp73b, rep3 (RNA-seq)


title: AAVtnfa_high_RPE_4


title: iPS Alice MIM P4 2


title: AAVtnfa_high_RPE_3


title: seedlings, swp73b, rep2 (RNA-seq)


title: seedlings, swp73b, rep1 (RNA-seq)


title: Patient_06_mDC

value: peripheral blood

value: nS


title: iPS Alice MIM P4 1


title: iPS Alice MIM P4 3


title: Patient_06_NK

value: NK


title: Patient_06_Monocytes

value: Monocytes


title: Patient_06_CD8


title: AAVtnfa_high_RPE_2


title: seedlings, pms2ab, rep3 (RNA-seq)


title: iPS Betty MIM Tag 5 P0 3


title: Patient_06_pDC

value: pDC


title: Patient_06_CD4


title: Patient_06_B


title: AAVtnfa_high_RPE_1

value: OS


title: seedlings, pms2ab, rep1 (RNA-seq)


title: seedlings, pms2ab, rep2 (RNA-seq)


title: iPS Betty MIM Tag 5 P0 2

value: induced Pluripotent stem cells


title: seedlings, bcl7a/b, rep1 (RNA-seq)


title: iPS Betty MIM Tag 5 P0 1


title: Patient_05_pDC


title: AAVstuffer_low_retina_6

value: Healthy

value: Retina

value: stuffer


title: seedlings, minu12, rep3 (RNA-seq)


title: Patient_05_NK


title: iPS Alice MIM Tag 5 P0 3

value: Mesoderm Induction Medium


title: Patient_05_Monocytes


title: seedlings, minu12, rep2 (RNA-seq)


title: seedlings, minu12, rep1 (RNA-seq)


title: AAVstuffer_low_retina_4

value: Y

value: FALSE


title: AAVstuffer_low_retina_3

value: OD


title: Patient_05_CD8


title: seedlings, sys123, rep2 (RNA-seq)

value: seedlings


title: AAVstuffer_low_retina_1


title: iPS Alice MIM Tag 5 P0 1


title: AAVstuffer_low_retina_5


title: Patient_05_mDC

value: mDC


title: iPS Alice MIM Tag 5 P0 2


title: AAVstuffer_low_RPE_6

value: RPE


title: seedlings, swi3d, rep3 (RNA-seq)


title: AAVstuffer_low_retina_2


title: seedlings, swi3d, rep2 (RNA-seq)


title: iPS Betty 3


title: seedlings, sys123, rep3 (RNA-seq)


title: Patient_04_pDC

value: peripheral blood


title: AAVstuffer_low_RPE_4


title: iPS Betty 2


title: Patient_05_CD4

value: nS


title: Patient_04_NK

value: NK


title: Patient_04_Monocytes

value: Monocytes


title: Patient_05_B

value: B


title: iPS Alice 3


title: iPS Alice 2


title: AAVstuffer_low_RPE_5

value: Failed R QC, but included

value: TRUE


title: seedlings, sys123, rep1 (RNA-seq)


title: AAVstuffer_low_RPE_2

value: Healthy


title: iPS Alice 1

value: induced Pluripotent stem cells


title: AAVstuffer_high_retina_5

value: Retina

value: OS

value: stuffer


title: seedlings, syd, rep3 (RNA-seq)

value: syd-/-


title: seedlings, brip12, rep3 (RNA-seq)


title: AAVstuffer_low_RPE_3

value: OD

value: Y

value: FALSE


title: seedlings, swi3d, rep1 (RNA-seq)

value: seedlings


title: MSPCs BMAC A 3

value: Mesenchymal stromal cells


title: OIR_hyperoxic_P16_3

data_processing:
Generation of genomic indices and read alignment was carried out via STAR (version 2.5.2b).
Quantification on gene level was performed using FeatureCounts (version 1.5.1) and RSEM (version 1.3.0), while discarding multimapping reads.
Assembly: GRCm38.96

growth_protocol: Pregnant females were purchased from Charles River (Sulzfeld, Germany) and male and female pups at P12 were used for the OIR experiment. Mice were housed in individually ventilated cages in groups of 2-5, constant temperature and a 12-hour light/dark cycle. Mice had ad libitum access to standard rodent chow and water.

extract_protocol:
Dissected retinae were stored in RNAlater (Invitrogen).  RNAlater-preserved tissues were disrupted and homogenized in CK14 tubes (VWR, 10144-496) with RLT buffer using a Precellys Evolution homogenizer (Bertin Technologies). Total RNA was then extracted using the MagMAX-96 total RNA isolation kit (Thermo Fisher Scientific, AM1830) including a DNase digestion prior to final elution.
Total RNA input of 100 ng was used for library construction with the TruSeq Stranded mRNA LT kit—Set A (Illumina, RS-122-2101), together with the SuperScript II Reverse Transcriptase (Thermo Fisher Scientific, 18064014), according to the manufacturer’s protocol. The quality of mRNA libraries was assessed for adapter and heterodimer presence using the DNA 1000 microfluidic chip (Agilent, 5067-1504), while library molarity was measured using the Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen, P11496). All 32 sequencing libraries were then normalized, pooled and spiked in with PhiX Control v3 (Illumina). The library pool was subsequently clustered using the TruSeq SR Cluster Kit v3 (Illumina, GD-401-3001), and sequenced with TruSeq SBS Kit v3 reagents (Illumina, FC-401-3002) on a HiSeq 2000 Sequencing System (Illumina) with single index, single-read reads at 1 x 51 bp length (Read parameters: Rd1: 52, Rd2: 7), reaching an average depth of 24.9 million Pass-Filter reads per sample (13.1% CV).

treatment_protocol: The OIR experiments were performed according to previously published protocols (Smith et al. 1994). In brief, 7-days-old male and female pups with their mothers were transferred to a hyperoxic chamber (75 % oxygen). At P12, oxygen concentration was slowly reduced back to normoxic conditions (21 % oxygen) within approximately 3 h. Control mice remained at normoxic conditions for the whole experiment. Mice were euthanized at P12, P13, P14, P15 and P16 by cervical dislocation and retinal tissue manually dissected.

value: Hyperoxia 75pc

tag: time

tag: timepoint


title: OIR_hyperoxic_P16_2


title: iPS Betty 1


title: AAVstuffer_high_retina_3

tag: well


title: seedlings, brip12, rep1 (RNA-seq)


title: AAVstuffer_high_retina_2

tag: angiogram


title: Patient_04_mDC

value: peripheral blood

value: mDC

value: nS


title: Patient_03_pDC

value: pDC

value: nM


title: Patient_03_NK

value: NK


title: seedlings, brip12, rep2 (RNA-seq)


title: MSPCs BMAC A 2


title: seedlings, syd, rep2 (RNA-seq)


title: AAVstuffer_low_RPE_1

value: Healthy

value: RPE

tag: eye


title: seedlings, brd1213, rep3 (RNA-seq)


title: seedlings, syd, rep1 (RNA-seq)


title: Patient_04_CD4


title: MSPCs BMAC A 1


title: OIR_hyperoxic_P16_1

value: Retina


title: AAVstuffer_high_retina_4

value: OS

tag: rin

value: stuffer


title: Patient_04_CD8


title: Patient_04_B

value: B


title: AAVstuffer_high_retina_6

value: Y

tag: replicate


title: OIR_hyperoxic_P15_3


title: OIR_hyperoxic_P15_2


title: AAVstuffer_high_RPE_6

value: FALSE

tag: transgene


title: seedlings, brd1213, rep1 (RNA-seq)

value: seedlings


title: seedlings, brd1213, rep2 (RNA-seq)


title: AAVstuffer_high_retina_1

value: OD


title: OIR_hyperoxic_P15_1

value: Hyperoxia 75pc


title: AAVstuffer_high_RPE_5


title: AAVstuffer_high_RPE_3


title: Patient_03_mDC

value: peripheral blood


title: Patient_03_CD4


title: Patient_03_CD8


title: Patient_03_B


title: OIR_hyperoxic_P14_2


title: seedlings, brm, rep1 (RNA-seq)

value: brm-/-


title: OIR_hyperoxic_P14_3


title: Patient_02_pDC

value: vS


title: AAVstuffer_high_RPE_2


title: seedlings, wt, rep3 (RNA-seq)

value: wild type


title: Patient_03_Monocytes

value: Monocytes

value: nM


title: OIR_hyperoxic_P13_3


title: Patient_02_NK

value: NK


title: AAVil6_high_retina_6

value: Retinopathy


title: OIR_hyperoxic_P13_2

value: Retina


title: Patient_02_Monocytes


title: seedlings, brm, rep2 (RNA-seq)


title: seedlings, wt, rep2 (RNA-seq)


title: OIR_hyperoxic_P13_1


title: AAVil6_high_retina_5

value: OS


title: Eva_Tuber_1

city: Davis

first: Patricia

last: Baldrich Gonzalez

state: CA

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

data_processing:
Sequencing adapters were removed using cutadapt (Martin 2011), retaining all reads between 18 and 34 nt in length without undetermined bases (cutadapt -a TGGAATTCTCGGGTGCCAAGG  -m 18 -M 34 -j 0 --max-n 0 -o sample.fastq).
The quality of reads was assessed using FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Assembly: RH potato genome (Zhou et al. 2020)
Supplementary files format and content: Count reads in txt file

organism: Solanum tuberosum

source_name: Tuber

growth_protocol: Desiree and Eva potatoes used in this study were from United States seed growers. To obtain root, leaf, and flower RNA, both cultivars were grown in a room at 16 h light and 22±3°C temperature.

extract_protocol:
Total RNA from leaves, flowers, and roots was extracted from three biological replicates of ground plant tissue TRIreagent (Ambion), following manufacturer’s recommendations. Correspondingly, total RNA from tuber was isolated using the RNeasy Mini kit (Qiagen, USA) following manufacturer’s recommendations, except that using a modified tuber extraction buffer (6 M guanidine hydrochloride, 20 mM MES hydrate, 20 mM EDTA, pH 8, 10% b-mecaptoethanol). Quality and quantity of the extracted RNA was measured by running an RNA denaturing agarose gel, and qubit fluorometer assay.
Small RNA libraries were generated using Somagenics RealSeq®-AC miRNA Library Kit according to the manufacturer's protocol using barcodes.
Libraries were pooled and sequenced using Illumina NextSeq 550 single end sequencing at the University of Delaware DNA Sequencing & Genotyping Center (Newark, DE, USA).

