title: bulk DNA from mid-log cultures 7min after the EdU pulse bound with RNAPII replicate 2

description:
RNApol2 (Rpb3HA) ChIP from a midlog culture 7 min after the EdU pulse
all_readsFandR_norm_50bpbins_FigS3BGEO.txt
Sonicated chromatin,7min after the EdU pulse, RNAPol2 on bulk DNA.paired end reads 2, replicate 2
7-Rpb3ChIP-2reads2FigS3BGEO

growth_protocol: Mid-log cells (grown o/n in SCD-URA at 30°C, OD600 ~0.68) were treated with 10µM EdU for 1min by mixing equal volumes of culture and preheated (30°C) premixed media containing 20µM EdU. EdU incorporation was stopped with the addition of Thymidine (Acros Organics , previously mixed into preheated SCD-URA media) to a final concentration of 10mM (1000 fold excess) to the culture. The culture was divided into two flasks and the ½ cultures were fixed with formaldehyde 7 or 15 minutes after EdU addition. Cell pellets were washed with cold PBS and flash frozen in liquid nitrogen and kept at -80°C until further processing.

extract_protocol:
Cross-linked frozen cell pellets were re-suspended in 1.5 ml NP lysis buffer (100 mM NaCl, 10 mM Tris 7.4, 5 mM MgCl2, 1 mM CaCl2, 10% NP-40, 50 mM EDTA, 0.1 % SDS (optional), 1 mM PMSF and 1xEDTA-free protease inhibitor cocktail (Roche)). The suspension was then split into aliquots each containing ~billion cells. Zirconium Sillicate beads (400 μl, 0.5 mm) were then added to each aliquot and cells were mechanically disrupted using a bullet blender (Next Advance) for 4 times x 3 min (intensity 8). Spheroplasts were treated with micrococcal nuclease or sonicated. Sonicated or digested chromatin was subject to ChIP with the indicated antibody. An aliquot was set aside for the input DNA fraction prior to ChIP. EdU incorporated into ChIPed and Input DNA fragments was biotinylated using Click chemistry and nascent DNA was purified with streptavidin coated beads (ChIP-NChAP and NChAP fractions, respectively). The supernatant after binding to  streptavidin beads was kept for the unreplicated ChIP fraction and an input DNA and a bulk ChIP DNA aliquot were set aside prior to biotinylation for the Input and ChIP fractions.
DNA samples from all fractions were treated with calf intestinal phosphatase (NEB). NGS libraries were constructed either with costum enzymes( blunt-ended, A-tailed, and ligated (Epicentre) to Illumina genomic PE adaptors with custom 5bp inline barcodes (first 5bp in raw data read)) or using the TrueSeq V2 LT Sample prep kit (Illumina) with the Illumina unique multiplexing indexes Set A and B. The custom library samples were amplified with the Phusion enzyme (NEB) for 18 PCR cycles with Illumina PE1 and PE2 primers.  The primer mix from the kit was  used in the PCR amplification step (also with Phusion) for the samples prepared with  TrueSeq V2 LT (15 cycles). For nascent (replicated NChAP and ChIPNChAP fractions) libraries, the nascent 'EdU containing) strand was separated from its complement with primer extension in the presence of dUTP and the dUTP strand was then digested with the USER enzyme cocktail prior to PCR amplification. All the steps for nascent libraries were done on streptavidine coated magnetic beads.
Strand specific sonicated-ChIP-seq  of replicated DNA fragments. The method which we call ChIP-NChAP (Nascent Chromtin Avidin Pulldown) was developed in the Radman-Livaja group.

value: mid-log 7min after an EdU pulse chased with excessed Thymidine

value: 1min EdU pulse

tag: antibody


title: replicated DNA  from mid-log cultures 7min after the EdU pulse bound with RNAPol2 replicate 2

status: Public on Dec 17 2021

type: SRA

city: Montpellier

first: Marta

last: Radman-Livaja

address: 1919 route de Mende

department: IGMM

country: France

institute: CNRS

description:
RNApol2 (Rpb3HA) ChIP followed by nascent DNA purification by EdU-biotin pulldown  from a midlog culture 7 min after the EdU pulse
all_readsFandR_norm_50bpbins_FigS3BGEO.txt
Sonicated chromatin,7 min after the EdU pulse,  RNAPol2 on replicated DNA.paired end reads 1, replicate 2
7-Rpb3ChIPNChAP-2reads1FigS3BGEO

library_source: genomic

data_processing:
Illumina OLB-1.8.0/CASAVA_v1.7.0 were used for base calling
time points and time point fractions  were separated either by in line barcodes and the 5bp barcode were removed from the read sequence and saved into separate fastq files from a unique fastq file obtained from the sequencing service using a custom perl script, or with Illumina unique indexes (Set A and B) and demultiplexed after sequencing into separate fastq files by the sequencing facility
reads were mapped to the yeast S288C genome using BLAT
Paired end read count distribution in 50bp windows was determined separately for Watson (marked as F in the processed data files) and Crick (marked as R in the processed data files) strands
the genome average read count value was calculated and the data were normalized to one
Genome_build: S288C (S. cerevisiae)
Supplementary_files_format_and_content: tab-delimited text files of indicated feature enrichment (columns) normalized to the average genome read count and distributed in 50bp bins. 50bp bins marked with R indicate repetitive sequences.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: wt yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2)

treatment_protocol: cell aliquots  were fixed with 1% (w/v) formaldehyde for 15 min at 30°C followed by 5 min of quenching in 125 mM Glycine. Cell pellets were then washed with cold PBS and flash frozen in liquid nitrogen and kept at -80°C until further processing.

tag: cell cycle

tag: edu incubation


title: replicated DNA  from mid-log cultures 15min after the EdU pulse bound with RNAPol2 replicate 1

description:
RNApol2 (Rpb3HA) ChIP followed by nascent DNA purification by EdU-biotin pulldown  from a midlog culture 15 min after the EdU pulse
all_readsFandR_norm_50bpbins_FigS3BGEO.txt
Sonicated chromatin, 15 min after the EdU pulse,RNAPol2 on replicated DNA.paired end reads 1, replicate 1
15-Rpb3ChIPNChAP-1reads1FigS3BGEO

value: mid-log 15min after an EdU pulse chased with excessed Thymidine


title: Subject 101730 NT

city: Vancouver

first: Annie

middle: Vogel

last: Ciernia

state: British Columbia

address: 2215 Wesbrook Mall room 4550, Centre for Brain Health

country: Canada

institute: University of British Columbia

library_source: transcriptomic

data_processing:
Raw sequencing reads were assessed for quality control using FastQC and multiqc (PreTrim_multiqc.html) and then trimmed to remove adapter contamination, polyA read through and low quality reads using the following call to BBDuk: bbduk.sh in=raw_sequences/${R1} out=${R1} ref=polyA.fa.gz,truseq_rna.fa.gz k=13 ktrim=r forcetrimleft=11 useshortkmers=t mink=5 qtrim=t trimq=10 minlength=20
All samples were then re-assessed for quality using FastQC and multiqc (PostTrim_multiqc.html). Following trimming and quality assessment, reads were concatenated for each sample down to a single fastq file. Each sample was then aligned to the human genome (GRCh38.p12) using STAR with the following: STAR --runThreadN 12 --genomeDir STAR/GRCh38.p12/star_indices/ --readFilesIn  trimmed_sequences/combinedfastq/${sample}.fastq --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI nM AS MD --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outFileNamePrefix star_out/${sample} command:
Alignment bam files were then compared using multiqc (STAR_Alignmentmultiqc.html), indexed using samtools and then reads per ensembl gene (Homo_sapiens.GRCh38.94.gtf) were counted using the following command to FeatureCounts: featureCounts -T 10 -s 1 -t exon -g gene_id -a STAR/GRCh38.p12/annotation/Homo_sapiens.GRCh38.94.gtf -o htcounts/${sample}.counts.txt star_out/${sample}Aligned.sortedByCoord.out.bam
Genome_build: GRCh38.94
Supplementary_files_format_and_content: Processed data files are the output count text files from FeatureCounts.

molecule: total RNA

organism: Homo sapiens

growth_protocol: Participants were enrolled in this study as part of the larger Autism Phenome Project (APP) conducted at UC Davis and the M.I.N.D. institute. Briefly, children were placed into one of three groups after clinical evaluation at the UC Davis M.I.N.D. Institute: (1) children diagnosed with autism spectrum disorder (ASD) (2) children diagnosed with pervasive development disorder, not otherwise specified or (3) typical developing (TD) children. Diagnoses were confirmed by the Autism Diagnostic Interview-Revised (ADI-R) [3] and the Autism Diagnostic Observation Schedule (ADOS) [4] based on the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition Text Revision (DSM-IVTR) [5].  Children were also assessed with the Repetitive Behaviors Scale - Revised; for behaviors that fell under the subdomains: (a) stereotypies, (b) self-injurious behavior, (c) ritualistic behavior, (d) sameness behavior, and (e) restricted behavior. Typically developing (TD) control children were assessed for development and screened for ASD-like behaviors using the Mullen’s Scale of Early Learning (MSEL) and the Social Communication Questionnaire. Criteria for placement in TD group included scores of <11 on the SCQ and scores within 2 standard deviations of the mean on all subscales of the MSEL. Exclusion criteria for TD children included any known neurological or behavioral problems, developmental delays, or speech language impairments. All subjects were screened for any known serious neurological conditions (including seizure disorders and Fragile X), psychiatric disorders, or immune-mediated medical conditions (such as celiac disease or other autoimmune disorder). Participants were also excluded if taking prescription medication, had reported illness or fever within 48 hours of blood draw, or had suspected or known vision or hearing problems. Written and informed consent was obtained from parent prior to participation, and approval for this study was approved by the institutional review boards at the University of California, Davis. To isolate peripheral mononuclear cells, each child had blood drawn into acid-citrate-dextrose Vacutainer tubes (BD Biosciences; San Jose, CA). Tubes were centrifuged for 10 min at 2300 rpm to separate plasma, which was then was removed and stored at -80°C. The remaining blood was diluted 1:1 with Hanks Balanced Salt Solution without Ca2+ or Mg2+ (HBSS; Gibco, Gaithersburg, MD), then carefully layered over a Ficoll-Paque gradient (Pharmacia Biotech, Piscataway, NJ) and centrifuged at room temperature for 30 minutes at 1700 rpm.  Peripheral blood mononuclear cells (PBMC) were harvested by carefully pipetting the interface layer and transferring to a new container where cells were then washed twice with HBSS. CD14+ cells were isolated using an anti-CD14 magnetic bead according to the manufactures protocol (Miltenyi).  Trypan blue exclusion was used to determine number of live versus dead cells.

extract_protocol:
RNA using the Qiagen RNeasy Mini kit (Germantown, MD) was used following the manufacturer’s instructions. Briefly cells were lysed and homogenized in lysis reagent using QIAshredder homogenizers. 70% ethanol was added to the lysate prior to passing through a spin column at 8000 x g to remove genomic DNA. Spin columns containing RNA were washed with ethanol + Buffer RPE multiple times and centrifuged at 8000 x g, then RNA was eluted from the column in 30uL RNAse-free water. RNA was treated with DNase and concentrated (Zymo Research, Cat No R1014). RNA quality was assessed by bioanalyzer and all samples had RNA Integrity Numbers >6.
QuantSeq 3’mRNA sequencing FWD (RNAseq) libraries (Lexogen, Cat 015.96) were prepared as stated in the Lexogen manual using 30ng of total input RNA per sample and 18 cycles of PCR amplification. 48 unique, dual index barcodes were used and samples were then pooled, exonuclease VII treated.
Samples sequenced across three lanes of a HiSeq4000 to generate Single End 100 base pair reads. Fastq files were generated by concatenating reads across all three lanes for each sample.

