title: Sth1-AA_Rapamycin_Ino80-ChEC_rep1

value: HHY221 (MATa tor1-1 fpr1::loxP-LEU2-loxP RPL13A-2x FKBP12::loxP ade 2-1 trp1-1 can1-100)  dBAR1::URA3 BrdU::HIS3(HIS+) Sth1-FRB::KAN INO80-MNase::HYG


title: Pa_43840_H

status: Public on Mar 25 2024

type: SRA

city: Milan

first: Pierluigi

last: Di Chiaro

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology (IEO)

library_source: transcriptomic

data_processing:
Reads were pre-processed (quality trimming and adapter clipping) using Trim Galore v0.6.5, then reads with a minimum of 20 bp were aligned to human genome build GRCh38/hg38 using Kallisto v0.46.0 with default parameters and in the correct orientation (--rf-stranded. Only uniquely mapped reads were retained.
Transcript-level expression were summarized to gene level using tximport v1.14.2 R-package and only protein coding genes were retained.
Differential expression analysis was performed using the DESeq2 R-package v1.26.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file providing raw read count values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: tumor

extract_protocol:
FFPE sections (4 μm) were mounted on polyethylene naphthalate membrane (PEN) slides, were deparaffinized in xylene and then partially rehydrated in an ethanol gradient up to 75% EtOH. After that sections were  counterstained with freshly prepared Cresyl Violet for 30 seconds, they were washed twice in 75% EtOH and air dried completely before proceeding to the microdissection using a UV-based LMD7 laser microdissection system (Leica Microsystems) at 20x magnification. Microdissected areas were collected by gravity into strip-tube caps.
Microdissected areas were digested with 10 mU of Proteinase K (ThermoFisher, #AM2546) for 1 hour at 60 C. 1 ml of 5 mM Proteinase K inhibitor (Calbiochem, #539470) was added to stop the reaction and samples were stored at -80 C until library preparation. They were then processed using the SMART-seq Stranded kit (Cat. 634444, protocol version 051018; Takara Bio USA, Inc.) according to the manufacturer’s protocol removing the initial fragmentation step.

tag: disease

value: primary pancreatic ductal adenocarcinoma (PDAC)

tag: tissue

value: tumor

tag: tumor area

value: Non-Gland forming


title: Sth1-AA_Vehicle_Ino80-ChEC_rep2

city: Geneva

first: Sevil

last: Zencir

address: 30, quai Ernest-Ansermet

department: Department of Molecular and Cellular Biology

country: Switzerland

institute: University of Geneva

library_source: genomic

data_processing:
library strategy: ChEC-seq
For MNase-seq, adapters were first removed from the paired-end reads using the Trim Galore Tool with default options from the Galaxy server (Afgan et al., 2018). Paired-end reads were aligned to sacCer3 genome assembly using Bowtie2 (Langmead et al., 2012). PCR duplicates were removed from the analysis. Then, deepTools 2.0 (Ramirez et al., 2016) was used through the bamCoverage function with size selection of fragments of 120–200 bp.
For ChEC-seq samples, adapters were first removed from the paired-end reads using the Trim Galore Tool with default options from the Galaxy server (Afgan et al., 2018). Paired-end reads were aligned to sacCer3 genome assembly using Bowtie2 (Langmead et al., 2012). PCR duplicates were removed from the analysis. Then, deepTools 2.0 (Ramirez et al., 2016) was used through the bamCoverage function with size selection of fragments of 0-200 bp.
Assembly: sacCer3
Supplementary files format and content: bigwig files were obtained using Galaxy server (Afgan et al., 2018).

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol:
MNase-seq: Yeast cells were grown at 30 °C in YEPD to mid-log phase before treatment.
ChEC-seq: Yeast cells were grown at 30 °C in YEPD to mid-log phase before treatment.

extract_protocol:
The ChEC-seq experiments were performed mainly as described in Gill et al. (2020) with following modifications; The yeast cells (at OD600 = 0.5-0.6) were washed once in 1 mL Buffer A [15 mM Tris-HCl pH 7.5, 80 mM KCl, 0.1 mM EGTA, 0.2 mM spermine, 0.5 mM spermidine and protease inhibitor tablet (Sigma-Aldrich)]. Cells were resuspended in 693 μL of buffer A and 7 μL of 10% digitonin (0.1% final concentration) were added to facilitate permeabilization of the cells for 5min at 30 °C. CaCl2 was added (final concentration 5 mM) to activate the MNase cleavage. For each samples 100 μL of cells were collected at 30 s after the induction of MNase digestion and and were immediately mixed with 200 mL of 2X Stop solution (400 mM NaCl, 20 mM EDTA, 4 mM EGTA, 1% SDS). The cells were treated with Proteinase K (0.4  μg/mL final concentration) and incubated at 55 °C for 30 min. The DNA was extracted using PCI extraction, and precipitated with Et-OH by adding 30  μg glycogen. Following to RNase treatment, size selection of DNA fragments was performed as follows; 100 μL of AmpureXP beads (Beckman Coulter) were added in 40 μL of RNase treated DNA and the reaction was mixed by pipetting up and down 10 times. The beads were incubated at room temperature for 5 minutes. The tubes then were placed on the magnetic rack and supernatant was transferred to the new tube containing 10 mM Tris and 0.2 M NaCl for each reaction. The DNA was purified by PCI extraction and Et-OH precipitation.
MNase-seq: NEBnext Ultra DNA library prep kit for Illumina (NEB, E7370L)
NEBnext Ultra DNA library prep kit for Illumina (NEB, E7370L)

treatment_protocol:
MNase-seq: Yeast cells from a fresh plate were grown overnight in YEPD medium at 30°C and diluted to OD600 = 0.3 in YEPD medium next morning. 50 mL of yeast cultures were used for each condition. After one cell cycle, rapamycin (1 μg/ mL, final) was added to corresponding samples at OD600 = 0.6 and incubated for 30 min for anchoring-away of targeted proteins. Nascent DNAs were labelled by addition of 5-Ethynyl-20-deoxyUridine (EdU) at a final concentration of 10 mM for 2 min. After labelling, cells were immediately fixed with formaldehyde at a final concentration of 1% for 15 minutes followed by glycine addition at a final concentration of 125 mM for 5 minutes. For MNase-seq of TSA treated cells, yeast strains were cultured the day before in YEPD medium and next morning they were diluted to OD600 = 0.2 in YEPD. The yeast cells treated with TSA (1 mM, final) for 30 min at OD600 = 0.5.
ChEC-seq: The yeast strains were cultured the day before in YEPD medium and next morning they were diluted to OD600 = 0.2 in YEPD. The 30 min rapamycin treatment (1 μg/ mL, final) was performed for anchoring away of targeted proteins and/or 30 min TSA treatment (1 mM, final) at OD600 = 0.5.

tag: strain

tag: genotype

tag: treatment

value: no rapamycin


title: RNA-24P-2

city: Xiamen

first: Huifen

last: Cao

email: hfcao_bnu@163.com, hfcao@hqu.edu.cn

state: Fujian

address: 668 Jimei Road

department: School of Biomedical Sciences

country: China

institute: Huaqiao University

description: ncRNAseq

data_processing:
SiNGLe method: The genomic site mapping was performed the same way as in the SSiNGLe-ILM protocol (https://protocolexchange.researchsquare.com/article/pex-920/v2) with the two additional filtering steps. One, PCR duplicates were removed. Two, a read-pair was used only if the first base of the read 2 aligned to the reference sequence. The coordinate of  the first aligning base of the read 2 was assigned as the position of the SSB site. SSiNGLe-AP methods: The analysis is identical with the SSiNGLe method except the coordinate of one base upstream of the first aligning base of the read 2 was assigned as the position of the AP site. RNA analysis: Quality-filtered NGS reads were aligned to the genome using RSEM (version 1.2.28). The TPM values for annotated transcripts were estimated using the “rsem-calculate-expression” function of RSEM (version 1.2.28) with a strand-specific strategy.
Assembly: Mm10 (GRCm38) for the mouse reads mapping
Supplementary files format and content: All BED files contain coordinates of SSB or AP sites mapped to mouse genomes. The 4th columns show the number of reads representing the SSB or AP site.
Supplementary files format and content: TPMs for RNA-seq

organism: Mus musculus

source_name: PBMC

extract_protocol:
2 male mice of C57BL/6J strain at 24-month-old were used to extract brains, hearts, livers, bone marrow, PBMCs and sperms. Red cells in bone marrow were removed by Red Blood Cell Lysis Buffer (Beyotime). PBMCs were isolated from blood using Ficoll-Paque PLUS (GE Healthcare). The motile spermatozoa were isolated from the mouse epididymal tail by collecting cells floating in the upper layer of RPMI 1640 (Thermo Fisher Scientific). The isolated tissues were immediately put into liquid nitrogen for quick freezing. The whole organs were cut into small pieces and ground into powder by tissue homogenizer in presence of liquid nitrogen to avoid heating. All ground tissue samples were stored at -80℃ prior to DNA isolation. Genomic DNA from the mouse brain, bone marrow, heart, liver and PBMCs was isolated using TIANamp Genomic DNA kit (Tiangen, DP304) with RNaseA treatment according to the manufacturer’s protocols. Genomic DNA from sperm cells was extracted using Sperm DNA Purification Kit (Simgen, 4202050) following the manufacturer’s instructions. All DNA samples were eluted in UltraPure™ DNase/RNase-Free Distilled Water (Invitrogen), measured the concentration using SMA6000 (Merinton) and stored at -20. Total RNA was isolated with TRNzol (TIANGEN, Beijing).
ncRNAseq:The RNA samples were used for RNA-seq library construction using rRNA depletion and a strand-specific strategy. The library construction and sequencing using the Illumina NovaSeq 6000 platform with the PE150 strategy on the 10-GB scale were outsourced to Novogene Corporation (Beijing).

value: PBMC

tag: development stage

value: 24 months


title: Sth1-AA_Vehicle_Ino80-ChEC_rep1


title: Pa_43840_G


title: U2AF1-WT,sgGPATCH8,seqrun1,rep2

city: New York

first: Jahan

last: Rahman

state: New York

address: 417 E 68th St

department: Center for Hematologic Malignancies

country: USA

institute: Memorial Sloan Kettering

data_processing:
A genome annotation (UCSC hg19/GRCh37) was created by combining the UCSC knownGene (PMID: 24270787), Ensembl 71 (PMID: 23203987), and MISO v2.0 (PMID: 21057496) annotations. Transcriptome mapping was accomplished using RSEM v1.2.4 (PMID: 21816040) with the argument ‘‘-v 2’’ which indicates Bowtie invocation (PMID: 19261174). Unaligned reads were mapped to the genome with TopHat v2.0.8b (PMID: 19289445), and to a custom annotation which includes all gene-level pairwise combinations of annotated 5’ and 3’ splice sites. The combined RSEM/Bowtie and TopHat alignments were inputted to MISO v2.0 (PMID: 21057496) to quantify isoform expression levels.
Assembly: hg19
Supplementary files format and content: tab-delimited text-files include raw isoform counts for each sample: isoform.expression.1.txt, isoform.expression.2.txt, isoform.expression.3.txt, isoform.expression.4.txt

molecule: polyA RNA

extract_protocol:
For cell line RNA sequencing (RNA-seq), RNA was extracted from K562 and293Tcells using the Qiagen RNeasy extraction kit, according to the manufacturer’s instructions. A minimum of 500 ng of high-quality RNA (as determined by Agilent Bioanalyzer) per replicate was used as input for library preparation.
Poly(A)-selected, strand-specific (dUTP method) Illumina libraries were prepared by the Integrated Genomics Operation (IGO) at Memorial Sloan Kettering with a modified TruSeq protocol and sequenced on the Illumina HiSeq 2000 to obtain∼60-80M paired-end 100 bp reads per sample.