treatment_protocol: Tuber RNA was extracted directly from seed tubers received from growers. Leaf and root RNA was extracted from six-week-old plants while flower RNA was isolated at flowering.

value: Tuber

tag: cultivar

value: Eva


title: AAVil6_high_retina_4

value: Y


title: seedlings, wt, rep1 (RNA-seq)


title: OIR_hyperoxic_P14_1


title: seedlings, brm, rep3 (RNA-seq)


title: Patient_02_mDC

tag: cell type

value: mDC


title: Patient_02_CD8


title: AAVstuffer_high_RPE_1

value: Healthy

value: RPE

tag: treatment

value: FALSE

value: stuffer


title: OIR_hyperoxic_P12_4

value: Hyperoxia 75pc


title: OIR_hyperoxic_P12_3


title: Patient_02_CD4

value: peripheral blood

value: vS


title: OIR_hyperoxic_P12_2


title: Patient_02_B

value: B


title: AAVil6_high_retina_3

tag: disease


title: AAVil6_high_retina_2

tag: tissue

value: OD


title: Eva_Tuber_2


title: Eva_Root_3

source_name: Root

value: Root


title: Patient_01_pDC

value: pDC

value: nS


title: Eva_Root_2


title: OIR_hyperoxic_P12_1

value: Retina

tag: strain


title: OIR_control_P16_3

value: Normoxia 21pc


title: Patient_01_NK

value: NK

tag: phenotype


title: AAVil6_high_RPE_5

value: Retinopathy

value: OS

value: Y

tag: comment

value: Tube was broken after bead homogenization > sample only partially recovered


title: Patient_01_Monocytes

value: Monocytes


title: Eva_Root_1

value: Eva


title: OIR_control_P16_2


title: Eva_Leaf_3

source_name: Leaf

value: Leaf


title: AAVil6_high_RPE_3

value: RPE

value: FALSE


title: Eva_Leaf_2


title: OIR_control_P16_1


title: Patient_01_mDC

value: peripheral blood

value: mDC


title: OIR_control_P15_3


title: Patient_01_CD8


title: Eva_Tuber_3

value: Tuber


title: AAVil6_high_RPE_2

value: OD


title: Eva_Leaf_1


title: Patient_01_CD4

value: nS


title: OIR_control_P15_2

value: Retina


title: AAVil6_high_RPE_6


title: AAVil6_high_retina_1


title: Eva_Flower_2

source_name: Flower

value: Flower


title: AAVil6_high_RPE_1


title: OIR_control_P14_3

value: Normoxia 21pc


title: OIR_control_P14_2


title: AAVil6_high_RPE_4

value: Retinopathy


title: OIR_control_P15_1


title: Eva_Flower_3


title: Patient_01_B

value: B


title: Desiree_Tuber_3

value: Desiree


title: Plasmodium_CLP1

city: xiamen

first: Qingxiang

address: Xiang'an south way

institute: Xiamen University

data_processing:
Basecalls performed using CASAVA version 1.4.
Sequence reads were aligned to the reference genome mm10 by Hisat2
feature-count was used to calculate raw counts.
Assembly: mm10
Supplementary files format and content: Fragment Per Kilobase of exon per Megabase of library size (FPKM) was used as the normalized method

source_name: lymphocytes

extract_protocol:
Total RNA were extracted by TRIzol.
The libraries were prepaered to Illmina sequence as strandard protocol described

treatment_protocol: Plasmodium was stimulated for 4 weeks, then CLP stimulation for 24h.

value: spleen

tag: genotype

value: Wild Type

value: Plasmodium 4 week CLP stimulate 24h


title: Eva_Flower_1

value: Eva


title: Plasmodium3

value: Plasmodium 4 week


title: Desiree_Tuber_2


title: OIR_control_P14_1

tag: time


title: Desiree_Root_3

value: Root


title: Plasmodium2


title: PBS_CLP3

value: PBS CLP stimulate 24h


title: OIR_control_P13_2

tag: timepoint


title: Desiree_Root_2


title: CM_P1_Dot1L_cKO_rep1_H3K27ac_ChIP

city: Milan

first: Paola

last: Cattaneo

address: Via Fantoli 16/15

department: Institute of Genetic and Biomedical Research

country: Italy

institute: National Research Council of Italy

data_processing:
fastq files were aligned to the mouse reference genome (mm10) using Bowtie2
Peak-calling was performed with MACS2
Diffbind was applied to determine the differential binding sites between controls and cKOs
Samtools and deeptools were used to generate bigWig files
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Cardiomyocytes

extract_protocol:
Cardiomyocytes were isolated using collagenase enzymatic reaction and FACS sorted based on the tdTomato fluorescence driven by the XMlc2-Cre. Purified Cardiomyocytes were cross-linked using 1% formaldehyde/PBS for 10 minutes at room temperature, the reactions quenched by adding 2.625 M glycine to 125 mM final 20% BSA to 0.5% final and cells pelleted by centrifugation for 5 minutes at 1,000 g, 4°C. Cells were washed twice with ice-cold 0.5% BSA/PBS and cell pellets were snap-frozen in liquid nitrogen and stored at −80°C. Fixed cells were thawed on ice and resuspended in 100 µl ice-cold RIPA buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 1% IGEPAL CA-630 0.25% Na-Deoxycholate, 0.1 % SDS, 1 mM EDTA, 1 × protease inhibitor cocktail). Chromatin was sheared for 90 minutes on an Active Motif PIXUL high-throughput sonicator using standard settings (Pulse [N]: 50, PRF:1 kHz, Burst Rate: 20 Hz). Two microliter of each lysate was kept to generate ChIP input libraries, and the remainder used to immunoprecipitate H3K27ac-associated DNA by adding 2 μg anti-H3K27ac antibody (Active Motif 39133, lot 31521015) and 20 μl of Dynabeads Protein A (Thermo) and rotating overnight at 8 RPM and 4°C. The next day, beads were collected on a magnet, washed thrice with 150 µl each of ice-cold wash buffer I (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA), wash buffer III (10 mM Tris/HCl pH 7.5, 250 mM LiCl, 1% IGEPAL CA-630, 0.7% deoxycholate, 1 mM EDTA), and twice with TET (10 mM Tris/HCl pH7.5, 1 mM EDTA, 0.2% Tween 20).
Libraries were prepared directly on the antibody/chromatin-bound beads: after the last TET wash, beads were suspended in 25 μl TT (10 mM Tris/HCl pH7.5, 0.05% Tween-20) and libraries were prepared using NEBNext Ultra II reagents according to the manufacturer’s protocol but with reagent volumes reduced by half, using 1 µl of 0.625 µM Bioo Nextflex DNA adapters per ligation reaction. DNA was eluted, proteins digested and crosslinks reversed by adding 4 μl 10% SDS, 4.5 μl 5 M NaCl, 3 μl EDTA, 1 μl proteinase K (20 mg/ml), 20 μl water, incubating for 1 h at 55°C, then overnight at 65°C. DNA was cleaned up by adding 2 μl SpeedBeads 3 EDAC (Cytiva) and 61 μl of 20% PEG 8000/1.5 M NaCl, mixing and incubating for 10 minutes at room temperature. SpeedBeads were collected on a magnet and washed twice by adding 150 μl 80% EtOH for 30 s each, then collecting beads and aspirating the supernatant. After air-drying the SpeedBeads, DNA was eluted with 25 μl TT buffer and the DNA contained in the eluate was amplified for 12 cycles in 50 μl PCR reactions using NEBNext Ultra II PCR master mix and 0.5 μM each of primers Solexa 1GA and Solexa 1GB. Libraries were cleaned up as above by adding 38.5 μl 20% PEG 8000/2.5 M NaCl and 2 μl Speedbeads, washing twice with 150 μl 80% EtOH for 30 s each, air-drying beads and eluting the DNA into 14 μl TT. ChIP library size distributions were estimated by 2% agarose/TBE gel electrophoresis of 2 μl library, and library DNA amounts were measured using a Qubit HS dsDNA kit on a Qubit fluorometer (Thermo). ChIP input material (1 percent of sheared DNA) was digested in 19 µl EB buffer (10 mM Tris pH 8, 0.5% SDS, 5 mM EDTA, 280 mM NaCl) with 1 µl Proteinase K for 1 h at 55°C and crosslinks reversed overnight at 65°C. DNA was cleaned up with 2 μl SpeedBeads 3 EDAC and 36 μl of 20% PEG 8000/1.5 M NaCl and washed with 80% ethanol as described above. DNA was eluted from the magnetic beads in 20 μl TT, DNA concentration determined and libraries prepared from 20 ng input DNA each as described for ChIP samples. Libraries were sequenced single-end for 76 cycles (SE76) to a depth of 15-22 million reads on an Illumina NextSeq 500 instrument.