treatment_protocol: CD14+ cells were seeded in RPMI 1640 (Gibco) at a concentration of 1 x 105 cells per well in 96 well cell culture plates. RPMI was supplemented with 10% low endotoxin heat inactivated fetal bovine serum (Omega Scientific; Tarzana, CA), 100 IU/ml penicillin, and 100 IU/ml streptomycin (Sigma, St Louis, MO). The cells were stimulated with RPMI alone, RPMI plus 1 µg/mL lipopolysaccharide (LPS; Escherichia coli serotype 0111:B4, Sigma, St. Louis, MO), or RPMI plus 10 µg/mL lipoteichoic acid (LTA; Staphylococcus aureus, Sigma) and cultured at 37°C with 5% CO2. After 24 hours cells were lysed and lysates were stored at -80°C.

tag: subject id

tag: tissue

value: PBMCs

tag: treatment

value: NT

tag: subject sex

value: Male

tag: diagnosis

value: Typical

tag: subject age (ears)


title: Subject 101730 LTA

value: LTA


title: MWMSmmWTNM1: Normoxia WT #1

city: LA

first: Madhuri

last: Wadehra

state: CA

address: 675 Charles Young Dr. South/ 4726 MRL

department: Pathology and Lab Medicine

country: USA

institute: UCLA

data_processing:
Data quality check was done on an Illumina SAV. Demultiplexing was performed with the Illumina Bcl2fastq2 v 2.17 program.
The STAR ultrafast universal RNA-seq aligner (v2.5.2b) was used to generate the genome index and perform single-end alignments. Reads were aligned to a genome index that includes both the genome sequence (GRCm38 primary assembly) and the exon/intron structure of known gene models (Gencode M12 genome annotation). Alignment files were used to generate strand-specific, gene-level count summaries with STAR's built-in gene counter. Differential expression analysis was performed with DESeq2.
Counts were normalized per-sample in units of RPKMs after correcting for gene mappable length and sample total counts.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab delimited, per-sample, gene expression estimates in units of RPKMs

organism: Mus musculus

source_name: Retina/coroid

growth_protocol: EMP2 KO mice bred on a C57BL/6 background were obtained from the laboratory of Dr. Carmen Williams [Williams 2017] and re-derived at UCLA.  Wildtype C57BL/6 mice were purchased from the UCLA Division of Laboratory and Animal Medicine colony.  All mice were housed  in 12:12 hour light-dark cycles with ad libitum access to a standard rodent chow diet (Pico Lab Rodent Diet 20, cat# 5053, Lab Diet, St. Louis, MO) and water.

extract_protocol:
RNA was extracted using the Zymo Direct-Zol RNA MiniPrep Plus (cat# R2070, Irvine, CA) as per the manufacturer’s instructions. Total RNA was quantified and 260/280 ratios determined using Nanodrop (all samples with a 260/280>1.97). 1μg of total RNA was used as starting material for each sample.
RNA sequencing and library preparation was performed by the UCLA Technology Center for Genomics and Bioinformatics with Kapa hyper Prep Kits with RiboErase. The workflow consists of rRNA depletion, cDNA generation, and end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane. Sequencing was performed on Illumina Hiseq3000 for a single read 50 run.

treatment_protocol: Oxygen-induced retinopathy was produced in the mouse according to standard guidelines published [Connor 2009]. Briefly, pups were designated at P0.5 the morning that they were found to be delivered. Mothers were maintained on the standard rodent chow diet, as above, during gestation and during suckling. Litters were culled to 8 pups, as per protocol recommendations. Mothers were randomly assigned to normoxia conditions or hyperoxia conditions. For those assigned to hyperoxia, on postnatal day 7, nursing mothers and their pups were subjected to hyperoxia (75% oxygen continuously) for 5 days by placing them in an airtight chamber (Biospherix Proox model 360). Conditions including humiditiy, temperature, and the health of the animals were assessed twice daily while in the chamber. On postnatal day 12, the mothers and their pups were removed from the chamber and placed back into room air (21% oxygen).

tag: strain

tag: Sex

value: Female

tag: age

tag: genotype/variation

value: Wild Type

value: Retina/coroid


title: D2HG_rep3 [bulk RNA-seq]

city: San Antonio

first: Meena

last: Kusi

state: TX

address: 7703 Floyd Curl Dr

department: Department of Molecular Medicine

institute: University of Texas Health Science Center at San Antonio

data_processing:
Raw sequence reads were checked for initial quality control using FastQC v0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and summarized using MultiQC v0.8 (https://multiqc.info/). Adapter sequences were trimmed using Cutadapt v1.18 (http://journal.embnet.org/index.php/embnetjournal/article/view/200/479).
The trimmed reads were then aligned to the human reference genome (GRCh38/hg38) using STAR v2.7.5a (Dobin et. al., 2013) with standard input parameters. Transcript counts were normalized and differentially expressed genes were estimated by using DESeq2 v1.26.0 (Love et. al., 2014).
Genome_build: hg38
Supplementary_files_format_and_content: Text file represents raw gene counts as described above.

extract_protocol:
Cells were collected, lysed and homogenized in TRI reagent (Zymo Research). Total RNA was extracted in triplicate from each condition according to Direct-zol RNA miniprep plus (Zymo Research) protocol. The quantity and quality of isolated RNA were assessed by NanoDrop 2000 (ThermoFisher) and Agilent 5200 Fragment Analyzer system. RNA quality scores ranged from 9.2 to 10.0.
Sequencing libraries were prepared with 500 ng of total RNA using Zymo RiboFree Total RNA Library Kit. Following first strand cDNA synthesis, rRNA depletion was carried out to enrich mRNA as per the protocol. A second strand of DNA was synthesized and adapter ligation was completed to obtain dual-indexed sequencing libraries. ERCC spike-in control mix (Ambion) was also added to each sample (1:10 dilution). The concentration and quality of libraries were evaluated using Qubit dsDNA assay on Qubit 2.0 fluorometer (Invitrogen) and High Sensitivity DNA Kit on Agilent 2100 Bioanalyzer system. RNA-seq libraries were sequenced on HiSeq 3000 platform using 50-bp, single-read Illumina chemistry with a coverage depth of 25-30 million reads per sample.

tag: cell type

value: Primary mammary epithelial cells (hMECs)

tag: passages


title: Subject 101736 LPS

value: LPS


title: replicated DNA  from mid-log cultures 7min after the EdU pulse bound with RNAPol2 replicate 1

description:
RNApol2 (Rpb3HA) ChIP followed by nascent DNA purification by EdU-biotin pulldown  from a midlog culture 7 min after the EdU pulse
all_readsFandR_norm_50bpbins_FigS3BGEO.txt
Sonicated chromatin, 7 min after the EdU pulse,RNAPol2 on replicated DNA.paired end reads 1, replicate 1
7-Rpb3ChIPNChAP-1reads1FigS3BGEO


title: bulk DNA from mid-log cultures 7min after the EdU pulse bound with RNAPII replicate 1

description:
RNApol2 (Rpb3HA) ChIP from a midlog culture 7 min after the EdU pulse
all_readsFandR_norm_50bpbins_FigS3BGEO.txt
Sonicated chromatin, 7 min after the EdU pulse, RNAPol2 on bulk DNA.paired end reads 1, replicate 1
7-Rpb3ChIP-1reads1FigS3BGEO


title: MWMSmmWTHP1: Hyperoxia WT #1


title: MWMSmmWTHP4: Hyperoxia WT #4


title: Subject 101730 LPS


title: Input DNA from mid-log cultures 7min after the EdU pulse replicate 1

description:
Input DNA from sonicated chromatin from midlog cultures 7min after the EdU pulse
all_readsFandR_norm_50bpbins_FigS3BGEO.txt
Sonicated chromatin 7 min after the EdU pulse, input DNA.paired end reads 1, replicate 1
7-Inpt-1reads1FigS3BGEO


title: MWMSmmWTHP2: Hyperoxia WT #2


title: replicated DNA  from mid-log cultures 15min after the EdU pulse bound with RNAPol2 replicate 2

description:
RNApol2 (Rpb3HA) ChIP followed by nascent DNA purification by EdU-biotin pulldown  from a midlog culture 15 min after the EdU pulse
all_readsFandR_norm_50bpbins_FigS3BGEO.txt
Sonicated chromatin,15 min after the EdU pulse,  RNAPol2 on replicated DNA.paired end reads 1, replicate 2
15-Rpb3ChIPNChAP-2reads1FigS3BGEO


title: Input DNA from mid-log cultures 7min after the EdU pulse replicate 2

description:
Input DNA from sonicated chromatin from midlog cultures 7min after the EdU pulse
all_readsFandR_norm_50bpbins_FigS3BGEO.txt
Sonicated chromatin,7 min after the EdU pulse, input DNA.paired end reads 1, replicate 2
7-Inpt-2reads1FigS3BGEO


title: MWMSmmWTHP3: Hyperoxia WT #3


title: Mcm2-3A55-NChAP-2-FVreadsFigS8GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 55min after G1 arrest with alpha factor
MCM23A_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,55min after release into S phase, replicated DNA.paired end reads, replicate 2

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm97

growth_protocol: Cells were grown overnight at 30°C in SCD-URA. The culture was diluted to OD600 ~0.3 the next morning and grown to OD600 ~0.65 and re-diluted to OD600 ~0.3  in fresh media. The culture was synchronized with the addition of 0.15 μg/ml α factor for 3h30min at 30°C. Cells were released from arrest in preheated (SCD-URA) + 10 μM EdU and grown at 30°C for indicated times before fixation with formaldehyde.

