title: 18KO-3

city: wenzhou

first: Gaozan

last: Tong

state: 浙江省

address: School of Pharmaceutical Science

institute: wenzhou medical university

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
For RNA-seq: The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0).
For RNA-seq: The reads mapped the genome were calculated using featureCounts (v1.6.3).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file include RPKM values for each Sample

source_name: liver

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent.
For RNA-seq: VAHTSTM Stranded mRNA-seq Library Prep Kit for Illumina v2 was used for library construction.

value: liver

value: FGF18 KNOCKOUT

value: hepatic ischemia reperfusion


title: control_mouse_rep2

status: Public on Sep 05 2023

type: RNA

city: Rochester

first: Charles

middle: L

last: Howe

state: MN

address: 200 First St SW

department: Neurology

country: USA

institute: Mayo Clinic

hyb_protocol: RNA was hybridized to Affymetrix GeneChip Mouse Gene 2.0 ST arrays following manufacturer's instructions by the University of Illinois at Chicago Core Genomics Facility.

scan_protocol: Arrays were scanned on the Affymetrix GeneTitan System following manufacturer's instructions by the University of Illinois at Chicago Core Genomics Facility.

data_processing: Raw data (CEL files) were imported into Transcriptome Analysis Console (Affymetrix) and normalized by robust multiarray average (RMA).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: neuron-specific polyribosomal RNA

label_protocol: RNA was labeled following manufacturer's instructions by the University of Illinois at Chicago Core Genomics Facility.

growth_protocol: All mice were housed and maintained in standard facilities in accordance with the guidelines of the Mayo Clinic Institutional Animal Care and Use Committee.

extract_protocol: RNA was extracted from anti-HA antibody immunoprecipitates using the RNeasy micro plus kit (Qiagen).

treatment_protocol: EAE = experimental autoimmune encephalomyelitis induced by MOG(35-55) peptide; CUP = Purina Test Diet 5LG6 containing 0.3% bis(cyclohexanone)oxaldihydrazone; CON = mice fed control chow.

tag: tissue

value: brain

tag: age

value: adult

tag: genotype

tag: treatment

value: Unmanipulated control mice.


title: PC3-Treated 01

type: SRA

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

country: China

institute: Chinese Academy of Sciences

description:
PE150 high throughout data
A_vs_B.deseq2.annot
DA02T1

library_source: transcriptomic

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 h38.p10 whole genome using bowtie v 0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Tab-delimited text files include TPM values and counts for each Sample

organism: Homo sapiens

source_name: Human prostate cancer cells

growth_protocol: Prostate cancer cells were routinely cultured and passaged (typically 0.5–1 × 10^6 cells in a T25 flask) in DMEM media supplemented with 10% FBS.

extract_protocol:
At the end of cell culture, media were removed, cells were lysed with Trizol reagent and total RNA was harvested. Illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101, RS-122-2102) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Upon 80% confluency, cancer cells were treated for 3 days with conditioned media derived from prostate stromal cells, either naive (control) or ectopically expressing human PDK4.

tag: cell line

tag: cell type

value: prostate cancer cells

tag: cell source

value: Carcinoma, derived from the metastatic site, bone of a prostate cancer patient

tag: passage

tag: name

value: PC3 treated (PSC27-PDK4 CM)

value: conditioned media from prostate stromal cells, ectopically expressing human PDK4


title: control_mouse_rep1


title: PC3-CTRL 02

description:
PE150 high throughout data
A_vs_B.deseq2.annot
DA01C2

value: PC3 control (PSC27 CM)

value: conditioned media from prostate stromal cells, naive (control)


title: PC3-CTRL 01

description:
PE150 high throughout data
A_vs_B.deseq2.annot
DA01C1


title: IR2

value: IR


title: IR3


title: C3H10T1/2 MSCs, H3K4me3, shNFIB, day 7

city: Incheon

first: Jangyhun

last: Choi

state: Incheon

address: 5N521, 100 Inha-ro, Michuhol-gu

department: Department of biological sciences

country: South Korea

institute: Inha University

library_source: genomic

data_processing:
Raw reads were trimmed to discard adaptor sequence and low quality sequence using Trimmomatic version 0.39 with the following parameters: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
Bowtie2 was used to align trimmed reads with the mouse genome assembly GRCm38 (mm10) on local mode (--local) with default parameters.
The resulting reads underwent three stages of processing using SAMtools version 1.12. First, high-quality mapped reads (MAPQ > 30) were converted into BAM file using view -bh -q 30 options. PCR duplicates were then removed by rmdup function with default parameters. Then, the resulting BAM files were sorted and indexed using sort and index function, respectively.
To call-peak analysis, BAM files were converted into BED files using Bedtools version 2.30.0 with the parameters: bamToBed -i.
ChIP-seq coverage tracks (bigwig files) were generated using bamCoverage of deepTools package version 3.5.1 as follows   parameters: --normalizeUsing RPGC –effectiveGenomeSize 1.87e9 -bs 1 -e.
Assembly: GRCm38/mm10
Supplementary files format and content: bigwig files

molecule: genomic DNA

growth_protocol: Mouse C3H10T1/2 mesenchymal stem cells were grown in DMEM (WelGENE) containing 10% FBS (WelGENE) and penicillin-streptomycin solution (Hyclone) in humidified atmosphere with 5% CO2 at 37ºC.

extract_protocol:
Cells were cross-linked with 1% formaldehyde (Sigma). Chromatins ranging from 200 and 700 base pairs were obtained following standard ChIP protocol. Chromatin (300 – 400 µg) was precleared with Protein A/G (Pierce) and incubated overnight with 8 µg of NFIB (Atlas, HPA003956), 8 µg of MLL1 (Bethyl, A300-086A), or 4 µg of H3K4me3 (Abcam, ab8580) antibodies. Immune complexes were reverse-crosslinked overnight. The resulting samples were treated with 10 µg of RNase A (Invitrogen) and 20 µg of Proteinase K (Invitrogen) and then ChIP'd DNA was purified with phenol-chloroform solution (Sigma).
The integrity of genomic DNA was assessed by an Agilent Bioanalyzer 2100 (Agilent Technologies). The libraries were constructed using a TruSeq ChIP library preparation kit (Illumina).

treatment_protocol: To induce osteogenic differentiation, cells were cultivated in osteogenic medium containing 20 mM β-glycerophosphate (Sigma), 100 μg/mL ascorbic acid 2-phosphate (Sigma), and 0.1 μM dexamethasone (Sigma) for 2 days. The osteogenic medium was replenished every other day for 21 days.

value: Mesenchymal stem cells

value: NFIB knockdown

tag: antibody

value: H3K4me3 (Abcam, ab8580)

tag: time point

value: Day 7

value: Osteogenic media


title: C3H10T1/2 MSCs, H3K4me3, shControl, day 7

value: WT


title: 18KO-1

value: liver

value: FGF18 KNOCKOUT

value: hepatic ischemia reperfusion


title: IR1


title: C3H10T1/2 MSCs, H3K4me3, shMLL1, day 0

value: MLL1 knockdown

value: Day 0

value: Untreated


title: C3H10T1/2 MSCs, H3K4me3, shMLL1, day 7


title: C3H10T1/2 MSCs, H3K4me3, shNFIB, day 0


title: 18KO-2


title: C3H10T1/2 MSCs, H3K4me3, shControl, day 0


title: C3H10T1/2 MSCs, NFIB, shMLL1, day 0

value: NFIB (Atlas, HPA003956)


title: C3H10T1/2 MSCs, NFIB, shNFIB, day 7


title: C3H10T1/2 MSCs, NFIB, shControl, day 0


title: C3H10T1/2 MSCs, MLL1, shControl, day 0

value: MLL1 (Bethyl, A300-086A)


title: C3H10T1/2 MSCs, NFIB, shControl, day 7


title: ATF4 KO cells, Vehicle treated [MM217]

city: Tempe

first: Blaise

last: Mariner

state: AZ

address: 427 E Tyler Mall, LSC 356

department: School of Life Sciences and Center for Evolution and Medicine

institute: Arizona State University

data_processing:
Reads were aligned and quantified using HISAT2 and HTSEQ after trimming.
Data analysis and differential expression utilized R programming and associated libraries such as limma.
Assembly: mm10
Supplementary files format and content: comma-delimited text files include raw reads

source_name: Mouse embryonic fibroblast

growth_protocol: Mouse embryonic fibroblasts cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and amino acids in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Quick-RNA Midiprep Kit (Zymo).
RNA libraries for RNA-seq were prepared by Azenta Sciences.

treatment_protocol:
7x ATF4 expression was induced with 600nM Borrelidin treatment
DMSO and Borrelidin were delivered in growth medium and incubated for 7 hours. Borrelidin was purchased from BioViotica (BVT-0098).

value: Mouse embryonic fibroblast

tag: biol rep

value: biol rep 9

value: ATF4 KO

value: DMSO

tag: time

value: 7 hours


title: C3H10T1/2 MSCs, NFIB, shNFIB, day 0

value: Mesenchymal stem cells

value: NFIB knockdown


title: ATF4 KO cells, Borrelidin treated [MM219]

value: biol rep 12

value: 600nM Borrelidin


title: C3H10T1/2 MSCs, input, shControl, day 0

value: WT


title: ATF4 KO cells, Vehicle treated [MM214]

value: biol rep 6


title: ATF4 KO, Vehicle treated [MM218]

value: biol rep 10


title: ATF4 KO cells, Vehicle treated [MM216]

value: biol rep 8


title: C3H10T1/2 MSCs, NFIB, shMLL1, day 7

value: MLL1 knockdown

value: Day 7

value: Osteogenic media


title: ATF4 KO, Vehicle treated [MM220]


title: ATF4 KO cells, Vehicle treated [MM215]

value: biol rep 7


title: ATF4 KO cells, Vehicle treated [MM213]

value: Mouse embryonic fibroblast

value: biol rep 5


title: ATF4 KO cells, Borrelidin treated [MM210]

value: biol rep 11

value: ATF4 KO


title: Wild type cells, Vehicle treated [MM211]

value: Wild type

value: DMSO

value: 7 hours


title: ATF4 KO cells, Borrelidin treated [MM205]


title: ATF4 KO cells, Borrelidin treated [MM208]

value: biol rep 9


title: ATF4 KO cells, Vehicle treated [MM212]

value: biol rep 4


title: ATF4 KO cells, Borrelidin treated [MM202]

value: biol rep 3

value: 600nM Borrelidin


title: ATF4 KO cells, Borrelidin treated [MM201]

value: biol rep 2


title: ATF4 KO cells, Vehicle treated [MM193]


title: ATF4 KO cells, Borrelidin treated [MM206]


title: ATF4 KO cells, Vehicle treated [MM192]


title: ATF4 KO cells, Borrelidin treated [MM199]

value: biol rep 1


title: ATF4 KO cells, Borrelidin treated [MM203]


title: MNaseseq_G1_1

city: Seattle

first: Eric

middle: Jan

last: Foss

state: WA

address: 1100 Fairview Ave N

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

description:
Sequencing was performed using an Illumina HiSeq 2500 in Rapid mode employing a paired-end, 50 base read length (PE50) sequencing strategy. Image analysis and base calling was per- formed using Illumina’s Real Time Analysis v1.18 software, followed by ‘demultiplexing’ of indexed reads and generation of FASTQ files, using Illumina’s bcl2fastq Conversion Software v1.8.4.
processed_data_for_MNase_seq_size_range_151bpto200bp_083023_1.txt

data_processing:
align to sacCer3 genome with bwa, using the -n 1 option
Picard's CleanSam
Picard's SortSam
Picard's FixMateInformation
Picard's AddOrReplaceReadGroups
Picard's ValidateSamFile
Picard's MergeSamFiles
perl script step_1_in_custom_quantification_of_bwa_aligned_reads_121222_1.pl
perl script step_2_if_quantifying_entire_lengths_of_library_inserts_121222_1.pl
perl script step_2_if_quantifying_midpoints_of_library_inserts_121222_1.pl
Assembly: sacCer3
Supplementary files format and content: processed_data_for_MNase_seq_size_range_151bpto200bp_083023_1.txt:  columns (1) chromosome; (2) coordinate; (3) 151-200 base pair library inserts, quantified along entire insert; (4)  151-200 base pair library inserts, quantified at insert midpoints.
Supplementary files format and content: 17618_CMBSs_chr_coord_rank_082923_1.txt:  columns (1) chromosome; (2) coordinate; (3) abundance; (4) rank