value: Cardiomyocytes

tag: developmental stage

value: postnatal day P1

value: Black Swiss

tag: chip antibody

value: anti-H3K27ac (Active Motif #39133, lot 31521015)


title: CM_P1_Dot1L_cKO_rep1-2_H3K27ac_input


title: CM_P1_Dot1L_cKO_rep2_H3K27ac_ChIP


title: Plasmodium_CLP3


title: CM_P1_Dot1L_Ctrl_rep2_H3K27ac_ChIP


title: PBS_CLP2


title: Desiree_Leaf_3

value: Leaf


title: OIR_control_P13_1

value: Retina


title: OIR_control_P12_4

value: Normoxia 21pc


title: CM_P1_Dot1L_Ctrl_rep1_H3K27ac_ChIP


title: CM_P1_Dot1L_Ctrl_rep1-2_H3K27ac_input


title: CM_E16_Dot1L_cKO_rep2_H3K27ac_input

value: emrbyonic day E16.5


title: OIR_control_P13_3


title: PBS_CLP1


title: Plasmodium1


title: Desiree_Leaf_2


title: Desiree_Leaf_1


title: CM_E16_Dot1L_cKO_rep1_H3K27ac_input


title: NS3

value: PBS


title: OIR_control_P12_2


title: OIR_control_P12_1


title: NS2


title: CM_E16_Dot1L_cKO_rep1_H3K27ac_ChIP


title: 2nd ktr3Δcap6Δ_Tunicamycin

city: Durham

first: EunJung

last: Thak

address: 2530 erwin rd

institute: eunjungthak

data_processing:
To perform high-throughput sequencing as paired-end 100 sequencing, NovaSeq 6000 (Illumina) was used.
The raw sequencing data was checked quality control using the FastQC. FASTX_Trimmer and BBMap were used to remove adapter and low-quality reads (<Q20), then the TopHat was used to map the trimmed reads with reference genome.
Gene expression levels were estimated using FPKM (fragments per kb per million reads) values, which normalized using EdgeR within R.
RNA-seq analysis was conducted using the ExDEGA (ebiogen).
Assembly: Cryptococcus neoformans var. grubii H99 (assembly CNA3)
Supplementary files format and content: mRNA-seq_Report_gene_processed data files 1/2:
mRNA-seq_Report_gene_processed data file 1  -  sample comparison in replication case (Group comparison 1: H99-plus/ H99-minus, Group comparison 2: KC-plus/ KC-minus)
mRNA-seq_Report_gene_processed data file 2  -  sample comparison in no replication case (comparison 1: H99-plus/ H99-minus, comparison 2: 1stKC-plus/ 1stKC-minus, comparison 3: 1stKC-minus/ 1stH99-minus, comparison 4: 2ndH99-plus/ 2ndH99-minus, comparison 5: 2ndKC-plus/ 2ndKC-minus, comparison 6: 2ndKC-minus/ 2ndH99-minus, comparison 7: 2ndH99-minus/ 1stH99-minus, comparison 8: 2ndH99-plus/ 1stH99-plus, comparison 9: 2ndKC-minus/ 1stKC-minus, comparison 10: 2ndKC-plus/ 1stKC-plus)

organism: Cryptococcus neoformans

source_name: yeast

growth_protocol: WT and mutant strains cells at OD600 (optical density at 600 nm) = 0.15 were cultured into 50 ml of YPD broth at 30°C in a shaking incubator until the OD600 reached 0.8, which is nearly the early phase of exponential growth.

extract_protocol:
The cell pellets were washed with diethyl pyrocarbonate (DEPC)-treated water twice, immediately frozen in liquid nitrogen, and disrupted thoroughly using a mortar and pestle. Total RNAs were extracted using the RNeasy Mini Kit (Qiagen
For RNA-sequencing, the NEBNext Ultra Ⅱ Directional RNA-Seq Kit (NEW ENGLAND BioLabs) was used to prepare libraries. The mRNA was isolated by using the Poly(A) RNA Selection Kit (LEXOGEN) and isolated mRNAs were used for the cDNA synthesis. The Illumina indexes 1–12 were used to perform indexing and enrichment step was carried out.

treatment_protocol: The cells were then treated with 5 ug/ml tunicamycin (TM) and further incubated at 30°C in a shaking incubator for 1 h.

value: Tunicamycin


title: NS1

value: spleen


title: Plas-1

data_processing:
Raw data was trimmed the adaptor by Trim_glore and qulity controlled via fastQC.
The clean reads were aligned to mm10 by bowtie2 and the options were as default.
The Peak identified by MACS2 and options were 'Fold [5,50], p value cut-off 0.01'.
The Bigwig file were built by bamCoverage with effective genome size of 2652783500.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Hematopoietic cell

extract_protocol:
Nuclei prepaed as previously described(William J Greenleaf 2013).
ATAC-seq libraries were prepared following standard protocol as described(Vazyme TD501).

treatment_protocol: Plasmodium was stimulated 6 weeks

value: Bone marrow

value: Hematopoietic cell

tag: cell markers

value: Wild Type


title: Plas-2


title: Desiree_Root_1

value: Desiree


title: 2nd ktr3Δcap6Δ

value: control


title: CM_E16_Dot1L_cKO_rep2_H3K27ac_ChIP


title: OIR_control_P12_3

source_name: Retina cells


title: CM_E16_Dot1L_Ctrl_rep2_H3K27ac_ChIP


title: CM_E16_Dot1L_Ctrl_rep2_H3K27ac_input


title: 2nd H99_Tunicamycin

value: MAT{alpha} (serotype A)


title: Desiree_Flower_3

value: Flower


title: Desiree_Tuber_1

value: Tuber


title: PBS-1


title: 1st ktr3Δcap6Δ_Tunicamycin


title: 2nd H99


title: Desiree_Flower_2


title: Desiree_Flower_1


title: Retina Day 28

city: Chongqing

first: Zongren

last: Xu

state: Chongqing

address: 1 Youyi Road, Yuzhong District, Chongqing, China

department: ophthalmology department

institute: The First Affiliated Hospital of Chongqing Medical University

data_processing:
Single cells were captured using a 10× Chromium System (10× Genomics) with the v2 single cell-reagent kit. The reads were aligned to the mouse genome using the Cell Ranger toolkit (version 2.1.1) provided by 10× Genomics and then used for unique molecular identifier (UMI) counting. Preliminary processing and filtration of single cells were performed using Cell Ranger (version 2.1.1). Generate three files matrix.mtx, genes.tsv and barcodes.tsv.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

source_name: Retina

extract_protocol:
Neuroretinal tissues were collected under a dissecting microscope, and the tissues were rinsed three times with PBS. First, the neuroretinas were digested using 0.25% trypsin for approximately 30 min at 37°C until a single-cell suspension was made. Complete DMEM was then used to neutralize the cell suspension. The single-cell samples were passed through a 40 μm cell strainer. Second, CD45-positive cells were obtained by sorting with magnetic beads. A hemocytometer with trypan blue was used to count the cells and ensure that the cell viability was approximately 90%. Finally, single-cell samples were subjected to scRNA-seq with a high-throughput droplet-mediated scRNA-seq platform (10× Genomics Chromium).
Each retinal tissue sample was diluted to contain approximately 5,000 CD45-positive cells in the appropriate volume. Subsequently, the single-cell suspension, gel beads and oils were added to the 10× Genomics single-cell A chip. After droplet generation, the samples were transferred into 200 μl PCR tubes, and reverse transcription was performed using a T100 Thermal Cycler (Bio-Rad). After reverse transcription, cDNA was recovered using a recovery agent provided by 10× Genomics. SPRIselect beads were used for clean-up of the cDNA, after which the cDNA was amplified for 10 cycles. The concentration of cDNA was detected with a Qubit2.0 fluorometer (Invitrogen). Single-cell cDNA libraries were prepared according to the Chromium Single Cell 3’ Reagent Kit v2 user guide (https://support.10xgenomics.com/single-cell-gene-expression/index/doc/user-guide-chromium-single-cell-3-reagent-kits-user-guide-v2-chemistry).

tag: tag

value: Tissue

tag: age

value: Adult

tag: condition

value: The inflammation response subsided to normal


title: 1st ktr3Δcap6Δ


title: CM_E16_Dot1L_Ctrl_rep1_H3K27ac_input

value: Cardiomyocytes

value: Black Swiss


title: Retina Day 21

value: Retina

value: Inflammation resolution


title: 1st H99_Tunicamycin

value: Tunicamycin


title: CM_E16_Dot1L_Ctrl_rep1_H3K27ac_ChIP

value: emrbyonic day E16.5

value: anti-H3K27ac (Active Motif #39133, lot 31521015)


title: CM_P1_cKO_rep2_input

data_processing:
fastq files were aligned to the mouse reference genome (mm10) using Bowtie2
Peak-calling was performed with MACS2
Diffbind was applied to determine the differential binding sites between controls and cKOs
Samtools and deeptools were used to generate bigWig files and to compute the coverage and fraction of gene body covered by H3K79me2
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: cardiomyocytes