extract_protocol:
Cross-linked frozen cell pellets were re-suspended in 1.5 ml NP lysis buffer (100 mM NaCl, 10 mM Tris 7.4, 5 mM MgCl2, 1 mM CaCl2, 10% NP-40, 50 mM EDTA, 0.1 % SDS (optional), 1 mM PMSF and 1xEDTA-free protease inhibitor cocktail (Roche)). The suspension was then split into aliquots each containing ~billion cells. Zirconium Sillicate beads (400 μl, 0.5 mm) were then added to each aliquot and cells were mechanically disrupted using a bullet blender (Next Advance) for 4 times x 3 min (intensity 8). Spheroplasts were treated with micrococcal nuclease or sonicated. Sonicated or digested chromatin was subject to ChIP with the indicated antibody. An aliquot was set aside for the input DNA fraction prior to ChIP. EdU incorporated into ChIPed and Input DNA fragments was biotinylated using Click chemistry and nascent DNA was purified with streptavidin coated beads (ChIP-NChAP and NChAP fractions, respectively). The supernatant after binding to  streptavidin beads was kept for the unreplicated ChIP fraction and an input DNA and a bulk ChIP DNA aliquot were set aside prior to biotinylation for the Input and ChIP fractions.
DNA samples from all fractions were treated with calf intestinal phosphatase (NEB). NGS libraries were constructed either with costum enzymes( blunt-ended, A-tailed, and ligated (Epicentre) to Illumina genomic PE adaptors with custom 5bp inline barcodes (first 5bp in raw data read)) or using the TrueSeq V2 LT Sample prep kit (Illumina) with the Illumina unique multiplexing indexes Set A and B. The custom library samples were amplified with the Phusion enzyme (NEB) for 18 PCR cycles with Illumina PE1 and PE2 primers.  The primer mix from the kit was  used in the PCR amplification step (also with Phusion) for the samples prepared with  TrueSeq V2 LT (15 cycles). For nascent (replicated NChAP and ChIPNChAP fractions) libraries, the nascent 'EdU containing) strand was separated from its complement with primer extension in the presence of dUTP and the dUTP strand was then digested with the USER enzyme cocktail prior to PCR amplification. All the steps for nascent libraries were done on streptavidine coated magnetic beads.
Strand specific MNase-CHIP-seq  or strand specific sonicated-ChIP-seq  of replicated DNA fragments. The method which we call ChIP-NChAP (Nascent Chromtin Avidin Pulldown) was developed in the Radman-Livaja group.

value: Mcm23A mutant

value: S-phase

value: from beginning of release from G1 arrest


title: Mcm2-3A55-NChAP-1-FVreadsFigS8GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 55min after G1 arrest with alpha factor
MCM23A_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,55min after release into S phase, replicated DNA.paired end reads, replicate 1

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm95


title: MWMSmmWTNM3: Normoxia WT #3


title: Subject 101728 NT

value: Full Autistic Disorder


title: Subject 101728 LPS


title: Subject 101728 LTA


title: MWMSmmKONM3: Normoxia EMP2 KO #3

value: EMP2 KO


title: MWMSmmKONM4: Normoxia EMP2 KO #4


title: Mcm2-3A55-Inpt-2readsFigS8GEO

description:
Input DNA from sonicated chromatin from S-phase 55min after G1 arrest with alpha factor
MCM23A_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,55min after release into S phase, input DNA.paired end reads, replicate 2

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm93


title: MWMSmmKONM2: Normoxia EMP2 KO #2


title: Subject 101736 NT


title: Mcm2-3A55-Inpt-1readsFigS8GEO

description:
Input DNA from sonicated chromatin from S-phase 55min after G1 arrest with alpha factor
MCM23A_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,55min after release into S phase, input DNA.paired end reads, replicate 1

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm91


title: Mcm2-3A48-NChAP-2-FVreadsFigS8GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 48min after G1 arrest with alpha factor
MCM23A_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,48min after release into S phase, replicated DNA.paired end reads, replicate 2

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm89


title: MWMSmmKONM1: Normoxia EMP2 KO #1


title: Mcm2-3A48-NChAP-1-FVreadsFigS8GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 48min after G1 arrest with alpha factor
MCM23A_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,48min after release into S phase, replicated DNA.paired end reads, replicate 1

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm87


title: MWMSmmKOHP4: Hyperoxia EMP2 KO #4


title: Mcm2-3A48-Inpt-2readsFigS8GEO

description:
Input DNA from sonicated chromatin from S-phase 48min after G1 arrest with alpha factor
MCM23A_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,48min after release into S phase, input DNA.paired end reads, replicate 2

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm85


title: MWMSmmKOHP3: Hyperoxia EMP2 KO #3


title: Mcm2-3A48-Inpt-1readsFigS8GEO

description:
Input DNA from sonicated chromatin from S-phase 48min after G1 arrest with alpha factor
MCM23A_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,48min after release into S phase, input DNA.paired end reads, replicate 1

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm83


title: Subject 101725 LTA


title: Subject 101725 LPS


title: Mcm2-3A40-NChAP-1-FVreadsFigS8GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 40min after G1 arrest with alpha factor
MCM23A_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,40min after release into S phase, replicated DNA.paired end reads, replicate 1

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm79


title: MWMSmmKOHP2: Hyperoxia EMP2 KO #2


title: Mcm2-3A40-Inpt-2readsFigS8GEO

description:
Input DNA from sonicated chromatin from S-phase 40min after G1 arrest with alpha factor
MCM23A_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,40min after release into S phase, input DNA.paired end reads, replicate 2

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm77


title: Mcm2-3A40-NChAP-2-FVreadsFigS8GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 40min after G1 arrest with alpha factor
MCM23A_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,40min after release into S phase, replicated DNA.paired end reads, replicate 2

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm81


title: MWMSmmKOHP1: Hyperoxia EMP2 KO #1


title: Subject 101717 LPS


title: Subject 101717 NT


title: Subject 101724 NT


title: MND-3

city: Wenzhou

first: Yanxuan

last: Li

address: Chashan

country: China

institute: Wenzhou Medical University

data_processing:
Reads were aligned against the miRBase (v21) using Bowtie allowing one mismatch.
Unaligned sequences were pooled together to identify novel miRNAs using the software package miRDeep (v2.0.0.5) with default parameters.
In order to investigate the expression profiles of miRNAs, the frequency of miRNA counts were normalized to TPM (tags per million) using the following formula: normalized expression = actual miRNA read count /total clean read count
Differentially expressed miRNAs between the paired groups were analyzed by using DEGseq
Genome_build: mm10
Supplementary_files_format_and_content: raw, FPKM

source_name: brain tissue

extract_protocol:
Total RNA was extract from each tissue sample using Trizol method.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

value: post-natal 21 day

value: maternal normal diet (MND)


title: MND-2


title: Subject 101713 NT

value: PBMCs

value: NT


title: MND-1


title: MHFD-3

value: Maternal high-fat diet (MHFD)


title: Subject 101713 LTA

value: LTA

value: Male

value: Typical


title: Subject 101725 NT


title: MHFD-2


title: Mcm2-3A40-Inpt-1readsFigS8GEO

description:
Input DNA from sonicated chromatin from S-phase 40min after G1 arrest with alpha factor
MCM23A_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,40min after release into S phase, input DNA.paired end reads, replicate 1

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm75


title: Mcm2-3A32-NChAP-2-FVreadsFigS8GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 32min after G1 arrest with alpha factor
MCM23A_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,32min after release into S phase, replicated DNA.paired end reads, replicate 2

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm73


title: Subject 101713 LPS


title: Mcm2-3A32-NChAP-1-FVreadsFigS8GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 32min after G1 arrest with alpha factor
MCM23A_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,32min after release into S phase, replicated DNA.paired end reads, replicate 1

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm71


title: Subject 101709 NT

value: Female


title: Mcm2-3A32-Inpt-2readsFigS8GEO

description:
Input DNA from sonicated chromatin from S-phase 32min after G1 arrest with alpha factor
MCM23A_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,32min after release into S phase, input DNA.paired end reads, replicate 2

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm69


title: Mcm2-3A32-Inpt-1readsFigS8GEO

description:
Input DNA from sonicated chromatin from S-phase 32min after G1 arrest with alpha factor
MCM23A_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,32min after release into S phase, input DNA.paired end reads, replicate 1

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm67


title: Subject 101709 LTA


title: VT191_Tissue_B

type: genomic

city: Sydney

first: Braydon

last: Meyer

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genetics and Epigenetics

country: Australia

institute: Garvan Institute of Medical Research

description:
202751300035_R08C01_Red.idat
202751300035_R08C01_Grn.idat

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

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

data_processing:
Raw intensity data (IDAT) files were imported into R using the minfi package (version 1.32.0) [PMID: 24478339]. The data was processed in minfi with background correction.  Poor quality probes with a detection p-value >0.01 in at least 10% samples were removed.  To reduce the risk of false discoveries we removed probes that mapped to multiple locations or overlapped SNPs as identified by Pidsley and colleagues [PMID: 27717381]. The resulting datasets comprised 804,805 CpG sites. β values were calculated from unmethylated (U) and methylated (M) signal [M/(U + M + 100)] and ranged from 0 to 1 (0 to 100% methylation).
beta_detp.csv = Normalized (FunNorm) Average Beta
raw_detp.csv= Unmethylated and methylated signal intensities

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Biopsys extracted at timepoints A, B and C, DNA isolation from microdissected formalin-fixed paraffin-embedded tissue was performed using the Gentra Puregene Genomic DNA purification tissue kit according to the manufacturer’s instructions (Qiagen).

treatment_protocol: Women enrolled in the observational study received neoadjuvant chemotherapy with 12 weeks of FEC100 (fluorouracil 500 mg/m2, epirubicin 100 mg/m2, and cyclophosphamide 500 mg/m2), and 12 weeks of docetaxel (100 mg/m2)

tag: gender

value: Breast

tag: timepoint

value: B

tag: response

value: Non


title: VT191_Tissue_A

description:
202751300035_R07C01_Red.idat
202751300035_R07C01_Grn.idat

value: A


title: VS065_Tissue_B

description:
202751300022_R04C01_Red.idat
202751300022_R04C01_Grn.idat

value: Complete


title: Mcm2-3A25-NChAP-1-FVreadsFigS8GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 25min after G1 arrest with alpha factor
MCM23A_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,25min after release into S phase, replicated DNA.paired end reads, replicate 1

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm63

value: Mcm23A mutant

tag: cell cycle

value: S-phase

value: from beginning of release from G1 arrest

tag: antibody


title: Mcm2-3A25-NChAP-2-FVreadsFigS8GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 25min after G1 arrest with alpha factor
MCM23A_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,25min after release into S phase, replicated DNA.paired end reads, replicate 2

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm65

tag: edu incubation


title: VS065_Tissue_A

description:
202751300022_R03C01_Red.idat
202751300022_R03C01_Grn.idat

tag: tissue


title: Subject 101709 LPS

tag: subject id

tag: treatment

value: LPS

value: Full Autistic Disorder


title: Mcm2-3A25-Inpt-2readsFigS8GEO

description:
Input DNA from sonicated chromatin from S-phase 25min after G1 arrest with alpha factor
MCM23A_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,25min after release into S phase, input DNA.paired end reads, replicate 2

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm61


title: Subject 101703 NT

value: PBMCs

tag: subject sex

tag: diagnosis


title: Subject 101703 LTA

tag: subject age (ears)


title: Subject 101703 LPS


title: Subject 101724 LPS


title: Mcm2-3A25-Inpt-1readsFigS8GEO

description:
Input DNA from sonicated chromatin from S-phase 25min after G1 arrest with alpha factor
MCM23A_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,25min after release into S phase, input DNA.paired end reads, replicate 1

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm59


title: Mcm2-3A18-NChAP-2-FVreadsFigS8GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 18min after G1 arrest with alpha factor
MCM23A_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,18min after release into S phase, replicated DNA.paired end reads, replicate 2