tag: cell line


title: Ino80-ChEC_PlusTSA_rep2

value: treated with TSA (1 mM final) for 30 min


title: RNA-24P-1

description: ncRNAseq


title: control, lung (C3_DCL11)

city: Fuzhou

first: Zhimin

last: Chen

address: Chazhong Road NO.20

institute: the First Affiliated Hospital, Fujian Medical University, Fuzhou

description:
C3_DCL11
lung_data_matrix.txt

library_source: transcriptomic single cell

data_processing:
The data matrix processed by Seurat is output through R language
Assembly: mm10
Supplementary files format and content: tab delimited text file includes data value for each sample

source_name: lung

extract_protocol:
Harvested cells at the required densities were combined with gel beads  containing the barcoded information along with a mixture of cells and  enzymes. Oil surfactant droplets in a microfluidic double-cross system were used for encapsulation to generate Gel Beads-In-Emulsions (GEMs). GEMs were passed through a reservoir and collected while the gel beads were lysed to release the barcode sequence.
The cDNA fragment was then reverse transcribed before the sample was labeled. The gel beads and the oil droplets are ruptured and PCR amplification was performed using the generated cDNA as a template. The products of all GEMs were mixed and a standard sequencing library is constructed. The cDNA was first enzymatically digested into fragments of about 200300 base pairs (bp), together with the library building process of traditional secondgeneration sequencing such as sequencing junction and primers. Finally, the DNA library was generated by PCR amplification

value: lung

value: wild type

value: control


title: U2AF1-S34F,sgRenilla,seqrun1,rep2


title: Pa_43840_F


title: RNA-24L-2

description: ncRNAseq

source_name: Liver

value: Liver


title: Pa_44228_G


title: Ino80-ChEC_PlusTSA_rep1


title: Pa_32572_F


title: U2AF1-S34F,sgGPATCH8,seqrun1,rep1


title: RNA-24L-1

description: ncRNAseq


title: Sth1-AA_Rapamycin_Ino80-ChEC_rep2

value: 30 minutes rapamycin (1  μg/ml final)


title: RNA-24S-1

description: ncRNAseq

source_name: Sperm

value: Sperm


title: Pa_32572_E


title: U2AF1-S34F,sgRenilla,seqrun1,rep1


title: Ino80-ChEC_MinusTSA_rep2

value: no TSA


title: RNA-24H-2

description: ncRNAseq

source_name: Heart

value: Heart


title: Ino80-ChEC_MinusTSA_rep1


title: U2AF1-WT,sgGPATCH8,seqrun1,rep1


title: RNA-24H-1

description: ncRNAseq


title: Pa_37672_G


title: Pa_44053_F


title: Sth1-ChEC_PlusTSA_rep2

value: HHY221 (MATa tor1-1 fpr1::loxP-LEU2-loxP RPL13A-2x FKBP12::loxP ade 2-1 trp1-1 can1-100)  dBAR1::URA3 BrdU::HIS3(HIS+) Sth1-Flag-MNase::HYG


title: U2AF1-WT,sgRenilla,seqrun1,rep1


title: RNA-24B-2

description: ncRNAseq

source_name: Brain

value: Brain


title: Pa_47691_F

value: primary pancreatic ductal adenocarcinoma (PDAC)


title: RNA-24B-1

description: ncRNAseq


title: U2AF1-WT,sgRenilla,seqrun1,rep2


title: Sth1-ChEC_PlusTSA_rep1


title: SRSF2-P95H,sgGPATCH8,seqrun2,rep3


title: SRSF2-P95H,sgGPATCH8,seqrun1,rep3


title: RNA-24M-2

description: ncRNAseq

source_name: Bone marrow

value: Bone marrow


title: Sth1-ChEC_MinusTSA_rep2


title: Pa_30866_H

value: tumor

value: Non-Gland forming


title: RNA-24M-1

description: ncRNAseq


title: SRSF2-P95H,sgRenilla,seqrun1,rep3


title: FreeMNase_2min

data_processing:
For MNase-seq, adapters were first removed from the paired-end reads using the Trim Galore Tool with default options from the Galaxy server (Afgan et al., 2018). Paired-end reads were aligned to sacCer3 genome assembly using Bowtie2 (Langmead et al., 2012). PCR duplicates were removed from the analysis. Then, deepTools 2.0 (Ramirez et al., 2016) was used through the bamCoverage function with size selection of fragments of 120–200 bp.
For ChEC-seq samples, adapters were first removed from the paired-end reads using the Trim Galore Tool with default options from the Galaxy server (Afgan et al., 2018). Paired-end reads were aligned to sacCer3 genome assembly using Bowtie2 (Langmead et al., 2012). PCR duplicates were removed from the analysis. Then, deepTools 2.0 (Ramirez et al., 2016) was used through the bamCoverage function with size selection of fragments of 0-200 bp.
Assembly: sacCer3
Supplementary files format and content: bigwig files were obtained using Galaxy server (Afgan et al., 2018).

extract_protocol:
The MNase-seq experiments were performed mainly as described in Gill et al. (2020) with the following modifications; For chromatin extraction, frozen cell pellets were resuspended in 600 mL cell lysis buffer (50 mM HEPES-KOH, pH 7.5, 140mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate, supplemented with 1 mM PMSF and EDTA-free protease inhibitors) mechanically lysed by bead beating. The cell extract was then centrifuged at 13,000 rpm for 30 min at 4˚C to collect chromatin. The chromatin was resuspended in 600 mL of NP buffer (0.5 mM Spermidine, 50 mM NaCl, 1mM b-mercaptoethanol, 0.075% NP-40, 10 mM Tris-HCl pH 7.4, 5 mM  μgCl2, 1 mM CaCl2) per reaction. The DNA concentration was measured using Qubit dsDNA BR assay kit (Invitrogen). Chromatin was diluted to »20 -30  μg/mL using NP buffer to adjust chromatin density in each reaction. MNase treatment was performed using 0.5 μL of MNase (ThermoScientific 100 units/mL), incubated at 37°C and 100 mL of digestion product was aliquoted for different time points (3, 6, 9 min). The MNase digestion was stopped by adding a stop buffer (20 mM EDTA, 0.5 % SDS, 0.5  μg/mL proteinase-K) in the reaction and incubated first at 42°C for 1 h and then at 65°C for overnight. After reversal of crosslinking, DNA was extracted with phenol- chloroform-iso amyl alcohol (PCI), treated with RNase and visualized on 2.5% agarose gel. The nucleosomal DNA sample for the best MNase digestion time point was purified again with PCI extraction before proceeding further steps.
MNase-seq: NEBnext Ultra DNA library prep kit for Illumina (NEB, E7370L)
NEBnext Ultra DNA library prep kit for Illumina (NEB, E7370L)

value: no rapamycin


title: Pa_30866_G


title: Pa_30866_F


title: Sth1-ChEC_MinusTSA_rep1


title: SRSF2-WT,sgGPATCH8,seqrun1,rep3


title: Sth1-AA_Ino80-AA_EdU_Rapamycin_rep2

value: HHY221 (MATa tor1-1 fpr1::loxP-LEU2-loxP RPL13A-2x FKBP12::loxP ade 2-1 trp1-1 can1-100)  dBAR1::URA3 BrdU::HIS3(HIS+) Sth1-FRB::KAN INO80-FRB::NAT

value: treated with rapamycin (1  μg/ml final) for 30 min and then with EdU (10 mM final) for 2 min


title: 24-S-1

description: AP site profiling

data_processing:
SiNGLe method: The genomic site mapping was performed the same way as in the SSiNGLe-ILM protocol (https://protocolexchange.researchsquare.com/article/pex-920/v2) with the two additional filtering steps. One, PCR duplicates were removed. Two, a read-pair was used only if the first base of the read 2 aligned to the reference sequence. The coordinate of  the first aligning base of the read 2 was assigned as the position of the SSB site. SSiNGLe-AP methods: The analysis is identical with the SSiNGLe method except the coordinate of one base upstream of the first aligning base of the read 2 was assigned as the position of the AP site. RNA analysis: Quality-filtered NGS reads were aligned to the genome using RSEM (version 1.2.28). The TPM values for annotated transcripts were estimated using the “rsem-calculate-expression” function of RSEM (version 1.2.28) with a strand-specific strategy.
Assembly: Mm10 (GRCm38) for the mouse reads mapping
Supplementary files format and content: All BED files contain coordinates of SSB or AP sites mapped to mouse genomes. The 4th columns show the number of reads representing the SSB or AP site.
Supplementary files format and content: TPMs for RNA-seq
Library strategy: SSiNGLe-AP

value: 24 months


title: SRSF2-WT,sgRenilla,seqrun1,rep3


title: 24-S-2

description: AP site profiling


title: Sth1-AA_Ino80-AA_EdU_Rapamycin_rep1


title: Pa_36203_F


title: 24-P-2

description: AP site profiling

value: PBMC


title: SRSF2-P95H,sgGPATCH8,seqrun1,rep2


title: Sth1-AA_Ino80-AA_EdU_Vehicle_rep2

value: no rapamycin, treated with EdU (10 mM final) for 2 min


title: Pa_36203_E


title: SRSF2-P95H,sgRenilla,seqrun1,rep2


title: Pa_36203_D


title: 24-P-1

description: AP site profiling


title: Sth1-AA_Ino80-AA_EdU_Vehicle_rep1


title: SRSF2-WT,sgGPATCH8,seqrun1,rep2


title: Sth1-AA_Ino80-AA_Input_Rapamycin_rep2


title: 24-L-2

description: AP site profiling

value: Liver


title: 24-L-1

description: AP site profiling


title: SRSF2-WT,sgRenilla,seqrun1,rep2


title: Sth1-AA_Ino80-AA_Input_Rapamycin_rep1

value: 30 minutes rapamycin (1  μg/ml final)


title: Pa_3791_C


title: 24-H-2

description: AP site profiling


title: Pa_37_C


title: Sth1-AA_Ino80-AA_Input_Vehicle_rep2


title: SRSF2-P95H,sgRenilla,seqrun1,rep1


title: Pa_1860_H


title: SRSF2-P95H,sgGPATCH8,seqrun1,rep1


title: 24-H-1

description: AP site profiling


title: Sth1-AA_Ino80-AA_Input_Vehicle_rep1


title: Pa_12_F


title: SRSF2-WT,sgGPATCH8,seqrun1,rep1


title: Ino80-AA_EdU_Rapamycin_rep1

value: HHY221 (MATa tor1-1 fpr1::loxP-LEU2-loxP RPL13A-2x FKBP12::loxP ade 2-1 trp1-1 can1-100)  dBAR1::URA3 BrdU::HIS3(HIS+) INO80-FRB::KAN


title: Pa_11_H


title: Pa_27_F


title: SRSF2-WT,sgRenilla,seqrun1,rep1


title: 24-B-1

description: AP site profiling


title: 24-B-2

description: AP site profiling


title: Ino80-AA_EdU_Vehicle_rep2


title: Pa_43840_E

value: Gland forming


title: 24-M-1

description: AP site profiling


title: Pa_38_G


title: 24-M-2

description: AP site profiling


title: Ino80-AA_EdU_Vehicle_rep1


title: Ino80-AA_Input_Rapamycin_rep2


title: SSB 24-S-2

description: SSB profiling from the same sample, 24-S-2, used for AP site and transcriptome profiling

data_processing:
SiNGLe method: The genomic site mapping was performed the same way as in the SSiNGLe-ILM protocol (https://protocolexchange.researchsquare.com/article/pex-920/v2) with the two additional filtering steps. One, PCR duplicates were removed. Two, a read-pair was used only if the first base of the read 2 aligned to the reference sequence. The coordinate of  the first aligning base of the read 2 was assigned as the position of the SSB site. SSiNGLe-AP methods: The analysis is identical with the SSiNGLe method except the coordinate of one base upstream of the first aligning base of the read 2 was assigned as the position of the AP site. RNA analysis: Quality-filtered NGS reads were aligned to the genome using RSEM (version 1.2.28). The TPM values for annotated transcripts were estimated using the “rsem-calculate-expression” function of RSEM (version 1.2.28) with a strand-specific strategy.
Assembly: Mm10 (GRCm38) for the mouse reads mapping
Supplementary files format and content: All BED files contain coordinates of SSB or AP sites mapped to mouse genomes. The 4th columns show the number of reads representing the SSB or AP site.
Supplementary files format and content: TPMs for RNA-seq
Library strategy: SSiNGLe

value: Sperm


title: Pa_32572_D


title: SSB 24-P-2

description: SSB profiling from the same sample, 24-P-2, used for AP site and transcriptome profiling


title: SSB 24-S-1

description: SSB profiling from the same sample, 24-S-1, used for AP site and transcriptome profiling


title: Ino80-AA_Input_Rapamycin_rep1


title: Input-K562-Ctr-IFN

city: Bethesda

first: Gary

last: Felsenfeld

address: 9000 Rockville Pike

institute: NIH

description: Input

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie2. Peaks were called using MACS2. Bigwig files were generated with Deeptools.
Assembly: Reads were mapped to hg19 whole genome using bowtie2. Peaks were called using MACS2. Bigwig files were generated with Deeptools.
Supplementary files format and content: Processed data files are in bigwig format

source_name: bone marrow

growth_protocol: HAP1 control cells and MAZ KO cells are cultured in IMDM with 10% FBS and 1% Pen/Strep. K562 control cells and MAZ knocking down cells were grown in RPMI 1640 medium (Invitrogen) supplemented with 10% fetal bovine serum, 10 mM HEPES (pH 7.3), and 1% penicillin-streptomycin.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed with a ChIP-IT Express kit.
ChIP-Seq libraries were prepared using the “NEBNext® Ultra™ II DNA Library Prep Kit”. MeDIP-Seq libraries were prepared using MagMeDIP-seq Package V2 MeDIP-seq library prep. kit. RNA-Seq Libraries were prepared with NEBNext® UltraTM Directional RNA Library Prep Kit.

treatment_protocol: HAP1 control cells and MAZ knocking out cells were purchased from Horizon Discovery. Knockdown of MAZ in K562 cells was conducted by using an electroporation system. SiRNAs against MAZ  were On-TARGET plus SMARTpool siRNA oligonucleotides purchased from Dhmarcon Inc.