extract_protocol:
Cardiomyocytes were isolated using collagenase enzymatic reaction and FACS sorted based on the tdTomato fluorescence driven by the XMlc2-Cre. Purified Cardiomyocytes were cross-linked using 1% formaldehyde/PBS for 10 minutes at room temperature, the reactions quenched by adding 2.625 M glycine to 125 mM final 20% BSA to 0.5% final and cells pelleted by centrifugation for 5 minutes at 1,000 g, 4°C. Cells were washed twice with ice-cold 0.5% BSA/PBS and cell pellets were snap-frozen in liquid nitrogen and stored at −80°C. Fixed cells were thawed on ice, resuspended in 500 µl ice-cold buffer L2 (0.5% Empigen BB, 1% SDS, 50 mM Tris/HCl pH 7.5, 1 mM EDTA, 1 × protease inhibitor cocktail) and chromatin was sheared to an average DNA size of 300–500 bp by administering 7 pulses of 10 s duration at 13 W power output with 30 s pause on wet ice using a Misonix 3000 sonicator. The lysate was diluted 2.5-fold with ice-cold L2 dilution buffer (20 mM Tris/HCl pH 7.4@20°C, 100 mM NaCl, 0.5% Triton X-100, 2 mM EDTA, 1 × protease inhibitor cocktail), and one percent of the lysate was kept as ChIP input. For each immunoprecipitation, aliquots of diluted lysate equivalent to 150,000 to 1 million cells, 20 μl of Dynabeads Protein A (for rabbit polyclonal antibodies) and 2 μg anti H3K79me2 antibody (Abcam #ab3594) were combined and rotated overnight at 8 RPM and 4°C. The following day, beads were collected on a magnet and washed three times each with wash buffer I (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA), wash buffer III (10 mM Tris/HCl pH 7.5, 250 mM LiCl, 1% IGEPAL CA-630, 0.7% Deoxycholate, 1 mM EDTA) and twice with ice-cold TET (10 mM Tris/HCl pH7.5, 1 mM EDTA, 0.2% Tween-20). Libraries were prepared directly on the antibody/chromatin-bound beads: after the last TET wash, beads were suspended in 25 μl TT (10 mM Tris/HCl pH7.5, 0.05% Tween-20).
Libraries were prepared using NEBNext Ultra II reagents according to the manufacturer’s protocol but with reagent volumes reduced by half. DNA was eluted and crosslinks reversed by adding 4 μl 10% SDS, 4.5 μl 5 M NaCl, 3 μl EDTA, 1 μl proteinase K (20 mg/ml), 20 μl water, incubating for 1 h at 55°C, then overnight at 65°C. DNA was cleaned up by adding 2 μl SpeedBeads 3 EDAC in 61 μl of 20% PEG 8000/1.5 M NaCl, mixing and incubating for 10 minutes at room temperature. SpeedBeads were collected on a magnet, washed twice by adding 150 μl 80% EtOH for 30 s each, collecting beads and aspirating the supernatant. After air-drying the SpeedBeads, DNA was eluted in 25 μl TT and the DNA contained in the eluate was amplified for 12 cycles in 50 μl PCR reactions using NEBNext High-Fidelity 2X PCR Master Mix or NEBNext Ultra II PCR master mix and 0.5 μM each of primers Solexa 1GA and Solexa 1GB. Libraries were cleaned up as above by adding 36.5 μl 20% PEG 8000/2.5 M NaCl and 2 μl Speedbeads, two washes with 150 μl 80% EtOH for 30 s each, air-drying beads and eluting the DNA into 20 μl TT. ChIP library size distributions were estimated following 2% agarose/TBE gel electrophoresis of 2 μl library, and library DNA amounts measured using a Qubit HS dsDNA kit on a Qubit fluorometer. ChIP input material (1 percent of sheared DNA) was treated with RNase for 15 min at 37°C in EB buffer (10 mM Tris pH 8, 0.5% SDS, 5 mM EDTA, 280 mM NaCl), then digested with Proteinase K for 1 h at 55°C and crosslinks reversed at 65°C for 30 min to overnight. DNA was cleaned up with 2 μl SpeedBeads 3 EDAC in 61 μl of 20% PEG 8000/1.5 M NaCl and washed with 80% ethanol as described above. DNA was eluted from the magnetic beads with 25 μl of TT and library prep and amplification were performed as described for ChIP samples. Libraries were sequenced single-end for 75 cycles (SE75) to a depth of 20-25 million reads on an Illumina NextSeq 500 instrument. .

value: cardiomyocytes

value: postnatal day P1


title: CM_P1_cKO_rep2_H3K79me2

value: H3K79me2 (abcam #ab3594)


title: CM_P1_cKO_rep1_input


title: Retina Day 14

value: At the peak of inflammation


title: PBS-2

value: Bone marrow

value: Hematopoietic cell

value: Wild Type

value: PBS


title: Retina Day 0

value: Tissue

value: Adult

value: Normal


title: AT1703 A. thaliana leaves 2 days post S. sclerotiorum inoculation [1703_2dpi_b]

city: Winnipeg

first: Philip

last: Walker

state: Manitoba

address: 104 Dunrobin Avenue

country: Canada

institute: Agriculture and AgriFood Canada

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads trimmed using trimmomatic v 0.36 for adaptor sequence and low-quality reads
Trimmed reads mapped to A. thaliana genome TAIR10 using hisat2
Raw count data was generated using featureCounts
Differential expression analysis performed using deseq2
Assembly: Arabidopsis thaliana TAIR 10 assembly
Supplementary files format and content: tab delimited count data

source_name: leaf tissue

growth_protocol: A. thaliana planted in sunshine mix #1 soil and grown at 22°C under long day conditions (16h light, 8h dark)

extract_protocol:
RNA was isolated using the Ambion RNaqueous micro kit according to manufacturer’s instructions. RNA quality was analyzed using the Agilent 6000 Pico LabChip and Agilent 2100 Bioanalyzer software
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: S. sclerotiorum ascospore inoculum was made by suspending a 1x10^6 spore/mL concentration of spores in a PDB and peptone solution. 10 µL of the solution was transferred onto mature transgenic and wild-type Col-0 A. thaliana leaves at a n = 15 leaves per treatment

value: leaf tissue

tag: agent

value: S. sclerotiorum infected


title: 1st H99

value: MAT{alpha} (serotype A)

value: control


title: AT1703 A. thaliana leaves 2 days post S. sclerotiorum inoculation [1703_2dpi_c]


title: CM_P1_cKO_rep1_H3K79me2

tag: cell type

value: Black Swiss


title: iSLK cells, STOP45-3

city: Guangzhou

first: Ersheng

last: Kuang

state: Guangdong

address: 74 Zhongshan 2nd Rd

department: Zhongshan School of Medicine

institute: Sun Yat-Sen University

data_processing:
The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Under the assumption that the number of reads derived from a gene (or transcript isoform) follows abinomial distribution, DEGseq is proposed based on MA-plot and widely used for differential gene expression analysis. The P-value could be assigned to each gene and adjusted by the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with q≤0.05 and |log2_ratio|≥1 are identified as differentially expressed genes (DEGs)
The KEGG enrichment of DEGs was implemented by the hypergeometric test, in which p-value was adjusted by multiple comparisons as q-value. KEGG terms with q<0.05 were considered to be significantly enriched.
Assembly: Homo_sapiens.GRCh38.94.chr
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

source_name: iSLK cells

extract_protocol:
Discard the supernatant, flash frozen on dry ice, and RNA was harvested using Trizol reagent.NEBNext® Ultra™ RNA Library Prep Kit for Illumina®（Cat #E7530L，NEB)was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: i SLK

value: wild type


title: LSK VaviCre+Rxrabfl/fl

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

data_processing:
For scRNA-Seq (10x Chromium 3’ version 2 chemistry) from Rxrabfl/fl and VaviCre+Rxrabfl/fl BM LSKs, the raw sequence data was aligned to genome version mm10 using Cell Ranger version 2.2.0 to obtain a filtered gene matrix files for further analysis. For Rxrabfl/fl 4,585 cells with 47,193 mean reads reported by Cell Ranger, whereas 4,382 cells with 50,633 mean reads were reported for VaviCre+Rxrabfl/fl LSKs. These filtered matrices were supplied to AltAnalyze version 2.1.4 for joint unsupervised analysis with the software Iterative Cluster and Guide-Gene Selection (ICGS) version 2, using default parameters (PMID: 32207533). ICGS2 identified 12 transcriptionally distinct cell populations, with all clusters containing generally similar proportions of cells from each capture. Cell-type annotations were obtained from ICGS2 biomarker and Gene Ontology gene-set enrichment predictions. UMAP visualization of hematopoietic stem and progenitor markers in AltAnalyze confirmed lineage assignments and suggested further heterogeneity of presumptive HSC-MPPs. To identify putative LT-HSC versus other HSC-MPP populations not in cell-cycle, we further subclustered these HSC-MPP (n=2,280 cells) using ICGS2 using a relaxed required marker gene cluster stability requirement (markerPearsonCutoff=0.20), to find four sub-clusters, denoted by distinct prior annotated HSC-subsets (gene-set enrichment of prior curated HSC marker genes in PMC7579674). For both the sub-clustering and broader LSK clusters, we performed comprehensive cell-population differential comparison analysis with the software cellHarmony (PMID: 31529053), comparing VaviCre+Rxrabfl/fl to Rxrabfl/fl (empirical Bayes t-test p<0.05, FDR corrected).
Genome_build: hg19
Supplementary_files_format_and_content: HDF5 sparse matrices and Excel workbook

source_name: Bone Marrow

extract_protocol:
Cell wer subjected to flow cytrometric sorting of bone marrow lineage-negative Sca1+ CD117+ cells (LSK). Cells were loaded onto a Chromium controller (10x Genomics).
The 10x Genomics Chromium 3’ v2 assay standard protocol was followed as previously described.
Sequencing was performed on the Illumina HiSeq-4000 platform at a target depth of 230 million reads per simple.

value: 5 month-old mice

value: LSK


title: CM_P1_Ctrl_rep2_input

value: cardiomyocytes

value: postnatal day P1


title: iSLK cells, BAC16-3


title: AT1703 A. thaliana leaves 3 days post S. sclerotiorum inoculation [1703_3dpi_b]


title: AT1703 A. thaliana leaves 3 days post S. sclerotiorum inoculation [1703_3dpi_c]


title: AT1703 A. thaliana leaves 2 days post S. sclerotiorum inoculation [1703_2dpi_a]


title: CM_P1_Ctrl_rep2_H3K79me2

value: H3K79me2 (abcam #ab3594)


title: LSK Rxrabfl/fl


title: AT1703 A. thaliana leaves 3 days post S. sclerotiorum inoculation [1703_3dpi_a]


title: CM_P1_Ctrl_rep1_input


title: uninfected AT1703 A. thaliana leaves [1703_0dpi_c]

value: uninfected


title: uninfected AT1703 A. thaliana leaves [1703_0dpi_b]


title: P05K

city: Hamburg

first: Yu

last: Zhao

address: Falkenried 94

department: Institute of Medical Systems Biology

institute: University Medical Center Hamburg-Eppendorf

description: scRNA-seq

library_source: transcriptomic single cell

data_processing:
10x Genomics raw sequencing data were processed using CellRanger software (version 5.0.0, 10x Genomics, Pleasanton, CA) and the human genome hg19-1.2.0 release or mouse mm10-3.0.0 as the reference (function cellranger count). The matrices of cells and the unique molecular identifier (UMI) count were obtained and further processed by the R package Seurat (version 4.0.1).
To remove potential doublets, cutoff values for number of expressed genes (nGene) were determined for samples following visual inspection of the distribution of nGene and nUMI for each cell. The cells with higher nGene values were excluded. We further removed low-quality cells with high mitochondrial genes of all detected genes.
Assembly: hg19-1.2.0 and mm10-3.0.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample (matrix.mtx, barcodes.tsv, features.tsv).

source_name: kidney steroid treated

growth_protocol: For single cell suspension kidneys were dissected and incubated for 40 min at 37°C in RPMI medium (including 0.01 M HEPES; 0.5 mL filtered FBS and 0.4µg/ mL DNase and 8 µg/ mL collagenase D). The samples were homogenized using a gentleMACS (Miltenyi Biotec).