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm57


title: VP035_Tissue_C

description:
200611820006_R08C01_Red.idat
200611820006_R08C01_Grn.idat

value: C


title: Subject 101699 NT

value: NT


title: VP035_Tissue_A

description:
200611820006_R07C01_Red.idat
200611820006_R07C01_Grn.idat


title: Mcm2-3A18-NChAP-2-FVbreadsFigS8GEO

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm55


title: MHFD-1

value: brain

value: post-natal 21 day

tag: strain

value: Maternal high-fat diet (MHFD)


title: Nav_BM_800

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

description: Naive.BM.BL.Rpkm.detected.csv

data_processing:
Raw sequencing reads were mapped to the hg38 using STAR and the UCSC KnownGene reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor and normalized to reads per kilobase per million (RPKM).
Genes were filtered for detection by requiring at least 3 RPM for all samples of at least one group
Genome_build: hg38
Supplementary_files_format_and_content: Naive.BM.BL.Rpkm.detected.csv

molecule: polyA RNA

source_name: Naïve B cell

extract_protocol:
Cells were FACS sorted into RLT+1%Bme using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research).
All purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara). Final libraries were constructed using 400 pg of cDNA as input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

tag: age

value: M

tag: race

value: Caucasian

tag: ethnicity

value: Non-Hispanic

value: Bone Marrow

value: Naive B cell


title: Mcm2-3A18-NChAP-1-FVreadsFigS8GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 18min after G1 arrest with alpha factor
MCM23A_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,18min after release into S phase, replicated DNA.paired end reads, replicate 1

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm53

tag: genotype/variation


title: Subject 101699 LPS

value: Male


title: Nav_BM_66294_516

description: Naive.BM.BL.Rpkm.detected.csv

tag: gender

value: F

tag: cell type


title: SN107_Tissue_B

description:
200611820002_R08C01_Red.idat
200611820002_R08C01_Grn.idat

value: Female

value: Breast

tag: timepoint

value: B

tag: response

value: Non


title: Mcm2-3A18-Inpt-2readsFigS8GEO

description:
Input DNA from sonicated chromatin from S-phase 18min after G1 arrest with alpha factor
MCM23A_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,18min after release into S phase, input DNA.paired end reads, replicate 2

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm51

value: Mcm23A mutant

tag: cell cycle

value: S-phase

value: from beginning of release from G1 arrest

tag: antibody


title: Sample 1: Src_Variant_Library

city: Seattle

first: Douglas

last: Fowler

state: WA

address: 3720 15th Ave NE, Foege Building, S041

department: Genome Sciences

institute: University of Washington

description:
Library and barcode sequencing from DNA
Src_Barcode_Map.txt

data_processing:
Sample 1 was sequenced on MiSeq (Illumina). Samples 2-5 were sequenced on NextSeq 500 (Illumina).
All reads were processed using  bcl2fastq v.2.16 and ea-utils v.1.1.2-537.
Sample 1: Custom scripts were used to process these reads. R2 files were trimmed to 230bp.
Samples 2-5: Functional scores were calculated using Enrich2 v1.2 software and Src_Barcode_Map.txt.
Genome_build: NA
Supplementary_files_format_and_content: Src_Barcode_Map.txt provides the linkage between the barcode sequence (first column) and the full length variant sequence of Src's catalytic domain (second column). This document was generated through the following steps: 1)Custom subassembly scripts to link barcode sequence with full length catalytic domain sequence. 2) Custom subassembly filtering script for high quality reads. 3) Filtering out  WT barcodes with aberrant activity score using 2x Std. Dev. of WT barcode mean activity score. 4) Spike in of 6 barcode sequences of control Src variants (3 each for K298M and T341I).
Supplementary_files_format_and_content: Src_Das_25_Score.csv, Src_DAS_100_Score.csv, Src_1_8000_Score.csv, Src_2_2000_Score.csv, and Src_4_800_Score.csv are the output of Enrich2 v1.2. The inputs for Enrich2 v1.2 were the corresponding "Raw Files" (Input, A, B, and C) that share the same Src Inhibitor and concentration. Variants are denoted by their amino acid level changes and each has a calculated functional score from Enrich2.

molecule: other

organism: Escherichia coli

source_name: Synthetic sequence

growth_protocol: TOP10 E.coli were grown in LB supplemented with 100 ug/mL Ampicillin. BY4741 ∆PDR5 or BY4741 Green Monster S. cerevisiae were grown in C-Leu media supplemented with 2% galactose.

extract_protocol:
Harvested cells (4 OD units worth) at each sampled time point were pelleted and stored at -20ºC. Plasmid DNA was extracted using Zymogen Yeast Miniprep Kit I following supplied protocol.
Extracted barcodes were amplifed and sample indices appended using 2x KAPA2G Robust HotStart ReadyMix with Thermocycler conditions of: Initial denaturation at 95ºC for 3 min, followed by 17 cycles of 95ºC for 15s, 60ºC for 15s, and 72ºC for 15s. Amplicons were quantified using KAPA Library Quantification Kit.
DNA amplicon sequencing using custom primers

treatment_protocol: S. cerevisiae harboring Src variant library were grown in 2% galactose containing media to induce Src expression and in varying concentrations of indicated Src kinase inhibitor. Library was grown and 4 OD unit timepoints were harvested throughout growth. The indicated concentration of Src inhibitor was added at the same time Src kinase expression was induced by galactose.

tag: treatment concentration

tag: molecule

value: Plasmid DNA


title: SN107_Tissue_A

description:
200611820002_R07C01_Red.idat
200611820002_R07C01_Grn.idat

tag: tissue

value: A


title: Subject 101697 LTA

tag: subject id

value: PBMCs

tag: treatment

value: LTA

tag: subject sex

value: Full Autistic Disorder


title: Nav_BM_66294_512

description: Naive.BM.BL.Rpkm.detected.csv

value: Caucasian

value: Non-Hispanic


title: SI114_Tissue_B

description:
202764140076_R08C01_Red.idat
202764140076_R08C01_Grn.idat

value: Partial


title: Mcm2-3A18-Inpt-1readsFigS8GEO

description:
Input DNA from sonicated chromatin from S-phase 18min after G1 arrest with alpha factor
MCM23A_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,18min after release into S phase, input DNA.paired end reads, replicate 1

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm49

tag: edu incubation


title: Nav_BM_66294_510

description: Naive.BM.BL.Rpkm.detected.csv

tag: age

value: M

value: Bone Marrow

value: Naive B cell


title: Subject 101696 NT

value: NT

value: Male

tag: diagnosis

tag: subject age (ears)


title: SI114_Tissue_A

description:
202764140076_R07C01_Red.idat
202764140076_R07C01_Grn.idat

value: Female

value: Breast


title: Subject 101696 LPS

value: LPS


title: Nav_BM_66294_513

description: Naive.BM.BL.Rpkm.detected.csv

value: F

tag: race

value: AA

tag: ethnicity


title: Nav_BM_2252

description: Naive.BM.BL.Rpkm.detected.csv

tag: gender

value: Not Indicated

tag: cell type


title: Subject 101697 LPS

value: PBMCs


title: 55-NChAP-WT-1-FVreadsFigS8GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 55min after G1 arrest with alpha factor
WT_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,55min after release into S phase, replicated DNA.paired end reads, replicate 1

source_name: wt yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2)

tag: genotype/variation

value: wt

value: S-phase

value: from beginning of release from G1 arrest


title: 55-NChAP-WT-2-FVreadsFigS8GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 55min after G1 arrest with alpha factor
WT_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,55min after release into S phase, replicated DNA.paired end reads, replicate 2

tag: cell cycle


title: Nav_BM_2206

description: Naive.BM.BL.Rpkm.detected.csv

value: Caucasian

value: Non-Hispanic


title: SH201_Tissue_A

description:
202764140076_R04C01_Red.idat
202764140076_R04C01_Grn.idat

tag: timepoint

value: A

tag: response

value: Partial


title: SS066_Tissue_A

description:
200811050082_R06C01_Red.idat
200811050082_R06C01_Grn.idat

value: Complete


title: Subject 101688 NT

value: NT

value: Full Autistic Disorder


title: Subject 101697 NT

value: Male


title: Nav_BM_208_2308

description: Naive.BM.BL.Rpkm.detected.csv

value: Bone Marrow

value: Naive B cell


title: 55-Inpt-WT-1readsFigS8GEO

description:
Input DNA from sonicated chromatin from S-phase 55min after G1 arrest with alpha factor
WT_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,55min after release into S phase, input DNA.paired end reads, replicate 1

tag: antibody


title: SH196_Tissue_A

description:
202764140076_R01C01_Red.idat
202764140076_R01C01_Grn.idat

value: Female

tag: tissue

value: Breast


title: Subject 101688 LTA

tag: subject id

value: LTA


title: Nav_BM_207_1177

description: Naive.BM.BL.Rpkm.detected.csv

value: F


title: 48-NChAP-WT-2-FVreadsFigS8GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 48min after G1 arrest with alpha factor
WT_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,48min after release into S phase, replicated DNA.paired end reads, replicate 2

value: wt


title: SF082_Tissue_B

description:
200611820002_R06C01_Red.idat
200611820002_R06C01_Grn.idat

value: B


title: SI114_Tissue_C

description:
202751300022_R01C01_Red.idat
202751300022_R01C01_Grn.idat

value: C


title: Subject 101688 LPS

value: PBMCs

tag: treatment

value: LPS


title: Nav_BM_1895

description: Naive.BM.BL.Rpkm.detected.csv

value: M

value: Caucasian

value: Hispanic


title: 48-NChAP-WT-1-FVreadsFigS8GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 48min after G1 arrest with alpha factor
WT_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,48min after release into S phase, replicated DNA.paired end reads, replicate 1

value: S-phase

value: from beginning of release from G1 arrest


title: Subject 101687 NT

value: NT

tag: subject sex

value: Male

value: Typical


title: 48-Inpt-WT-2readsFigS8GEO

description:
Input DNA from sonicated chromatin from S-phase 48min after G1 arrest with alpha factor
WT_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,48min after release into S phase, input DNA.paired end reads, replicate 2

tag: edu incubation


title: RP186_Tissue_B

description:
202751300035_R06C01_Red.idat
202751300035_R06C01_Grn.idat

value: Female

value: Partial


title: SF082_Normal_N

description:
200611820002_R04C01_Red.idat
200611820002_R04C01_Grn.idat

value: Breast

value: N

value: Complete


title: 40-NChAP-WT-2-FVreadsFigS8GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 40min after G1 arrest with alpha factor
WT_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,40min after release into S phase, replicated DNA.paired end reads, replicate 2

value: wt


title: Nav_BL_83

description: Naive.BM.BL.Rpkm.detected.csv

tag: age

value: F

value: Asian

value: Non-Hispanic

value: Blood

value: Naive B cell


title: Subject 101687 LPS

value: PBMCs

value: LPS

tag: diagnosis


title: Nav_BL_82

description: Naive.BM.BL.Rpkm.detected.csv


title: 55-Inpt-WT-2readsFigS8GEO

description:
Input DNA from sonicated chromatin from S-phase 55min after G1 arrest with alpha factor
WT_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,55min after release into S phase, input DNA.paired end reads, replicate 2

value: S-phase

value: from beginning of release from G1 arrest


title: Subject 101685 NT

value: NT

value: Male

value: Full Autistic Disorder

tag: subject age (ears)


title: Nav_BL_81

description: Naive.BM.BL.Rpkm.detected.csv

tag: race

value: AA


title: 40-NChAP-WT-1-FVbreadsFigS8GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 40min after G1 arrest with alpha factor
WT_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,40min after release into S phase, replicated DNA.paired end reads, replicate 1