value: bone marrow

tag: cell type

value: erythroleukemia

tag: chip antibody

value: Inp

value: IFNg treated


title: Ino80-AA_EdU_Rapamycin_rep2


title: Input-K562-siMAZ

description: Input

value: untreated


title: Input-K562-siMAZ-IFN

description: Input


title: Ino80-AA_Input_Vehicle_rep2


title: Pa_32572_C

value: primary pancreatic ductal adenocarcinoma (PDAC)

value: tumor


title: SSB 24-P-1

description: SSB profiling from the same sample, 24-P-1, used for AP site and transcriptome profiling


title: Pa_47691_C


title: MAZ-ChIPseq-K562-siMAZ

description: ChIP-Seq


title: MAZ-ChIPSeq-K562-Ctr-IFN

description: ChIP-Seq


title: Pa_30866_D


title: Ino80-AA_Input_Vehicle_rep1

value: no rapamycin


title: Sth1-AA_EdU_Rapamycin_rep2

value: HHY221 (MATa tor1-1 fpr1::loxP-LEU2-loxP RPL13A-2x FKBP12::loxP ade 2-1 trp1-1 can1-100)  dBAR1::URA3 BrdU::HIS3(HIS+) Sth1-FRB::KAN

value: treated with rapamycin (1  μg/ml final) for 30 min and then with EdU (10 mM final) for 2 min


title: Pa_32572_H


title: SSB 24-L-2

description: SSB profiling from the same sample, 24-L-2, used for AP site and transcriptome profiling

value: 24 months


title: Pa_29919_F


title: MAZ-ChIPSeq-k562-Ctr

description: ChIP-Seq


title: Pa_26967_C


title: Sth1-AA_EdU_Rapamycin_rep1


title: SSB 24-L-1

description: SSB profiling from the same sample, 24-L-1, used for AP site and transcriptome profiling


title: MAZ-ChIPSeq-HAP1-MAZko-IFN-2

description: ChIP-Seq

value: myelogenous leukemia


title: SSB 24-H-2

description: SSB profiling from the same sample, 24-H-2, used for AP site and transcriptome profiling

value: Heart


title: MAZ-ChIPSeq-K562-siMAZ-IFN

description: ChIP-Seq


title: Sth1-AA_EdU_Vehicle_rep2

value: no rapamycin, treated with EdU (10 mM final) for 2 min


title: SSB 24-H-1

description: SSB profiling from the same sample, 24-H-1, used for AP site and transcriptome profiling


title: Sth1-AA_EdU_Vehicle_rep1


title: Pa_36203_B


title: SSB 24-B-2

description: SSB profiling from the same sample, 24-B-2, used for AP site and transcriptome profiling

value: Brain


title: MAZ-ChIPSeq-HAP1-MAZko-IFN-1

description: ChIP-Seq


title: MAZ-ChIPSeq-HAP1-MAZko-2

description: ChIP-Seq


title: Pa_36203_A

value: Gland forming


title: Sth1-AA_Input_Rapamycin_rep2

value: 30 minutes rapamycin (1  μg/ml final)


title: Pa_3791_G


title: SSB 24-B-1

description: SSB profiling from the same sample, 24-B-1, used for AP site and transcriptome profiling


title: MAZ-ChIPseq-HAP1-MAZko-1

description: ChIP-Seq

value: bone marrow


title: Sth1-AA_Input_Rapamycin_rep1


title: Pa_3791_F


title: MAZ-ChIPSeq-HAP1-P-IFN-2

description: ChIP-Seq


title: Input-K562-Ctr

description: Input

value: erythroleukemia


title: SSB 24-M-2

description: SSB profiling from the same sample, 24-M-2, used for AP site and transcriptome profiling

value: Bone marrow


title: MAZ-ChIPSeq-HAP1-P-IFN-1

description: ChIP-Seq

value: IFNg treated


title: SSB 24-M-1

description: SSB profiling from the same sample, 24-M-1, used for AP site and transcriptome profiling


title: Sth1-AA_Input_Vehicle_rep1


title: Pa_26768_G


title: Pa_26768_F


title: Rsc3-AA_EdU_Rapamycin_rep2

value: HHY221 (MATa tor1-1 fpr1::loxP-LEU2-loxP RPL13A-2x FKBP12::loxP ade 2-1 trp1-1 can1-100)  dBAR1::URA3 BrdU::HIS3(HIS+) Rsc3-FRB::KAN


title: OCT6_KO_EpiLCs_Rep3

city: Belen de Escobar

first: Santiago

last: Miriuka

state: Buenos Aires

address: Ruta 9 Km 52.5

department: LIAN-CONICET

country: Argentina

institute: FLENI

data_processing:
Quality checked reads (FastQC) were processed in Fastp tool to remove any leftover adapters and low-quality ends.
Processed reads were mapped to the mouse reference genome (GRCm39/mm39) using STAR aligner in two-pass mode, producing gene abundance quantification as well.
Raw counts were then fed into DESeq2 for differential expression analysis (fdr<0.1)
Assembly: GRCm39
Supplementary files format and content: raw counts file

source_name: 46C mESCs (Oct6-KO)

growth_protocol: Undifferentiated mESCs were cultured in N2B27 defined medium with 2i+LIF in gelatin-coated dishes. Differentiation to EpiLCs was performed by culturing WT or KO cells in N2B27 supplemented with 1%KSR, 12 ng/ml bFGF and 20 ng/ml ActivinA for 48h in fibronectin-coated dishes

extract_protocol:
Cells were washed once in PBS and whole cell lysates were prepared using Trizol reagent (Invitrogen). Total RNA was obtained according to manufacturer specifications.
Total RNA was used to prepare libraries with TruSeq Stranded Total RNA LT Sample Prep Kit (Gold) (Illumina) according to the TruSeq Stranded Total RNA Sample Prep Guide, Part # 15031048 Rev. E protocol, followed by paired-end sequencing

treatment_protocol: WT and Oct6 KO mESCs were differentiated for 48h to EpiLCs

value: 46C mESCs (Oct6-KO)


title: MAZ-ChIPSeq-HAP1-P-2

description: ChIP-Seq

value: untreated


title: WT_EpiLCs_Rep3

source_name: 46C mESCs (WT)

value: 46C mESCs (WT)

value: Wild-type


title: Pa_23_A

value: primary pancreatic ductal adenocarcinoma (PDAC)

value: tumor


title: Rsc3-AA_EdU_Rapamycin_rep1

value: treated with rapamycin (1  μg/ml final) for 30 min and then with EdU (10 mM final) for 2 min


title: MAZ-ChIPSeq-HAP1-P-1

description: ChIP-Seq

value: myelogenous leukemia


title: STAT1-ChIPSeq-K562-siMAZ-IFN-2

description: ChIP-Seq


title: Rsc3-AA_EdU_Vehicle_rep2

value: no rapamycin, treated with EdU (10 mM final) for 2 min


title: WT_EpiLCs_Rep2


title: Pa_06_E


title: STAT1-ChPSeq-K562-siMAZ-IFN-1

description: ChIP-Seq


title: Rsc3-AA_EdU_Vehicle_rep1


title: Pa_22_H


title: Pa_01_B


title: STAT1-CHIPSeq-K562-siMAZ-2

description: ChIP-Seq


title: OCT6_KO_EpiLCs_Rep1


title: Sth1-AA_Input_Vehicle_rep2

value: HHY221 (MATa tor1-1 fpr1::loxP-LEU2-loxP RPL13A-2x FKBP12::loxP ade 2-1 trp1-1 can1-100)  dBAR1::URA3 BrdU::HIS3(HIS+) Sth1-FRB::KAN

value: no rapamycin


title: STAT1-ChIPSeq-K562-siMAZ-1

description: ChIP-Seq


title: WT_EpiLCs_Rep1


title: Rsc3-AA_Input_Rapamycin_rep1

value: 30 minutes rapamycin (1  μg/ml final)


title: Pa_37672_F

value: Non-Gland forming


title: STAT1-ChIPSeq-K562Ctr-IFN-2

description: ChIP-Seq

value: bone marrow

value: erythroleukemia


title: Pa_47691_H


title: Rsc3-AA_Input_Vehicle_rep2


title: Rsc3-AA_Input_Vehicle_rep1


title: STAT1-ChIPSeq-K562-Ctr-IFN-1

description: ChIP-Seq

value: IFNg treated


title: OCT6_KO_EpiLCs_Rep2


title: Pa_47691_G


title: STAT1-ChIPSeq-K562-Ctr-2

description: ChIP-Seq


title: Reb1-AA_EdU_Rapamycin_rep2

value: HHY221 (MATa tor1-1 fpr1::loxP-LEU2-loxP RPL13A-2x FKBP12::loxP ade 2-1 trp1-1 can1-100)  dBAR1::URA3 BrdU::HIS3(HIS+) Reb1-FRB::KAN


title: Pa_1860_G


title: STAT1-ChIPSeq-K562-Ctr-1

description: ChIP-Seq


title: Rsc3-AA_Input_Rapamycin_rep2

value: HHY221 (MATa tor1-1 fpr1::loxP-LEU2-loxP RPL13A-2x FKBP12::loxP ade 2-1 trp1-1 can1-100)  dBAR1::URA3 BrdU::HIS3(HIS+) Rsc3-FRB::KAN


title: Input-ChIPseq-HAP1-MAZko-IFN

description: Input

value: Inp


title: Reb1-AA_EdU_Rapamycin_rep1


title: Pa_37672_H


title: Input-HAP1-MAZko

description: Input

value: untreated


title: Reb1-AA_EdU_Vehicle_rep1


title: Pa_10663_H


title: Input-HAP1-P-IFN

description: Input


title: Reb1-AA_Input_Rapamycin_rep2


title: Pa_3791_E


title: Input-HAP1-P

description: Input


title: Pa_32572_G


title: Reb1-AA_Input_Rapamycin_rep1


title: Reb1-AA_EdU_Vehicle_rep2


title: Reb1-AA_Input_Vehicle_rep2


title: STAT1-ChIPSeq-HAP1-MAZko-IFN-2

description: ChIP-Seq


title: STAT1-ChPSeq-HAP1-MAZko-IFN-1

description: ChIP-Seq


title: Pa_44054_H


title: Reb1-AA_Input_Vehicle_rep1


title: Pa_26967_E


title: Pa_44054_G


title: STAT1-ChIPSeq-HAP1-MAZko-2

description: ChIP-Seq


title: Pa_10663_G


title: Pa_44054_F


title: Abf1-AA_EdU_Rapamycin

value: HHY221 (MATa tor1-1 fpr1::loxP-LEU2-loxP RPL13A-2x FKBP12::loxP ade 2-1 trp1-1 can1-100)  dBAR1::URA3 BrdU::HIS3(HIS+) Abf1-FRB::KAN


title: Abf1-AA_EdU_Vehicle


title: Pa_44053_H

value: primary pancreatic ductal adenocarcinoma (PDAC)


title: STAT1_ChIPSeq-HAP1-P_IFN-2

description: ChIP-Seq


title: diquat, lung (E3_DCL15)

description:
E3_DCL15
lung_data_matrix.txt

value: lung

value: wild type

value: diquat


title: Abf1-AA_Input_Vehicle


title: Abf1-AA_Input_Rapamycin


title: STAT1_ChIPSeq-HAP1-P_IFN-1

description: ChIP-Seq

value: myelogenous leukemia


title: Pa_47264_G

value: tumor


title: STAT1-ChIPSeq-HAP1-P-2

description: ChIP-Seq


title: SEF1-VP16_YPGly_repeat 4

type: RNA

city: Taipei

first: Po-Chen

last: Hsu

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description: Gene expression after 5.5 h of subculture

hyb_protocol: The Agilent Gene Expression Hybridization Kit (5188-5242, Agilent Technologies) was used for hybridization according to the manufacturer's instruction. Briefly, 16 ml of Alexa dye labeled cDNA in water was denatured at 98°C for 3 min in a reaction volume of 40 ml containing 4 ml Agilent 10x blocking Agent and 20 ml of Agilent 2x GEx Hybridization Buffer HI-RPM. Denatured dye-labeled cDNAs were subsequently hybridized to a Agilent Yeast V2 gene expression 8x15K microarray (Design ID: 016322, Agilent Technologies) at 65°C and rotated at 10 rpm on an Agilent hybridizer for 17 h. After hybridization, the microarrays were washed using the Agilent Gene Expression Wash Kit (5188-5327, Agilent Technologies). Briefly, microarrays were washed 1 min at room temperature with GE Wash Buffer 1 and 1 min with 37°C GE Wash buffer 2, and then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned at 535 nm (for Alexa Flour® 555 dye) on the Agilent DNA Microarray Scanner (US9230696) using one color scan setting for 8x15k array slides (scan area: 61 x 21.6 mm; scan resolution: 5 mm; dye channel: green; green PMT: 100%; tiff: 16 bit; XDR: 0.10).

data_processing: Scanned images were analyzed with the Feature Extraction 10.5.1.1 Software (Agilent Technologies) using default parameters (protocol: GE1_105_Dec08 and grid: 023206_D_F_20131222; provided by the IMB Genomics Core Lab, Academia Sinica, Taiwan) to obtain the background subtracted and spatially detrended Processed Signal intensities. Features flagged in the Feature Extraction Software as the feature non-uniform outlierswere excluded.

label: Alexa Flour® 555

source_name: log-phase SEF1-VP16 mutant cells, YPGly, 30°C, 5.5 h, biological repreat 4

label_protocol: For Alexa dye-labeled cDNA synthesis, the kit SuperScriptTM Plus Indirect cDNA Labeling System (L101402, Invitrogen by Thermo Fisher Scientific) was used according to the manufacturer's instruction. Briefly, 10 mg of DNase-treated RNA were reverse-transcribed using the anchored oligo[(dT)20-VN] primers and the cDNA was labeled with aminoallyl-dUTP followed by a column purification (28106, QIAquick DNA Purification Kit, Qiagen).  The aa-cDNA was then labeled with Alexa Flour® 555 dye (A-32756, Invitrogen by Thermo Fisher Scientific) and purified with the QIAGEN column (28106, QIAquick DNA Purification Kit, QIAGEN).

growth_protocol: Cells were grown in the YPD medium at 30°C overnight.

extract_protocol: Total RNA were extracted by phenol-chloroform followed by ethanol precipitation. gDNA contaminations wete removed by the TURBO DNA-free kit (AM1907, Ambion). The final RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was checked with the Agilent 2100 Bioanalyzer.

treatment_protocol: Cells from overnight cutures were subsequently diluted into YPD and YPGly in a cell density of 0.2 OD600/ml, incubated for 5.5 h at 30°C, and harvested.