organism: Saccharomyces cerevisiae

source_name: yeast cells

extract_protocol:
ChEC-seq was carried out as previously described (Foss et al., 2019; Foss et al., 2021). Briefly, cells were centrifuged at 1,500 x g for 2 mins, and washed twice in cold Buffer A (15 mM Tris pH 7.5, 80 mM KCl, 0.1 mM EGTA) without additives. Washed cells were carefully resuspended in 570 μL Buffer A with additives (0.2 mM spermidine, 0.5 mM spermine, 1 mM PMSF, ½ cOmplete ULTRA protease inhibitors tablet, Roche, per 5 mL Buffer A) and permeabilized with 0.1% digitonin in 30 ̊ C water bath for 5 min. Permeabilized cells were cooled at room temperature for 1 min and 1/5th of cells were transferred in a tube with freshly made 2x stop buffer (400 mM NaCl, 20 mM EDTA, 4 mM EGTA)/1% SDS solution for undigested control. Micrococcal nuclease was activated with 5.5 μL of 200 mM CaCl2 at various times (30 sec, 1 min, 5 mins, and 10 mins) and the reaction stopped with 2x stop buffer/1% SDS. Once all time points were collected, proteinase K was added to each collected time points and incubated at 55 ̊ C water bath for 30 mins. DNA was extracted using phenol/chloroform and precipitated with ethanol. Micrococcal nuclease digestion was analyzed via gel electrophoresis prior to proceeding to library preparation. Library was prepared as previously described used using total DNA, without any fragment size selection (Foss et al., 2019; Foss et al., 2021).
We carried out MNase-Seq as previously described (Foss et al., 2017). Briefly, cells grown to log phase in rich medium, Yeast Peptone Agar with 2% glucose (YEPD), from an overnight 25 mL culture were synchronized with 3 μM alpha-factor for 1.5 hrs. at 30 ̊ C. Arrested cells were crosslinked with 1% formaldehyde for 30 min at room temperature water bath with shaking. Formaldehyde was quenched with 125 mM glycine and cells were centrifuged at 3000 rpm for 5 min. Cells were washed twice with water and resuspended in 1.5 mL Buffer Z (1 M sorbitol, 50 mM Tris-HCl pH 7.4) with 1 mM beta-mercaptoethanol (1.1 μL of 14.3 M beta-mercaptoethanol diluted 1:10 in Buffer Z) per 25 mL culture. Cells were treated with 100 μL 20 mg/ mL zymolyase at 30 ̊ C for 20–30 min depending on cell density. Spheroplasts were centrifuged at 5000 rpm for 10 min and resuspended in 5 mL NP buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris pH 7.4, 5 mM MgCl2, 1 mM CaCl2) supplemented with 500 μM spermidine, 1 mM beta-mercaptoethanol and 0.075% NP-40. Nuclei were aliquoted in tubes with varying concentrations of micrococcal nuclease (Worthington), mixed via tube inversion, and incubated at room temperature for 20 mins. Chromatin digested with 1.9 U– 7.5 U micrococcal nuclease per 1/5th of spheroplasts from a 25 mL culture yielded appropriate mono-, di-, tri- nucleosome protected fragments for next- generation sequencing. Digestion was stopped with freshly made 5x stop buffer (5% SDS, 50 mM EDTA) and proteinase K was added (0.2 mg/ml final concentration) for an overnight incubation at 65 ̊ C to reverse crosslinking. DNA was extracted with phenol/chloroform and precipitated with ethanol. Micrococcal nuclease digestion was analyzed via gel electrophoresis prior to proceeding to library preparation.
as described previously (PMID: 22025700)

treatment_protocol: alpha factor (G1) arrest:  shift log phase culture to 3µM alpha factor for 1.5 hours; HU arrest:  shift log phase culture to 200 mM HU for 50 minutes

value: yeast cells

value: Mat A, his3, leu2, met15, ura3, hmla::HYG

value: G1 arrest with alpha factor; MNase-seq


title: MCM2ChEC_HU_1

description:
Sequencing was performed using an Illumina HiSeq 2500 in Rapid mode employing a paired-end, 50 base read length (PE50) sequencing strategy. Image analysis and base calling was per- formed using Illumina’s Real Time Analysis v1.18 software, followed by ‘demultiplexing’ of indexed reads and generation of FASTQ files, using Illumina’s bcl2fastq Conversion Software v1.8.4.
17618_CMBSs_chr_coord_rank_082923_1.txt

growth_protocol: cells grown to log phase in rich medium, Yeast Peptone Agar with 2% glucose (YEPD)

value: Mat A, his3, leu2, ura3, met15, hmla::NAT, MCM2 3x Flag Mnase tag with KanMX

value: HU arrest (shift log phase culture to 200 mM HU); Chromatin Endogenous Cleavage (ChEC)


title: MCM2ChEC_log_1

value: Mat A, his3, leu2, met15, ura3, hmla::HYG, with MCM2 MNase 3xFlag Tag with KanMx

value: log phase; Chromatin Endogenous Cleavage (ChEC)


title: MCM2ChEC_HU_2


title: MCM4ChEC_G1_1

value: Mat A, his3, leu2, met15, ura3, hmla::HYG, with MCM4 MNase 3xFlag Tag with KanMx

value: G1 arrest with alpha factor; Chromatin Endogenous Cleavage (ChEC)


title: Wild type cells, Borrelidin treated [MM186]

value: Mouse embryonic fibroblast

value: biol rep 12

value: Wild type


title: MCM2ChEC_G1_4


title: MCM2ChEC_G1_5


title: Wild type cells, Borrelidin treated [MM185]

value: biol rep 11

value: 7 hours


title: MCM2ChEC_log_2


title: ATF4 KO cells, Borrelidin treated [MM209]

value: biol rep 10

value: ATF4 KO

value: 600nM Borrelidin


title: ATF4 KO cells, Borrelidin treated [MM207]

value: biol rep 8


title: ATF4 KO cells, Vehicle treated [MM188]

value: biol rep 1

value: DMSO


title: Wild type cells, Borrelidin treated [MM183]

value: biol rep 9


title: ATF4 KO cells, Borrelidin treated [MM204]

value: biol rep 5


title: MCM6ChEC_G1_2

value: yeast cells

value: Mat A, his3, leu2, met15, ura3, hmla::HYG, with MCM6 MNase 3xFlag Tag with KanMx


title: Wild type cells, Borrelidin treated [MM182]


title: MCM2ChEC_G1_2

value: Mat A, his3, leu2, ura3, met15, hmla::NAT, MCM2 3x Flag Mnase tag with KanMX


title: MCM6ChEC_G1_1

value: G1 arrest with alpha factor; Chromatin Endogenous Cleavage (ChEC)


title: MCM2ChEC_G1_1

value: Mat A, his3, leu2, met15, ura3, hmla::HYG, with MCM2 MNase 3xFlag Tag with KanMx


title: Wild type cells, Borrelidin treated [MM181]

value: Mouse embryonic fibroblast

value: biol rep 7


title: ANT 3

city: Guangzhou

first: Neng

last: Jiang

address: 651 Dongfeng East Road, Guangzhou 510060, P. R. China

institute: Sun Yat-sen University Cancer Center

description: Patient 3 (tumor). Exiqon miRNA Array: Prepare the RNA Sample and RNA Sample QC; miRNA labeling; miRNA array hybridization; miRNA array scanning and analysis

hyb_protocol: After stopping the labeling procedure, briefly spin the reaction and leave it at 4°C. The labeled sample is now ready for hybridization on the array. Hybridization should preferably occur within 1-2h. Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to array manual.

scan_protocol: The hybridized chips were scanned with an Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: GenePix pro V6.0 is used to read the raw intensity of the image. The intensity of green signal is calculated after background. subtraction and four Replicated spots of each probe on the same slide have been averaged.

source_name: primary lung cancer

label_protocol: miRNAs were  labeled with the miRCURYTM Array Power Labeling kit (Cat #208032-A, Exiqon) according to the manufacturer’s guideline for miRNAs labelling.

extract_protocol: Total RNA was extracted from fresh tissue samples by TRIzol Reagent (Invitrogen life technologies).

value: adjacent nontumor tissues

tag: status after 5 years

value: Alive

tag: histology

value: NSCLC

value: 61 years

tag: Sex

value: Female

tag: Stage

value: IB


title: Wild type cells, Borrelidin treated [MM179]

value: Wild type

value: 600nM Borrelidin

value: 7 hours


title: Wild type cells, Borrelidin treated [MM184]

value: biol rep 10


title: Wild type cells, Borrelidin treated [MM178]

value: biol rep 4


title: Wild type cells, Vehicle treated [MM174]

value: DMSO


title: Wild type cells, Borrelidin treated [MM176]

value: biol rep 2


title: MCM2ChEC_G1_3

value: yeast cells

value: G1 arrest with alpha factor; Chromatin Endogenous Cleavage (ChEC)


title: ANT 2

description: Patient 2 (non-tumor). Exiqon miRNA Array: Prepare the RNA Sample and RNA Sample QC; miRNA labeling; miRNA array hybridization; miRNA array scanning and analysis

tag: tissue

value: Dead

value: 70 years

value: Male

value: IIIA


title: Wild type cells, Borrelidin treated [MM175]

value: Mouse embryonic fibroblast

value: biol rep 1


title: Wild type cells, Vehicle treated [MM173]

value: biol rep 9


title: Wild type cells, Vehicle treated [MM169]

value: biol rep 6


title: Tumor 2

description: Patient 2 (tumor). Exiqon miRNA Array: Prepare the RNA Sample and RNA Sample QC; miRNA labeling; miRNA array hybridization; miRNA array scanning and analysis

value: primary lung cancer

value: NSCLC

tag: age


title: Tumor 1

description: Patient 1 (tumor). Exiqon miRNA Array: Prepare the RNA Sample and RNA Sample QC; miRNA labeling; miRNA array hybridization; miRNA array scanning and analysis

value: Alive

value: 55 years

value: IIB


title: G1_Input

city: Bengaluru

first: Amit

last: Singh

state: KARNATAKA

address: Sir CV Raman Road

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

description: Samples without undergoing immunoprecipitation served as Input control (Replicate 1)

data_processing:
The single-end reads with raw read quality of Phred score ≥ 20 were mapped using bwa (version 0.7.12-r1039) to the reference genome (Mycobacterium tuberculosis H37Rv, NC_000962.3) obtained from the NCBI database.
Samtools (version 0.1.19-96b5f2294a) were used to map the reads with a mapping quality of at least 1 resulting in.sam file.
After the conversion of.sam file to.bam, the bam files were sorted using samtools sort command.
The sorted bam files of each pulldown-input pair were used to call peaks using Macs2 (version 2.2.6) callpeak function with the following parameters; --mfold 2 80 s 50 --nomodel --keep-dup all.
A peak was associated with a gene only if both the biological replicates have at least a peak for that gene.
The peaks obtained were at least 1.5- fold enriched with ≤ 0.01 Q value (FDR).
To obtain the genes having overlap with the peaks, gene positions were extracted using the.gff file of the reference file (NC_000962.3), and a custom.bed format file was made.
Based on the peak positions and overlap with the genes/regulatory region (−500,+30 from the start codon), genes were identified using in-house python script.
For visualisation of the peaks, the sorted bam files were converted to bigwig format with the following parameters; --binsize 100 --effectiveGenomeSize 4411532 --normalizeUsing RPGC (reads per genomic content), which were further uploaded on integrative genomics viewer (IGV) software.
To prepare for the line plots for the pull-down regions, bedtools coverage (version 2.30.0) was used to make coverage using a bed file made from the sorted bam file (bamtobed option) and a custom bed file of chromosome positions with 100 base pairs intervals.
From the coverage file, normalised values corresponding to every bin were obtained by dividing the total number of mapped reads for every sample.
Averages of both the replicates for every sample (both pull-down and input) were calculated which were further used to calculate the Fold change using the formula: (Average CPM of Pull-down samples)/(Average CPM of Input samples).
Assembly: NC_000962.3
Supplementary files format and content: peaks.txt (macs2 output pull down sample vs input sample), bigwig file

organism: Mycobacterium tuberculosis H37Rv

source_name: bacteria grown with 0.3 % glucose as sole C source

growth_protocol: rv0158 KO Mtb was transformed with ATc-inducible expression vector (pexCF-rv0158) and transformants were grown in the presence of 50 μg/mL- hygromycinB to maintain the plasmid. This strain was grown in 7H9-ADS to log phase at 37 degrees Celcius at 180 rpm.