title: RD061_Tissue_B

description:
200611820006_R04C01_Red.idat
200611820006_R04C01_Grn.idat

value: Female

value: Breast

value: B


title: Subject 101685 LPS


title: 40-Inpt-WT-2readsFigS8GEO

description:
Input DNA from sonicated chromatin from S-phase 40min after G1 arrest with alpha factor
WT_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,40min after release into S phase, input DNA.paired end reads, replicate 2

value: wt


title: Nav_BL_77

description: Naive.BM.BL.Rpkm.detected.csv

value: F

tag: ethnicity


title: RD061_Tissue_A

description:
200611820006_R03C01_Red.idat
200611820006_R03C01_Grn.idat

tag: gender

value: A

value: Complete


title: Subject 101684 NT

value: Typical


title: Nav_BL_57983_163

description: Naive.BM.BL.Rpkm.detected.csv

value: Asian

value: Non-Hispanic

value: Blood

tag: cell type

value: Naive B cell


title: 40-Inpt-WT-1readsFigS8GEO

description:
Input DNA from sonicated chromatin from S-phase 40min after G1 arrest with alpha factor
WT_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,40min after release into S phase, input DNA.paired end reads, replicate 1

tag: genotype/variation

value: S-phase

value: from beginning of release from G1 arrest


title: Nav_BL_57983_162

description: Naive.BM.BL.Rpkm.detected.csv


title: PR068_Tissue_A

description:
200811050082_R08C01_Red.idat
200811050082_R08C01_Grn.idat

value: Partial


title: SF082_Tissue_A

description:
200611820002_R05C01_Red.idat
200611820002_R05C01_Grn.idat


title: 32-NChAP-WT-2-FVreadsFigS8GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 32min after G1 arrest with alpha factor
WT_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,32min after release into S phase, replicated DNA.paired end reads, replicate 2

tag: cell cycle


title: Nav_BM_1464

description: Naive.BM.BL.Rpkm.detected.csv

value: Bone Marrow


title: Subject 101682 NT

value: PBMCs

value: NT


title: Subject 101687 LTA

value: LTA

value: Male


title: Nav_BL_2206

description: Naive.BM.BL.Rpkm.detected.csv

value: M

value: Caucasian


title: Subject 101682 LTA

value: Female


title: 40-NChAP-WT-1-FVreadsFigS8GEO

value: wt


title: PR068_Normal_N

description:
200811050082_R02C01_Red.idat
200811050082_R02C01_Grn.idat

value: Breast

tag: timepoint

value: N


title: NS028_Tissue_B

description:
200611820006_R02C01_Red.idat
200611820006_R02C01_Grn.idat

value: B

tag: response


title: Subject 101682 LPS

value: LPS

value: Typical


title: Nav_BL_1895

description: Naive.BM.BL.Rpkm.detected.csv

value: Hispanic

value: Blood

value: Naive B cell


title: RP186_Tissue_A

description:
202751300035_R05C01_Red.idat
202751300035_R05C01_Grn.idat

value: A

value: Partial


title: NS028_Tissue_A

description:
200611820006_R01C01_Red.idat
200611820006_R01C01_Grn.idat


title: Subject 101680 NT

value: PBMCs

value: NT

value: Full Autistic Disorder


title: Nav_BL_115_2267

description: Naive.BM.BL.Rpkm.detected.csv

value: F

value: Asian

value: Non-Hispanic


title: 32-Inpt-WT-1readsFigS8GEO

description:
Input DNA from sonicated chromatin from S-phase 32min after G1 arrest with alpha factor
WT_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,32min after release into S phase, input DNA.paired end reads, replicate 1

value: wt

value: S-phase

value: from beginning of release from G1 arrest

tag: antibody


title: NH032_Tissue_C

description:
202751300075_R06C01_Red.idat
202751300075_R06C01_Grn.idat

value: Female

tag: tissue

value: Breast

value: C

value: Non


title: Subject 101680 LTA

tag: subject id

value: LTA

value: Male


title: Nav_BL_114_2266

description: Naive.BM.BL.Rpkm.detected.csv

value: Caucasian

value: Blood

value: Naive B cell


title: 25-NChAP-WT-2-FVreadsFigS8GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 25min after G1 arrest with alpha factor
WT_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,25min after release into S phase, replicated DNA.paired end reads, replicate 2


title: 25-NChAP-WT-2breadsFigS8GEO


title: NH032_Tissue_A

description:
202751300075_R04C01_Red.idat
202751300075_R04C01_Grn.idat

value: A


title: RNA_PopD_800_S8

data_processing:
Bases were trimmed to remove bases with low PHRED scores in Partek Genomics Suite
Trimmed bases were then aligned to human genome hg38 using Partek Geonmics Suite
Gene counts were quantified using HTSeq algorithm with union model in Partek Genomics Suite
Gene counts were library size and log normalized using the rlog function in DESeq2 (v1.28.1; default parameter) in R
Genome_build: hg38
Supplementary_files_format_and_content: text file of log2 normalized read counts

value: M

value: Bone Marrow

tag: cell subset


title: Subject 101679 NT

value: PBMCs

tag: treatment

value: NT

tag: subject sex

value: Full Autistic Disorder


title: NH032_Tissue_B

description:
202751300075_R05C01_Red.idat
202751300075_R05C01_Grn.idat

value: B


title: RNA_PopD_66294_513_S87

tag: age

value: F

value: AA

value: Non-Hispanic


title: Subject 101679 LTA

value: Female

tag: diagnosis


title: 25-NChAP-WT-1-FVbreadsFigS8GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 25min after G1 arrest with alpha factor
WT_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,25min after release into S phase, replicated DNA.paired end reads, replicate 1

value: wt

value: S-phase

tag: edu incubation

value: from beginning of release from G1 arrest


title: MV158_Tissue_A

description:
202751300035_R01C01_Red.idat
202751300035_R01C01_Grn.idat

value: Breast

value: Partial


title: 25-Inpt-WT-2readsFigS8GEO

description:
Input DNA from sonicated chromatin from S-phase 25min after G1 arrest with alpha factor
WT_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,25min after release into S phase, input DNA.paired end reads, replicate 2


title: 32-Inpt-WT-2readsFigS8GEO

description:
Input DNA from sonicated chromatin from S-phase 32min after G1 arrest with alpha factor
WT_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,32min after release into S phase, input DNA.paired end reads, replicate 2


title: Subject 101679 LPS

value: LPS

tag: subject age (ears)


title: 32-NChAP-WT-1-FVreadsFigS8GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 32min after G1 arrest with alpha factor
WT_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,32min after release into S phase, replicated DNA.paired end reads, replicate 1


title: Subject 101680 LPS

value: Male


title: MS168_Tissue_A

description:
202751300022_R07C01_Red.idat
202751300022_R07C01_Grn.idat

value: A

value: Non


title: RNA_PopD_66294_510_S79

value: M

tag: race

value: Caucasian

tag: ethnicity

value: Bone Marrow


title: Subject 101676 LTA

value: PBMCs

value: LTA

value: Full Autistic Disorder


title: RNA_PopD_2252_S28

tag: gender

value: Not Indicated


title: 25-Inpt-WT-1readsFigS8GEO

description:
Input DNA from sonicated chromatin from S-phase 25min after G1 arrest with alpha factor
WT_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,25min after release into S phase, input DNA.paired end reads, replicate 1

tag: genotype/variation


title: RNA_PopD_2206_S24

value: Non-Hispanic


title: 18-NChAP-WT-2-FVreadsFigS8GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 18min after G1 arrest with alpha factor
WT_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,18min after release into S phase, replicated DNA.paired end reads, replicate 2

value: wt

tag: cell cycle


title: 18-NChAP-WT-1-FVreadsFigS8GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 18min after G1 arrest with alpha factor
WT_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,18min after release into S phase, replicated DNA.paired end reads, replicate 1

value: S-phase


title: MM139_Tissue_B

description:
202764140076_R06C01_Red.idat
202764140076_R06C01_Grn.idat

value: Female

tag: timepoint

value: B


title: Subject 101676 LPS


title: MV158_Tissue_B

description:
202751300035_R02C01_Red.idat
202751300035_R02C01_Grn.idat

value: Breast

tag: response

value: Partial


title: Subject 101676 NT

value: NT

value: Male


title: RNA_PopD_208_2308_S71

value: F

value: AA


title: 18-NChAP-WT-1-FVbreadsFigS8GEO

value: from beginning of release from G1 arrest

tag: antibody


title: MM139_Tissue_A

description:
202764140076_R05C01_Red.idat
202764140076_R05C01_Grn.idat

tag: tissue

value: A


title: RNA_PopD_207_1177_S67

tag: subject id

value: Caucasian

value: Bone Marrow


title: 18-Inpt-WT-2readsFigS8GEO

description:
Input DNA from sonicated chromatin from S-phase 18min after G1 arrest with alpha factor
WT_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,18min after release into S phase, input DNA.paired end reads, replicate 2


title: Subject 101668 NT

value: PBMCs

value: Full Autistic Disorder


title: Subject 101668 LTA

value: LTA


title: RNA_PopD_1895_S16

value: M

value: Hispanic

tag: cell subset


title: MS168_Tissue_B

description:
202751300022_R08C01_Red.idat
202751300022_R08C01_Grn.idat

value: Female

value: Non


title: 18-Inpt-WT-1readsFigS8GEO

description:
Input DNA from sonicated chromatin from S-phase 18min after G1 arrest with alpha factor
WT_all_readsFandR_norm_50bp_Fig_S8BGEO.txt
Sonicated chromatin,18min after release into S phase, input DNA.paired end reads, replicate 1

value: wt

value: S-phase


title: MG098_Tissue_A

description:
202751300032_R07C01_Red.idat
202751300032_R07C01_Grn.idat

value: Breast

value: Complete


title: MG098_Tissue_B

description:
202751300032_R08C01_Red.idat
202751300032_R08C01_Grn.idat

value: B


title: RNA_PopD_1464_S4

value: F

value: AA

value: Non-Hispanic


title: MD193_Tissue_B

description:
202751300075_R08C01_Red.idat
202751300075_R08C01_Grn.idat

value: Partial


title: Subject 101660 NT

tag: treatment

value: NT

value: Male

value: Typical


title: RNA_PopB_800_S7

value: Caucasian

value: Bone Marrow


title: RNA_PopB_66294_516_S90


title: MD193_Tissue_A

description:
202751300075_R07C01_Red.idat
202751300075_R07C01_Grn.idat

value: A


title: 20min-H3K56Ac-ChIPNChAP-MCM23A-2readsFigS7BGEO

description:
H3K56Ac ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 20min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_6_S7BGEO.txt
Sonicated chromatin,20min after release into S phase, H3K56Ac on replicated DNA.paired end reads, replicate 2

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm16

value: Mcm23A mutant

value: early S-phase (67% of the genome is unreplicated)

value: from beginning of release from G1 arrest


title: LO170_Tissue_B

description:
202751300032_R02C01_Red.idat
202751300032_R02C01_Grn.idat

value: Female


title: Subject 101660 LPS

value: PBMCs

value: LPS

tag: subject sex


title: 20min-H3K36me3-ChIPNChAP-McM23A-2readsFigS7BGEO

description:
H3K36me3 ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 20min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_6_S7BGEO.txt
Sonicated chromatin,20min after release into S phase, H3K36me3 on replicated DNA.paired end reads, replicate 2