title: Rpo21-AA_EdU_Rapamycin

value: HHY221 (MATa tor1-1 fpr1::loxP-LEU2-loxP RPL13A-2x FKBP12::loxP ade 2-1 trp1-1 can1-100)  dBAR1::URA3 BrdU::HIS3(HIS+) Rpo21-FRB::KAN

value: treated with rapamycin (1  μg/ml final) for 30 min and then with EdU (10 mM final) for 2 min


title: STAT1-ChPSeq-HAP1-MAZko-1

description: ChIP-Seq


title: SEF1-VP16_YPGly_repeat 3

source_name: log-phase SEF1-VP16 mutant cells, YPGly, 30°C, 5.5 h, biological repreat 3


title: Pa_47264_F

value: Non-Gland forming


title: SEF1-VP16_YPGly_repeat 1

source_name: log-phase SEF1-VP16 mutant cells, YPGly, 30°C, 5.5 h, biological repreat 1


title: SEF1-VP16_YPGly_repeat 2

source_name: log-phase SEF1-VP16 mutant cells, YPGly, 30°C, 5.5 h, biological repreat 2


title: Pa_44053_G


title: Rpo21-AA_EdU_Vehicle

value: no rapamycin, treated with EdU (10 mM final) for 2 min


title: ChIPSeq-HAP1-P-IFN-InpSiM-lib8-51821_S23

description: Input

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie2. Peaks were called using MACS2. Bigwig files were generated with Deeptools.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed with a ChIP-IT Express kit following manufacturer's instructions.
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor plus (Diagenode).
ChIP-Seq libraries were prepared using the “NEBNext® Ultra™ II DNA Library Prep Kit”.  Libraries were amplified using 15 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Input

value: IFNγ

tag: treatment time_(hr)


title: Rpo21-AA_Input_Rapamycin

value: 30 minutes rapamycin (1  μg/ml final)


title: ChIPSeq-HAP1-P-Inp-lib8-51821_S17_L003

description: Input


title: Pa_47264_D


title: Rpo21-AA_Input_Vehicle

value: no rapamycin


title: STAT1-ChPSeq-HAP1-P-1

description: ChIP-Seq

value: bone marrow


title: sef1_YPGly_repeat 3

source_name: log-phase sef1 deletion mutant cells, YPGly, 30°C, 5.5 h, biological repreat 3


title: Input_S phase

value: HHY221 (MATa tor1-1 fpr1::loxP-LEU2-loxP RPL13A-2x FKBP12::loxP ade 2-1 trp1-1 can1-100)  dBAR1::URA3 BrdU::HIS3(HIS+)

value: S-phase arrested cells, non-labeled


title: Pa_26967_G

value: primary pancreatic ductal adenocarcinoma (PDAC)


title: AVC-6h

city: Blacksburg

first: John

last: Maurer

state: VA

address: 175 West Campus Dr.

department: School of Animal Sciences

institute: Virginia Tech

hyb_protocol: Hybridizations were performed on NimbleGen slides, and carried out in Corning Hybridization Chambers at 42°C overnight. Dye swapping was performed for the different replicates to minimize dye-associated effects on cDNA synthesis. The slides were washed at increasing stringencies (2× SSC [1× SSC is 0.15 M NaCl plus 0.015 M sodium citrate], 0.1% sodium dodecyl sulfate [SDS], 42°C; 0.1% SSC, 0.1% SDS, room temperature; 0.1% SSC, room temperature). Following hybridization, the microarrays were scanned for the Cy3 and Cy5 fluorescent signals.

scan_protocol: Microarray chips were scanned with a ScanArray 5000 laser scanner (GSI Lumonics; Watertown, MA).

data_processing: The data was analyzed using QuantArray v.2.01 software. Background intensity was subtracted from spot boundary signal intensities to derive Cy3 and Cy5 median signal intensities.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: STM YC1104 cells grown for 6h in dialysis tube, AV3

label_protocol: Twenty mg of total RNA was reverse-transcribed using random hexamers, SuperScript II reverse transcriptase (Invitrogen) in the presence of RNAse inhibitor (Roche) and Cy3- or Cy5-labeled dCTP, according to Invitrogen instructions.

growth_protocol: Salmonella enterica was grown inside dialysis tubing either without any microflora (CTRL), with commercial competitive exclusion product Aviguard outside of the tubing (AV), or with cecal content with high Salmonella load (CECAL35-4) outside of the tubing, at 37C. Samples were taken after 6 hours or 9 hours of growth.

extract_protocol: Total RNA was harvested from Salmonella grown in the dialysis tubing and microarray analysis was performed as follows: the samples were treated with 0.1 ml volume of 95% ethanol, 5% acidic phenol (pH 4.3) and total RNA was extracted using MasterPure Complete DNA and RNA purification kits (Epicentre; Madison, WI) and the High Pure RNA isolation kit (Roche; Indianapolis, IN).  The samples were subsequently treated twice with the Turbo DNA-free kit (Ambion; Austin, TX).

value: SL1344-derivative YC1104

value: bacterial cell

tag: external milieu

value: Ex vivo chicken cecal medium with Aviguard at 10^8 cells / ml

tag: time


title: IpH3K27AcChPSeq-HAP1-siMZ-lib6-4122021_S23_L003


title: CECAL354B-6h

source_name: STM YC1104 cells grown for 6h in dialysis tube, CECAL354-2

value: Ex vivo chicken cecal medium with cecal content containing high Salmonella load, 10^8 cells/ml


title: sef1_YPGly_repeat 4

source_name: log-phase sef1 deletion mutant cells, YPGly, 30°C, 5.5 h, biological repreat 4


title: Pa_26967_H

source_name: tumor

value: tumor


title: Pa_47264_E


title: AVB-6h

source_name: STM YC1104 cells grown for 6h in dialysis tube, AV2


title: CECAL354A-6h

source_name: STM YC1104 cells grown for 6h in dialysis tube, CECAL354-1


title: AVA-9h

source_name: STM YC1104 cells grown for 9h in dialysis tube, AV1


title: sef1_YPGly_repeat 2

source_name: log-phase sef1 deletion mutant cells, YPGly, 30°C, 5.5 h, biological repreat 2


title: CECAL354C-6h

source_name: STM YC1104 cells grown for 6h in dialysis tube, CECAL354-3


title: WT_YPGly_repeat 4

source_name: log-phase wild type cells, YPGly, 30°C, 5.5 h, biological repreat 4


title: CTRLB-6h

source_name: STM YC1104 cells grown for 6h in dialysis tube, CTRL2

value: Ex vivo chicken cecal medium without bacteria


title: EdU_S phase

value: S-phase arrested cells, treated with EdU (10 mM final)


title: IPH3K27AcChpSeq-HAP1IFN-lib6-4122021_S10_L002


title: Pa_1860_F

value: Non-Gland forming


title: EdU_G1 phase

value: G1-phase arrested cells, treated with EdU (10 mM final)


title: AVA-6h

source_name: STM YC1104 cells grown for 6h in dialysis tube, AV1


title: IpH3K27AcChPSeq-HAP1-Lib6-4122021_S4_L001


title: CTRLC-6h

source_name: STM YC1104 cells grown for 6h in dialysis tube, CTRL3


title: Pa_26967_F


title: rdr1 rdr2 rdr6 ddm1/+ hp5 ONT 5mC

city: Cold Spring Harbor

first: Robert

middle: A

last: Martienssen

state: NY

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

description: PromethION P2 Solo

data_processing:
For ChIPseq: Adapter trimming with cutadapt, mapping with Bowtie2 and bigwigs generated with Deeptools.
For ONT: Base calling was performed with dorado, reads were aligned with minimap2 and consensus methylation calls were produced with modkit. Methylaiton ratios were extracted with bedtools and converted to bigwigs with UCSC tools.
Assembly: ColCEN v1.2
Supplementary files format and content: For ChIPseq: Bigwig files representating log fold change of count per million IP/Input for each biological replicate or normalized coverage for Inputs.
Supplementary files format and content: For ONT: Bigwigs files of scaled methylation ratio [0-1] at each cytosine, with ratios on the negative strand being multiplied by -1. One file for each sequence context: CG (.cpg), CHG (.chg) and CHH (.chh).

organism: Arabidopsis thaliana

source_name: rosette leaves

growth_protocol: Plants were grown on MS media for ChIPseq and on soil for ONT sequencing.

extract_protocol:
ChIP was performed as previously described (Inagaki et al., 2017). Genomic DNA was extracted with Qiagen Dneasy Plant for ONT.
ChIP-seq libraries were made with NEBNext Ultra II DNA Library Prep Kit. ONT libraries were made with ONT SQK-NBD114.24 Ligation sequencing
ChIP-seq and direct methylation sequencing (WGS)

treatment_protocol: Crosslinking with 1% FA followed by quencing with 0.125M Glycine

value: rosette leaves

value: rdr1 rdr2 rdr6 ddm1/+ ATHILA-hp5


title: ChIPSeq-HAP1-siMZ-IFN-IpH3K4me3-Lib5-51821_S39

value: IFNγ


title: CTRLA-9h

source_name: STM YC1104 cells grown for9h in dialysis tube, CTRL1


title: WT_YPGly_repeat 3

source_name: log-phase wild type cells, YPGly, 30°C, 5.5 h, biological repreat 3


title: rdr1 rdr2 rdr6 ddm1 hp5 ONT 5mC

description: PromethION P2 Solo

value: rdr1 rdr2 rdr6 ddm1 ATHILA-hp5


title: ChIPSeq-HAP1-siMZ-IpH3K4me3-lib5-51821_S29_L005


title: rdr1 rdr2 rdr6 ddm1/+ ONT 5mC

description: PromethION P2 Solo

value: rdr1 rdr2 rdr6 ddm1/+


title: Pa_17780_F


title: CTRLA-6h

source_name: STM YC1104 cells grown for 6h in dialysis tube, CTRL1


title: WT_YPGly_repeat 2

source_name: log-phase wild type cells, YPGly, 30°C, 5.5 h, biological repreat 2


title: ChIPSeq-HAP1-P-IFN-IpH3K4me3-lib5-51821_S22_L004


title: Pa_31330_E


title: sef1_YPGly_repeat 1

source_name: log-phase sef1 deletion mutant cells, YPGly, 30°C, 5.5 h, biological repreat 1


title: WT_YPGly_repeat 1

source_name: log-phase wild type cells, YPGly, 30°C, 5.5 h, biological repreat 1


title: Pa_44228_D

source_name: tumor

value: Gland forming


title: rdr1 rdr2 rdr6 ddm1 ONT 5mC

description: PromethION P2 Solo

value: rdr1 rdr2 rdr6 ddm1


title: Pa_17780_H

value: primary pancreatic ductal adenocarcinoma (PDAC)


title: SEF1-VP16_YPD_repeat 4

source_name: log-phase SEF1-VP16 mutant cells, YPD, 30°C, 5.5 h, biological repreat 4


title: IpH3K3me3ChPSeq-HAP1-Lib5-4122021_S1_L001


title: Pa_44228_C


title: melan-a UVR 5

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

description: UVR

data_processing:
Adapter sequences were removed using TrimGalore!
Sequencing reads were mapped using Bowtie2 for each SmaI/XmaI site in the genome and signatures to methylated (5'CCGGG) and unmethylated (5'GGG) CpG were enumerated for each SmaI/XmaI site. Mouse genome (mm9) and human genome (hg19) was used.
For every CpG site within the SmaI/XmaI recognition site, the methylation was calculated. Let m be the number of tags corresponding to methylated CpG's (tags starting with CCGGG) and u be the number of tags corresponding to unmethylated CpG's (tags starting with GGG), the methylation percent was calculated as 100*(c*m)/(c*m+u), where c is the correction factor based on the observed vs expected methylation of spiked-in standards.
Genome_build: hg19 / mm9
Supplementary_files_format_and_content: The processed data are in tab-delimited text file. The columns of the file are: ID_SmaI_hg19 or ID_SmaI_mm9 (CCCGGG site ID), chromosome (chromosome of the CCCGGG site), position (position of the CCCGGG site), meth_reads (observed number of reads corresponding to methylated CpG, XmaI), unmeth_reads (observed number of reads corresponding to unmethylated CpG, SmaI), total_reads, raw_methylation (unadjusted methylation value), adjusted_methylation (methylation value adjusted based on spiked in standards). Summary table lists methylation percent values supported by more than 19 sequencing reads at individual CCCGGG sites.

source_name: melan-a

growth_protocol: HEMn-DP1 cells were cultured in Medium 254 (Gibco) supplemented with human melanocyte growth supplement (Gibco) and phorbol 12-myristate acetate (200nM). Melan-a cells were cultured in RPMI 1640 media supplemented with 10% fetal bovine serum, 1% L-glutamine, and 0.1% gentamicin antibiotic [50mg/ml].

extract_protocol:
Cells were pelleted and lysed in 2% SDS, 25 mM EDTA; proteins were precipitated by the addition of 10M ammonium acetate and removed by centrifugation. DNA was precipitated by the addition of isopropanol and washed twice with 70% ethanol. The DNA pellet was dissolved in TE (Tris 10 mM, EDTA 1mM). High molecular DNA was recovered by immobilization on 0.4x AMPure XP beads (Beckman Coulter) prior to methylation analysis.
Two micrograms of genomic DNA were spiked with methylation standards and then sequentially digested with SmaI and XmaI restriction enzymes. DNA was digested with 20 units of SmaI for 8 h at 25°C. 20 units of XmaI was added and the digestion was continued for an additional 16 h at 37°C. 3' end filling and dA tailing was performed by 15 units of Klenow Fragment (3'>5' exonuclease deficient; NEB) with nucleotide mix (0.4 mM final concentration of each dCTP, dGTP, dATP).
Libraries were prepared by ligation of NEBNext adapters  at a 10:1 adapter to fragment ratio using T4 DNA ligase (NEB) at 16°C overnight. Hairpin loops of the adapters were cleaved with USER enzyme at 37°C for 15 min. Ligated DNA was dual-size selected using AMPure XP beads for fragments between 250 to 450 bp. Adapter-ligated DNA fragments were indexed with NEBNext Index  i7 primers (NEB). Libraries were amplified for 14 cycles and cleaned with AMPure XP beads prior to sequencing. Libraries were were pooled to 10 nM and spiked with 25% phiX library to ensure sequence diversity.
OTHER: DREAM

treatment_protocol: Cells were plated in 60mm tissue culture dishes in biological replicates 2 days before UVR exposure.  Cells were at 80% confluence at time of treatment. Cells were washed with DPBS and covered with a small amount of DPBS and Saran wrap for UVR exposure.  Two TL-20 lamps emitting a broad band UVR spectrum (35% UVA and 65% UVB) were used.  Cells received a total dose of 175 J/m2 over 90 s at a rate of 1.94 W/m2. The majority of the cells survive this exposure.  Cells were cultured for one month after UVR treatment before detecting changes in DNA methylation.