extract_protocol:
DNA–protein interactions were established by cross-linking 50 ml of the culture of Mtb strains with 1% formaldehyde while agitating cultures at 37 °C/ 180 RPM for 30 min. Crosslinking was quenched by the addition of glycine to a final concentration of 250 mM. Cells were pelleted, washed in 1 X PBS + 1 X protease inhibitor cocktail (Sigma Aldrich, cat. no.- 11873580001), and resuspended in IP Buffer (20 mM K-HEPES pH 7.9, 50 mM KCl, 0.5 mM dithiothreitol, 10% glycerol and 1 X protease inhibitor cocktail). Cells were lysed and the supernatant was subjected to Covaris S2 ultrasonicator at settings: Duty factor = 10%, Peak power = 174 W, cycles per burst = 200, for 20 min (4 times 5 min with 1 min gap) to shear chromatin to a uniform size centred around 200 bp. Following shearing, the sample was adjusted to buffer IPP150 (10 mM Tris-HCl—pH 8.0, 150 mM NaCl and 0.1% NP40) and shearing of DNA to an average size of 100–400 bp was confirmed by running a de-crosslinked aliquot on Agilent Bioanalyzer. Immunoprecipitation of FLAG-tagged proteins was initiated by incubating samples overnight rotating at 4 °C with Anti-FLAG M2 Magnetic Beads (Sigma Aldrich cat. no.- M8823), following manufacturer’s instructions. Samples without undergoing immunoprecipitation served as Input control for each condition. Beads were washed twice with IP buffer and once with Tris-EDTA buffer pH 7.5. Elution was performed in 50 mM Tris–HCl pH 7.5, 10 mM EDTA, 1% SDS for 40 min at 65 °C. All Samples were finally treated with RNAse A (1 mg/ ml) for 1 hr at 37 °C, and cross-links were reversed by incubation for 2 hr at 50 °C and for 9 hr at 65 °C in elution buffer with Protease K (10 mg/ ml). Input and Immunoprecipitated DNA were subsequently purified using QIAquick PCR purification Kit and the concentration of the DNA was measured using the Qubit HS DNA kit.
NEBNExt UltraTM II DNA library Prep with sample purification beads (NEB, cat. no.- E7103L) was used for the library preparation.

treatment_protocol: Log phase cultures at an OD600 of 0.35 was washed twice with 1X PBS, and induced for 24 hr using a low ATc concentration 12.5 ng/mL in presence of either 0.3% (w/v) D-glucose or 0.3% (w/v) sodium propionate as sole C sourcewereinduced for 24 hoursr (one generation time) using a low ATc concentration 12.5 ng/mLculture.

tag: genotype

value: rv0158 knockout:pexCF-rv0158

value: 24 hr with ATc concentration 12.5 ng/mL


title: P1_ChIP

description: Immunoprecipitation with Anti-FLAG M2 Magnetic Beads (Sigma Aldrich cat. no.- M8823) (Replicate 1)

source_name: bacteria grown with 0.3% propionate as sole C source

tag: treatment


title: G2_Input

description: Samples without undergoing immunoprecipitation served as Input control (Replicate 2)

value: bacteria grown with 0.3 % glucose as sole C source


title: P1_Input

value: bacteria grown with 0.3% propionate as sole C source


title: P2_ChIP

description: Immunoprecipitation with Anti-FLAG M2 Magnetic Beads (Sigma Aldrich cat. no.- M8823) (Replicate 2)


title: Tumor 3

value: 61 years

value: Female

value: IB


title: Wild type cells, Vehicle treated [MM171]

value: biol rep 8

value: Wild type

value: DMSO

value: 7 hours


title: P2_Input


title: Wild type cells, Vehicle treated [MM170]

value: Mouse embryonic fibroblast

value: biol rep 7


title: Wild type cells, Vehicle treated [MM167]

value: biol rep 4


title: Wild type cells, Vehicle treated [MM168]

value: biol rep 5


title: Wild type cells, Vehicle treated [MM166]

value: biol rep 3


title: G2_ChIP

value: Anti-FLAG M2 Magnetic Beads (Sigma Aldrich cat. no.- M8823)


title: Wild type cells, Borrelidin treated [MM180]

value: biol rep 6

value: 600nM Borrelidin


title: Wild type cells, Borrelidin treated [MM177]


title: Wild type cells, Vehicle treated [MM164]

value: biol rep 2


title: G1_ChIP

value: bacteria grown with 0.3 % glucose as sole C source

value: rv0158 knockout:pexCF-rv0158

value: 24 hr with ATc concentration 12.5 ng/mL


title: ANT 1

description: Patient 1 (non-tumor). Exiqon miRNA Array: Prepare the RNA Sample and RNA Sample QC; miRNA labeling; miRNA array hybridization; miRNA array scanning and analysis

value: adjacent nontumor tissues

value: Alive

value: NSCLC

value: 55 years

value: Male

value: IIB


title: Wild type cells, Vehicle treated [MM163]

value: Mouse embryonic fibroblast

value: biol rep 1

value: Wild type

value: DMSO

value: 7 hours


title: YN1_DMEM_NPC3

city: New Orleans

first: Giovane

middle: G

last: Tortelote

state: LA

address: 1430 Tulane Ave. School of Medicine, Room 5112

department: Pediatrics

institute: Tulane University School of Medicine

description: E13NPC ctrl vs YN1 diff genes.xlsx

data_processing:
Alignment and differential expression FASTQ files are checked for quality control using FASTQC. Alignment of the reads was done using STAR to the mm9 and mm10 genomes. This produced wiggle files for visualizing tracts. RSEM package was used to quantifiy read counts and normalized counts to create a relative molar concentration for the reads from the FASTQ files. The generated final files contain normalized expression files (transcripts per million/tpm), beta (biased estimates of natural log fold-change), and statistics values for each gene and transcripts across all samples. The steps above were implemented in the Tulane University NextGen sequence Core.
Assembly: mm10
Supplementary files format and content: The generated final files contain normalized expression files (transcripts per million/tpm), beta (biased estimates of natural log fold-change), and statistics values for each gene and transcripts across all samples.

source_name: Primary E13 Nephron Progenitor cell (NPC)

growth_protocol: Female CD1 mice were time-paired with Six2GFP+ or GFP- males for E13.5 embryonic kidney harvest. E13.5 NPC were isolated by MACS and expanded as described in the paper.

extract_protocol:
Total RNA was isolated using Qiagen RNeasy Mini-kit (cat# 74104) with on column DNase digestion. Samples were sent to Genewiz and passed quality control. RNA sequencing was non-strand specific and sequenced on Illumina-HiSeq 2x75 bp per lane. The RNA library was prepared with poly-A tail selection.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: After 2-3 passages, NPC were cultured in differentiation media with either CHIR99021 or YN1. The differentiation media was made with: DMEM + KO serum replacement (ThermoFisher, cat# 10828028), 200 ng/mL Fgf2 (R7D systems, cat# 3718-GMP), 3.5 µM CHIR99021 (Tocris, cat #4423) or in differentiation media replacing CHIR with 20 µM YN1 (Sigma SML0947). After 24h treatment NPC were harvested for quantitative proteome profiling by TMT LC-MS or transcriptome profiling by bulk RNASeq.

value: nephron progenitor cells

value: WT

value: YN1_DMEM Treat


title: YN1_DMEM_NPC2


title: YN1_DMEM_NPC


title: CHIR_DMEM_NPC3

value: CHIR_DMEM Treat


title: DMEM_NPC2

value: DMEM media ctrl


title: DMEM_NPC


title: DMEM_NPC3


title: CHIR_DMEM_NPC2

description: E13 NPC ctrl vs ChIR diff.xlsx


title: NPEM_NPC3

value: NPEM media ctrl


title: NPEM_NPC


title: Hypothalamus_P-group_1

city: bunkyo

first: yoshikazu

last: saito

state: tokyo

country: Japan

institute: university of tokyo

hyb_protocol: cRNA 15µg were flagmentated, and hybridized for 16hr at 45 on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained with Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were normalized using the statistical software R, and the qFARMS method.

organism: Rattus norvegicus

source_name: Hypothalamus_powder diet

label_protocol: Biotin-labeled cRNA was synthesized from 100ng total RNA according to the manufacture's protocol.

growth_protocol: Rats were housed under controlled conditions at a temperature of 20–26°C and humidity of 40–60% under a 12/12-h light-dark cycle, with ad libitum feed and water intake.

extract_protocol: Total RNA was extracted from the hypothalamus sample using TRIzol Reagent(Thermo Fisher Scientific) , according to the manufacture's protocol. The extracted total RNA was cleaned up with RNeasy Mini Kit (QIAGEN).

treatment_protocol: Rats were administered powdered or solid feed for 8 days.

tag: gender

value: male

value: 4 weeks old

tag: diet

value: powder chow


title: Hypothalamus_P-group_5


title: NPEM_NPC2

tag: cell type


title: Hypothalamus_P-group_4


title: SRK018-79

city: Farmington

first: Laura

last: Haynes

state: CT

address: 263 Farmington Avenue

department: Center on Aging

institute: UCONN Health

data_processing:
Paired-end 151-bp sequencing was performed on an Illumina HiSeq 2000 (Illumina, Shelton, CT).
Sequencing reads were trimmed with trimmomatic (Bolger, Lohse et al. 2014) to remove the universal Illumina adaptor and mapped to the UCSC mouse reference genome (mm9) and a custom splice junction library in parallel using hisat2/2.1.0
We continued our analysis with samples that contained at least 36 million mapped reads. Uniquely Mapped reads were quantifed using HTSeq
Genes were considered not expressed if they had zero reads in all technical and biological replicates.
Mapped reads in were counted using HTSeq and then diferential expression was performed with DESeq2
Assembly: mm9
Supplementary files format and content: comma separated values (.csv) file includes raw counts for each sample

source_name: gastrocnemius muscle

extract_protocol:
The gastrocnemius muscle was dissected and placed in RNAlater (Qiagen Inc., Germantown, MD) overnight at 4 °C. RNAlater was removed the following day, and the muscle was frozen at−80°C until RNA isolation. The muscle was homogenized and RNA was extracted via miRNeasy extraction per manufacturer’s instructions (Qiagen Inc., Germantown, MD).
mRNA-seq libraries were structured according to the standard Illumina TruSeq-stranded mRNA protocol from 2 rounds of the same experiment run together

treatment_protocol: Young (n=10/time point) and aged (n=9–10/time point) C57BL/6 mice were intranasally infected with 500 EID50 of PR8 infuenza and analyzed at various DPI. The gastrocnemius muscle was harvested at various days post infection (DPI) and RNA was isolated

value: gastrocnemius muscle

value: Aged

tag: days post_infection

value: infected with 500 EID50 of PR8 infuenza


title: SRK018-74

value: Young


title: SRK018-80


title: SRK018-75


title: SRK018-76


title: SRK018-77


title: Hypothalamus_P-group_2


title: Hypothalamus_C-group_5

source_name: Hypothalamus_chow diet

value: solid chow


title: Hypothalamus_C-group_3


title: Hypothalamus_C-group_2


title: Hypothalamus_C-group_4


title: Hypothalamus_C-group_1


title: Hypothalamus_P-group_3


title: Lgr5_m_Y_rep2 (total RNA-seq)

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

description: transcriptional profiling (RNA sequencing)

data_processing:
Fastq files quality check was performed using FastQC v0.11.5.
The fastq files were mapped to the mm9 genome using TopHat v2.1.0 with the following parameters --bowtie1 --no-coverage-search -a 5.
The number of reads covered by each gene is calculated by HTSeq-Count 0.11.2 with -s no -a 0 -t exon -m intersection-nonempty parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Htseq-count text file

source_name: Lgr5 positive cells from small intestine (intestinal stem cells)

growth_protocol: Young (2 months old) and old (18-26 months old) male and female wild-type C57BL6/J mice were group housed and maintained in a specific pathogen-free animal facility in Fritz Lipmann Institute with 12 h of light/dark cycle and fed with a standard mouse chow.

extract_protocol:
For the Lgr5-eGFP ISCs isolation, the villi-free intestinal pieces (2 cm) were incubated in 5mM EDTA/PBS on ice for 45 min. The tissue was then shaken vigorously for 1 min, the crypt solution was filtered through a 100 µm cell strainer and centrifuged at 300xg for 5 min at 4°C. The crypts were dissociated with the mixture of 18 ml TrypLE Express, 2 ml of 10X DNase I Buffer (100 mM Tris HCl pH 7.5, 25 mM MgCl2, 5 mM CaCl2) and 1 ml DNase I (10 mg/ml) for 30 min at 37°C with brief vortexing every 10 min. The single-cell suspension was then passed through a 20 µm cell strainer and centrifuged at 450xg for 5 minutes at 4°C. The pellet was resuspended in 3 ml FSM (2% FBS, 2.5 mM EDTA) containing 10 µM Y27632 and DAPI (1:1000). The single cell suspension was applied to FACS LSRII (BD Biosciences) and the Lgr5-eGFPHi ISCs were sorted for downstream analysis.
Total ribo-depleted RNA-seq library preparation was performed as described previously (Neri et al., Nature 2017) . In brief, 50 to 500 ng of total RNA were depleted of ribosomal RNA using the Ribo-Zero™ Gold Kit H/M/R Kit (illumina) following manufacturer’s instructions. Ribo-depleted RNA was resuspended in 17 μl of EFP buffer (illumina), heated to 94°C for 8 min, and used as input for first strand synthesis, using the TruSeq™ RNA Library Preparation Kit v2 (illumina) following manufacturer’s instructions.