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm6


title: RNA_PopB_66294_513_S86

tag: age


title: LO170_Tissue_A

description:
202751300032_R01C01_Red.idat
202751300032_R01C01_Grn.idat

value: Breast

value: Complete


title: Subject 101313 NT

tag: diagnosis


title: 20min-H3-ChIPNChAP-McM23A-2readsFigS7BGEO

description:
H3 ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 20min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_6_S7BGEO.txt
Sonicated chromatin,20min after release into S phase, H3 on replicated DNA.paired end reads, replicate 2

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm4

tag: edu incubation


title: LL053_Tissue_B

description:
202751300032_R06C01_Red.idat
202751300032_R06C01_Grn.idat

value: B


title: RNA_PopB_66294_512_S82

value: F

value: Non-Hispanic


title: 25min-Rpb3-ChIPNChAP-WT-2readsFigS7GEO

description:
RNApol2 (Rpb3HA) ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_5_S7AGEO.txt
Sonicated chromatin,25min after release into S phase, RNAPol2 on replicated DNA.paired end reads, replicate 2

value: wt

value: mid early S-phase (39% of the genome is unreplicated)


title: LL053_Tissue_A

description:
202751300032_R05C01_Red.idat
202751300032_R05C01_Grn.idat


title: RNA_PopB_66294_510_S78

value: M


title: Subject 101288 NT

value: NT

value: Typical

tag: subject age (ears)


title: 20min-Rpb3-ChIPNChAP-MCM23A-2readsFigS7BGEO

description:
RNApol2 (Rpb3HA) ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 20min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_6_S7BGEO.txt
Sonicated chromatin,20min after release into S phase, RNAPol2 on replicated DNA.paired end reads, replicate 2

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm24


title: Subject 101668 LPS

value: Male

value: Full Autistic Disorder


title: RNA_PopB_2252_S27

tag: race

value: Caucasian

value: Not Indicated

value: Bone Marrow


title: Subject 101313 LTA

value: PBMCs

value: LTA


title: LK051_Tissue_A

description:
200811050082_R07C01_Red.idat
200811050082_R07C01_Grn.idat

value: Female

value: Breast

value: A


title: 25min-NChAP-WT-2readsFigS7GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_5_S7AGEO.txt
Sonicated chromatin,25min after release into S phase, replicated DNA.paired end reads, replicate 2

value: from beginning of release from G1 arrest


title: RNA_PopB_2206_S23

tag: ethnicity

value: Non-Hispanic


title: Subject 101288 LTA


title: 20min-H3K4me3-ChIPNChAP-McM23A-2readsFigS7BGEO

description:
H3K4me3 ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 20min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_6_S7BGEO.txt
Sonicated chromatin,20min after release into S phase, H3K4me3 on replicated DNA.paired end reads, replicate 2

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm10

value: Mcm23A mutant

value: early S-phase (67% of the genome is unreplicated)


title: 25min-H3K56Ac-ChIPNChAP-WT-2techrepreadsFigS7GEO

description:
H3K56Ac ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_5_S7AGEO.txt
Sonicated chromatin,25min after release into S phase, H3K56Ac on replicated DNA.paired end reads, replicate 2

value: wt

value: mid early S-phase (39% of the genome is unreplicated)


title: JS207_Tissue_B

description:
202751300032_R04C01_Red.idat
202751300032_R04C01_Grn.idat

tag: gender

value: B

value: Partial


title: RNA_PopB_208_2308_S70

value: F

value: AA


title: Subject 101288 LPS

value: LPS

value: Typical


title: JS207_Tissue_A

description:
202751300032_R03C01_Red.idat
202751300032_R03C01_Grn.idat


title: Subject 101280 NT

value: PBMCs

value: NT

value: Male


title: RNA_PopB_207_1177_S66

value: Caucasian

value: Bone Marrow


title: 25min-H3K4me3-ChIPNChAP-WT-2techrepreadsFigS7GEO

description:
H3K4me3 ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_5_S7AGEO.txt
Sonicated chromatin,25min after release into S phase, H3K4me3 on replicated DNA.paired end reads, replicate 2

tag: genotype/variation

value: from beginning of release from G1 arrest


title: Subject 101280 LTA

value: LTA


title: JR058_Tissue_A

description:
200811050082_R04C01_Red.idat
200811050082_R04C01_Grn.idat

value: Female

value: Breast

value: A

value: Non


title: Subject 101313 LPS


title: 25min-H3K4me3-ChIPNChAP-WT-2readsFigS7GEO

value: wt

tag: cell cycle

value: mid early S-phase (39% of the genome is unreplicated)


title: RNA_PopB_1895_S15

value: M

value: Hispanic


title: Subject 101280 LPS

value: LPS


title: EL197_Tissue_A

description:
202764140076_R02C01_Red.idat
202764140076_R02C01_Grn.idat

tag: timepoint

value: Complete


title: 25min-H3K36me3-ChIPNChAP-WT-2readsFigS7GEO

description:
H3K36me3 ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_5_S7AGEO.txt
Sonicated chromatin,25min after release into S phase, H3K36me3 on replicated DNA.paired end reads, replicate 2


title: Subject 101254 NT

value: PBMCs

value: Typical


title: RNA_PopA_800_S6

value: Non-Hispanic


title: EH093_Tissue_A

description:
200811050082_R05C01_Red.idat
200811050082_R05C01_Grn.idat

tag: response

value: Partial


title: Subject 101254 LTA

value: Male


title: RNA_PopA_66294_516_S89

value: F

value: Caucasian

value: Bone Marrow


title: DB125_Tissue_A

description:
202751300022_R02C01_Red.idat
202751300022_R02C01_Grn.idat

value: Female

value: Breast


title: Subject 101254 LPS


title: RNA_PopA_66294_513_S85

value: AA


title: 20min-Rpb3-ChIPNChAP-WT-2readsFigS7GEO

description:
RNApol2 (Rpb3HA) ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 20min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_5_S7AGEO.txt
Sonicated chromatin,20min after release into S phase, RNAPol2 on replicated DNA.paired end reads, replicate 2

value: wt

value: early S-phase (70% of the genome is unreplicated)

value: from beginning of release from G1 arrest

tag: antibody


title: 25min-H3K56Ac-ChIPNChAP-WT-2readsFigS7GEO

value: mid early S-phase (39% of the genome is unreplicated)


title: 25min-H3-ChIPNChAP-WT-2readsFigS7GEO

description:
H3 ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_5_S7AGEO.txt
Sonicated chromatin,25min after release into S phase, H3 on replicated DNA.paired end reads, replicate 2


title: CM102_Tissue_B

description:
200611820002_R03C01_Red.idat
200611820002_R03C01_Grn.idat

tag: tissue

value: B


title: Subject 101241 NT

tag: subject id

value: NT


title: CM102_Tissue_A

description:
200611820002_R02C01_Red.idat
200611820002_R02C01_Grn.idat

value: A


title: 20min-H3K56Ac-ChIPNChAP-WT-2readsFigS7GEO

description:
H3K56Ac ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 20min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_5_S7AGEO.txt
Sonicated chromatin,20min after release into S phase, H3K56Ac on replicated DNA.paired end reads, replicate 2


title: Subject 101241 LTA

value: PBMCs

value: LTA

value: Typical


title: 20min-NChAP-WT-2readsFigS7GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 20min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_5_S7AGEO.txt
Sonicated chromatin,20min after release into S phase, replicated DNA.paired end reads, replicate 2


title: RNA_PopA_66294_512_S81

value: Non-Hispanic

tag: cell subset


title: EL197_Tissue_B

description:
202764140076_R03C01_Red.idat
202764140076_R03C01_Grn.idat

value: Complete


title: 20min-H3K4me3-ChIPNChAP-WT-2readsFigS7GEO

description:
H3K4me3 ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 20min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_5_S7AGEO.txt
Sonicated chromatin,20min after release into S phase, H3K4me3 on replicated DNA.paired end reads, replicate 2


title: CM102_Normal_N

description:
200611820002_R01C01_Red.idat
200611820002_R01C01_Grn.idat

value: N

value: Partial


title: Subject 101221 NT

tag: treatment

value: Male


title: RNA_PopA_66294_510_S77

value: M

value: Caucasian

value: Bone Marrow


title: RNA_PopB_1464_S3

value: F

value: AA


title: 20min-H3K36me3-ChIPNChAP-WT-2readsFigS7GEO

description:
H3K36me3 ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 20min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_5_S7AGEO.txt
Sonicated chromatin,20min after release into S phase, H3K36me3 on replicated DNA.paired end reads, replicate 2

value: wt

value: early S-phase (70% of the genome is unreplicated)

value: from beginning of release from G1 arrest


title: RNA_PopA_2252_S26

value: Not Indicated


title: Subject 101221 LTA

value: PBMCs

tag: subject sex


title: CC046_Tissue_C

description:
200611820006_R06C01_Red.idat
200611820006_R06C01_Grn.idat

value: Female

value: Breast

value: C

value: Non


title: RNA_PopA_208_2308_S69

tag: age

value: Non-Hispanic


title: CC046_Tissue_A

description:
200611820006_R05C01_Red.idat
200611820006_R05C01_Grn.idat

value: A


title: RNA_PopA_207_1177_S65


title: Subject 101221 LPS

value: LPS

value: Male

tag: diagnosis

value: Typical


title: BT084_Tissue_B

description:
202751300022_R06C01_Red.idat
202751300022_R06C01_Grn.idat

value: B

value: Complete


title: RNA_PopA_1895_S14

value: M

value: Caucasian

value: Hispanic

value: Bone Marrow


title: Subject 101213 NT

value: NT


title: 25min-Rpb3-ChIPNChAP-MCM23A-1readsFig6GEO

description:
RNApol2 (Rpb3HA) ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_6_S7BGEO.txt
Sonicated chromatin,25min after release into S phase, RNAPol2 on replicated DNA.paired end reads, replicate 1

source_name: Mcm23A mutant yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and mcm2-3A::HYG that replaced the endogenous mcm2

value: Mcm23A mutant

value: mid early S-phase (20% of the genome is unreplicated)

tag: edu incubation

value: from beginning of release from G1 arrest


title: BT084_Tissue_A

description:
202751300022_R05C01_Red.idat
202751300022_R05C01_Grn.idat

value: Female

value: Breast


title: 25min-Rpb3-ChIP-MCM23A-1readsFig6GEO

description:
RNApol2 (Rpb3HA) ChIP from S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_6_S7BGEO.txt
Sonicated chromatin,25min after release into S phase, RNAPol2 on bulk DNA.paired end reads, replicate 1


title: RNA_PopA_1464_S2

value: F

value: AA

value: Non-Hispanic


title: Subject 101213 LPS

value: PBMCs

value: LPS

value: Male

tag: subject age (ears)


title: 25min-NChAP-MCM23A-1readsFig6GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_6_S7BGEO.txt
Sonicated chromatin,25min after release into S phase, replicated DNA.paired end reads, replicate 1