extract_protocol:
Cells were loaded on a 10x Chromium single cell instrument.
All steps were performed according to standard protocol of the Chromium single cell 3' v2 or 5' v1.1 kit to generate high-quality cDNA libraries.

value: kidney T cells

tag: disease

value: ANCA-GN

tag: treatment

value: steroid

tag: patient id


title: uninfected AT1703 A. thaliana leaves [1703_0dpi_a]

tag: tissue


title: P04K

description: scRNA-seq


title: CM_E16_cKO_rep2_input

tag: strain

value: embryonic day E16.5


title: P03K

description: scRNA-seq


title: CM_E16_cKO_rep2_H3K79me2

tag: genotype


title: CM_E16_cKO_rep1_input


title: P02K

description: scRNA-seq


title: CM_E16_cKO_rep1_H3K79me2


title: Col-0 A. thaliana leaves 3 days post S. sclerotiorum inoculation [WT_3dpi_a]

value: leaf tissue


title: Col-0 A. thaliana leaves 3 days post S. sclerotiorum inoculation [WT_3dpi_b]

value: S. sclerotiorum infected


title: TGF_day_12

type: RNA

city: Boston

first: Andrew

last: Emili

address: 72 East Concord St

department: Biochemistry

institute: Boston University

description: mRNA expression

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The arrays were normalized together using the Robust Multiarray Average (RMA) algorithm and a CDF (Chip Definition File) that maps the probes on the array to unique Entrez Gene identifiers

label: biotin

source_name: MCF10A cells treated with TGFbeta for 12 days

label_protocol: standard Affymetrix protocol

growth_protocol: Standard culture conditions for MCF10A

extract_protocol: Qiagen Rneasy kit

treatment_protocol: 10 ng/mL TGFbeta in complete growth medium for indicated time points

value: Normal breast epithelial cell line

value: TGFbeta for 12 days


title: TGF_day_8

description: mRNA expression

source_name: MCF10A cells treated with TGFbeta for 8 days

value: TGFbeta for 8 days


title: TGF_day_6

description: mRNA expression

source_name: MCF10A cells treated with TGFbeta for 6 days

value: TGFbeta for 6 days


title: P01K

description: scRNA-seq


title: TGF_day_4

description: mRNA expression

source_name: MCF10A cells treated with TGFbeta for 4 days

value: TGFbeta for 4 days


title: TGF_day_5

description: mRNA expression

source_name: MCF10A cells treated with TGFbeta for 5 days

value: TGFbeta for 5 days


title: Col-0 A. thaliana leaves 2 days post S. sclerotiorum inoculation [WT_2dpi_b]


title: Col-0 A. thaliana leaves 3 days post S. sclerotiorum inoculation [WT_3dpi_c]


title: CM_E16_Ctrl_rep2_input

value: Black Swiss


title: CM_P1_Ctrl_rep1_H3K79me2

value: cardiomyocytes


title: uninfected Col-0 A. thaliana leaves [WT_0dpi_c]


title: Col-0 A. thaliana leaves 2 days post S. sclerotiorum inoculation [WT_2dpi_a]


title: TGF_day_3

description: mRNA expression

source_name: MCF10A cells treated with TGFbeta for 3 days

value: TGFbeta for 3 days


title: uninfected Col-0 A. thaliana leaves [WT_0dpi_b]


title: THP1 cells stably expressing scrambled siRNA

city: New Delhi

first: Vivek

last: Rao

address: Sukhdev Vihar

department: Immunology and Infectious Disease Biology

country: India

institute: CSIR-Institute of Genomics and Integrative Biology

description: PMA differentited macrophages VR_PA_11

data_processing:
Adaptor sequence and low quality sequence were trimmed using Trimmomatic-0.39
Mapped to hg38 whole genome using STAR
Read counts were generated using HTSeq
Assembly: hg38
Supplementary files format and content: tab-delimited text files with counts for each sample

source_name: THP1 cells

growth_protocol: The cells were cultured in RPMI with 10% fetal bovinbe serum and 1mM sodium pyruvate. Cells were differentiated with 100 nM PMA for 24 hours and rested for 48 hours. Post 72 hours the macrophages were used to extract RNA.

extract_protocol:
Total RNA was extracted using RNAzol reagent. Eluted RNA was treated with turbo Dnase and purified with RNeasy mini kit from Qiagen. 1 μg of total RNA was used library preparation.
Truseq RNA Library Prep Kit protocol was used to prepare the libraries for total RNA sequencing. Briefly mRNAs were fragmented in fragmentation buffer after which cDNA was synthesized using oligo-dT as primers. The complementary strand of the cDNA was synthesized using DNA polymerase I, in dNTPs mixture dTTP was replaced with dUTP. The double stranded DNA was purified using AMPureXP beads. Then the dUTP containing strands were degraded by USER Enzyme, and strands were amplified using PCR and purified using AMPure XP beads. These cDNA libraries used for sequencing.

treatment_protocol: THP1 cells expressing different plasmid contructs

value: human monocytic cell line derived from an acute monocytic leukemia patient

tag: antibiotic selection

value: Neomycin

tag: variation

value: Scrambled siRNA control cells


title: THP1 cells stably expressing siRNA targeting CMPK2

description: PMA differentited macrophages VR_PA_12

value: CMPK2 silenced cells


title: CM_E16_Ctrl_rep2_H3K79me2

tag: developmental stage

value: H3K79me2 (abcam #ab3594)


title: THP1 cells stably expressing CMPK2 tagged with mCherry

description: PMA differentited macrophages VR_PA_10

value: Puromycin

value: CMPK2 overexpressing cells


title: CM_E16_Ctrl_rep1_input

value: embryonic day E16.5

tag: chip antibody


title: THP1 cells stably expressing mCherry

description: PMA differentited macrophages VR_PA_9

value: Vector control cells


title: CM_E16_Ctrl_rep1_H3K79me2


title: cKO IFNγ rgc rep1 [ckoifn1]

status: Public on Nov 10 2022

city: Hong Kong

first: Xu

last: Wang

state: New Territories

address: HKUST

department: LIFS

country: Hong Kong

institute: HKUST

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using TrimGalore with parameters trim_galore -q 20 --phred33 --stringency 5 --length 20 -e 0.1 --paired.
Trimed reads were mapped to GrCM38/mm10 genome using STAR.
Mapped reads (Bam) were quantified using Rsubred package.
Assembly: mm10
Supplementary files format and content: csv file showing raw reads of each sample

source_name: retina

extract_protocol:
Single cells were transfered to lysis buffer and cDNA was captured by oligodT. The smart-seq2 protocol was used for whole transcriptome amplification.
Smart-seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA-seq.

value: retina

value: retina ganglion cell

value: IFNγ injection

value: Ptpn2 KO

value: optiv nerve injury


title: cKO IFNγ rgc rep2 [ckoifn2]


title: TGF_4_hours

description: mRNA expression

source_name: MCF10A cells treated with TGFbeta for 4 hours

value: Normal breast epithelial cell line

value: TGFbeta for 4 hours


title: TGF_day_2

description: mRNA expression

source_name: MCF10A cells treated with TGFbeta for 2 days

value: TGFbeta for 2 days


title: TGF_day_1

description: mRNA expression

source_name: MCF10A cells treated with TGFbeta  for 1 day

value: TGFbeta  for 1 day


title: cKO IFNγ rgc rep3 [ckoifn3]


title: cKO rgc rep2 [cko2]

value: PBS injection


title: uninfected Col-0 A. thaliana leaves [WT_0dpi_a]

value: leaf tissue

value: uninfected


title: IFNγ rgc rep3 [ifn3]

value: wt


title: cKO rgc rep3 [cko3]


title: Untreated_Control

description: mRNA expression

source_name: Untreated MCF10A cells

value: none; untreated


title: IFNγ rgc rep2 [ifn2]


title: cKO rgc rep1 [cko1]


title: IFNγ rgc rep1 [ifn1]


title: BMMSCs_rep4

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Gene expression data from bone marrow mesenchymal stem cells

hyb_protocol: Fragmented cRNA was hybridized for 16 h at 45 ℃ to Affymetrix GeneChip Human Gene 1.0 ST arrays (Affymetrix).

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

data_processing: Data were analyzed by GeneChip Operating Software 1.4.

source_name: Bone marrow mesenchymal stem cells from human

label_protocol: Biotin-labeled, fragmented (B200 nt) cRNA was hybridized to Affymetrix GeneChip Human Gene 1.0 ST arrays (Affymetrix).

growth_protocol: Dental pulp stem cells and bone marrow stem cells were expanded in a GMP-compliant facility with ISO 8 clean room standards equipped with class II and class III bio-safety cabinets and all other standard tissue culture equipment.

extract_protocol: Total RNA was extracted using Trizol Reagent (Life Technologies). Following purification with a RNeasy kit (Qiagen, Valencia, CA, USA)

treatment_protocol: All DPSCs and BMMSCs were seeded in 10 cm2 dishes and cultured until they reached 80 % confluence and used for further analysis.

tag: gender

value: Male

value: bone marrow

value: Bone marrow mesenchymal stem cells


title: wt rgc rep3 [wt3]

value: retina


title: DPSCs_rep4

description: Gene expression data from dental pulp stem cells

source_name: Dental pulp stem cells from human

value: dental pulp

value: Dental pulp stem cells


title: DPSCs_rep2


title: wt rgc rep2 [wt2]

value: retina ganglion cell


title: BMMSCs_rep1


title: DPSCs_rep1


title: BMMSCs_rep3


title: BMMSCs_rep2


title: wt rgc rep1 [wt1]

value: optiv nerve injury


title: SD3

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

data_processing:
Basic read quality was verified using summaries produced by FastQC. Trimmomatic was used to remove low quality reads and bases
The reads for each sample were mapped to the rat (Rnor_6.0) genome using Bowtie2
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 1000 bp windows. The edgeR Pvalue was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR P value less than an arbitrarily chosen threshold were considered DMR. The DMR edges were extended until no genomic window with an edgeR P value less than 0.1 remained within 1000 bp of the DMR.
The selected DMR were then summarized and annotated.
Assembly: Rnor_6.0
Supplementary files format and content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window and other summary values.