tag: strain

value: Young (2 months old)


title: Lgr5_m_O_rep2 (total RNA-seq)

value: old (18-26 months old)


title: CHIR_DMEM_NPC


title: Lgr5_m_Y_rep1 (total RNA-seq)


title: SRK018-72


title: Lgr5_m_Y_rep3 (total RNA-seq)


title: Lgr5_m_O_rep1 (total RNA-seq)


title: SRK018-71


title: SRK018-70


title: SRK018-73


title: SRK018-69


title: SRK018-66


title: SRK018-67


title: SRK018-65


title: SRK018-64


title: Spinal cord organoids, VPA+Rapamycin 1

city: brisbane

first: Giovanni

last: Pietrogrande

state: QLD

address: Corner College and Cooper Rds, Bldg 75, AIBN

country: Australia

institute: University of Queensland

description:
C4_RAPA
deg.txt

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: Reference genome and gene model annotation files were downloaded from genome website 2 directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools
Supplementary files format and content: txt files with raw counts, fpkms, and DGE

source_name: Whole spinal cord organoid

extract_protocol:
NEBNext® Ultra™ RNA Library Prep Kit for Illumina®
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers.

treatment_protocol: Indicated treatment for 96 hours

value: Whole spinal cord organoid

tag: cell line

value: WTC

value: VPA+Rapamycin


title: Spinal cord organoids, VPA 3

description:
C6_VPA
deg.txt

value: WT

value: VPA


title: Spinal cord organoids, VPA+Rapamycin 2

description:
C5_RAPA
deg.txt


title: Spinal cord organoids, VPA 2

description:
C5_VPA
deg.txt


title: Spinal cord organoids, FGF 1

description:
C4_FGF
deg.txt

value: Vehicle


title: SRK018-62


title: SRK018-63


title: Spinal cord organoids, VPA+Rapamycin 3

description:
C6_RAPA
deg.txt


title: Spinal cord organoids, VPA 1

description:
C4_VPA
deg.txt


title: SRK018-59


title: SRK018-61


title: Lgr5_m_O_rep3 (total RNA-seq)


title: Spinal cord organoids, FGF 2

description:
C5_FGF
deg.txt


title: Spinal cord organoids, FGF 3

description:
C6_FGF
deg.txt


title: SRK018-57


title: SRK018-58


title: SRK018-56


title: n12_proseq_90m_2

city: Ithaca

first: Joel

last: Baines

state: NY

address: Hungerford Hill Rd

department: Baker Institute for Animal Health

institute: Cornell University

description: PRO-Seq

data_processing:
Adapter trimming, genome alignment and conversion to strand-specific BigWigs using pipeline available here: https://github.com/Danko-Lab/proseq2.0
Normalised bedgraphs files generated by extracting read counts from the BigWig file on the HSV-1 genome using multiBigWigSummary from deepTools. Reads for each sample were scaled based on drosophila spike-in reads to normalise for sequencing depth for each sequencing experiment.  The resulting txt file was then converted to bedgraph.
Supplementary files format and content: Hg38 human genome build, Dm3 drosophila genome build, HSV-1 KOS in-house genome builds with external repeats deleted (available here: https://github.com/Baines-Lab/Public/tree/main/HSV-1)
Supplementary files format and content: Drosophila normalised strand-specific bedgraph files
Library strategy: PRO-Seq

molecule: nuclear RNA

growth_protocol: HEp-2 cells were maintained in DMEM supplemented with 10% NBS and pen/strep

extract_protocol:
Nuclei were extracted and nuclear run-on with biotinylated nucleotides performed as described in: Nature Protocols. Aug 11(8):1455-76 doi:10.1038/nprot.2016.086 and Journal of virology 92.8 (2018): doi:10.1128/JVI.02184-17
Constructed as detailed in: bioRxiv 2020.05.18.102277; doi: https://doi.org/10.1101/2020.05.18.102277

treatment_protocol: Cells were infected with HSV-1 n12  or repair at a MOI of 5 and infection allowed to proceed for 0, 30, 60 or 90 min. Time 0 indicates time after 1h viral adsorption at 4°C. Performed in duplicates.

value: lung epithelial carcinoma cells

tag: minutes post-infection

tag: viral infection

value: infected with HSV-1 ICP4 null mutant n12

tag: virus strain

value: HSV-1 KOS


title: n12_proseq_90m_1

description: PRO-Seq


title: n12_repair_proseq_90m_1

description: PRO-Seq

value: infected with HSV-1 ICP4 null mutant repair


title: n12_repair_proseq_90m_2

description: PRO-Seq


title: n12_repair_proseq_60m_2

description: PRO-Seq


title: n12_repair_proseq_60m_1

description: PRO-Seq


title: SRK018-55

value: gastrocnemius muscle


title: SRK018-60

value: Aged


title: SRK018-54

value: infected with 500 EID50 of PR8 infuenza


title: SRK018-53

value: Young


title: SRK018-52


title: n12_proseq_60m_2

description: PRO-Seq


title: SRK018-50


title: n12_repair_proseq_30m_2

description: PRO-Seq


title: SRK018-51


title: SRK018-45


title: SRK018-49


title: n12_repair_proseq_0m_2

description: PRO-Seq


title: SRK018-48


title: n12_proseq_30m_2

description: PRO-Seq


title: n12_repair_proseq_0m_1

description: PRO-Seq


title: n12_proseq_30m_1

description: PRO-Seq


title: SRK018-44


title: SRK018-43


title: n12_proseq_0m_2

description: PRO-Seq


title: SRK018-42


title: SRK018-41


title: n12_repair_procap_3h_1

description: PRO-Cap

data_processing:
Adapter trimming, genome alignment and conversion to strand-specific BigWigs using pipeline available here: https://github.com/Danko-Lab/proseq2.0
Normalised bedgraphs files generated by extracting read counts from the BigWig file on the HSV-1 genome using multiBigWigSummary from deepTools. Reads for each sample were scaled based on drosophila spike-in reads to normalise for sequencing depth for each sequencing experiment.  The resulting txt file was then converted to bedgraph.
Supplementary files format and content: Hg38 human genome build, Dm3 drosophila genome build, HSV-1 KOS in-house genome builds with external repeats deleted (available here: https://github.com/Baines-Lab/Public/tree/main/HSV-1)
Supplementary files format and content: Drosophila normalised strand-specific bedgraph files
Library strategy: PRO-Cap

extract_protocol:
Nuclei were extracted and nuclear run-on with biotinylated nucleotides performed as described in: Nature Protocols. Aug 11(8):1455-76 doi:10.1038/nprot.2016.086 and Journal of virology 92.8 (2018): doi:10.1128/JVI.02184-17
Constructed as detailed in Nature Protocols. Aug 11(8):1455-76 doi:10.1038/nprot.2016.086

treatment_protocol: Cells were infected with HSV-1 n12  or repair at a MOI of 5 and infection allowed to proceed for 0,1.5 or 3 hours. Time 0 indicates time after 1h viral adsorption at 4°C. Performed in duplicates.

tag: hour post-infection


title: SRK018-40


title: n12_repair_procap_3h_2

description: PRO-Cap


title: n12_procap_3h_2

description: PRO-Cap


title: n12_proseq_60m_1

description: PRO-Seq


title: SRK018-37


title: n12_procap_3h_1

description: PRO-Cap


title: n12_repair_procap_1.5h_2

description: PRO-Cap


title: SRK018-35


title: SRK018-36


title: n12_procap_1.5h_2

description: PRO-Cap


title: SRK018-34


title: n12_repair_procap_1.5h_1

description: PRO-Cap


title: n12_repair_procap_0h_2

description: PRO-Cap


title: SRK018-32


title: SRK018-31


title: n12_repair_proseq_30m_1

description: PRO-Seq


title: n12_procap_1.5h_1

description: PRO-Cap


title: n12_repair_procap_0h_1

description: PRO-Cap


title: n12_procap_0h_2

description: PRO-Cap


title: n12_repair_groseq_10m_2

description: PRO-Seq

data_processing:
Adapter trimming, genome alignment and conversion to strand-specific BigWigs using pipeline available here: https://github.com/Danko-Lab/proseq2.0
Normalised bedgraph files generated using bamCoverage from deepTools. Each sample was scaled based on drosophila spike-in reads reads to normalize for sequencing depth.
Supplementary files format and content: Hg38 human genome build, Dm3 drosophila genome build, HSV-1 KOS in-house genome builds with external repeats deleted (available here: https://github.com/Baines-Lab/Public/tree/main/HSV-1)
Supplementary files format and content: Drosophila normalised strand-specific bedgraph files
Library strategy: GRO-Seq

extract_protocol:
Nuclei were extracted and nuclear run-on with Br-UTP performed for 5, 7.5 or 10m as described in Nat Protoc. 2015 Aug;10(8):1198-211. doi: 10.1038/nprot.2015.076.
Constructed using magnetic bead protocol described as detailed in Nat Protoc. 2015 Aug;10(8):1198-211. doi: 10.1038/nprot.2015.076 using PRO-Seq library protocol as in: bioRxiv 2020.05.18.102277; doi: https://doi.org/10.1101/2020.05.18.102277

treatment_protocol: Cells were infected with HSV-1 n12  or repair at a MOI of 5 and infection allowed to proceed for 1.5h. Time 0 indicates time after 1h viral adsorption at 4°C. Performed in duplicates

tag: run-on time_(min)


title: SRK018-33


title: SRK018-39


title: SRK018-28


title: SRK018-30


title: n12_repair_groseq_10m_1

description: PRO-Seq


title: SRK018-29


title: n12_procap_0h_1

description: PRO-Cap


title: SRK018-27


title: SRK018-38


title: n12_proseq_0m_1

description: PRO-Seq


title: SRK018-25


title: n12_groseq_10m_1

description: PRO-Seq


title: SRK018-26


title: n12_repair_groseq_7.5m_2

description: PRO-Seq


title: SRK018-24


title: SRK018-23


title: n12_groseq_7.5m_2

description: PRO-Seq


title: n12_repair_groseq_7.5m_1

description: PRO-Seq


title: SRK018-21


title: n12_groseq_7.5m_1

description: PRO-Seq


title: SRK018-22


title: n12_repair_groseq_5m_2

description: PRO-Seq


title: SRK018-20


title: n12_groseq_10m_2

description: PRO-Seq


title: SRK018-18


title: n12_groseq_5m_2

description: PRO-Seq


title: n12_repair_groseq_5m_1

description: PRO-Seq


title: SRK018-19


title: SRK018-17


title: n12_groseq_5m_1

description: PRO-Seq


title: SRK018-16


title: TB-preDM_Week 2_Romania_ROM14

city: London

first: Jackie

last: Cliff

address: Keppel Street

department: Immunology and Infection

country: United Kingdom

institute: London School of Hygiene & Tropical Medicine

data_processing:
Alignment STAR version 2.5.1b
Quantification HT-seq count version 0.6.1
Normalisation DESeq2 version 1.12.4
Assembly: Human_g1k_v37
Supplementary files format and content: read count for each ensembl gene id, un-normalised, un-filtered

source_name: Whole Blood

extract_protocol:
Whole blood stored in PAXgene Blood RNA collection tubes and extracted using the PAXgene blood miRNA kit (Qiagen)
Bioscientific NEXTflex-Rapid-Directional mRNA-seq sample preparation (Bioscientific)