title: BH174_Tissue_B

description:
202751300035_R04C01_Red.idat
202751300035_R04C01_Grn.idat

value: B

value: Non


title: Subject 101213 LTA

value: LTA

value: Typical


title: RNA_Pop3_82_S58

tag: race

value: Asian

value: Blood


title: 25min-H3K56Ac-ChIPNChAP-MCM23A-1readsFig6GEO

description:
H3K56Ac ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_6_S7BGEO.txt
Sonicated chromatin,25min after release into S phase, H3K56Ac on replicated DNA.paired end reads, replicate 1

value: Mcm23A mutant


title: RNA_Pop3_83_S62

tag: ethnicity


title: Subject 101178 NT

value: NT


title: BH174_Tissue_A

description:
202751300035_R03C01_Red.idat
202751300035_R03C01_Grn.idat

tag: gender

value: A


title: RNA_Pop3_81_S55


title: AF013_Tissue_C

description:
202751300075_R03C01_Red.idat
202751300075_R03C01_Grn.idat

value: Female

value: C

value: Partial


title: Subject 101178 LTA


title: Subject 101178 LPS


title: 20min-H3-ChIPNChAP-WT-2readsFigS7GEO

description:
H3 ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 20min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_5_S7AGEO.txt
Sonicated chromatin,20min after release into S phase, H3 on replicated DNA.paired end reads, replicate 2

tag: genotype/variation

value: wt

value: early S-phase (70% of the genome is unreplicated)

value: from beginning of release from G1 arrest


title: 25min-H3K4me3-ChIPNChAP-MCM23A-1readsFig6GEO

description:
H3K4me3 ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_6_S7BGEO.txt
Sonicated chromatin,25min after release into S phase, H3K4me3 on replicated DNA.paired end reads, replicate 1

tag: cell cycle

value: mid early S-phase (20% of the genome is unreplicated)


title: 25min-H3K56Ac-ChIP-MCM23A-1readsFig6GEO

description:
H3K56Ac ChIP from S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_6_S7BGEO.txt
Sonicated chromatin,25min after release into S phase, H3K56Ac on bulk DNA.paired end reads, replicate 1


title: AF013_Tissue_B

description:
202751300075_R02C01_Red.idat
202751300075_R02C01_Grn.idat

value: Breast

tag: timepoint


title: 25min-H3K4me3-ChIP-MCM23A-1readsFig6GEO

description:
H3K4me3 ChIP from S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_6_S7BGEO.txt
Sonicated chromatin,25min after release into S phase, H3K4me3 on bulk DNA.paired end reads, replicate 1


title: 25min-H3K36me3-ChIPNChAP-McM23A-1readsFig6GEO

description:
H3K36me3 ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_6_S7BGEO.txt
Sonicated chromatin,25min after release into S phase, H3K36me3 on replicated DNA.paired end reads, replicate 1


title: Subject 101157 NT

value: PBMCs

value: Male


title: AF013_Tissue_A

description:
202751300075_R01C01_Red.idat
202751300075_R01C01_Grn.idat

tag: response


title: RNA_PopD_66294_512_S83

value: F

value: Caucasian

value: Non-Hispanic

value: Bone Marrow


title: RNA_Pop3_57983_163_S48

value: Asian

value: Blood


title: RNA_Pop3_57983_162_S44


title: 25min-H3K36me3-ChIP-MCM23A-1readsFig6GEO

description:
H3K36me3 ChIP from S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_6_S7BGEO.txt
Sonicated chromatin,25min after release into S phase, H3K36me3 on bulk DNA.paired end reads, replicate 1

value: Mcm23A mutant

tag: antibody


title: BT084_Normal_N

description:
200811050082_R01C01_Red.idat
200811050082_R01C01_Grn.idat

value: Female

tag: tissue

value: N

value: Complete


title: RNA_Pop3_2206_S19

tag: subject id

value: M


title: Subject 101157 LTA

value: LTA

value: Typical


title: Subject 101157 LPS

value: LPS


title: Subject 101152 NT

value: NT

value: Full Autistic Disorder


title: 20min-Rpb3-ChIPNChAP-MCM23A-1readsFig6GEO

description:
RNApol2 (Rpb3HA) ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 20min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_6_S7BGEO.txt
Sonicated chromatin,20min after release into S phase, RNAPol2 on replicated DNA.paired end reads, replicate 1

value: early S-phase (52% of the genome is unreplicated)

value: from beginning of release from G1 arrest


title: RNA_Pop3_115_2267_S41

value: F

tag: cell subset


title: TL3

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

data_processing:
Base calling was done using Illumina RTA3
Illumina bc12fastq v2.20 was used for demultiplexing and fastq file generation
Reads were aligned using STAR aligner to get gene counts (Gen_Counts.tsv)
Genome_build: Ensembl Drosophila ananassae genome (release 37)
Supplementary_files_format_and_content: Gene_Counts.tsv contains raw read counts

organism: Drosophila ananassae

source_name: Hemocytes from hemolymph

extract_protocol:
single cell cytosol extraction via patch pipette
Nextera XT DNA Library Preparation Kit (Illumina)

tag: cell type

value: Blood cells

tag: time

tag: treatment

value: uninduced


title: TL4


title: RNA_Pop3_1895_S11

tag: age

value: Caucasian

value: Hispanic


title: Subject 101152 LTA

value: PBMCs

tag: subject sex

value: Male

tag: diagnosis


title: RNA_Pop3_77_S52

tag: race

value: Asian

value: Non-Hispanic

value: Blood


title: 20min-NChAP-MCM23A-1readsFig6GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 20min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_6_S7BGEO.txt
Sonicated chromatin,20min after release into S phase, replicated DNA.paired end reads, replicate 1

value: Mcm23A mutant

tag: edu incubation


title: TL2


title: 20min-Input-MCM23A-1readsFig6GEO

description:
Input DNA from sonicated chromatin from S-phase 20min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_6_S7BGEO.txt
Sonicated chromatin,20min after release into S phase, input DNA.paired end reads, replicate 1


title: RNA_Pop3_114_2266_S35

tag: gender

tag: ethnicity


title: TL1


title: RNA_Pop3_113_2265_S31


title: Subject 101150 NT

value: Typical

tag: subject age (ears)


title: Subject 101150 LTA

value: LTA


title: GC7

value: Multinucleated giant cells

value: induced


title: RNA_Pop2_83_S61


title: 20min-H3K4me3-ChIP-MCM23A-1readsFig6GEO

description:
H3K4me3 ChIP from S-phase 20min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_6_S7BGEO.txt
Sonicated chromatin,20min after release into S phase, H3K4me3 on bulk DNA.paired end reads, replicate 1

tag: genotype/variation

tag: cell cycle

value: early S-phase (52% of the genome is unreplicated)


title: Subject 101150 LPS

value: LPS


title: TL5


title: GC6


title: 25min-H3-ChIPNChAP-MCM23A-1readsFig6GEO

description:
H3 ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_6_S7BGEO.txt
Sonicated chromatin,25min after release into S phase, H3 on replicated DNA.paired end reads, replicate 1

value: mid early S-phase (20% of the genome is unreplicated)

value: from beginning of release from G1 arrest

tag: antibody


title: 20min-H3K36me3-ChIPNChAP-MCM23A-1readsFig6GEO

description:
H3K36me3 ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 20min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_6_S7BGEO.txt
Sonicated chromatin,20min after release into S phase, H3K36me3 on replicated DNA.paired end reads, replicate 1


title: RNA_Pop2_82_S57

value: F

tag: tissue


title: Subject 101138 NT

tag: subject id

value: NT

value: Full Autistic Disorder


title: GC5


title: RNA_Pop2_81_S54

value: AA

tag: cell subset


title: 20min-H3-ChIPNChAP-MCM23A-1readsFig6GEO

description:
H3 ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 20min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_6_S7BGEO.txt
Sonicated chromatin,20min after release into S phase, H3 on replicated DNA.paired end reads, replicate 1


title: Subject 101138 LTA

value: PBMCs

value: Male


title: Subject 101152 LPS


title: RNA_Pop2_77_S51

value: Asian

value: Non-Hispanic


title: GC1

tag: cell type


title: GC4

tag: time


title: Subject 101138 LPS

tag: treatment


title: RNA_Pop2_57983_163_S47

tag: age

value: Blood


title: rtt109D_Rpb3ChipNChAP25min_Sphase_rep2readsFig4GEO

description:
RNApol2 (Rpb3HA) ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig4GEO.txt
Sonicated chromatin,25min after release into S phase, RNAPol2 on replicated DNA.paired end reads, replicate 2

source_name: rtt109D yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2) and rtt109::KanMX6

value: wt

value: S-phase (10% of the genome is unreplicated)


title: 20min-H3-ChIP-MCM23A-1readsFig6GEO

description:
H3 ChIP from S-phase 20min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_6_S7BGEO.txt
Sonicated chromatin,20min after release into S phase, H3 on bulk DNA.paired end reads, replicate 1

value: Mcm23A mutant


title: P15

value: Plasmatocytes

value: induced


title: 20min-H3K56Ac-ChIPNChAP-McM23A-1readsFig6GEO

description:
H3K56Ac ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 20min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Figs_6_S7BGEO.txt
Sonicated chromatin,20min after release into S phase, H3K56Ac on replicated DNA.paired end reads, replicate 1

value: early S-phase (52% of the genome is unreplicated)


title: Subject 101134 NT

tag: subject sex

value: Female

value: Typical


title: P14


title: rtt109D_Rpb3ChipNChAP25min_Sphase_rep1readsFig4GEO

description:
RNApol2 (Rpb3HA) ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig4GEO.txt
Sonicated chromatin,25min after release into S phase, RNAPol2 on replicated DNA.paired end reads, replicate 1

value: from beginning of release from G1 arrest


title: RNA_Pop2_57983_162_S43

value: F


title: RNA_Pop2_2206_S18

value: M

value: Caucasian


title: Subject 101134 LTA

value: PBMCs

value: LTA

tag: diagnosis


title: rtt109D_Rpb3chip25min_Sphase_rep2readsFig4GEO

description:
RNApol2 (Rpb3HA) ChIP from S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig4GEO.txt
Sonicated chromatin,25min after release into S phase, RNAPol2 on bulk DNA.paired end reads, replicate  2


title: Subject 101134 LPS

value: LPS


title: rtt109D_Rpb3Chip25min_Sphase_rep1readsFig4GEO

description:
RNApol2 (Rpb3HA) ChIP from S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig4GEO.txt
Sonicated chromatin,25min after release into S phase, RNAPol2 on bulk DNA.paired end reads, replicate 1


title: P2


title: Subject 101132 NT

value: NT


title: RNA_Pop2_1895_S10

tag: race

value: Hispanic

value: Blood


title: RNA_Pop2_115_2267_S38

value: Asian

value: Non-Hispanic


title: P3

value: Plasmatocytes


title: rtt109D_NChAP25min_Sphase_rep2readsFig4GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig4GEO.txt
Sonicated chromatin,25min after release into S phase, replicated DNA.paired end reads, replicate 2

value: wt

value: S-phase (10% of the genome is unreplicated)

tag: edu incubation


title: RNA_Pop2_113_2265_S30

tag: gender


title: P1

value: induced


title: Subject 101132 LTA

value: Female

value: Typical


title: RNA_Pop2_114_2266_S34

value: F

tag: ethnicity


title: RNA-Seq of HEK293 cells expressing GFP-N treated for with Sodium arsenite for oxidative stress, replicate 2