value: melanocyte cell line

tag: sample type

value: batch 2


title: SEF1-VP16_YPD_repeat 3

source_name: log-phase SEF1-VP16 mutant cells, YPD, 30°C, 5.5 h, biological repreat 3


title: Pa_43840_D


title: VncS T245A Replicate 2

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 2.10. Only sequences at least 25 nt in length were considered for further analysis.
Bowtie version 2.5.1, with default parameters, was used for alignment on the reference genome
Genes were counted using featureCounts version 2.0.0 from Subreads package (parameters: -t locus_tag -g ID -s 1).
Count data were analyzed using R version 4.0.5 and the Bioconductor package DESeq2 version 1.30.1. The normalization and dispersion estimation were performed with DESeq2 using the default parameters but statistical tests for differential expression were performed with(out) applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between the biological condition. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p-value lower than 0.05 were considered differentially  expressed.
Assembly: Streptococcus agalactiae BM110 (from NCBI id=318722 , NCBI RefSeq reference NZ_LT714196)
Supplementary files format and content: DESeq 2 output matrix

organism: Streptococcus agalactiae

source_name: cultures

growth_protocol: Bacterial cultures in rich media (THY) incubated at 37°C in static condition are harvested in exponential growth phase (OD600 = 0.5).

extract_protocol:
Total RNA are extracted after cell wall mechanical lysis with 0.1 µm beads (Precellys Evolution, Bertin Technologies) in RNApro reagent (MP Biomedicals), and purified by chloroform extraction and ethanol precipitation.
Depletion of rRNA (FastSelect Bacterial, Qiagen) and libraries construction ((TruSeq Stranded mRNA, Illumina) are done following manufacturer instructions.

treatment_protocol: Bacterial pellets are washed with cold PBS containing RNA stabilization reagents (RNAprotect, Qiagen) before flash freezing and storage at -80°C.

value: cultures

value: VncS T245A


title: melan-a UVR 4

description: UVR


title: VncS T245A Replicate 3


title: VncS T245A Replicate 1


title: melan-a UVR 3

description: UVR

value: batch 1


title: SEF1-VP16_YPD_repeat 2

source_name: log-phase SEF1-VP16 mutant cells, YPD, 30°C, 5.5 h, biological repreat 2


title: Pa_43840_B

value: tumor


title: sef1_YPD_repeat 4

source_name: log-phase sef1 deletion mutant cells, YPD, 30°C, 5.5 h, biological repreat 4


title: Pa_43840_C


title: melan-a UVR 2

description: UVR


title: SEF1-VP16_YPD_repeat 1

source_name: log-phase SEF1-VP16 mutant cells, YPD, 30°C, 5.5 h, biological repreat 1


title: Pa_37672_E


title: VikS T221A Replicate 1

value: VikS T221A


title: VikS T221A Replicate 2


title: Pa_37672_D


title: SaeS T133A Replicate 3

value: SaeS T133A


title: melan-a control 5

description: Control


title: Pa_37672_B


title: melan-a control 4

description: Control


title: sef1_YPD_repeat 3

source_name: log-phase sef1 deletion mutant cells, YPD, 30°C, 5.5 h, biological repreat 3


title: WT_YPD_repeat 4

source_name: log-phase wild type cells, YPD, 30°C, 5.5 h, biological repreat 4


title: IPH3K27AcChPSeq-HAP1-siMZIFN-lib6-4122021_S25


title: SaeS T133A Replicate 2


title: Pa_44054_E


title: sef1_YPD_repeat 2

source_name: log-phase sef1 deletion mutant cells, YPD, 30°C, 5.5 h, biological repreat 2


title: VikS T221A Replicate 3


title: melan-a control 3

description: Control


title: sef1_YPD_repeat 1

source_name: log-phase sef1 deletion mutant cells, YPD, 30°C, 5.5 h, biological repreat 1


title: Pa_44054_D


title: melan-a UVR 1

description: UVR


title: WT_YPD_repeat 3

source_name: log-phase wild type cells, YPD, 30°C, 5.5 h, biological repreat 3


title: Pa_44054_C


title: RelS T208A Replicate 3

value: RelS T208A


title: Pa_44054_B


title: WT_YPD_repeat 2

source_name: log-phase wild type cells, YPD, 30°C, 5.5 h, biological repreat 2


title: melan-a control 1

description: Control


title: PROseq_SUDHL4_FOXO1_FKBP_2hB

city: Nashville

first: Scott

last: Hiebert

state: Tennessee

address: 2220 Pierce Ave, Hiebert Lab PRB 512

institute: Vanderbilt University

library_source: other

data_processing:
Adaptor trimming: Adaptors were trimmed using Trimmomatic with flollowing settings CROP:75, ILLUMINACLIP:adaptorfile:2:30:7, TRAILING:15, MINLEN:15
Reverse complement: Reverse complements of the R1 files were created using fastx_reverse_complement from the FASTX toolkit.
Alignment: The reverse complement reads were aligned to a concatenated genome containing the hg19 and dm3 assembiles by Bowtie2.
File conversion and read filtering: SAM fies were converted to BAM files using samtools view with the options -S -b. Low quality reads were removed using samtools view with the following options -F 4 and -q 10. Filtered BAM files were sorted and indexed using samtools sort and samtools index respectively.
Spike-in quantication and removal: OCI-LY1 and NU-DUL-1 -Spike-in reads were quantified using samtools idxstats to quantify reads aligned to each chromosome. Reads aligned to dm3 chromosomes were summed in R to calculate the total number of spike-in reads. A bam file containing only hg19 reads was created using samtools view with the following options -bh and the names of the hg19 chromosomes. These files were resorted and indexed as described in the previous step. SU-DHL-4 - Spike-in reads were quantified using the grep command to quantify and remove reads aligned to the GFP, NeoR, Luciferase, and Gal4 sequences.
Differential analysis: Peak calling, read quantification, and differential expression were performed with NRSA.
Assembly: hg19/dm3
Supplementary files format and content: Normalized counts for promoter proximal and gene body polymerase. Tab delimted file containing Transcript ID, Gene Name, promoter proximal counts (ppc) for each replicate, promoter proximal density (ppd) for each replicate, gene body counts (gbc) for each replicate, and gene body density (gdb) for each replicate. Counts were noramlized in DEseq2.
Supplementary files format and content: Normalized counts for intergenic polymerase (enhancers). Tab delimted file containing Enhancer ID, chr, start, end, and counts for each replicate. Counts were noramlized in DEseq2.
Library strategy: PRO-seq

molecule: other

source_name: DLBCL Cell Line

growth_protocol: NU-DUL-1 and SU-DHL-4 cells were cultured in RPMI 1640 + 10% Fetalplex +1% L-Glutamine + 1% PenStrep. OCI-LY1 cells were cultured in IDMDM + 10% FetalPlex +1% L-Glutamine + 1% PenStrep. Cells were subcultured the day before the experiment, incubated at 37C with 5% CO2, and harvested while in log phase growth.

extract_protocol:
Biotinylated RNAs were extracted with Trizol LS after nuclear run on.
Libraries were constructed as previously described (Mahat et al., Nature Protocols, 2016).

treatment_protocol: dTAG-47 was added to culture medium to a final concentration of 500 nm at the indicated timepoints.

value: DLBCL Cell Line

value: GC-DLBCL

value: 2h dTAG-47


title: RelS T208A Replicate 1


title: Pa_44053_E

data_processing:
Reads were pre-processed (quality trimming and adapter clipping) using Trim Galore v0.6.5, then reads with a minimum of 20 bp were aligned to human genome build GRCh38/hg38 using Kallisto v0.46.0 with default parameters and in the correct orientation (--rf-stranded. Only uniquely mapped reads were retained.
Transcript-level expression were summarized to gene level using tximport v1.14.2 R-package and only protein coding genes were retained.
Differential expression analysis was performed using the DESeq2 R-package v1.26.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file providing raw read count values for each sample


title: PROseq_SUDHL4_FOXO1_FKBP_2hA


title: PhoS T345A Replicate 3

value: PhoS T345A


title: PROseq_SUDHL4_FOXO1_FKBP_1hB

value: 1h dTAG-47


title: SaeS T133A Replicate 1


title: Pa_44053_C

value: Gland forming


title: PhoS T345A Replicate 2


title: PhoS T345A Replicate 1


title: Pa_44053_B


title: LiaS Q149A Replicate 3

value: LiaS Q149A


title: RelS T208A Replicate 2


title: WT_YPD_repeat 1

source_name: log-phase wild type cells, YPD, 30°C, 5.5 h, biological repreat 1


title: Pa_41866_E

value: primary pancreatic ductal adenocarcinoma (PDAC)


title: PROseq_SUDHL4_FOXO1_FKBP_0.5hB


title: PROseq_SUDHL4_FOXO1_FKBP_0.5hA


title: PROseq_SUDHL4_FOXO1_FKBP_0hB

value: 0h (untreated)


title: Pa_41866_D


title: Pa_44053_D


title: LiaS Q149A Replicate 2


title: LiaS Q149A Replicate 1


title: Pa_30866_B


title: HssS T150A Replicate 3

value: HssS T150A


title: PROseq_SUDHL4_FOXO1_FKBP_0hA


title: PROseq_SUDHL4_FOXO1_FKBP_1hA


title: Pa_30866_E


title: plasmid DNA fragments, amplified, after acetic screening

city: Tianjin

first: Qianxi

last: He

address: Yaguan road 135

institute: Tianjin University

data_processing:
The original data of sequencing results were subjected to image Base calling by using the software CASAVA(v1.8.2), and the quality was preliminarily analyzed.
The overlap regions of paired-end sequencing results were merged.
Through sequences alignment, the abundance of spacer of every sgRNA plasmid could be determined.
Assembly: YarliW29
Supplementary files format and content: xlsx.tab-Abundance of sgRNA spacers before screening
Supplementary files format and content: xlsx.tab-Abundance of sgRNA spacers after acetic acid screening
Supplementary files format and content: xlsx.tab-Abundance of sgRNA spacers after furfural screening
Library strategy: CRISPR screen

organism: synthetic construct

growth_protocol: Y. lipolytica transformed with the whole-genome sgRNA plasmid library was inoculated in SD-Leu medium. When cell growth reached the late exponential phase (after approximately 36 hours), 1 mL of culture was collected for plasmid extraction.

extract_protocol:
Plasmid extraction was performed using ZymoprepTM Yeast Plasmid Miniprep II (Zymo Research Corporation).
Sequences containing spacers in sgRNA plasmids were amplified via PCR, purified, fragmented, and their ends were repaired and reformed to become clusters.

value: yeast cell


title: HssS T150A Replicate 2

value: cultures


title: Pa_29919_G


title: HssS T150A Replicate 1


title: plasmid DNA fragments, amplified, after furfural screening


title: Pa_29919_E


title: plasmid DNA fragments, amplified, before screening


title: Pa_26967_D


title: HK11030 T245A Replicate 3


title: Glucosamine treated parasites 3

city: São Paulo

first: Gerhard

last: Wunderlich

state: SP

address: Av. Professor Lineu Prestes, 1374, ICB2

country: Brazil

institute: Institute for Biomedical Sciences, University of São Paulo

description:
TPM_GlcNtreated
TPM_3

data_processing:
FastQ groomer (Galaxy version 1.0.4)
Trimmomatic (Galaxy Version 0.36.5)
HISAT2 (Galaxy Version 2.0.5)
bamCoverage (Galaxy Version 3.2.0.0.0)
htseq-count (Galaxy version Htseq: SAMTOOLS:1.2; PICARD:1.134)
HTseqCountToTPM (Galaxy Version TPMtool 1)
Assembly: PlasmoDB_51_Pfalciparum3D7Genome
Supplementary files format and content: csv format depicting TPMs of triplicates per gene locus

organism: Plasmodium falciparum

source_name: trophozoites

extract_protocol:
RNA from 0.1% saponin treated infected red blood cells (10^8 trophozoites per replicate) was Trizol extracted following exactly the protcol provided by Invitrogen.
The library construction followed the exact instructions of the Illumina NextSeq 500/550 Mid Output Kit v2.5 (150 Cycles) and Agilent SureSelect Strand Specific RNA-Seq Library Preparation kit for 16 samples for the Illumina platform, using the components of these kits.