organism: Rattus norvegicus

source_name: Sperm

growth_protocol: Female and male rats of an outbred strain Hsd:Sprague Dawley SD (Harlan) at 70 to 100 days of age were fed ad lib with a standard rat diet and ad lib tap water. All animal cages were housed in the same room and environment with gestating females and females with litters being housed individually within cages. Conditions were designed to minimize differences that would cause maternal effects. The breeding of unrelated males and females within specific exposure lineages (interbreeding) was used to optimize the maternal and paternal lineage contributions to the phenotypes observed. No inbreeding within the colonies was performed. Generally, six unrelated breeding pairs at the F0 generation were used to generate the subsequent generations. The gestating female rats exposed to DDT or DMSO were designated as the F0 generation. F1- F3 generation control and exposure lineages were housed in the same room and racks with lighting, food and water. Non-littermate females and males aged 70-100 days from the F1 generation of exposure or control lineages were bred within their treatment group to obtain F2 generation offspring. Unrelated F2 generation rats were bred to obtain F3 generation offspring. No sibling or cousin breeding was used to avoid any inbreeding artifacts. All animals were aged to 1 year for pathology and epigenetic analysis. All experimental protocols for the procedures with rats were pre-approved by the Washington State University Animal Care and Use Committee (IACUC approval # 2568 & 6931).

extract_protocol:
For sperm collection, the epididymis was dissected free of fat and connective tissue, then, after cutting open the cauda, placed into 6 ml of phosphate buffer saline (PBS) for 20 minutes at room temperature. Further incubation at 4ºC will immobilize the sperm. The tissue was then minced, the released sperm pelleted at 4ºC 3,000 x g for 10 min, then resuspended in 250 µL NIM buffer and stored at -80ºC for intracytoplasmic sperm injection or further processing. Adult female SD rats at 6-12 weeks of age with body weight > 125 grams were used as egg donors. These females were superovulated by intraperitoneal injection of 300 IU/kg of Pregnant Mare's Serum Gonadotropin (PMSG), followed by intraperitoneal injection of 300 IU/kg of human Chorionic Gonadotropin (hCG) 48 h later. Mature oocytes (MII stage) were collected from the oviducts 16 h after hCG injection, and freed from cumulus cells by treatment with 0.1% bovine testicular hyaluronidase (Sigma, Cat# H3506) in the M2 medium (Millipore, Cat# MR-015-D) at 37°C for 5 min.  The cumulus-free oocytes were washed and kept in the KSOM-AA medium (Millipore, MR-121-D) in an incubator (Sanyo, Cat# 19AIC) at 37°C with air containing 5% CO2 before ICSI.   For ICSI, sperm frozen in TE buffer (10 mM Tris and 1 mM EDTA, pH 8.0) were thawed at 37°C for 3 min. An aliquot of 2 µl sperm TE suspension was mixed immediately with 50 µl of 4% PVP (Sigma, Cat# P5288) in water (Millipore, Cat# TMS-006-C).  A single sperm head was picked up and injected into the mature oocytes using a glass pipette equipped with a piezo drill under the control of an electric micromanipulator (TransferMan NK2, Eppendorf). Injected oocytes were then transferred to the KSOM+AA medium (Millipore, Cat# MR-121-D) covered by mineral oil and cultured in an incubator at 37°C with humidified air containing 5% CO2. After 24 h of culture in KSOM+AA, embryos were transferred into mR1ECM (Cosmo, CSR-R-M191) for further incubation. Morula stage embryos were collected at 100-104 h post-ICSI and into cryovials (Olympus, Cat#: 27-125), which were snap-frozen in liquid nitrogen followed by storage at -80C until shipment on dry ice for MeDIP-seq. Embryos development were observed at 100-104h and 116-120h after ICSI, and morula stage embryos were collected into cryovials (Olympus, Cat#: 27-125), which were snap-frozen in liquid nitrogen followed by storage at -80C until shipment on dry ice for MeDIP-seq. For molecular analysis, an appropriate amount of rat sperm suspension (approximately 50 µL) was used for DNA extraction. Somatic cell contamination and debris were removed by brief sonication (Fisher Sonic Dismembrator, model 300, power level 25), which destroys the somatic cells, then centrifugation and washing 1-2 times in 1X PBS. The resulting purified sperm pellet was resuspended in 820 µL DNA extraction buffer and 80 µl 0.1M DTT added, then incubated at 65°C for 15 minutes. Proteinase K (80 µl of 20 mg/ml) was added and the sample was incubated at 55°C for 2-3 hours under constant rotation. Protein was removed by addition of protein precipitation solution (300 µl, Promega A795A), incubation for 15 min on ice, then centrifugation at 13,500 ? g for 30 minutes at 4°C. One ml of the supernatant was precipitated with 2 µl of GlycoBlue (Invitrogen, AM9516) and 1 ml of cold 100 % isopropanol. After incubation, the sample was spun at 13,500 ? g for 30 min at 4°C, then washed with 70% cold ethanol. The pellet was air-dried for about 5 minutes then resuspended in 100 µl of nuclease free water. For the MeDIP, genomic DNA was sonicated and run on 1.5% agarose gel for fragment size verification. The sonicated DNA was then diluted with 1X TE buffer to 400 ?l, then heat-denatured for 10 min at 95?C, and immediately cooled on ice for 10 min to create single-stranded DNA fragments. Then 100 ?l of 5X IP buffer and 5?g of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added, and the mixture was incubated overnight on a rotator at 4?C. The following day magnetic beads (Dynabeads M280 Sheep anti-Mouse IgG; Life Technologies 11201D) were pre-washed per manufacturer’s instructions, and 50 ?l of beads were added to the 500 ?l of DNA-antibody mixture from the overnight incubation, then incubated for 2h on a rotator at 4?C. After this incubation, the samples were washed three times with 1X IP buffer using a magnetic rack. The washed samples were then resuspended in 250 ?l digestion buffer (5mM Tris PH 8, 10.mM EDTA, 0.5% SDS) with 3.5 ?l Proteinase K (20 mg/ml), and incubated for 2-3 hours on a rotator at 55?C. DNA clean-up was performed using a Phenol-Chloroform-Isoamyl-Alcohol extraction, and the supernatant precipitated with 2 ?l of GlycoBlue (20 mg/ml), 20 ?l of 5M NaCl and 500 ?l ethanol in -20?C freezer for one to several hours. The DNA precipitate was pelleted, washed with 70% ethanol, then dried and resuspended in 20 ?l H2O or 1X TE. DNA concentration was measured in a Qubit apparatus (Life Technologies) with the ssDNA analysis kit (Molecular Probes Q10212).
MeDIP DNA was used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra RNA Library Prep Kit for Illumina (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA from the single-stranded DNA resulting from MeDIP. After this step, the manufacturer’s protocol was followed indexing each sample individually with NEBNext Multiplex Oligos for Illumina.

treatment_protocol: Timed-pregnant females were mated and on embryonic days 8 through 14 (E8-E14) of gestation were administered daily intraperitoneal injections of the treatment compound (DDT) or vehicle control dimethyl sulfoxide (DMSO). Only the F0 generation received exposure treatments.

tag: treatment group

value: DDT


title: SD4


title: DPSCs_rep3


title: SD1


title: SD2


title: SC3

value: Control


title: B3

city: Hefei

first: Shihai

last: Xing

state: Anhui

address: No.1 Qianjiang Road, Xinzhan District

institute: Anhui University of Chinese Medicine

data_processing:
Raw reads were filtered via SOAPnuke (v1.4.0) by removing reads containing adaptors, poly-N or low quality, and then clean reads were obtained.
Trinity (v2.0.6) was used to assemble the clean reads and Tgicl (v2.0.6) to perform clustering and eliminate redundant data in the assembled transcripts to obtain unique genes. The assembled transcripts were processed for further expression analysis and functional annotation.
Clean reads were mapped to the assembled unique genes by Bowtie2 (v2.2.5)and the expression level of genes were calculated by RSEM (v1.2.8) and normalized to FPKM (Fragments per kilo base of transcript per million mapped reads). Functional annotation of genes was achieved by mapping genes to different databases (NT, NR, KOG, KEGG) using the software BLAST (v2.2.23). GO annotation was performed by Blast2GO (v 2.5.0) with NR annotations. DEseq2 was used to detect DEGs (Different expressed genes), and DEGs with fold change > 2 or <-2 and adjusted P value <= 0.001 were considered to be significantly different expressed genes. GO enrichment analysis and KEGG enrichment analysis were performed using Phyper, a function of R. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value < 0.05).
Assembly: transcript.fa
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Dendrobium huoshanense

source_name: whole seedlings

growth_protocol: Annual plants were randomly selected as experimental materials for freezing stress, and  were cultured at a temperature of 4 ° C, light cycle of 11 h· d-1, light intensity of 1500～ 2000 Lx.

extract_protocol:
75μL EB（0.25M, NaCl; 0.05M, Tris-HCl (pH = 7.5); 20mM, EDTA; 1%(w/v) sodium dodecyl sulphate）, 750μL CI and 30μL β-mercaptoethanol were mixed in a 2.0mL RNase-free micro-centrifuge tube.Grinded tissue samples of the whole D. huoshanense seedlings at about 80 mg with liquid nitrogen into powder and transferred the milled powder samples to 2 mL tubes.  Vortex vigorously. Place at 20˚C for 5 minutes before centrifuging the samples at 4˚C for 5 min at 12000×g.1/10 volume of 3M sodium acetate (pH = 5.2) and 2.5 volume of absolute ethanol were added to the supernatant. Mix gently and incubate at 4˚C for 30 minutes.Centrifuge at 4˚C for 10 min at 12000×g to recover the nucleic acids.200 μL of DEPC-treated water was added to dissolve the nucleic acids and 500μL of 10M LiCl was added to the solution. Mix gently and then place on ice for 60 minutes.Centrifuge at 4˚C for 10 min at 12000×g. Discard the supernatant and wash the pellet with 800μL of 75% (V/V) ethanol. Air-dry in a ventilator for 5-10min.50 μL of DEPC-treated water was added to dissolve RNA.RNA integrity and quality were evaluated by 1% agarose gel electrophoresis and spectrophotometric analysis using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT) attached magnetic beads were used to purified mRNA with eliminating rRNA and tRNA in the total RNA. Purified mRNA of control sample and cold treated samples of the whole D. huoshanense seedlings were fragmented into small pieces with fragment buffer at appropriate temperature. Then, First-strand cDNA was generated by random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. After that, RNA Index Adapters and A-Tailing Mix were added by incubating to end repair. The fragments of cDNA obtained from previous steps were amplified by PCR, and the PCR products were purified by Ampure XP Beads firstly, dissolved in EB solution. The products were validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products obtained from previous steps were heated to denature and circularized by the splint oligo sequence to get the final library, and the single stranded circular DNA (ssCir DNA) was formatted as the final library.
The constructional final library was further amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of each molecular, DNBs were loaded into the patterned nano-array and single end of 50 bases reads were generated on MGI2000 platform (BGI-Shenzhen, China).