city: Toronto

first: Jack

last: Greenblatt

address: 160 College Street

institute: University of Toronto

description:
pau_results_QAPA.txt
diff_table_N_Ar_vs_N_noAr.tab
groups_N_Ar_N_noAr_deseq2_results.tab

data_processing:
Base calls were processed with bcl2fastq2 (Illumina) version 2.18.
RNA-seq reads were processed for alternative splicing and expression analysis using vast-tools, version 1.0 (Tapial et al., (2017))
Alternative splicing analysis: From primary vast-tools output, events with poor coverage or junction balance were filtered out (vast-tools quality column score 3 other than SOK/OK/LOW for cassette exon [CE], microexon [MIC] and alternative 5'/3'-ss events or coverage less than 15 reads for intron retention [IR] events; score 4 other than OK/B1 for CE and MIC events or less than 0.05 for IR events). Significantly differential AS was assessed with the diff module of vast-tools under development and were additionally required to have a PSI difference >10.
Expression analysis: Expression differences were calculated based on vast-tools raw read counts per gene using the R package edgeR.
For differential mRNA expression analysis, gene-level read counts were quantified using Salmon (version 0.8.2) and normalized by variance-stabilizing transformation using DESeq2.
To estimate the differential poly(A) site usage, we used QAPA with default settings, essentially as previously described (Ha KCH et. al. 2018. Genome Biology). To quantify the relative usage of proximal poly(A) sites, QAPA calculates the percentage of expression of a single 3′ UTR over the total expression level of all 3′ UTRs for a given gene. Lengthening events were defined as those with percentage of proximal Poly(A) Usage Index (PAU) group difference between N andGFP (PAU_Group_diff) < −20% and shortening events with PAU_Group_diff > 20%.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files for PAU from QAPA analysis, PAU difference between N and GFP from QAPA analysis, and differential gene expression from DESeq2 analysis

source_name: Human embryonic kidney cells

growth_protocol: Human embryonic kidney cells (HEK293) cells were grown in DMEM supplemented with 10% FBS, sodium pyruvate, MEM non-essential amino acids, and penicillin/streptomycin, and maintained at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted with the Qiagen RNasy Mini kit.
1000 ng per sample was used in the library preparation. To obtain larger insert size (540 nt on average after size selection), Illumina’s TruSeq Stranded mRNA sample preparation protocol was modified as follows: 1) fragmentation time and temperature was reduced from 8 minutes at 98 C to 2 minutes at 80 C. Average size distribution prior to library preparation was 232 nt versus 740 nt, respectively; 2) after the final library was generated, the samples were loaded onto a 2% agarose gel (Cat # 1613101, BioRad) and run for 1 hour at 100 V. The libraries were size selected between 400 and 600 bp. Excised gel fragments were purified using the Qiagen MinElute Gel Extraction kit (Cat # 28604, Qiagen). The rest of the protocol was adapted as described in Illumina’s TruSeq Stranded mRNA sample preparation guide (Part# 15031047 Rev. E, Illumina).

treatment_protocol: GFP-N or GFP alone was expressed in an HEK293 cell line engineered with the Flp-in system under the control of doxycyclin, and expression was induced for 24 hours prior to UV crosslinking.Cells were treated with Sodium Arsenite for 1hour prior to harvesting.

tag: cell line

tag: overexpression

value: SARS-CoV-2 N protein fused with GFP


title: rtt109D_Input25min_Sphase_rep1readsFig4GEO

description:
Input DNA from sonicated chromatin from S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig4GEO.txt
Sonicated chromatin,25min after release into S phase, input DNA.paired end reads, replicate 1

tag: genotype/variation

tag: cell cycle

value: from beginning of release from G1 arrest


title: RNA-Seq of HEK293 cells expressing GFP-N treated with Sodium arsenite for oxidative stress, replicate 1

description:
pau_results_QAPA.txt
diff_table_N_Ar_vs_GFP_Ar.tab
groups_N_Ar_GFP_Ar_deseq2_results.tab


title: rtt109D_NChAP25min_Sphase_rep1readsFig4GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig4GEO.txt
Sonicated chromatin,25min after release into S phase, replicated DNA.paired end reads, replicate 1

tag: antibody


title: rtt109D_Input25min_Sphase_rep2readsFig4GEO

description:
Input DNA from sonicated chromatin from S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig4GEO.txt
Sonicated chromatin,25min after release into S phase, input DNA.paired end reads, replicate 2


title: Subject 101123 LPS

tag: subject id

tag: tissue

value: PBMCs

value: Male

tag: subject age (ears)


title: 12_CAMHB + PBT2 + zinc + tetracycline

city: Brisbane

first: David

middle: Manuel Pereira

last: De Oliveira

state: QLD

address: St Lucia

department: School of Chemistry and Molecular Biosciences

institute: The University of Queensland

description: A. baumannnii MS14413 RNAseq data

data_processing:
HiSeq 2500 ultra-high-throughput sequencing system was used for base-calling
Samples were uploaded to the Galaxy web platform (public server at usegalaxy.org), trimmed and mapped to the reference genome (A. baumannii MS14413 accession number: NZ_CP054302) using bowtie2 with default parameters
Read counts were determined using featureCounts and differential gene expression was analyzed with edgeR with the CPM threshold set at 2.0
Genome_build: NZ_CP054302
Supplementary_files_format_and_content: xlsx files

organism: Acinetobacter baumannii

source_name: Bacteria

growth_protocol: Bacteria were grown in cation-adjusted Mueller-Hinton broth (CA-MHB) as per CLSI guidelines at 37°C under aerobic conditions.

extract_protocol:
RNA was isolated using the RNeasy Plus Kit (Qiagen). Briefly, bacteria were grown to OD600 of 0.5 in CA-MHB in the presence or absence of PBT2 + ZnSO4 + tetracycline. Two volumes of RNAprotect (Qiagen) were added to the cultures and the samples were then centrifuged at 5,000 x g for 25 min at 4°C to pellet cells. RNA was isolated from the dry pellet as per the manufacturer’s instructions. To ensure complete removal of DNA, the RNA was then further purified using the TURBO DNA-free kit (Thermo Fisher Scientific) according to the manufacturer’s instructions.
RNASeq analysis was performed at the Australian Genome Research Facility. The cDNA library was prepared using a Ribo-zero stranded protocol. In brief, rRNA was depleted with Ribo Zero, RNA was fragmented (heat and divalent cations) and 1st strand cDNA synthesis was done with SuperScript II Reverse Transcriptase (Invitrogen). For the 2nd strand cDNA synthesis, the strand was “marked” with dUTP.  A 3’ adenylation of DNA fragments was performed followed by sequencing adapter ligation (utilizing T-A pairing of adapter and DNA fragments). The library was amplified by PCR (amplification of “unmarked” 1st strand only). Libraries were assessed using either Agilent’s Bioanalyzer DNA 1000 chip or TapeStation D1K TapeScreen system. qPCR was used to quantify individual libraries before normalizing (2 nM) and pooling. Libraries were pooled and clustered through the Illumina cBot system using TruSeq PE Cluster Kit v3 reagents followed by sequencing on the Illumina HiSeq 2500 system with TruSeq SBS Kit v3 reagents with 110 (101 read 1, 9 cycles index read). Libraries were sequenced with a HiSeq 2500 ultra-high-throughput sequencing system (Illumina) to produce 50-base-single end reads. An average of 30 million reads per sample were generated, uploaded to the Galaxy web platform (public server at usegalaxy.org), and mapped to the reference genome (S. pneumoniae ATCC 700669 accession number: NC_011900) using bowtie2 with default parameters. Read counts were determined using featureCounts and differential gene expression was analyzed with edgeR with the CPM threshold set at 2.0. Figures were generated using ggplot2 and ggpubr packages in R-studio

treatment_protocol: Bacteria were grown to  OD600 of 0.5 in CA-MHB in the presence or absence of PBT2 (64 µM), ZnSO4 (8 µM) and tetracycline (1 µg/mL).

tag: strain

tag: treatment condition

value: CAMHB + 64 uM PBT2  + 8 uM ZnSO4 + 1 ug/mL tetracycline


title: Subject 101119 NT

tag: treatment

value: NT

value: Full Autistic Disorder


title: 11_CAMHB + PBT2 + zinc + tetracycline

description: A. baumannnii MS14413 RNAseq data


title: Subject 101123 LTA

value: LTA

tag: subject sex


title: mid-Sphase_H3K56ac_ChIPreadsFig3GEO

description:
H3K56ac ChIP from mid S-phase 35min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig3GEO.txt
MNase digested chromatin,35min after release into S phase, H3K56ac on bulk DNA.paired end reads

value: mid S-phase (6% of the genome is unreplicated)


title: Subject 101123 NT

tag: diagnosis


title: 8_CAMHB + PBT2 + zinc

description: A. baumannnii MS14413 RNAseq data

value: CAMHB + 64 uM PBT2  + 8 uM ZnSO4


title: 10_CAMHB + PBT2 + zinc + tetracycline

description: A. baumannnii MS14413 RNAseq data


title: 7_CAMHB + PBT2 + zinc

description: A. baumannnii MS14413 RNAseq data


title: 9_CAMHB + PBT2 + zinc

description: A. baumannnii MS14413 RNAseq data


title: Subject 101132 LPS

value: LPS


title: Midlog_inputreadsFig3GEO

description:
Input DNA from MNAse digested chromatin in log phase
all_readsFandR_norm_50bp_Fig3GEO.txt
MNase digested chromatin,log phase, input DNA.paired end reads

value: wt

value: log phase


title: mid-Sphase_H3K56ac_ChIPNChAPreadsFig3GEO

description:
H3K56ac ChIP followed by nascent DNA purification by EdU-biotin pulldown from mid S-phase 35min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig3GEO.txt
MNase digested chromatin,35min after release into S phase, H3K56ac on replicated DNA.paired end reads


title: RNA-Seq of HEK293 cells expressing GFP-N, replicate 1

description:
pau_results_QAPA.txt
diff_table_N_noAr_vs_GFP_noAr.tab
groups_N_noAr_GFP_noAr_deseq2_results.tab


title: RNA-Seq of HEK293 cells expressing GFP alone treated with Sodium arsenite for oxidative stress,, replicate 2

value: GFP alone


title: Subject 101119 LPS


title: Subject 101119 LTA


title: RNA-Seq of HEK293 cells expressing GFP alone treated with Sodium arsenite for oxidative stress, replicate 1

description:
pau_results_QAPA.txt
diff_table_GFP_Ar_vs_GFP_noAr.tab
groups_GFP_Ar_GFP_noAr_deseq2_results.tab


title: 6_CAMHB + PBT2

description: A. baumannnii MS14413 RNAseq data

value: CAMHB + 64 uM PBT2


title: 5_CAMHB + PBT2

description: A. baumannnii MS14413 RNAseq data


title: mid-Sphase_inputreadsFig3GEO

description:
Input DNA from MNAse digested chromatin mid S-phase 35min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig3GEO.txt
MNase digested chromatin,35min after release into S phase,input DNA.paired end reads


title: RNA-Seq of HEK293 cells expressing GFP-N, replicate 2