tag: patient id

value: TB-preDM

value: Romania

tag: timepoint

value: Week 2


title: TB-IH_Diagnosis_Romania_ROM3

value: TB-IH

value: Diagnosis


title: SRK018-15

tag: tissue


title: SRK018-14

tag: age


title: TB-preDM_Week 2_Romania_ROM1


title: TB-IH_Month 2_Romania_ROM5

value: Month 2


title: SRK018-12


title: TB-preDM_Diagnosis_Romania_ROM13


title: SRK018-11


title: TB-preDM_Month 2_Romania_ROM11


title: SRK018-10


title: SRK018-13


title: TB-preDM_Month 6_Romania_ROM9

value: Month 6


title: TB-preDM_Diagnosis_Romania_ROM1


title: SRK018-08


title: SRK018-07


title: TB-preDM_Week 2_Romania_ROM13


title: SRK018-06


title: TB-preDM_Month 2_Romania_ROM1


title: SRK018-05


title: TB-IH_Diagnosis_Romania_ROM5


title: TB-preDM_Month 2_Romania_ROM13


title: SRK018-04


title: TB-preDM_Week 2_Romania_ROM9


title: TB-preDM_Month 2_Romania_ROM14


title: SRK018-02


title: TB-IH_Month 2_Romania_ROM3


title: TB-preDM_Diagnosis_Romania_ROM11


title: SRK018-03


title: TB-IH_Week 2_Romania_ROM5


title: SRK017-77


title: TB-IH_Week 2_Romania_ROM3


title: TB-IH_Month 6_Romania_ROM3


title: SRK017-79


title: SRK017-78


title: TB-preDM_Month 6_Romania_ROM14


title: SRK017-75


title: SRK018-09


title: TB-preDM_Diagnosis_Romania_ROM9


title: SRK017-74


title: TB-preDM_Month 6_Romania_ROM13


title: TB-DM_Diagnosis_Indonesia_UNPAD82

data_processing:
Alignment STAR version 2.5.1b
Quantification HT-seq count version 0.6.1
Normalisation DESeq2 version 1.12.4
Genome_build: Human_g1k_v37
Supplementary_files_format_and_content: read count for each ensembl gene id, un-normalised, un-filtered

value: TB-DM

value: Indonesia


title: SRK017-72


title: SRK017-73


title: TB-IH_Diagnosis_South_Africa_SUN121


title: TB-only_Diagnosis_Romania_ROM8

value: TB-only


title: SRK017-71


title: SRK018-01


title: SRK017-68


title: TB-IH_Month 2_Indonesia_UNPAD2


title: SRK017-67


title: SRK017-69


title: SRK017-66


title: TB-only_Month 6_Indonesia_UNPAD14


title: SRK017-64


title: TB-only_Month 6_South_Africa_SUN103


title: SRK017-76


title: SRK017-65


title: TB-preDM_Month 6_South_Africa_SUN55


title: SRK017-63


title: TB-DM_Month 6_Romania_ROM10


title: SRK017-62


title: TB-DM_Week 2_Romania_ROM2


title: SRK017-61


title: TB-IH_Diagnosis_South_Africa_SUN50


title: TB-preDM_Week 2_South_Africa_SUN55


title: SRK017-60


title: TB-DM_Week 2_Indonesia_UNPAD4


title: TB-DM_Week 2_South_Africa_SUN112


title: TB-only_Diagnosis_Indonesia_UNPAD20


title: SRK017-59


title: TB-IH_Month 6_South_Africa_SUN136


title: SRK017-58


title: SRK017-57


title: TB-only_Diagnosis_Indonesia_UNPAD34


title: TB-IH_Month 6_Indonesia_UNPAD11


title: SRK017-55


title: SRK017-54


title: SRK017-53


title: TB-DM_Diagnosis_Indonesia_UNPAD19


title: TB-DM_Month 6_Indonesia_UNPAD29


title: SRK017-52


title: TB-DM_Month 2_Romania_ROM4


title: TB-IH_Month 6_Indonesia_UNPAD15


title: SRK017-51


title: TB-preDM_Diagnosis_South_Africa_SUN55


title: SRK017-48


title: SRK017-56


title: TB-DM_Month 2_Indonesia_UNPAD82


title: SRK017-46


title: TB-DM_Month 2_South_Africa_SUN162


title: TB-preDM_Month 6_South_Africa_SUN54


title: TB-IH_Week 2_Indonesia_UNPAD7


title: SRK017-45


title: TB-IH_Month 2_South_Africa_SUN121


title: TB-DM_Diagnosis_Romania_ROM4


title: SRK017-44


title: TB-DM_Diagnosis_South_Africa_SUN144


title: SRK017-41


title: TB-DM_Month 2_Indonesia_UNPAD10


title: SRK017-42


title: TB-only_Diagnosis_Indonesia_UNPAD3


title: SRK017-47


title: SRK017-40


title: SRK017-49


title: TB-DM_Diagnosis_South_Africa_SUN68


title: TB-IH_Week 2_Indonesia_UNPAD13


title: SRK017-50


title: TB-only_Diagnosis_Indonesia_UNPAD30


title: SRK017-38


title: SRK017-37


title: TB-DM_Diagnosis_Indonesia_UNPAD25


title: TB-IH_Month 6_Indonesia_UNPAD7


title: SRK017-39


title: TB-IH_Week 2_South_Africa_SUN50


title: SRK017-36


title: TB-only_Month 2_Indonesia_UNPAD3


title: SRK017-35


title: TB-only_Month 2_Indonesia_UNPAD30


title: SRK017-32


title: TB-IH_Month 6_South_Africa_SUN119


title: SRK017-34


title: SRK017-43


title: TB-DM_Week 2_Indonesia_UNPAD29


title: SRK017-33


title: TB-DM_Month 6_Indonesia_UNPAD6


title: SRK017-31


title: SRK017-30


title: TB-DM_Week 2_South_Africa_SUN144


title: SRK017-29


title: TB-preDM_Month 6_South_Africa_SUN140


title: TB-preDM_Diagnosis_South_Africa_SUN133


title: SRK017-27


title: TB-DM_Week 2_South_Africa_SUN163


title: TB-only_Month 6_Romania_ROM8


title: TB-DM_Month 6_South_Africa_SUN126


title: SRK017-24


title: SRK017-26


title: TB-DM_Month 2_Indonesia_UNPAD8


title: SRK017-22


title: TB-DM_Month 6_Romania_ROM12


title: TB-DM_Month 6_Indonesia_UNPAD24


title: TB-DM_Week 2_South_Africa_SUN155


title: SRK017-17


title: SRK017-20


title: TB-preDM_Month 2_South_Africa_SUN54


title: TB-DM_Diagnosis_Indonesia_UNPAD32


title: SRK017-19


title: SRK017-18


title: TB-only_Month 6_Indonesia_UNPAD27


title: SRK017-16


title: SRK017-28


title: SRK017-15


title: TB-preDM_Month 2_South_Africa_SUN55


title: SRK017-14


title: SRK017-25


title: TB-DM_Month 2_Indonesia_UNPAD6


title: TB-DM_Diagnosis_Romania_ROM2


title: SRK017-13


title: TB-IH_Diagnosis_South_Africa_SUN105


title: SRK017-12


title: SRK017-23


title: SRK017-21


title: SRK017-11


title: TB-IH_Month 2_Indonesia_UNPAD7


title: SRK017-09


title: TB-DM_Diagnosis_Indonesia_UNPAD28


title: TB-DM_Month 2_Romania_ROM7


title: SRK017-07


title: SRK017-08


title: SRK017-06


title: TB-DM_Diagnosis_Indonesia_UNPAD12


title: TB-only_Diagnosis_South_Africa_SUN141


title: SRK017-04


title: TB-DM_Week 2_South_Africa_SUN159


title: SRK017-03


title: TB-DM_Diagnosis_Indonesia_UNPAD10


title: TB-DM_Month 2_South_Africa_SUN59


title: TB-IH_Diagnosis_South_Africa_SUN120


title: SRK017-05


title: SRK017-01


title: SRK017-10


title: TB-DM_Diagnosis_Indonesia_UNPAD4


title: TB-only_Month 2_South_Africa_SUN141


title: TB-only_Month 2_Romania_ROM15


title: Fat1, EtOH replicate 1

city: Louisville

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
base calling was performed offsite by GeneWiz
QA/QC of raw fastq files was performed using FastQC v 0.10.1
Raw fastq sequences were aligned to the mm10 genome using STARv2.5.2b using the Ensembl gtf with the parameters --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --sjdbGTFfile Mus_musculus.Ensembl.GRCm38.82.gtf --outReadsUnmapped Fastx  --runThreadN 16
Differentially expressed genes were determined using cuffdiff2 v2.2.1 with the parameters –p 5 –library-type fr-firststrand Homo_sapiens.GRCh38.82.chrAdded.gtf
Assembly: mm10
Supplementary files format and content: genes.fpkm_table
Supplementary files format and content: Matrix of cuffnorm (v2.2.1) normalized FPKM values for each gene within each sample.

molecule: polyA RNA

extract_protocol:
Total RNA was purified from liver tissue and BMDMs with Trizol reagent (Thermo Fisher Scientific) as described by the manufacturer, and any contaminating genomic DNA was removed by digestion with DNase I (Thermo Fisher Scientific). cDNA was synthesized with qScript cDNA Supermix (Quanta Biosciences, Beverly, MA) from 1 μg of RNA.
Liver RNA was extracted and purified via Trizol Reagent (Thermo Fisher Scientific, Waltham, MA) as described by the manufacturer.  Any carryover genomic DNA was removed by digestion with TURBOÔ DNase I (Thermo Fisher Scientific) followed by further purification with the RNeasy MinElute Cleanup Kit (Qiagen, Germantown, MD). RNA integrity numbers were a minimum of 7.5 as determined on the Agilent Bioanalyzer instrument (Agilent Technologies, Santa Clara, CA). RNA samples were then provided to GENEWIZ (South Plainfield, NJ) for RNAseq. RNA was subjected to poly-A selection followed by 2X150 paired end sequencing on the Illumina HiSeq platform