treatment_protocol: Annual plants were randomly selected as experimental materials for freezing stress, and the total plants were then collected and frozen in liquid nitrogen at different time points (0 and 7 d) after treatment. All samples had three biological repeats.

value: whole seedlings

value: cold stress treatments


title: B1


title: SC2


title: A3

value: normal growth


title: D1

source_name: Morula


title: A2


title: D3


title: B2


title: SC1


title: D2


title: C3


title: A1


title: C2


title: C1


title: normal, patient 3

city: SHENYANG

first: KAI

last: TAO

state: State

address: Reconstructive and Plastic Surgery, The General Hospital of Northern Theater Command, No. 83, Wenhua Road, Shenhe District

description: Control

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://geneglobe.qiagen.com/cn/analyze/
For the normalization it uses the average of five housekeeping genes: SNORD61, SNORD68, SNORD72, SNORD95, SNORD96A.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: SYBR Green

source_name: skin

label_protocol: RT2 miRNA qPCR Assay were performed using the Custom RT2 PCR Arrays (QIAGEN, Hilden, Germany) following the Manufacturer’s instructions. 400ng RNA was reverse transcribed to cDNA in 20μl system by First Strand cDNA Synthesis Kit for RT-PCR (Merck & Co., Inc., Kenilworth, NJ, USA). Real-time PCR was performed using the Mx3000P real-time PCR system (Thermo Fisher Scientific, Waltham, MA, USA). PCR was carried out as follows: 40 cycles of 94 °C for 15s, 60 °C for 10s and 72 °C for 20s.

growth_protocol: Tumor tissues were collected simultaneously. All the resected samples were placed immediately into liquid nitrogen and stored at - 80°C.

extract_protocol: RNA was extracted by RNA isolation kit (Cat.No.83913, Sigma-Aldrich) per the manufacturer's protocol. 250 ng amount of RNA was reverse transcribed to cDNA by a Reverse Transcription Reaction kit (Qiagen, Hilden, Germany).

tag: disease state

value: normal

tag: Sex

value: male


title: diabetes, patient 3

institute: Reconstructive and Plastic Surgery, The General Hospital of Northern Theater Command, No. 83, Wenhua Road, Shenhe District

description: Test

value: diabetes


title: diabetes, patient 2

description: Test


title: CLB-GAR

type: genomic

city: Gothenburg

first: Susanne

middle: Marie

last: Fransson

address: Medicinaregatan 3

department: Laboratory medicine

country: Sweden

institute: Gothenburg University

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing: Affymetrix GeneChip Command Console

source_name: Cell line CLB-GAR

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines cultured under standard conditions

extract_protocol: Genomic DNA extracted using Qiagen DNA extraction kik

value: CLB-GAR

value: Neuroblastoma


title: NGP

source_name: Cell line NGP

value: NGP


title: CLB-BAR

source_name: Cell line CLB-BAR

value: CLB-BAR


title: CLB-GE

source_name: Cell line CLB-GE

value: CLB-GE


title: CLB-PE

source_name: Cell line CLB-PE

value: CLB-PE


title: diabetes, patient 1

description: Test


title: LS

source_name: Cell line LS

value: LS


title: Patient 57 KGH329

city: Kingston

first: David

last: LeBrun

state: Ontario

address: 88 Stuart street

department: Pathology and Molecular Medicine

institute: Queen's University

description: NanoString codeset was used to enumerate transcripts from 58 KHSC samples. This codeset was designed to quantify expression of 135 genes, including the 92 TCF3 target genes, 35 genes implicated in myelodysplastic syndrome (MDS), and 8 “housekeeping” genes whose expression we expected to be relatively invariant from case to case

hyb_protocol: Transcripts were enumerated using the NanoString nCounter® system (NanoString Technologies, Seattle, WA)

scan_protocol: According to manufacturer's instructions

data_processing: Quality assessment and normalization were performed with NSolver Analysis Software (NanoString Technologies, Inc., v3.0) using geometric mean for background correction and positive control normalization. ARHGAP27, RB1, NRF1, BAALC and ZNF19 showed very low variability among samples and were used as reference genes for normalization. Expression according to probes associated with the same gene (2 probes each for SAMHD1 and EPB41L5) was averaged.

source_name: biopsy

label_protocol: 500 ng of total RNA from each sample was used to enumerate transcripts using the NanoString nCounter® system (NanoString Technologies, Seattle, WA)

extract_protocol: Total RNA was purified from 1 mm cores of FFPE tissue from representative areas of paraffin blocks using the Qiagen AllPrep FFPE kit

tag: diagnosis

value: DLBCL

tag: age at dx

value: F

tag: b symptoms?

value: no

tag: bulky disease?

tag: biopsy site

value: left jugulodigastric LN

tag: ipi score

tag: ecog >= 2

tag: ldh > uln

tag: extranodal sites > 1

tag: Stage

tag: chemotherapy

value: R-CHOP

tag: # of cycles

tag: response chenson

value: complete

tag: relapse?

tag: status

value: Alive

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

tag: ihc myc high?1=yes,0=no

tag: myc fish

value: Translocated

tag: bcl2 fish

tag: coo by lymph2cx

value: ABC

tag: classification

value: Group A

value: FFPE tissue


title: Patient 58 KGH330

tag: diagnosis

tag: age at dx

tag: gender

value: M

tag: b symptoms?

tag: bulky disease?

tag: biopsy site

value: left posterior cervical LN

tag: ipi score

value: yes

value: Normal

value: GCB

value: Group B

tag: tissue


title: IMR32

source_name: Cell line IMR32

tag: cell line

tag: disease state

value: Neuroblastoma


title: normal,patient 1

description: Control

value: normal

tag: Sex

value: male


title: KELLY

source_name: Cell line KELLY

value: KELLY


title: SH-SY-5Y

source_name: Cell line SH-SY-5Y


title: SK-N-SH

source_name: Cell line SK-N-SH

value: SK-N-SH


title: SK-N-DZ

source_name: Cell line SK-N-DZ

value: SK-N-DZ


title: SK-N-FI

source_name: Cell line SK-N-FI

value: SK-N-FI


title: SK-N-BE(2)

source_name: Cell line SK-N-BE(2)


title: Patient 55 KGH327

value: DLBCL

value: F

value: no

value: left neck LN

tag: ecog >= 2

tag: ldh > uln

tag: extranodal sites > 1

tag: Stage

tag: chemotherapy

value: R-CHOP

tag: # of cycles

tag: response chenson

value: complete

tag: relapse?

tag: status

value: Alive

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

value: CNI


title: Patient 56 KGH328

tag: diagnosis

tag: age at dx

tag: gender

tag: b symptoms?

value: yes

tag: bulky disease?

tag: biopsy site

value: left tibia mass

tag: ihc myc high?1=yes,0=no

tag: myc fish

value: Translocated

tag: bcl2 fish

tag: coo by lymph2cx

value: GCB

tag: classification

value: FFPE tissue


title: Patient 53 KGH324

value: inguinal LN

tag: ipi score

tag: ecog >= 2

tag: ldh > uln

tag: extranodal sites > 1

tag: Stage

tag: chemotherapy

tag: # of cycles

value: nd

value: Normal

value: Group B

tag: tissue


title: Patient 54 KGH326

tag: diagnosis

value: DLBCL

tag: age at dx

tag: gender

value: M

value: left inguinal LN

tag: response chenson

tag: relapse?

tag: status

value: Dead

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

value: ABC

value: Group A


title: normal,patient 2

description: Control

tag: disease state

value: normal

tag: Sex

value: male


title: Patient 51 KGH322

tag: b symptoms?

value: no

tag: bulky disease?

value: yes

tag: biopsy site

value: neck LN

tag: ipi score

tag: ecog >= 2

value: R-CHOP

value: complete

value: Alive

tag: ihc myc high?1=yes,0=no

tag: myc fish

tag: bcl2 fish

tag: coo by lymph2cx

tag: classification


title: Patient 52 KGH323

tag: diagnosis

tag: age at dx

tag: gender

value: mesenteric LN

tag: ldh > uln

tag: extranodal sites > 1

tag: Stage

tag: chemotherapy

tag: # of cycles

tag: response chenson

value: CNI

value: Translocated

value: GCB

tag: tissue

value: FFPE tissue


title: SK-N-AS

source_name: Cell line SK-N-AS

tag: cell line

value: SK-N-AS

tag: disease state

value: Neuroblastoma


title: Patient 49 KGH320

value: DLBCL

value: M

tag: b symptoms?

tag: bulky disease?

tag: biopsy site

value: gastric

tag: ipi score

tag: ecog >= 2

tag: relapse?

tag: status

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

tag: ihc myc high?1=yes,0=no

value: Normal

value: Group B


title: Patient 50 KGH321

tag: diagnosis

tag: age at dx

tag: gender

value: F

value: no

value: medial canthus

tag: ldh > uln

tag: extranodal sites > 1

tag: Stage

tag: myc fish

value: nd

tag: bcl2 fish

tag: coo by lymph2cx

tag: classification


title: NB69

source_name: Cell line NB69

tag: cell line

tag: disease state


title: Patient 48 KGH319

tag: b symptoms?