value: trophozoites

value: JmjC2 tagged with HA-glmS

value: 2.5 mM Glucosamine for 24 h


title: HK11030 T245A Replicate 2


title: HK11030 T245A Replicate 1


title: genomic DNA from SDC HF2927 TMZ sample replicate 3

type: genomic

city: Detroit

first: oluwademilade

last: Nuga

state: MI

address: 540 E canfield

department: Pharmacology

institute: Wayne State University

hyb_protocol: Illumina protocols

scan_protocol: Illumina protocols

data_processing: Average beta

source_name: HF2927 SDCs

label_protocol: Illumina protocols

extract_protocol: genomic DNA extraction

tag: Sex

value: Male

value: HF2927 SDCs


title: Pa_1860_C

source_name: tumor

extract_protocol:
FFPE sections (4 μm) were mounted on polyethylene naphthalate membrane (PEN) slides, were deparaffinized in xylene and then partially rehydrated in an ethanol gradient up to 75% EtOH. After that sections were  counterstained with freshly prepared Cresyl Violet for 30 seconds, they were washed twice in 75% EtOH and air dried completely before proceeding to the microdissection using a UV-based LMD7 laser microdissection system (Leica Microsystems) at 20x magnification. Microdissected areas were collected by gravity into strip-tube caps.
Microdissected areas were digested with 10 mU of Proteinase K (ThermoFisher, #AM2546) for 1 hour at 60 C. 1 ml of 5 mM Proteinase K inhibitor (Calbiochem, #539470) was added to stop the reaction and samples were stored at -80 C until library preparation. They were then processed using the SMART-seq Stranded kit (Cat. 634444, protocol version 051018; Takara Bio USA, Inc.) according to the manufacturer’s protocol removing the initial fragmentation step.

value: tumor


title: Glucosamine treated parasites 1

description:
TPM_GlcNtreated
TPM_1


title: HK10655 T267A Replicate 3


title: Pa_10663_E


title: HK10655 T267A Replicate 2


title: Pa_26967_B


title: Glucosamine treated parasites 2

description:
TPM_GlcNtreated
TPM_2


title: Pa_10663_D


title: Untreated control parasites 2

description:
TPMcontrols.csv
TPM_2

value: control


title: genomic DNA from SDC HF2927 ionizing radiation sample replicate 1


title: HK10655 T267A Replicate 1


title: genomic DNA from SDC HF2927 ionizing radiation sample replicate 2


title: genomic DNA from SDC HF2927 TMZ sample replicate 2


title: Pa_10663_C


title: Untreated control parasites 1

description:
TPMcontrols.csv
TPM_1


title: HK02290 H288A Replicate 3


title: genomic DNA from SDC HF2927 control sample replicate 3


title: genomic DNA from SDC HF2927 control sample replicate 2


title: Sample 11_NNAT-negative beta cells 4

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
Sequencing was conducted on an Illumina NextSeq 500 system with 40 basepair paired-end reads
Sequencing reads were mapped to mm10 genome using STAR aligner (version 2.7.1a)
Gene based counting was performed using the STAR aligner
Gene expression analysis was performed using the DESeq2 Bioconductor package (DESeq2_1.32.0)
Assembly: mm10
Supplementary files format and content: comma-delimited text file include raw counts for each Sample generated by STAR aligner.

source_name: NNAT-negative beta cells

growth_protocol: Mouse primary islets were digested from the pancreas using Liberase TM in RPMI, purified using a Histopaque graadient and hand-picked into RPMI supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
RNA was harvested from FACS-sorted populations using RNeasy kits (Qiagen). 20 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using a NEBNext Ultra II Directional RNA library Prep Kit for Illumina paired with a Poly(A) mRNA magnetic isolation module and AMPure XP SPRIselect beads (Beckman Coulter),

treatment_protocol: Single cells from purified islets were obtained via digestion with Accutase, resupended into FACS buffer and sorted by FACS.

value: male

tag: age

value: 10 week old

value: primary mouse islet cells

value: NNAT-negative beta cells

value: rat insulin promoter (RIP)-Cre x STOP-tdTomato x Nnat-EGFP

value: Chow fed


title: HK02290 H288A Replicate 2


title: Pa_31330_G

city: Milan

first: Pierluigi

last: Di Chiaro

address: Via Adamello 16

institute: European Institute of Oncology (IEO)

value: primary pancreatic ductal adenocarcinoma (PDAC)

value: Gland forming


title: genomic DNA from SDC HF2927 TMZ sample replicate 1


title: Sample 10_NNAT-positive beta cells 4

source_name: NNAT-positive beta cells

value: NNAT-positive beta cells


title: melan-a control 2

description: Control

source_name: melan-a

value: melanocyte cell line

value: batch 1


title: HK02290 H288A Replicate 1

source_name: cultures

value: cultures


title: Untreated control parasites 3

description:
TPMcontrols.csv
TPM_3

value: trophozoites

value: JmjC2 tagged with HA-glmS


title: Sample 9_NNAT-negative beta cells 3


title: Pa_31330_H


title: genomic DNA from CSC HF2927 TMZ sample replicate 1

source_name: HF2927 CSCs

value: Male

value: HF2927 CSCs


title: DltS T184A Replicate 3

value: DltS T184A


title: genomic DNA from SDC HF2927 ionizing radiation sample replicate 3

value: HF2927 SDCs


title: Pa_29919_H

value: tumor

value: Non-Gland forming


title: genomic DNA from CSC HF2927 TMZ sample replicate 3


title: ureC::bla_LB+urea_biol_rep_3

city: Ann Arbor

first: Madison

last: Fitzgerald

address: 1150 W. Medical Center Drive

department: Microbiology & Immunology

institute: University of Michigan

description:
ureC_urea-induced_transcriptome.xlsx
ureC_urea_vs_ureR_urea.xlsx
ureC_urea_vs_WT_urea.xlsx

data_processing:
Geneious Prime 2022.1 software was used for data analysis (www.geneious.com). Reads were paired as fastq files and were imported into Geneious Prime using the average insert size for each sample.
The BBduk plug-in was used to remove Illumina adapter sequences and perform quality trimming (maq=20, maxns=1, trimq=14, minlength=20).
Trimmed reads were mapped to the HI4320 genome (GenBank: NC_010554.1) using the Geneious read mapper.
Geneious calculated expression levels of genes in each sample, and the DeSeq2 plug-in was used to calculate differential expression (fit type=parametric).
Assembly: NCBI Reference Sequence: NC_010554.1
Supplementary files format and content: Excel files containing differential gene expression data between the two indicated samples, as calculated by DeSeq2.

organism: Proteus mirabilis

source_name: bacterial

growth_protocol: Overnight cultures of bacterial strains were sub-cultured in duplicate in 3 mL LB buffered with 250 mM HEPES and incubated at 37°C with aeration. After 2 hours, one culture of each strain was supplemented with urea to a final concentration of 50 mM while the other culture remained unperturbed. Samples were collected after 15 minutes of growth post-urea addition.

extract_protocol:
RNA was isolated using RNeasy kit (Qiagen). Samples were incubated with lysozyme (0.5 mg/mL) for 15 minutes with agitation to lyse cells. Subsequent RNA isolation was performed according to the manufacturer’s instructions. Genomic DNA was depleted using the Turbo-DNAfree Kit (Invitrogen). rRNA was removed using the NEBNext rRNA Depletion Kit (bacteria).
Sequencing libraries were prepared using the xGen Broad-range RNA Library Prep (IDT) and xGen Normalase UDI Primer Plate 1 (IDT) according to the manufacturer's instructions.

treatment_protocol: 1 mL of each culture was preserved in 2 mL of RNAprotect Bacterial Reagent. After incubating for ~15 minutes at room temperature, samples were centrifuged, supernatants removed, and pellets frozen at -20°C for at least one day.

value: bacterial

tag: condition

value: LB +urea


title: Sample 8_NNAT-positive beta cells 3

value: male

value: 10 week old

value: primary mouse islet cells

value: rat insulin promoter (RIP)-Cre x STOP-tdTomato x Nnat-EGFP

value: Chow fed


title: DltS T184A Replicate 2


title: genomic DNA from SDC HF2927 control sample replicate 1


title: ureC::bla_LB+urea_biol_rep_2


title: Sample 7_non-beta cells 3

source_name: non-beta cells

value: non-beta cells


title: DltS T184A Replicate 1

value: cultures


title: ureC::bla_LB+urea_biol_rep_1


title: genomic DNA from CSC HF2927 ionizing radiation sample replicate 2


title: genomic DNA from CSC HF2927 ionizing radiation sample replicate 3


title: genomic DNA from CSC HF2927 ionizing radiation sample replicate 1


title: ureC::bla_LB_biol_rep_3

description:
ureC_urea-induced_transcriptome.xlsx
ureC_LB_vs_ureR_LB.xlsx
ureC_LB_vs_WT_LB.xlsx

value: LB


title: genomic DNA from CSC HF2927 control sample replicate 2


title: genomic DNA from CSC HF2927 control sample replicate 1


title: genomic DNA from CSC HF2927 control sample replicate 3


title: ureC::bla_LB_biol_rep_2


title: CovS T282A Replicate 1

value: CovS T282A


title: genomic DNA from CSC HF2927 TMZ sample replicate 2

value: Male


title: Sample 6_NNAT-negative beta cells 2

value: NNAT-negative beta cells


title: CovS T282A Replicate 2


title: Sample 5_NNAT-positive beta cells 2

value: NNAT-positive beta cells


title: Sample 3_NNAT-negative beta cells 1


title: Sample 4_non-beta cells 2


title: CiaH T228A Replicate 3

value: CiaH T228A


title: ureR::aphA_LB+urea_biol_rep_3

description:
ureR_urea-induced_transcriptome.xlsx
ureC_urea_vs_ureR_urea.xlsx
ureR_urea_vs_WT_urea.xlsx


title: CiaH T228A Replicate 2


title: Sample 2_NNAT-positive beta cells 1


title: ureC::bla_LB_biol_rep_1


title: genomic DNA from SDC HF2303 TMZ sample replicate 2

source_name: HF2303 SDCs

value: Female

value: HF2303 SDCs


title: genomic DNA from SDC HF2303 TMZ sample replicate 3


title: Sample 1_non-beta cells 1


title: CiaH T228A Replicate 1


title: CovS T282A Replicate 3


title: PD-treated with 24 mM oxamate and 0.3 mM octyl-L2HG_C

city: Jerusalem

first: Eli

last: Pikarsky

address: Ein Karem

department: The Lautenberg Center for Immunology and Cancer Research

country: Israel

institute: The Hebrew University-Hadassah Medical School

data_processing:
Raw reads were created with bcl2fastq, v2.18.0.12, then processed to remove bad quality and adapter bases with cutadapt, v1.18, using parameters -q32,32, -O 1, --match-read-wildcards and -m 15. Processed reads were further filtered by fastq_quality_filter, FASTX v0.0.14, with parameters -q 20 and -p 90.
Processed reads were aligned to the mouse genome with tophat, v2.1.1, using parameters -N 5, --read-gap-length 5, --read-edit-dist 10, --segment-length 18, --read-realign-edit-dist 3, --no-coverage-search, --library-type fr-firststrand, and gene annotations from Ensembl release 99.
Counts per gene were calculated with htseq-count, v0.6.0, using -s 'reverse' and masking for short genes (e.g. miRNAs).
Statistical testing was done with DESeq2, v1.22.2, taking genes with at least 10 counts and incorporating the mouse of origin as a batch factor in the model.
Genome_build: GRCm38
Supplementary_files_format_and_content: An Excel file with a single header row, followed by a row for each gene. Columns A-K have general gene information, L-T have raw counts for each sample, U-AC have normalized counts for each sample, AD is the average expression (baseMean), then 5 columns for each comparison with the output of DESeq2 results.

source_name: isolated and cultured cells

extract_protocol:
RNA was isolated using Qiagen mini kit
Libraries were prepared with poly-A capturing and the KAPA Stranded mRNA-Seq Kit

value: cultured germ cells

tag: developmental stage

value: Pachytene/Diplotene

value: Treated with 24 mM oxamate and  0.3 mM octyl-L2HG


title: genomic DNA from SDC HF2303 TMZ sample replicate 1


title: ureR::aphA_LB+urea_biol_rep_1

value: bacterial

value: LB +urea


title: genomic DNA from SDC HF2303 ionizing radiation sample replicate 3


title: BceS V124A Replicate 3

tag: tissue

value: BceS V124


title: PD-treated with 24 mM oxamate and 0.3 mM octyl-L2HG_B


title: ureR::aphA_LB_biol_rep_3

description:
ureR_urea-induced_transcriptome.xlsx
ureC_LB_vs_ureR_LB.xlsx
ureR_LB_vs_WT_LB.xlsx


title: PD-treated with 24 mM oxamate and 0.3 mM octyl-L2HG_A


title: ureR::aphA_LB+urea_biol_rep_2


title: ureR::aphA_LB_biol_rep_2


title: BceS V124A Replicate 1


title: ureR::aphA_LB_biol_rep_1

description:
WT_urea-induced_transcriptome.xlsx
ureC_LB_vs_ureR_LB.xlsx
ureR_LB_vs_WT_LB.xlsx


title: PD-treated with 24 mM oxamate_C

description: PD-treated with 24 mM oxamate

value: Treated with 24 mM oxamate


title: BM110 B Replicate 3

value: WT


title: HI4320_LB+urea_biol_rep_3

description:
WT_urea-induced_transcriptome.xlsx
ureC_urea_vs_WT_urea.xlsx
ureR_urea_vs_WT_urea.xlsx


title: BceS V124A Replicate 2

value: cultures


title: genomic DNA from SDC HF2303 ionizing radiation sample replicate 1


title: genomic DNA from SDC HF2303 ionizing radiation sample replicate 2


title: PD-treated with 24 mM oxamate_B

description: PD-treated with 24 mM oxamate


title: PD-treated with 24 mM oxamate_A

description: PD-treated with 24 mM oxamate


title: BM110 B Replicate 1


title: HI4320_LB_biol_rep_3

description:
WT_urea-induced_transcriptome.xlsx
ureC_LB_vs_WT_LB.xlsx
ureR_LB_vs_WT_LB.xlsx

value: LB


title: PD-nontreated_C

description: PD-nontreated

value: Untreated


title: PD-nontreated_B

description: PD-nontreated


title: genomic DNA from SDC HF2303 control sample replicate 1


title: BM110 A Replicate 3


title: N2, atp-2 RNAi treatment

first: chun-liang

last: Pan

address: Taipei City , Taiwan (R.O.C.)