value: liver

tag: Sex

value: male

tag: genotype

value: EtOH


title: Fat1, EtOH replicate 2

tag: treatment


title: Fat1, EtOH replicate 3


title: TB-DM_Month 6_South_Africa_SUN149


title: TB-IH_Week 2_South_Africa_SUN120


title: Wild-type, EtOH replicate 3

value: Wild-type


title: TB-only_Month 2_Romania_ROM8


title: TB-only_Week 2_South_Africa_SUN103


title: SRK017-02

value: gastrocnemius muscle


title: TB-only_Month 2_Indonesia_UNPAD20


title: Wild-type, EtOH replicate 2


title: Wild-type, EtOH replicate 1


title: TB-IH_Month 2_Indonesia_UNPAD11


title: Fat1, pair-fed, LPS replicate 3

value: pair-fed, LPS


title: TB-only_Diagnosis_Romania_ROM15


title: TB-only_Diagnosis_South_Africa_SUN103


title: Fat1, pair-fed, LPS replicate 2


title: Fat1, pair-fed, LPS replicate 1


title: TB-IH_Diagnosis_Indonesia_UNPAD15


title: TB-IH_Month 2_Indonesia_UNPAD15


title: Wild-type, pair-fed, LPS replicate 3


title: TB-DM_Week 2_Indonesia_UNPAD24


title: Wild-type, pair-fed, LPS replicate 2


title: TB-only_Week 2_Indonesia_UNPAD34


title: TB-only_Week 2_Romania_ROM6


title: Wild-type, pair-fed, LPS replicate 1


title: TB-DM_Week 2_Romania_ROM4


title: TB-IH_Diagnosis_South_Africa_SUN119


title: TB-IH_Month 6_Indonesia_UNPAD23


title: Fat1+/-, EtOH, LPS + RvD1 replicate 4

value: EtOH, LPS + RvD1


title: Fat1+/-, EtOH, LPS + RvD1 replicate 1


title: Fat1+/-, EtOH, LPS + RvD1 replicate 2


title: TB-DM_Month 6_Indonesia_UNPAD28


title: Fat1+/-, EtOH, LPS + RvD1 replicate 3


title: TB-DM_Diagnosis_South_Africa_SUN51


title: Fat1+/-, EtOH, LPS + RvE1 replicate 3

value: EtOH, LPS + RvE1


title: Fat1+/-, EtOH, LPS + RvE1 replicate 4


title: TB-only_Month 6_Romania_ROM6

value: Romania


title: TB-IH_Month 2_South_Africa_SUN136


title: Fat1+/-, EtOH, LPS replicate 4

value: EtOH, LPS


title: Fat1+/-, EtOH, LPS + RvE1 replicate 1


title: TB-DM_Month 2_South_Africa_SUN68


title: TB-IH_Month 2_South_Africa_SUN127

value: TB-IH


title: Fat1+/-, EtOH, LPS replicate 3


title: TB-DM_Month 6_Indonesia_UNPAD4


title: TB-only_Month 6_South_Africa_SUN141


title: Fat1+/-, EtOH, LPS replicate 1


title: Wild-type, EtOH, LPS replicate 4


title: TB-DM_Month 2_Romania_ROM10


title: Wild-type, EtOH, LPS replicate 2


title: TB-only_Diagnosis_Indonesia_UNPAD27

value: Diagnosis


title: Wild-type, EtOH, LPS replicate 3


title: Fat1+/-, pair-fed replicate 4

value: pair-fed


title: TB-DM_Month 2_South_Africa_SUN135


title: Wild-type, EtOH, LPS replicate 1


title: Fat1+/-, EtOH, LPS + RvE1 replicate 2


title: TB-only_Week 2_South_Africa_SUN132


title: TB-IH_Week 2_Indonesia_UNPAD17


title: Fat1+/-, pair-fed replicate 2


title: Fat1+/-, pair-fed replicate 3


title: TB-DM_Month 2_Indonesia_UNPAD4


title: Fat1+/-, pair-fed replicate 1


title: Wild-type, pair-fed replicate 4


title: TB-DM_Diagnosis_South_Africa_SUN162


title: TB-DM_Month 6_South_Africa_SUN144


title: TB-IH_Diagnosis_South_Africa_SUN136


title: TB-DM_Month 2_Indonesia_UNPAD18


title: Wild-type, pair-fed replicate 2


title: Wild-type, pair-fed replicate 3


title: TB-DM_Month 2_South_Africa_SUN112


title: TB-DM_Diagnosis_South_Africa_SUN71


title: Wild-type, pair-fed replicate 1


title: TB-IH_Month 6_South_Africa_SUN50


title: Fat1+/-, EtOH, LPS replicate 2


title: TB-IH_Month 2_Indonesia_UNPAD23


title: TB-only_Week 2_Indonesia_UNPAD30


title: TB-preDM_Month 6_South_Africa_SUN133

value: TB-preDM


title: TB-IH_Diagnosis_Indonesia_UNPAD7


title: TB-DM_Diagnosis_Indonesia_UNPAD18

value: TB-DM


title: TB-IH_Diagnosis_Indonesia_UNPAD2

value: Indonesia


title: TB-IH_Month 2_Indonesia_UNPAD13


title: TB-IH_Month 2_South_Africa_SUN50


title: TB-DM_Week 2_Indonesia_UNPAD82


title: TB-DM_Month 6_Indonesia_UNPAD31


title: TB-IH_Month 2_South_Africa_SUN120


title: RNA-seq, -met, rep2

city: UNIVERSITY PARK

first: Lu

last: Bai

state: PENNSYLVANIA

address: 406 SOUTH FREAR, UNIVERSITY PARK

department: BMB

institute: Penn State University

data_processing:
50 bp paired-end reads were aligned to S. cerevisiae genome (sacCer3), FPKM was counted by featureCounts (version 2.0.3).
Supplementary files format and content: tab-delimited txt files include FPKM counts for each sample

growth_protocol: Yeast strains were grown in 50 mL synthetic media with methionine to OD660 = 0.2.

extract_protocol:
Standard RNA extraction protocol was used for the preparation of RNA-seq samples
The RNA-seq libraries were prepared with NEBNext Ultra II DNA Library Prep Kit. Next generation sequencing was performed on NextSeq 2000.

tag: chip antibody

tag: condition

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, CDC20::MET3pr-mCherry::URA3, CWC23::MET3pr-GFP::KanMX

value: methionine depletion


title: TB-only_Week 2_Romania_ROM15

value: TB-only


title: RNA-seq, -met, rep1


title: TB-IH_Week 2_South_Africa_SUN105


title: porcine embryos  SiTF 02

city: Changchun

first: Daoyu

last: Zhang

address: Xinzhu street 1977

institute: Jilin University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt genomic benchwork
Trimmed sequence reads were mapped to Sscrofa11.1 using bowtie2(v2.3.5)
Read count extraction and normalization were performed using stringTie(v2.1.7)
Supplementary files format and content: Sscrofa11.1
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Sus scrofa

source_name: 4-cell embryos

growth_protocol: Embryo culture medium

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: siRNA micromanipulation of cytoplasmic injection

value: 4-cell embryos

value: embryos

tag: cell type

value: TFAP2C KD

value: siRNA injection


title: M.CviPI, MeDIP, rep2

data_processing:
Paired-end reads of 50 bp or 150 bp were processed with fastp (version 0.23.2) to remove low quality reads. Processed reads were aligned to S. cerevisiae genome (sacCer3) with BWA (version 0.7.17). Aligned bam files were deduplicated with Picard MarkDuplicates (version 3.0.0). bigwig files were generated by deeptools bamCoverage (version 3.5.1) for visualization purposes. To detect differentially methylated NDRs, aligned reads on each NDR were counted by Subread featureCounts (version 2.0.3) using a list of NDR coordinates generated from a previous study, with the following parameters “-p -O”. Fold change and P-value were generated by DEseq2 (1.38.0) without outliers filtering. log2 (Fold Change) > 0.7 and the adjusted P-value < 0.05 were used as the cutoff for identifying differentially methylated regions.
Assembly: sacCer3
Supplementary files format and content: table generated by DEseq2
Supplementary files format and content: bigwig

growth_protocol: Yeast strains were grown in 50 mL synthetic media with/without methionine at 30°C to OD660 = 0.3.

extract_protocol:
Standard MeDIP protocol for preparation of methylated genomic DNA
MeDIP-Seq libraries were prepared with NEBNext Ultra II DNA Library Prep Kit (NEB, E7645L). Next generation sequencing was performed on NextSeq 2000 (Illumina).

treatment_protocol: β-estradiol (Sigma, 50-28-2) was added to a final concentration of 2 nM for 1/2 hrs, allowing the LacI-NLS-M.CviPI fusion protein to express. For MATa and MATalpha viewpoint, glucose (D) or galactose(G) was added according to the experimental conditions.

tag: strain

value: 2hr, 10nM Beta-estradiol

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2


title: porcine embryos  SiTF 01

tag: cell line


title: TB-IH_Diagnosis_Indonesia_UNPAD26


title: M.CviPI, MeDIP, rep1


title: TB-IH_Month 6_South_Africa_SUN127


title: TB-DM_Month 2_Indonesia_UNPAD24


title: porcine embryos  control 02

value: Control


title: TB-only_Month 2_South_Africa_SUN103


title: TB-DM_Diagnosis_Romania_ROM12

value: Romania


title: TB-DM_Month 6_South_Africa_SUN51


title: Mlp1_M.CviPI, MeDIP, rep2

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-Mlp1-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2


title: TB-DM_Diagnosis_Romania_ROM7

value: Diagnosis


title: TB-DM_Week 2_South_Africa_SUN162


title: Mlp1_M.CviPI, MeDIP, rep1


title: TB-only_Month 2_Romania_ROM17


title: TB-DM_Month 2_Indonesia_UNPAD29


title: TB-DM_Month 6_South_Africa_SUN163


title: Ctrl_alpha, G, MeDIP, 2hr, 0X, rep2

value: 2hr, 2nM Beta-estradiol

value: MAT-alpha, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, GAL10pr::GAL10pr-HO::URA3


title: Donor1-CD4 cells treated with PHA-1

city: Beerse

first: Filmon

last: Eyassu

address: Turnhoutseweg 30

country: Belgium

institute: Janssen Pharmaceutica

description: Donor1-CD4 cells treated with PHA-1

hyb_protocol: Target hybridization was processed on the GeneTitan® Instrument according to the instructions provided in the User Guide for Expression Array Plates

scan_protocol: Images were analyzed using the GeneChip® Command Console Software (AGCC) (Affymetrix).

data_processing: All microarray data were processed using the statistical computing program R (R version 3.2.2) and Bioconductor packages. The microarray dataset was background corrected and normalized with robust multiarray analysis [50]] and summarized with the metadata package hgu219hsentrezg (CDF version 15.1.0). Quality assessment was performed with arrayQualityMetrics [52].

source_name: Donor1-CD4 cells treated with PHA-1

label_protocol: For all the target preparation, including the amplification of total RNA and labeling, were carried out as described in the GeneChip Express Kit User Manual (Affymetrix 2004). Biotin-labeled target samples were hybridized to the GeneChip® HG-U219 containing probes for ~18500 genes

extract_protocol: RNA extraction was prepared with the RNeasy plus mini kit (Qiagen, Germany). Amplification and labelling of total RNA were performed using the GeneChip® PICO Reagent Kit following the manufacturer’s protocol (ThermoFisher 2016).

treatment_protocol: Following an overnight stimulation of bulk CD4+ T-cells isolated from PLWIH on cART with the T66 protein (4µM), PHA (10 µg/mL) or PBS, 100,000 cells were transferred to a tube containing 100 µl of RLT buffer (Qiagen). Cells were stored at –80 °C until further processing.

value: CD4 cells

value: PHA


title: TB-DM_Month 2_South_Africa_SUN51

value: TB-DM


title: porcine embryos  control 01


title: Ctrl_alpha, G, MeDIP, 2hr, 0X, rep1


title: TB-DM_Month 6_Indonesia_UNPAD19

value: Indonesia


title: TB-only_Month 6_Romania_ROM15

value: TB-only


title: MATalpha, G, MeDIP, 2hr, 256X, rep2

value: MAT-alpha, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, TAF2::256XLacO::HIS3, GAL10pr::GAL10pr-HO::URA3


title: MATalpha, G, MeDIP, 2hr, 256X, rep1


title: TB-DM_Month 2_Indonesia_UNPAD28


title: TB-IH_Month 2_South_Africa_SUN105

value: TB-IH


title: Donor4-CD4 cells treated with PHA-4

description: Donor4-CD4 cells treated with PHA-4

source_name: Donor4-CD4 cells treated with PHA-4


title: Ctrl_alpha, D, MeDIP, 2hr, 0X, rep2


title: TB-DM_Diagnosis_Indonesia_UNPAD83


title: TB-DM_Month 2_South_Africa_SUN159


title: Donor3-CD4 cells treated with PHA-3

description: Donor3-CD4 cells treated with PHA-3

source_name: Donor3-CD4 cells treated with PHA-3


title: Donor1-CD4 cells treated with T66-1

description: Donor1-CD4 cells treated with T66-1

source_name: Donor1-CD4 cells treated with T66-1


title: TB-DM_Diagnosis_Indonesia_UNPAD84


title: TB-DM_Month 2_South_Africa_SUN163


title: Ctrl_alpha, D, MeDIP, 2hr, 0X, rep1


title: Donor2-CD4 cells treated with PHA-2

description: Donor2-CD4 cells treated with PHA-2

source_name: Donor2-CD4 cells treated with PHA-2


title: TB-IH_Month 6_Indonesia_UNPAD13


title: MATalpha, D, MeDIP, 2hr, 256X, rep2


title: TB-only_Week 2_Indonesia_UNPAD20


title: TB-preDM_Week 2_South_Africa_SUN133

value: TB-preDM


title: MATalpha, D, MeDIP, 2hr, 256X, rep1


title: Donor4-CD4 cells treated with T66-4

description: Donor4-CD4 cells treated with T66-4

source_name: Donor4-CD4 cells treated with T66-4


title: genomic DNA from Adh5-/- sample [205730000030_R06C01]

type: genomic

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: Josep Carreras Leukaemia Research Institute (IJC)

description: Liver samples from Adh5–/– mice

hyb_protocol: Samples were bisulfite converted using EZ DNA Methylation-Gold™ Kit (Zymo Research, CA, USA) following the manufacturer’s protocol with modifications for Illumina Infinium Methylation Assay.

scan_protocol: Infinium Mouse Methylation BeadChip (Illumina) arrays were used to profile genome wide DNA methylation. This platform interrogates over 285,000 methylation sites per sample at single-nucleotide resolution. Samples were hybridized in the array following the manufacturer’s instructions.

data_processing: The DNA methylation status of the studied samples was obtained using the Infinium Mouse Methylation BeadChip Array (~285,000 methylation sites). Raw signal intensities were preprocessed and analyzed using SeSAMe (v1.14.2). DNA methylation beta values were obtained from raw IDAT files using the openSesame pipeline within R statistical environment (v4.0.3). Briefly, this pipeline includes a data preprocessing procedure consisting of strain-specific masking for mouse methylation array probes, followed by masking of non-uniquely mapped probes (poor design), channel inference for Infinium I probes, non-linear dye bias correction, detection p-value masking (P > 0.05) using the pOOBAH algorithm and background subtraction using the noob method.

label: Cy5 and Cy3

source_name: High molecular weight DNA

label_protocol: Standard Illumina labelling protocol

extract_protocol: DNA from fresh-frozen mouse liver samples was extracted and purified using DNeasy Blood and Tissue Kit (Qiagen GmbH, Hilden, Germany) according to manufacturer’s instructions. Purified genomic DNA was quantified with Qubit (Invitrogen, Carlsbad, CA, USA) according to manufacturer’s instructions.