value: yes

tag: bulky disease?

tag: biopsy site

value: pleura

tag: ipi score

tag: ecog >= 2

tag: chemotherapy

value: R-CHOP

tag: # of cycles

tag: response chenson

value: complete

tag: relapse?

value: Alive

value: Unclassified

tag: tissue


title: Patient 45 KGH315

tag: diagnosis

tag: age at dx

tag: gender

value: axilla LN

tag: ldh > uln

tag: extranodal sites > 1

tag: Stage

tag: status

value: Dead

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

tag: ihc myc high?1=yes,0=no

value: Translocated

value: GCB

value: FFPE tissue


title: HCT116 cells, Wild-type transposon and piggyBat replicate 3

city: Bethesda

first: Pavol

last: Genzor

state: MD

address: 6720A Rockledge Drive, Suite 100

department: ACESO

institute: Henry M Jackson Foundation

data_processing:
To generate *_peaks.bed files: The reads were trimmed twice using cutadapt (v3.4), first to remove the seqeuncing adapters, and second time to remove TIR seqeunce. Trimmed reads were alligned to human genome (hg38) using Hisat aligner (v2.2.1.0) using standard settings. Generated bam files were loaded into R using custom function and paired-end reads converted into read fragments. To call peaks, read fragments were used to generate genomic coverage, and any region with at least five reads coverage was considered as a peak and was reported in the *peaks.bed files. For exact methods and custom code please visit related github fount at https://github.com/HaaseLab.
Assembly: GRCh38.p5.v24
Supplementary files format and content: Tab delimited text files in standard bed format with following colums: chromosome, start, end, peakID, peak_area_under_the_curve, strand, peak_maximum_height, peak_width, total_read_fragments_analyzed_in_sample

source_name: Large intestine, colon

extract_protocol:
RNA was extracted using RNaesy Mini Kit (Qiagen #74106).
Total RNA was reverse-transcribed to cDNA using M-MLV (Promega #M3681) and primer SMART-dT18VN (5`-AAGCAGTGGTATCAACGCAGAGTACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN). Next, cDNA was amplified using different pairs of primers containing regions within specific tranpsoson used in this study (see suplemental information) and primer Smart (5`-AAGCAGTGGTATCAACGCAGAGT). Amplified cDNA was purified using PCR gel purification column (Macherey-Nagel #740609) and 500 ng of purified cDNA was was fragmented and tagged using Illumina DNA Prep (Illumina #20060060). Tagged DNA was PCR amplified (Read1-TnME: 5`-ACACTCTTTCCCTACACGACGCTCTTCCGATCTAGATGTGTATAAGAGACA*G; Read2 primer was specific to transposase species, see suplemental information) and amplicons from 100-500 bp were size selected on 2% agarose gel. Dual index primers (NEB #E7780S) for seqeuncing were added by amplifying tagmented libraries usign Q5 Polymerase (NEB #M0544S) following the NEBnext protocol (NEB #E7645S - Section 4.1). The PCR products were purified using AMPure XP beads (Beckman Coulter #A63881) using 0.9x bead volume. The quality of final library was verified using TapeStation.
See the publication 10.1016/j.cell.2020.06.037 for detailed methods to construct library from self-reporting transposons (SRTs).

treatment_protocol: Cells transfected with different self-reporting transposon construct were grown in presence of 3 µg/ml puromycin for two weeks.

value: Large intestine, colon

tag: cell line

tag: cell type

value: colorectal carcinoma

tag: genotype

tag: transfection

value: transfected with self-reporting transposon (SRT)

tag: treatment

value: Wild-type transposon and piggyBat


title: HCT116 cells, Wild-type transposon and piggyBat replicate 2


title: HCT116 cells, Wild-type transposon and piggyBat replicate 1


title: Patient 46 KGH316

value: DLBCL

value: F

tag: b symptoms?

tag: bulky disease?

value: no

tag: biopsy site

value: small bowel resection

tag: ipi score

tag: ecog >= 2

tag: chemotherapy

tag: # of cycles

tag: response chenson

value: partial

tag: relapse?

tag: myc fish

value: Normal

tag: bcl2 fish

value: CNI

tag: coo by lymph2cx

value: ABC

tag: classification

value: Group A


title: Patient 44 KGH313

tag: diagnosis

tag: age at dx

tag: gender

value: M

value: rigt lower lid lump

tag: ldh > uln

tag: extranodal sites > 1

tag: Stage

value: R-CHOP

value: complete

value: yes

tag: status

value: Dead

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

tag: ihc myc high?1=yes,0=no

value: nd

value: Unclassified

tag: tissue


title: HCT116 cells, Symmetric transposon with re-engineered hyperactive piggyBac replicate 3

value: Large intestine, colon

tag: cell line

tag: cell type

value: colorectal carcinoma

tag: genotype

tag: transfection

value: transfected with self-reporting transposon (SRT)

tag: treatment


title: HCT116 cells, Symmetric transposon with re-engineered hyperactive piggyBac replicate 1


title: HCT116 cells, Symmetric transposon with re-engineered hyperactive piggyBac replicate 2


title: Patient 43 KGH312

value: DLBCL

value: F

tag: b symptoms?

value: no

tag: bulky disease?

tag: biopsy site

value: right breast lump

tag: ipi score

tag: ecog >= 2

tag: chemotherapy

tag: # of cycles

tag: response chenson

tag: relapse?

tag: myc fish

tag: bcl2 fish

tag: coo by lymph2cx

value: GCB

tag: classification

value: Group B

value: FFPE tissue


title: Patient 42 KGH310

tag: diagnosis

tag: age at dx

tag: gender

value: M

value: right inguinal LN

tag: ldh > uln

tag: extranodal sites > 1

tag: Stage

tag: status

value: Alive

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

tag: ihc myc high?1=yes,0=no

value: Normal

value: Group A

tag: tissue


title: HCT116 cells, Symmetric transposon with re-engineered piggyBac replicate 2

tag: cell line

tag: cell type

tag: genotype

tag: transfection

tag: treatment


title: HCT116 cells, Symmetric transposon with re-engineered piggyBac replicate 3


title: NB1

source_name: Cell line NB1

tag: disease state

value: Neuroblastoma


title: HCT116 cells, Symmetric transposon with re-engineered piggyBac replicate 1


title: HCT116 cells, Short transposon with hyperactive piggyBac replicate 3


title: Patient 41 KGH309

tag: diagnosis

tag: b symptoms?

tag: bulky disease?

tag: biopsy site

value: right testicle

tag: ipi score

tag: ecog >= 2

tag: chemotherapy

value: R-CHOP

tag: # of cycles

tag: response chenson

value: complete

tag: relapse?

tag: myc fish

value: CNI

tag: bcl2 fish

tag: coo by lymph2cx

value: ABC

tag: classification


title: Patient 40 KGH307

value: DLBCL

tag: age at dx

tag: gender

value: parotid

tag: ldh > uln

tag: extranodal sites > 1

tag: Stage

tag: status

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

tag: ihc myc high?1=yes,0=no

value: Translocated

tag: tissue


title: Patient 47 KGH318

tag: diagnosis

tag: b symptoms?

value: yes

tag: bulky disease?

tag: biopsy site

value: left nek LN

tag: ipi score

tag: ecog >= 2

value: no

tag: chemotherapy

tag: # of cycles

value: partial

value: Dead


title: Patient 39 KGH306

tag: age at dx

tag: gender

value: F

value: left neck

tag: response chenson

tag: relapse?

value: nd

tag: myc fish

tag: bcl2 fish

tag: coo by lymph2cx

value: Unclassified

tag: classification

value: FFPE tissue


title: HCT116 cells, Short transposon with hyperactive piggyBac replicate 2

tag: tissue

value: Large intestine, colon

tag: cell line

tag: cell type

value: colorectal carcinoma

tag: genotype

tag: transfection

value: transfected with self-reporting transposon (SRT)

tag: treatment


title: Patient 38 KGH305

tag: diagnosis

tag: b symptoms?

tag: bulky disease?

tag: biopsy site

value: left neck LN

tag: ipi score

tag: ecog >= 2

tag: ldh > uln

tag: extranodal sites > 1

tag: Stage

value: R-CHOP

value: complete

tag: status

value: Alive

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

tag: ihc myc high?1=yes,0=no

value: Normal

value: GCB

value: Group B


title: HCT116 cells, Short transposon with wild-type piggyBac replicate 2

tag: tissue

tag: cell line

tag: cell type


title: Patient 37 KGH304

value: DLBCL

tag: age at dx

tag: gender

value: M

value: yes

value: no

value: left tonsil

tag: chemotherapy

tag: # of cycles

tag: response chenson

tag: relapse?

tag: myc fish

tag: bcl2 fish

tag: coo by lymph2cx

value: ABC

tag: classification

value: Group A


title: Patient 35 KGH302

tag: diagnosis

tag: b symptoms?

tag: bulky disease?

tag: biopsy site

value: left neck

tag: ipi score

tag: ecog >= 2

tag: ldh > uln

tag: extranodal sites > 1

tag: Stage

value: stable disease

tag: status

value: Dead

value: CNI

value: FFPE tissue


title: Patient 36 KGH303

tag: age at dx

tag: gender

value: left neck mass

tag: chemotherapy

value: R-CHOP

tag: # of cycles

value: complete

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

tag: ihc myc high?1=yes,0=no

value: Translocated

tag: tissue


title: HCT116 cells, Short transposon with wild-type piggyBac replicate 3

value: Large intestine, colon

tag: cell line

tag: cell type

value: colorectal carcinoma

tag: genotype

tag: transfection

value: transfected with self-reporting transposon (SRT)

tag: treatment


title: Patient 33 KGH300

tag: diagnosis

value: DLBCL

value: M

tag: b symptoms?

value: yes

tag: bulky disease?

tag: biopsy site

value: portal LN

tag: ipi score

tag: ecog >= 2

tag: ldh > uln

tag: response chenson

tag: relapse?

tag: myc fish

tag: bcl2 fish

value: Normal

tag: coo by lymph2cx

tag: classification