institute: National Taiwan University

data_processing:
Illumina GA Pipeline software bcl2fastq v2.0
A sample were expected to generate 60M sequence reads.
Qualified reads were analyzed using TopHat/Cufflinks  and gene expression level was quantified as TPM (Transcripts Per Million mapped reads)
Statistical analysis of gene expression profiles was done with CummeRbund.
The reference genome (WBcel235(GCA_000002985.3)) and gene annotations were retrieved from the Ensembl genome browser.
Assembly: WBcel235(GCA_000002985.3
Supplementary files format and content: Excel file include FPKM values for two samples

organism: Caenorhabditis elegans

source_name: Whole worms

growth_protocol: C. elegans were cultured on nematode growth medium with HT115 E. coli strain

extract_protocol:
RNA was extracted by GENEzol RNA Isolation Kit (Geneaid)
RNA libraries for RNA-seq were prepared by using Agilent's SureSelect Strand specific RNA Library Preparation Kit.

treatment_protocol: HT115 with construct which allowed the bacterial to express atp-2 dsRNA was fed to the wroms in the experimental group.

value: Whole worms

value: HT115 expressing atp-2 dsRNA


title: genomic DNA from CSC HF2303 TMZ sample replicate 3

source_name: HF2303 CSCs

value: HF2303 CSCs


title: HI4320_LB+urea_biol_rep_2


title: HI4320_LB_biol_rep_2


title: BM110 A Replicate 2


title: HI4320_LB_biol_rep_1


title: PD-nontreated_A

description: PD-nontreated


title: N2, RNAi control

value: HT115 with empty vector


title: genomic DNA from CSC HF2303 TMZ sample replicate 2

value: Female


title: BM110 A Replicate 1


title: genomic DNA from CSC HF2303 TMZ sample replicate 1


title: genomic DNA from CSC HF2303 ionizing radiation sample replicate 3


title: Gut lamina propria macrophages sham vs pMCAO 24 h ( (pMCAO biol rep 5)

status: Public on Mar 24 2024

city: Melbourne

first: Deanna

middle: S

last: Deveson Lucas

state: Victoria

address: 15 Innovation walk, Monash University, Clayton

country: Australia

institute: Monash University

data_processing:
Raw fastq files have been analysed with RNAsik pipeline (Tsyganov et al. 2018) to produce raw genes count matrix and various quality control metrics.
For this analysis RNAsik pipeline (Tsyganov et al. 2018) ran with STAR aligner option (Dobin et al., 2013) mapping raw reads to the mus musculus GRCm38-mm10 (GCF_000001635.20, NCBI) reference genome, reads were quantified with featureCounts (Liao, Smyth, and Shi 2014).
Raw counts were then analysed with Degust (Powell 2015) web tool to do differential expression analysis to produce list of differentially expressed genes and several quality plots including classical multidimensional scaling (MDS) and MA plots
In this analysis limma voom (Law et al. 2014) was used for differential expression analysis. Degust (Powell 2015) largely follows limma voom workflow with typical counts per million (CPM) library size normalisation and trimmed mean of M values (TMM) normalisation (Robinson and Oshlack 2010) for RNA composition normalisation.
Assembly: GRCm38-mm10 (GCF_000001635.20, NCBI)
Supplementary files format and content: raw gene counts, text file, tab separated, includes all samples

source_name: not applicable

extract_protocol:
RNA was harvested using Rneasy micro plus kit (Qiagen). extracted RNA was tested using an RNA 6000 Pico kit on the Agilent 2100 Bioanalyser, 2.0 ng of total RNA was used for the construction of sequencing libraries.
An RNA cleavage approach was carried out to remove ribosomal RNA. Library construction and cDNA synthesis were performed using the Trio RNA-sequencing library preparation kit (protocol M01440v2, 2017; Tecan). Manual denaturing and on-board clustering were carried out using 70pM of library pool containing 1% PhiX (protocol 1000000109376 v3, 2020; Illumina). Sequencing was carried out on the NextSeq 2000 (Illumina) with P3 reagents and paired-end reading of 100 base pairs. Approximately 35 million reads were sequenced for each sample

treatment_protocol:
Sham or pMCAO surgery for 24 hours
Lamina propria macrophages from the whole small intestines were isolated via FACS

value: not applicable

value: Small intestine lamina propria macrophage

value: pMCAO


title: Gut lamina propria macrophages sham vs pMCAO 24 h  (pMCAO biol rep 4)


title: Gut lamina propria macrophages sham vs pMCAO 24 h (sham biol rep 4)

value: Sham


title: Gut lamina propria macrophages sham vs pMCAO 24 h  (pMCAO biol rep 2)


title: Gut lamina propria macrophages sham vs pMCAO 24 h  (pMCAO biol rep 3)


title: Gut lamina propria macrophages sham vs pMCAO 24 h (sham biol rep 2)


title: Gut lamina propria macrophages sham vs pMCAO 24 h (sham biol rep 1)


title: genomic DNA from CSC HF2303 ionizing radiation sample replicate 2


title: HI4320_LB+urea_biol_rep_1

value: bacterial


title: genomic DNA from CSC HF2303 ionizing radiation sample replicate 1


title: Gut lamina propria macrophages sham vs pMCAO 24 h (pMCAO biol rep 1)


title: Gut lamina propria macrophages sham vs pMCAO 24 h (sham biol rep 5)


title: genomic DNA from CSC HF2303 control sample replicate 3


title: Gut lamina propria macrophages sham vs pMCAO 24 h (sham biol rep 3)


title: Gut muscularis macrophages sham vs pMCAO 24 h (sham bio rep 4)

treatment_protocol:
Sham or pMCAO surgery for 24 hours
Muscularis macrophages

value: Small intestine muscularis macrophage


title: Gut muscularis macrophages sham vs pMCAO 24 h (sham bio rep 1)


title: Gut muscularis macrophages sham vs pMCAO 24 h (pMCAO rep 2)


title: Gut muscularis macrophages sham vs pMCAO 24 h (sham bio rep 3)


title: Gut epithelial cells sham vs pMCAO 24 h (pMCAO biol rep 1) [KP_58_S19]

source_name: Gut epithelial cells sham vs pMCAO 24 h (pMCAO)

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). extracted RNA was tested using an RNA 6000 Pico kit on the Agilent 2100 Bioanalyser, 2.0 ng of total RNA was used for the construction of sequencing libraries.
An RNA cleavage approach was carried out to remove ribosomal RNA. Library construction and cDNA synthesis were performed using the Trio RNA-sequencing library preparation kit (protocol M01440v2, 2017; Tecan). Manual denaturing and on-board clustering were carried out using 70pM of library pool containing 1% PhiX (protocol 1000000109376 v3, 2020; Illumina). Sequencing was carried out on the NextSeq 2000 (Illumina) with P3 reagents and paired-end reading of 100 base pairs. Approximately 35 million reads were sequenced for each sample

treatment_protocol:
Sham or pMCAO surgery for 24 hours
Epithelial cells from the whole small intestines were isolated via FACS

value: Small intestine epithelial cell


title: Gut epithelial cells sham vs pMCAO 24 h (pMCAO biol rep 2) [KP_62_S23]


title: Gut muscularis macrophages sham vs pMCAO 24 h (pMCAO rep 1)


title: Gut muscularis macrophages sham vs pMCAO 24 h (pMCAO rep 3)


title: genomic DNA from CSC HF2303 control sample replicate 2


title: Gut epithelial cells sham vs pMCAO 24 h (pMCAO biol rep 5) [KP_67_S28]


title: Gut muscularis macrophages sham vs pMCAO 24 h (sham bio rep 2)


title: Gut epithelial cells sham vs pMCAO 24 h (pMCAO biol rep 4) [KP_66_S27]


title: genomic DNA from CSC HF2303 control sample replicate 1


title: Gut epithelial cells sham vs pMCAO 24 h (pMCAO biol rep 3) [KP_63_S24]


title: Gut epithelial cells sham vs pMCAO 24 h (sham bio rep 7) [KP_72_S30]

source_name: Gut epithelial cells sham vs pMCAO 24 h (sham)


title: Gut epithelial cells sham vs pMCAO 24 h (sham bio rep 6) [KP_68_S29]


title: Gut epithelial cells sham vs pMCAO 24 h (sham biol rep 3) [KP_61_S22]


title: Gut epithelial cells sham vs pMCAO 24 h (sham biol rep 4)  [KP_64_S25]


title: Gut epithelial cells sham vs pMCAO 24 h (sham biol rep 1) [KP_59_S20]


title: Gut epithelial cells sham vs pMCAO 24 h (sham bio rep 5) [KP_65_S26]


title: morula_RAGxWT_26, mRNA-seq

city: Philadelphia

first: Natalie

middle: Alyce

last: Trigg

state: Pennsylvania

address: 421 Curie Blvd

institute: Children's Hospital of Philadelphia

data_processing:
Reads were mapped using RSEM and normalized to transcripts per million (tpm).
Assembly: mm10
Supplementary files format and content: xlsx spreadsheet with one tab per tissue type/comparison

source_name: Morula embryo

extract_protocol:
Single embryos, sired by control, germ-free or Rag2−/− sperm or eggs from control or GF mice were collected for single-embryo/egg RNA-sequencing. Embryos were transferred to a 96-well plate and fresh 1 × TCL buffer with 1% β-mercaptoethanol was added.
Nextera XT kit (Illumina)

value: Morula embryo

value: RAG KO x WT

tag: environment


title: Gut epithelial cells sham vs pMCAO 24 h (sham biol rep 2) [KP_60_S21]