value: liver


title: TB-DM_Month 2_Indonesia_UNPAD84


title: Donor3-CD4 cells treated with T66-3

description: Donor3-CD4 cells treated with T66-3

source_name: Donor3-CD4 cells treated with T66-3


title: genomic DNA from Adh5-/- sample [205730000030_R04C02]

description: Liver samples from Adh5–/– mice


title: Donor2-CD4 cells treated with T66-2

description: Donor2-CD4 cells treated with T66-2

source_name: Donor2-CD4 cells treated with T66-2


title: Donor4-CD4 cells treated with PBS-4

description: Donor4-CD4 cells treated with PBS-4

source_name: Donor4-CD4 cells treated with PBS-4

value: PBS


title: TB-only_Month 2_Indonesia_UNPAD27


title: Ctrl_a, G, MeDIP, 2hr, 0X, rep2

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, GAL10pr::GAL10pr-HO::URA3


title: TB-only_Month 6_Romania_ROM17


title: TB-IH_Week 2_Indonesia_UNPAD23


title: TB-IH_Week 2_South_Africa_SUN121


title: Ctrl_a, G, MeDIP, 2hr, 0X, rep1


title: MATa, G, MeDIP, 2hr, 256X, rep2

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, TAF2::256XLacO::HIS3, GAL10pr::GAL10pr-HO::URA3


title: TB-DM_Diagnosis_Indonesia_UNPAD24


title: TB-IH_Week 2_Indonesia_UNPAD26


title: genomic DNA from Adh5-/- sample [205730000030_R03C02]

description: Liver samples from Adh5–/– mice


title: TB-DM_Month 6_Romania_ROM4

value: Romania


title: MATa, G, MeDIP, 2hr, 256X, rep1


title: gcGBM4

city: Boston

first: Adrian

last: Dubuc

state: Massachussetts

address: 75 Francis St, 5-5066 Shapiro Building

institute: Brigham and Women's Hospital

hyb_protocol: Eighty (80) nanogram of genomic DNA were hybrieized to the ThermoFisher Oncoscna FFPE assay, in accordance with the manufacturers protocols

scan_protocol: Microarrays were washed and scanned using a GeneChip Fluidics station to generate DDAT files. ThermoFisher GeneChip Command Console software was used to gneerate a .CEL file based on probe signal intensity

data_processing: Data was evaluated using ThermoFisher Chromosome Analysis Suite (version 4.0) to generate log2-ratio data and copy-neutral loss of heterozygosity calls.

source_name: brain tumor

label_protocol: biotin

extract_protocol: DNA was extracted from FFPE specimens using QIAamp DNA FFPE Tissue kit and quantified via Nanodrop

value: giant cell glioblastomas


title: TB-IH_Month 6_Indonesia_UNPAD17


title: genomic DNA from Wildtype sample [205730000030_R03C01]

description: Liver samples from WT mice

value: Wildtype


title: Donor2-CD4 cells treated with PBS-2

description: Donor2-CD4 cells treated with PBS-2

source_name: Donor2-CD4 cells treated with PBS-2


title: TB-DM_Diagnosis_Indonesia_UNPAD6

value: Diagnosis


title: genomic DNA from Wildtype sample [205730000030_R01C01]

description: Liver samples from WT mice


title: TB-IH_Month 2_South_Africa_SUN119


title: genomic DNA from Adh5-/- sample [205730000030_R01C02]

description: Liver samples from Adh5–/– mice


title: TB-DM_Diagnosis_South_Africa_SUN126


title: TB-DM_Month 6_South_Africa_SUN71


title: Donor1-CD4 cells treated with PBS-1

description: Donor1-CD4 cells treated with PBS-1

source_name: Donor1-CD4 cells treated with PBS-1


title: Donor3-CD4 cells treated with PBS-3

description: Donor3-CD4 cells treated with PBS-3

source_name: Donor3-CD4 cells treated with PBS-3


title: genomic DNA from Adh5-/- sample [205730000030_R05C02]

description: Liver samples from Adh5–/– mice


title: Myopic right eyes - Rep 3

city: Sheridan

first: Kenneth

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

library_source: transcriptomic single cell

data_processing:
CellRanger version 3.1.0 count was used to create the matrix table for further processing.
Matrix files were then imported into Seurat version 4.1.1 for normalization, clustering and visualization.
Assembly: Chicken_GRCg6a
Supplementary files format and content: tab-delimited text file containing gene symbols with their respective expression for each cell/barcode.

organism: Gallus gallus

source_name: Choriod

growth_protocol: White Leghorn male chicks (Gallus gallus) were obtained as 2-day-old hatchlings from Ideal Breeding Poultry Farms (Cameron, TX). Chicks were housed in temperature-controlled brooders with a 12-hour light/dark cycle and were given food and water ad libitum.

extract_protocol:
Choroidal cells were isolated as described previously (Coulombe & Nishi, 1991) with minor modifications: Choroids were cut into small pieces, and digested with collagenase [Worthington; 2mg/ml in HBSS containing Ca++ and Mg++; 2ml/ sample] for 20 min at 37°C. Following centrifugation at 834 x g at 4°C for 15 min, the supernatants were removed and samples were digested with 2 ml trypsin (Sigma; 0.2% in PBS for 20 min at 37°C). Choroids were again centrifuged as described above, trypsin removed, and replaced with another 2ml of collagenase solution (2 mg/ml in HBSS) and incubated at 37°C with occasional trituration using a glass Pasteur pipette until the digest was able to pass freely through the glass Pasteur pipette. Following a second centrifugation as described above, supernatants were removed and the pelleted choroidal digests were resuspended in PBS + 0.04% BSA (1 ml/sample). The dissociated cell suspensions were passed through small, individual 105 μm metal mesh screens held in place with 25 mm Swinnex filter holders (MilliporeSigma, Burlington, MA ) using  5 cc syringes (6 filters and 6 syringes in total).  Each filtrate was collected in 4 ml snap cap tubes. Each filter was rinsed with an additional 1 ml PBS + 0.04% BSA and added to each original filtrate.  Each cell sample was then passed through a 40 μm pipette tip cell strainer (FLOWMI; SP Bel-Art, Wayne, NJ).  Living and dead cells were identified by simultaneously staining with green-fluorescent calcein-AM and red-fluorescent ethidium homodimer-1, respectively.
10xChromium single cell libraries were prepared according to the standard protocol outlined in the manual. Briefly, sorted single cell suspension, 10x barcoded gel beads, and oil were loaded into Chromium™ Single Cell A Chip to capture single cells in nanoliter-scale oil droplets by Chromium™ Controller and to generate Gel Bead-In-EMulsions (GEMs). Full length cDNA libraries were prepared by incubation of GEMs in a thermocycler machine. GEMs containing cDNAs were broken and all single cell cDNA libraries were pooled together, cleaned using DynaBeads MyOne™ Silane beads (Fisher PN 37002D), and pre-amplified by PCR to generate sufficient mass for sequencing library construction. Sequencing libraries were constructed by following the steps: cDNA fragmentation, end repair & A-tailing, size selection by SPRIselect beads (Beckman Coulter, PN B23318), adaptor ligation, sample index PCR amplification, and a repeat of SPRIselect beads size selection. The final constructed single cell libraries were sequenced with a total reads per cell targeted for a minimum of 50,000.

treatment_protocol: Form deprivation myopia (FDM) was induced in 3 to 4 day-old chicks by applying translucent plastic goggles to the right eye, as previously described (Rada et al., 1991). The contralateral eyes (left eyes) of all chicks remained untreated and served as controls. Chicks were checked daily for the condition of the goggles. Goggles remained in place for 10 days. At the start of the light cycle on the 11th day (7 am) the goggles were removed and chicks were allowed to experience unrestricted vision (recover) for 24 hrs.

value: Choriod

value: Myopic


title: Ctrl_a, D, MeDIP, 2hr, 0X, rep1

value: 2hr, 2nM Beta-estradiol


title: TB-DM_Week 2_South_Africa_SUN135

source_name: Whole Blood

value: TB-DM


title: Ctrl_a, D, MeDIP, 2hr, 0X, rep2


title: Myopic right eyes - Rep 2


title: genomic DNA from Wildtype sample [205730000030_R02C01]

description: Liver samples from WT mice


title: TB-only_Week 2_South_Africa_SUN141


title: MATa, D, MeDIP, 2hr, 256X, rep2


title: genomic DNA from Wildtype sample [205730000030_R05C01]

description: Liver samples from WT mice


title: TB-DM_Week 2_Indonesia_UNPAD32

value: Indonesia


title: genomic DNA from Adh5-/- sample [205730000030_R02C02]

description: Liver samples from Adh5–/– mice


title: TB-IH_Week 2_South_Africa_SUN127


title: MATa, D, MeDIP, 2hr, 256X, rep1


title: Myopic right eyes - Rep 1


title: TB-preDM_Diagnosis_South_Africa_SUN54


title: TB-DM_Month 6_South_Africa_SUN135


title: TB-only_Month 2_South_Africa_SUN129

value: TB-only


title: Ctrl, +met, MeDIP, 2hr, 0X, rep2

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2


title: TB-only_Diagnosis_South_Africa_SUN132


title: Control left eyes - Rep 3

value: Control


title: TB-only_Week 2_Indonesia_UNPAD16


title: TB-DM_Month 6_Romania_ROM2


title: TB-DM_Week 2_Romania_ROM10


title: TB-IH_Month 6_Indonesia_UNPAD26

value: TB-IH


title: TB-DM_Month 6_Indonesia_UNPAD83


title: Control left eyes - Rep 1


title: Control left eyes - Rep 2


title: TRP2, +met, MeDIP, 2hr, 256X, rep1

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, TRP2::256XLacO::HIS3


title: TRP2, +met, MeDIP, 2hr, 256X, rep2


title: Ctrl, +met, MeDIP, 2hr, 0X, rep1


title: TB-DM_Month 6_Romania_ROM7


title: TB-IH_Week 2_Indonesia_UNPAD2


title: Ctrl, -met, MeDIP, 2hr, 0X, rep1


title: Abcg1cKO_biol rep 4

city: Bern

first: Emanuele

last: Pignatti

address: Freiburgstrasse 15

country: Switzerland

institute: University of bern

data_processing:
The produced paired-end reads which passed Illumina’s chastity filter were demultiplexed using Illumina’s bcl2fastq software version 2.20.0.422 (no further refinement or selection).
Illumina adapter residuals were trimmed using cutadapt (v4.0 with Python 3.9.16).
Quality of the reads in fastq format was checked with the software FastQC (version 0.11.9). Raw reads shorter than 10 bp, having average Q-values below 24 or incorporating uncalled ‘N’ bases were filtered out using the BBTools software suite (version 38.86).
The splice aware RNA mapping software STAR (version 2.7.10a) was used to map the remaining reads.
To count the uniquely mapped reads to annotated genes, the software htseq-count (HTSeq version 0.13.5) was used. Normalization of the raw counts and differential gene expression analysis was carried out with the R software package DESeq2 (version 1.38.3)
Assembly: mm10 reference genome provided by IGenomes (archive-2015-07-17-14-33-26).
Supplementary files format and content: The processed data file submitted containes normalized expression values for Abca1cKO+Cre controls, and Abcg1cKO values, their respective averages, log2fold, IfcSE, p value and p adjusted value for the comparison.

source_name: Adrenal gland

extract_protocol:
RNA was isolated from whole adrenals cleaned of the adherent fat and homogenized in TRI Reagent (Sigma) using the Direct-zol miniprep RNA kit (Zymo Research)
Illumina Stranded mRNA Prep Preparation including polyA enrichment was used according to manufacturer’s recommendations to construct libraries from total RNA.