tag: strain


title: morula_RAGxWT_27, mRNA-seq

tag: genotype


title: morula_RAGxWT_25, mRNA-seq


title: morula_RAGxWT_24, mRNA-seq


title: morula_RAGxWT_23, mRNA-seq


title: morula_RAGxWT_22, mRNA-seq


title: morula_RAGxWT_18, mRNA-seq


title: genomic DNA from SDC HF2303 control sample replicate 3

value: HF2303 SDCs


title: morula_RAGxWT_19, mRNA-seq


title: morula_RAGxWT_16, mRNA-seq


title: morula_RAGxWT_17, mRNA-seq


title: morula_RAGxWT_20, mRNA-seq


title: morula_RAGxWT_14, mRNA-seq


title: morula_RAGxWT_15, mRNA-seq


title: morula_RAGxWT_11, mRNA-seq


title: morula_RAGxWT_28, mRNA-seq


title: morula_RAGxWT_10, mRNA-seq


title: morula_RAGxWT_9, mRNA-seq


title: morula_RAGxWT_12, mRNA-seq


title: morula_RAGxWT_8, mRNA-seq


title: morula_RAGxWT_5, mRNA-seq


title: morula_RAGxWT_6, mRNA-seq


title: morula_RAGxWT_3, mRNA-seq


title: morula_RAGxWT_4, mRNA-seq


title: morula_RAGxWT_21, mRNA-seq


title: morula_GFxCR_15, mRNA-seq

value: WT


title: morula_RAGxWT_1, mRNA-seq


title: morula_GFxCR_17, mRNA-seq


title: morula_GFxCR_16, mRNA-seq


title: morula_RAGxWT_2, mRNA-seq


title: morula_RAGxWT_13, mRNA-seq


title: morula_GFxCR_12, mRNA-seq


title: morula_GFxCR_13, mRNA-seq


title: morula_GFxCR_9, mRNA-seq


title: BM110 B Replicate 2

value: cultures


title: morula_GFxCR_6, mRNA-seq


title: morula_GFxCR_7, mRNA-seq


title: morula_GFxCR_5, mRNA-seq


title: morula_GFxCR_11, mRNA-seq


title: morula_GFxCR_8, mRNA-seq


title: morula_GFxCR_14, mRNA-seq


title: morula_GFxCR_3, mRNA-seq


title: morula_CRxCR_42, mRNA-seq


title: morula_GFxCR_1, mRNA-seq


title: morula_GFxCR_2, mRNA-seq


title: morula_GFxCR_10, mRNA-seq


title: morula_GFxCR_4, mRNA-seq


title: morula_RAGxWT_7, mRNA-seq


title: morula_CRxCR_40, mRNA-seq


title: morula_CRxCR_39, mRNA-seq


title: morula_CRxCR_37, mRNA-seq


title: morula_CRxCR_41, mRNA-seq


title: morula_CRxCR_38, mRNA-seq


title: morula_CRxCR_36, mRNA-seq


title: morula_CRxCR_35, mRNA-seq


title: morula_CRxCR_32, mRNA-seq


title: morula_CRxCR_34, mRNA-seq


title: morula_CRxCR_31, mRNA-seq


title: morula_CRxCR_30, mRNA-seq


title: morula_CRxCR_28, mRNA-seq


title: morula_CRxCR_26, mRNA-seq


title: morula_CRxCR_24, mRNA-seq


title: morula_CRxCR_21, mRNA-seq


title: morula_CRxCR_23, mRNA-seq


title: morula_CRxCR_22, mRNA-seq


title: morula_CRxCR_27, mRNA-seq


title: morula_CRxCR_25, mRNA-seq


title: morula_CRxCR_19, mRNA-seq


title: morula_CRxCR_20, mRNA-seq


title: morula_CRxCR_43, mRNA-seq


title: morula_CRxCR_15, mRNA-seq


title: morula_CRxCR_17, mRNA-seq


title: morula_CRxCR_13, mRNA-seq


title: morula_CRxCR_14, mRNA-seq


title: morula_CRxCR_18, mRNA-seq


title: morula_CRxCR_11, mRNA-seq


title: morula_CRxCR_33, mRNA-seq


title: morula_CRxCR_10, mRNA-seq


title: morula_CRxCR_8, mRNA-seq


title: morula_CRxCR_6, mRNA-seq


title: morula_CRxCR_9, mRNA-seq


title: morula_CRxCR_7, mRNA-seq


title: morula_CRxCR_5, mRNA-seq


title: morula_CRxCR_29, mRNA-seq


title: morula_CRxCR_3, mRNA-seq


title: morula_CRxCR_4, mRNA-seq


title: morula_CRxCR_2, mRNA-seq


title: morula_CRxCR_1, mRNA-seq


title: 4cell_RAGxWT_20, mRNA-seq

source_name: 4 cell embryo

value: 4 cell embryo


title: 4cell_RAGxWT_21, mRNA-seq


title: 4cell_RAGxWT_18, mRNA-seq


title: morula_CRxCR_16, mRNA-seq


title: 4cell_RAGxWT_14, mRNA-seq


title: 4cell_RAGxWT_16, mRNA-seq


title: 4cell_RAGxWT_19, mRNA-seq


title: 4cell_RAGxWT_13, mRNA-seq


title: 4cell_RAGxWT_17, mRNA-seq


title: 4cell_RAGxWT_10, mRNA-seq


title: 4cell_RAGxWT_11, mRNA-seq


title: 4cell_RAGxWT_12, mRNA-seq


title: 4cell_RAGxWT_9, mRNA-seq


title: morula_CRxCR_12, mRNA-seq


title: 4cell_RAGxWT_8, mRNA-seq


title: 4cell_RAGxWT_7, mRNA-seq


title: 4cell_RAGxWT_6, mRNA-seq


title: 4cell_RAGxWT_4, mRNA-seq


title: 4cell_GFxCR_14, mRNA-seq


title: 4cell_GFxCR_15, mRNA-seq


title: 4cell_RAGxWT_3, mRNA-seq


title: 4cell_GFxCR_12, mRNA-seq


title: 4cell_GFxCR_13, mRNA-seq


title: 4cell_RAGxWT_15, mRNA-seq


title: 4cell_GFxCR_8, mRNA-seq


title: 4cell_GFxCR_11, mRNA-seq


title: 4cell_GFxCR_6, mRNA-seq


title: 4cell_GFxCR_3, mRNA-seq


title: 4cell_GFxCR_4, mRNA-seq


title: 4cell_GFxCR_5, mRNA-seq


title: 4cell_GFxCR_1, mRNA-seq


title: 4cell_GFxCR_10, mRNA-seq


title: 4cell_GFxCR_2, mRNA-seq


title: 4cell_CRxGF_8, mRNA-seq


title: 4cell_CRxGF_6, mRNA-seq


title: 4cell_RAGxWT_5, mRNA-seq


title: 4cell_CRxGF_7, mRNA-seq


title: 4cell_RAGxWT_2, mRNA-seq


title: 4cell_CRxGF_5, mRNA-seq


title: 4cell_RAGxWT_1, mRNA-seq


title: 4cell_CRxGF_2, mRNA-seq


title: 4cell_CRxGF_3, mRNA-seq


title: 4cell_CRxGF_1, mRNA-seq


title: 4cell_CRxCR_24, mRNA-seq


title: 4cell_GFxCR_9, mRNA-seq


title: 4cell_CRxCR_23, mRNA-seq


title: 4cell_CRxCR_25, mRNA-seq


title: 4cell_GFxCR_7, mRNA-seq


title: 4cell_CRxCR_22, mRNA-seq


title: 4cell_CRxCR_20, mRNA-seq


title: 4cell_CRxCR_21, mRNA-seq


title: 4cell_CRxCR_19, mRNA-seq


title: 4cell_CRxCR_17, mRNA-seq


title: 4cell_CRxGF_4, mRNA-seq


title: 4cell_CRxCR_14, mRNA-seq


title: 4cell_CRxCR_15, mRNA-seq


title: 4cell_CRxCR_13, mRNA-seq


title: 4cell_CRxCR_10, mRNA-seq


title: 4cell_CRxCR_8, mRNA-seq


title: 4cell_CRxCR_11, mRNA-seq


title: 4cell_CRxCR_9, mRNA-seq


title: 4cell_CRxCR_7, mRNA-seq


title: 4cell_CRxCR_5, mRNA-seq


title: 4cell_CRxCR_3, mRNA-seq


title: 4cell_CRxCR_6, mRNA-seq


title: 4cell_CRxCR_4, mRNA-seq


title: 4cell_CRxCR_2, mRNA-seq


title: liver_CRxCR_F1_4, mRNA-seq

data_processing:
Transcriptomic analysis was performed in the R statistical computing environment version 4.2 and RStudio version 2022.02.1 using a pipeline adopted from an open-source toolkit for RNA sequencing analysis (Berry et al. 2021).
Assembly: GRCm39cDNA
Supplementary files format and content: xlsx spreadsheet with one tab per tissue type/comparison

source_name: Liver

extract_protocol:
Liver tissue was snap frozen and stored at −80°C until further processing. RNA was extracted from tissue using TRIzol extraction
Illumina stranded mRNA kit

value: Liver

tag: generation


title: liver_CRxCR_F1_2, mRNA-seq


title: 4cell_CRxCR_18, mRNA-seq


title: liver_CRxCR_F1_1, mRNA-seq


title: liver_GFxCR_F1_3, mRNA-seq


title: liver_CRxCR_F1_3, mRNA-seq


title: liver_GFxCR_F1_2, mRNA-seq


title: liver_GFxCR_F1_1, mRNA-seq


title: 4cell_CRxCR_16, mRNA-seq


title: 4cell_CRxCR_12, mRNA-seq


title: S_small_v2

city: Tallahassee

first: Li

last: Guo

address: Thrasher Medical Researcher Building, Suite 2300-D

department: College of Medicine

institute: Florida State University

description: 10X Genomics

data_processing:
FASTQ files were aligned to mm10 using Cell Ranger V.5.0.1.  Data quality control, filter, dimension reduction, clustering, and differential expression analysis  was performed in Seurat V4.1.1. Briefly, cells were filtered with nFeature_RNA > 200, nFeature_RNA < 6000,  percent.mt < 5, and nCount_RNA < 50000. Sctransform was used to normalize the data and regress out potential sample batch effect. RunPCA, RunUMAP, FindNeighbors, and FindClusters (resolution of 0.6) were then sequentially applied to perform dimension reduction and cell clustering. FindAllMarkers were then called with min.pct=0.1 and logfc.threshold=0.25 to identify markers for each clusters.
Assembly: mm10
Supplementary files format and content: seurat objects containing gene expression matrix, cell clustering, and other metadata

source_name: small ducts

extract_protocol:
Whole pancreas ducts were isolated, seperated manually by size under a fluorescent stereoscope. Small, medium, and big ducts were further digested using 1mL of trypLE Express for 5-10min (depending on the size of the ducts) at 37ºC, vigorously shaking the digestion mix every 2-3 min. After digestion, tryPLE was neutralized by adding 10mL of blocking buffer, centrifuged, and washed twice. Sox9:eGFP positive cells were sorted from small, medoim and large ducts via FACS. Ten thousand sorted cells from each ductal fraction were pooled from 3 male mice in two independent experiments.
3’ mRNA library was prepared following 10xGenomics manufacturing instructions.
scRNA-seq, Sequencing was carried out as paired-end (PE77) using NovaSeq6000.

value: pancreas

value: small ducts

value: Sox9:eGFP positive cells


title: S_small

description: 10X Genomics


title: M_medium_v2

description: 10X Genomics

source_name: medium ducts

value: medium ducts


title: M_medium

description: 10X Genomics


title: Neurospora crassa AtrR mutant, Control, rep3

city: Beijing

first: pengju

last: YU

address: No.1 Beichen West Road

institute: Institute of Microbiology, Chinese Academy of Sciences

data_processing:
Basecalling was performed using a software developed for DNBSEQ-T7.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke v1.5.2, then mapped to Neurospora crassa whole genome (GCA_000182925.2) using HISAT v2.0.4 with parameters -p 8 --phred64 --sensitive -I 1 -X 10000
After analyzing the efficiency of aligned clean reads to reference genome by Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200, gene expression were calculated as Fragments Per Kilobase of exon per Megabase of library size (FPKM) using RSME v1.2.12 with default parameters.
Differential expressed genes were caracterized using a protocol from Audic S. et al.,  Genome Research, 1997.
Assembly: GCA_000182925.2
Supplementary files format and content: excel file include FPKM values for all Samples and data for differential expressed genes between each two Samples, as well as the annotation of each genes.

organism: Neurospora crassa

source_name: mycelia

growth_protocol: Briefly, 14 small pieces of mycelial mats (1-2 mm2) were grown in liquid Vogel’s medium for 12 h and then treated with or without sterol biosynthesis inhibitors for 12 h.

extract_protocol:
Harvested samples were immediately frozen, and then ground into fine powder in liquid nitrogen. Total RNA extraction was performed according to the standard TRIzol protocol (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Sterol biosynthesis inhibitors, including ketoconazole (Sigma), terbinafine (J&K), and amorolfine (J&K), were added, with final concentrations of 1.5, 2.5 and 0.375 μg/mL, respectively.

value: mycelia

value: atrR knockout

tag: treatment

value: No treatment


title: Neurospora crassa AtrR mutant, AMO, rep1

value: Amorolfine


title: Neurospora crassa, AMO-AtrR, rep1


title: Neurospora crassa, Control-AtrR, rep3


title: Neurospora crassa, AMO-AtrR, rep3


title: Neurospora crassa AtrR mutant, Control, rep1


title: Neurospora crassa, Control-AtrR, rep2


title: Neurospora crassa, AMO-AtrR, rep2


title: 4cell_CRxCR_1, mRNA-seq


title: Neurospora crassa, Control-AtrR, rep1


title: B_big_v2

description: 10X Genomics

source_name: big ducts

value: big ducts


title: genomic DNA from SDC HF2303 control sample replicate 2

value: Female

tag: cell line


title: Neurospora crassa AtrR mutant, AMO, rep2


title: Neurospora crassa AtrR mutant, Control, rep2


title: B_big

description: 10X Genomics

tag: cell type


title: Neurospora crassa AtrR mutant, AMO, rep3


title: Neurospora crassa SAH2 mutant, AMO, rep2

value: sah-2 knockout


title: Neurospora crassa SAH2 mutant, AMO, rep3


title: Neurospora crassa SAH2 mutant, Control, rep3


title: 4cell_CRxGF_9, mRNA-seq


title: Neurospora crassa SAH2 mutant, AMO, rep1


title: NMCM, CVB3,rep2

city: Wuhan

first: Yan

last: Zhuang

state: Hubei

address: 1095# Jiefang Ave

department: Tongji Hospital

institute: Huazhong University of Science and Technology

data_processing:
The libraries were subjected to quality validation using the Agilent 2100 TapeStation system (Agilent).
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions.
After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Differential expression analysis was performed using the DESeq2 R package (1.20.0).
Assembly: mm10
Supplementary files format and content: Office open XML excel spreadsheet includes raw count for each sample.
Supplementary files format and content: Office open XML excel spreadsheet includes FPKM values for each sample.

source_name: Primary cell

growth_protocol: DMEM containing 10% FBS with 5%CO2 at 37°C.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA).
For RNA-seq,the RNA was then reverse-transcribed, using the TruSeq RNA Library Prep Kit (Illumina).

treatment_protocol: Mice or mouse primary cardiomyocytes were treated with CVB3 and ST2

value: Primary cell

value: mouse primary cardiomyocyte

value: CVB3 treatment


title: NMCM, CVB3 and ST2，rep3

value: CVB3 and ST2 treatment


title: Neurospora crassa SAH2 mutant, Control, rep2


title: NMCM, CVB3 and ST2，rep2


title: NMCM, CVB3 and ST2，rep1


title: Neurospora crassa, AMO-SAH2, rep3

value: WT


title: Neurospora crassa SAH2 mutant, Control, rep1


title: NMCM, sST2, rep4

value: sST2 treatment


title: Neurospora crassa, AMO-SAH2, rep2


title: NMCM, sST2, rep1


title: NMCM, sST2, rep3


title: NMCM, Control,rep4


title: Neurospora crassa, Control-SAH2, rep1


title: Neurospora crassa NcSR mutant, KTC, rep3

value: ncSR knockout

value: Ketoconazole


title: Neurospora crassa, AMO-SAH2, rep1


title: Neurospora crassa, Control-SAH2, rep2


title: Neurospora crassa, Control-SAH2, rep3


title: NMCM, Control,rep3


title: NMCM, Control,rep2


title: NMCM, sST2, rep2


title: Heart,CVB3 and ST2, rep3

source_name: Heart

value: Heart


title: Neurospora crassa NcSR mutant, KTC, rep1


title: Heart,CVB3 and ST2, rep2


title: Heart,CVB3 and ST2, rep1


title: Neurospora crassa NcSR mutant, KTC, rep2


title: NMCM, Control,rep1


title: Heart,CVB3,rep2


title: Neurospora crassa NcSR mutant, Control, rep1


title: Heart,CVB3,rep1


title: Neurospora crassa, AMO, rep3


title: Neurospora crassa, AMO, rep2


title: Heart,Control,rep2


title: NMCM, CVB3,rep1


title: Neurospora crassa, AMO, rep1


title: Neurospora crassa, KTC, rep3


title: Neurospora crassa, KTC, rep2


title: Neurospora crassa, KTC, rep1


title: Neurospora crassa, TERB, rep3

value: Terbinafine


title: Heart,Control,rep1