value: Adrenal gland


title: Abcg1cKO_biol rep 3


title: TB-DM_Diagnosis_Indonesia_UNPAD8


title: TB-DM_Month 2_South_Africa_SUN155


title: Abcg1cKO_biol rep 2


title: Ctrl, -met, MeDIP, 2hr, 0X, rep2


title: genomic DNA from Wildtype sample [205730000030_R04C01]

description: Liver samples from WT mice

value: liver


title: TB-DM_Week 2_Indonesia_UNPAD28


title: TB-DM_Month 6_South_Africa_SUN68


title: TRP2, -met, MeDIP, 2hr, 256X, rep2


title: Abcg1cKO_biol rep 1


title: TB-DM_Month 2_Romania_ROM12


title: TB-preDM_Week 2_South_Africa_SUN140

value: TB-preDM


title: TRP2, -met, MeDIP, 2hr, 256X, rep1


title: TB-DM_Month 2_Indonesia_UNPAD32


title: gcGBM3


title: TB-DM_Diagnosis_South_Africa_SUN135


title: Control_biol rep 2


title: TB-only_Diagnosis_Romania_ROM17

value: Romania


title: TB-only_Month 2_Romania_ROM6


title: Control_biol rep 4


title: TB-DM_Diagnosis_Romania_ROM10


title: Control_biol rep 3


title: TB-only_Month 2_Indonesia_UNPAD34


title: TB-DM_Month 2_Indonesia_UNPAD83


title: Abca1cKO_biol rep 2


title: TB-IH_Month 6_Indonesia_UNPAD2


title: TB-DM_Week 2_Indonesia_UNPAD6


title: TB-only_Week 2_Romania_ROM16


title: TB-DM_Week 2_South_Africa_SUN71


title: TB-DM_Week 2_Indonesia_UNPAD10


title: TB-IH_Week 2_South_Africa_SUN119


title: Abca1cKO_biol rep 1


title: TB-only_Month 6_Indonesia_UNPAD34


title: TB-DM_Month 6_Indonesia_UNPAD18


title: WTL7

city: guangzhou

first: Hao-Xian

last: ZHU

state: Guangdong

address: No. 106, Zhongshan 2nd Road

institute: Guangdong Provincial People’s Hospital

data_processing:
STAR-2.5.2b software was used to map reads to the reference genome.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for bulk RNA-seq Samples

source_name: murine liver tissue

extract_protocol:
Total RNA was extracted utilizing RNA iso Plus (TaKaRa, 9109) from liver tissues
RNA libraries were prepared for sequencing using standard Illumina protocols

value: murine liver tissue

value: CTRL mice


title: WTL8


title: TB-DM_Month 6_Indonesia_UNPAD10


title: TB-DM_Week 2_Romania_ROM12


title: Abca1cKO_biol rep 4


title: TB-DM_Month 6_Indonesia_UNPAD84


title: TB-DM_Month 2_South_Africa_SUN144


title: TB-only_Week 2_Indonesia_UNPAD14


title: TB-only_Month 6_Romania_ROM16


title: WTL4


title: WTL3


title: TB-DM_Month 6_South_Africa_SUN112


title: TB-DM_Week 2_South_Africa_SUN68


title: Abca1cKO_biol rep 3


title: WTL6


title: TB-IH_Month 6_South_Africa_SUN120


title: TB-DM_Diagnosis_Indonesia_UNPAD31

value: Diagnosis


title: TB-DM_Month 6_Indonesia_UNPAD25


title: WTL1


title: TB-DM_Week 2_South_Africa_SUN149


title: WTL2


title: TB-DM_Month 2_South_Africa_SUN71


title: L10

value: CTRL-T infusion


title: TB-DM_Diagnosis_South_Africa_SUN159


title: L9


title: TB-IH_Month 6_South_Africa_SUN105


title: L8


title: TB-preDM_Week 2_South_Africa_SUN54


title: NRCMs, Ad-Otud1-3

city: Shanghai

first: Kai

last: Huang

address: 168 Changhai Road, Yangpu District, Shanghai, China

department: Department of Cardiovascualr Surgery

institute: Changhai Hospital

data_processing:
Fastp (0.23.2) was used for data quality control (--n_base_limit 15,--qualified_quality_phred 20).
Filtered data was mapped to  Rnor_6.0 by hisat2 (2.2.1)
Read counts were extracted by featureCounts (1.6.1)
Assembly: Rn6
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: primary culture cell

growth_protocol: Heart ventricles were dissected, cut into pieces as small as possible, and digested with 0.1% Collagenase Ⅱ (LS004176, Worthington, USA) for 15 min at 37 ℃. The supernatant was collected and mixed with culture medium (High glucose DEME with 10% FBS, 1% Penicillin/streptomycin). This digestion procedure was repeated several times until tissue sediment almost disappeared. After that, all the collected cell suspension was filtered through 100 μm cell strainer and subjected to centrifuge at 1500 rpm for 3 min. Cells were resuspended with culture medium and placed in a cell incubator for 120 min. Newborn rat cardiomyocytes (NRCMs) were in the supernatant.

extract_protocol:
RNA was harvested using TRNzol Univeral Reagent (TIANGEN). 1.5 μg total RNA was used for the  construction of  sequencing libraries.
RNA libraries for RNA-seq were prepared  using Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit for Illumina according to manufacturer's instruction.

treatment_protocol: NRCMs were infected with Ad-Otud1 and then subjected to AngⅡ(10 μM) stimulation for 24h.

value: primary culture cell

value: Neonatal neonatal rat cardiomyocytes

value: Ad-Otud1 + Ang II


title: TB-only_Diagnosis_Romania_ROM16


title: Control_biol rep 1


title: TB-DM_Week 2_Indonesia_UNPAD31

value: TB-DM

value: Indonesia


title: NRCMs, Ad-Otud1-1


title: TB-only_Week 2_Romania_ROM8

value: TB-only


title: TB-DM_Month 2_South_Africa_SUN149


title: TB-DM_Diagnosis_South_Africa_SUN149


title: NRCMs, Ad-GFP-3

value: Ad-GFP + Ang II


title: TB-DM_Month 2_Indonesia_UNPAD12


title: L4

value: CAR-T infusion


title: TB-only_Month 6_Indonesia_UNPAD20


title: L7


title: L6


title: L3


title: NRCMs, Ad-GFP-2


title: cbl7, infected, biolgical rep 3

city: Pozuelo de Alarcón

first: Stephan

last: Pollmann

state: Madrid

address: Campus de Montegancedo, Autovia M-40 (km 38)

institute: CBGP (UPM-INIA/CSIC)

data_processing:
Novogene Novogene Co., LTD Genomics Service (Cambridge, UK)
Original image data files from the Illumina platform were transformed to sequenced reads by CASAVA base recognition.
Sequence reads were trimmed for the adaptor sequence/low-quality reads were deleted using a Novogene in-house script (quality parameter limit: 0.05)
Trimmed sequence reads were mapped against the TAIR10 Arabidopsis genome using Tophat v2.0.12 (mismatch = 2).
Read count extraction and normalization was performed using HTSeq v0.6.3 (–m union parameter).
Assembly: TAIR10 Arabidopsis genome
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample.

organism: Arabidopsis thaliana

source_name: Roots

growth_protocol: Seedlings were grown vertically for seven days on 0.5x MS medium. Then, they were transferred to solidified Plant Nutrition Medium. Root tissue was harvested after 14 days.

extract_protocol:
DNA-free total RNA was extracted by employing the phenol/chloroform method described by Oñate-Sánchez & Vicente-Carbajosa, 2008, BMC Res. Notes.
Sequencing libraries were generated using a NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer’s recommendations.

treatment_protocol: Each seedling was either mock-infected by associating a 5 mm Ø medium plug extracted from sterile AP plates (control) or from AP plates harbouring a 1‐week‐old S. indica mycelium (co-cultivation).

value: Roots

tag: ecotype

value: cbl7 T-DNA insertion line

value: S. indica infected


title: L1


title: TB-DM_Week 2_Indonesia_UNPAD18


title: cbl7, infected, biolgical rep 2


title: TB-only_Diagnosis_Romania_ROM6


title: NRCMs, Ad-GFP-1


title: TB-DM_Month 6_South_Africa_SUN59


title: TB-only_Week 2_Indonesia_UNPAD3


title: YBP2, MeDIP, 1hr, 256X, rep2

value: 1hr, 2nM Beta-estradiol

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, YBP2::256XLacO::HIS3


title: NRCMs, Ad-Otud1-2


title: cbl7, infected, biolgical rep 1


title: mESC_Mettl3KO_m6A-CT2

city: Singapore

first: Kiyofumi

last: Hamashima

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology (IMCB)

data_processing:
Adapter sequences of paired-end raw reads were trimmed using Trim Galore with parameters -q 30.
Trimmed reads were aligned to the hg19 & mm9 genome assembly using STAR aligner version 2.7.2 with the following parameters: --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 30  --outFilterMismatchNmax 3 --outFilterMultimapNmax 1.
Peaks were called using Macs2 with parameters -f BAM -B -q 0.01 --nomodel --extsize 100 --keep-dup all and called peaks with log-q-value > 10 were used in downstream analyses.
Assembly: hg19 and mm9
Supplementary files format and content: Bed files were narrowPeak files generated by Macs2.
Library strategy: Cut & Tag

source_name: C57BL/6 Mettl3-/- (KO)

extract_protocol: For bulk m6A-CT library preparation, E14, EPSC, MEF and HEK293T nuclei were isolated with the following conditions: 1 min on ice in 0.020 % Triton X-100 for E14, 0.015 % Triton X-100 for EPSC; 5 min on ice in 0.2 % NP-40 for MEF, 0.02 % NP-40 for HEK293T. Aliquots of nuclei (5,000–100,000 nuclei) were bound to pre-activated Concanavalin A (Con-A) Conjugated Paramagnetic Beads (EpiCypher, #21-1411) and used in assay. All wash steps were performed on a magnetic separation rack. Undirected cDNA/RNA hybrid tagmentation for INPUT RNA was carried out as described previously. Briefly, nuclei were resuspended in 50 μL Reverse Transcription & Tagmentation Buffer, and incubated for 1 hour at 37 °C. 2.5 μL pAG-Tn5 was then added and vortexed briefly, and incubated for 1 hour at 37 °C.  Antibody directed tagmentation for m6A-CT was carried out as  same as sc-m6A-CT using 1 μg anti-m6A antibody (Synaptic Systems, #202003). When tagmentation was done, 54.5 μL of 0.5 M EDTA, 1 μL of 20 mg/mL Proteinase K and 5.5 μL of 10% SDS were sequentially added to the sample and incubated at 58 °C for 1 hour. An equal amount of Phenol-chloroform-isoamyl alcohol 25:24:1 (PCI), pH 6.7 was added to each sample, and PCI extraction followed by ethanol precipitation were performed. To perform gap-filling, the purified RNA/DNA samples were mixed with 0.32 U/μL Bst 3.0 DNA Polymerase (New England Biolabs) and Q5 High-Fidelilty 2× PCR Master mix (New England Biolabs), and incubated for 5 min at 58 °C, 5 min at 72 °C, and then at 5 min at 80 °C to inactivate Bst 3.0. A qPCR cycle check can be performed at this stage using 1:100 templates. A successful experiment can be identified by comparing cycle threshold values to IgG-CT. A universal i5 and a uniquely barcoded i7 primer, and Q5 HiFi 2× PCR Master mix were used to amplify libraries with the following cycling conditions: 45 sec at 98 °C, followed by 14-21 cycles of 15 sec at 98 °C and 10 sec at 60 °C, with a final extension at 1 min at 72 °C. Post-PCR clean-up was performed by 0.5× right-side followed by 1.2× left-side SPRI beads (Beckman Counter) selection.

value: C57BL/6 Mettl3-/- (KO)

value: Mouse embryonic stem cells

tag: antibody

value: m6A (MilliporeSigma, #ABE572)

tag: replicate


title: YBP2, MeDIP, 1hr, 256X, rep1


title: L5

value: murine liver tissue


title: TB-IH_Diagnosis_Indonesia_UNPAD13

value: TB-IH

value: Diagnosis


title: cbl7, mock, biolgical rep 3

value: Control


title: TB-IH_Diagnosis_Indonesia_UNPAD17


title: mESC_WT_m6A-CT2

source_name: C57BL/6 wild-type

value: C57BL/6 wild-type


title: YBP2, MeDIP, 1hr, 16X, rep1

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, YBP2::16XLacO::HIS3


title: mESC_WT_m6A-CT1

description:
mESC_Control_MeTPeak.csv
mESC_Control_vs_Mettl3KO_exomePeak2.csv


title: L2


title: YBP2, MeDIP, 1hr, 16X, rep2


title: YBP2, MeDIP, 1hr, 8X, rep2

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, YBP2::8XLacO::HIS3


title: TB-IH_Diagnosis_Indonesia_UNPAD11

value: Indonesia


title: cbl7, mock, biolgical rep 2


title: WT, infected, biolgical rep 3

value: wildtype


title: TB-preDM_Month 2_South_Africa_SUN133

value: TB-preDM


title: cbl7, mock, biolgical rep 1

value: Roots

value: cbl7 T-DNA insertion line


title: YBP2, MeDIP, 1hr, 4X, rep2

value: 1hr, 2nM Beta-estradiol

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, YBP2::4XLacO::HIS3


title: mESC_Mettl3KO_Input2

value: C57BL/6 Mettl3-/- (KO)


title: mESC_Mettl3KO_Input1

value: Mouse embryonic stem cells


title: YBP2, MeDIP, 1hr, 8X, rep1


title: mESC_WT_Input2


title: WT, infected, biolgical rep 1

value: S. indica infected


title: mESC_Mettl3KO_m6A-CT1

value: m6A (MilliporeSigma, #ABE572)


title: YBP2, MeDIP, 1hr, 4X, rep1


title: TB-only_Month 6_South_Africa_SUN132

value: TB-only


title: WT, mock, biolgical rep 3


title: mESC_WT_Input1


title: Ctrl, MeDIP, 1hr, 0X, rep2

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2


title: TB-preDM_Month 2_South_Africa_SUN140