title: Huh7_NC1_E3_R2

source_name: Huh7, Negative Control1, Experiment3, Replicate2

value: Negative Control siRNA #1


title: 2691_B

status: Public on Dec 18 2021

type: SRA

city: Amsterdam

first: Esther

last: Lips

address: Plesmanlaan 121

department: Molecular Pathology

country: Netherlands

institute: NKI-AVL

description:
2691_B
3597_17_2691_B_AAGGTACA

library_source: transcriptomic

data_processing:
Reads were aligned to the human transcriptome (Homo_sapiens.GRCh37.75.gtf) using Tophat v2.1[54]. Readcounts per gene were calculated using lcount[55], and normalized using DESeq2[56]. The SVA R package[57] was used to combine and batch correct gene expression datasets. Gene expression levels were associated with chemotherapy response using samr[58]; differential gene expression between pre- and post-treatment samples was analyzed using DESeq2[56]. Subsequent pathway / GO-term enrichment was performed using the Reactome Cytoscape plugin[59, 60] and geneset enrichment was performed using GSEA[61]. The most significant genes from the samr analysis (FDR < 5%) were selected for a ‘core enrichment’ set, based on unsupervised clustering and pathway and GO-term enrichment (Supplementary Table S1). Metagene scores for all three processes were created by calculating the median expression of genes assigned to each cluster. Expression above or below the metagene median was used to stratify patients into a HHL (Proliferation High, Immune High, ECM Low) or LLH (Proliferation Low, Immune Low, ECM High) profile. RNA-seq reads of the pre-post dataset were also aligned to the human reference genome version 37.75 (hg19) using bwa[45] to be able to confirm somatic mutations and indels in the expression data.
Genome_build: 37.75 (hg19)
Supplementary_files_format_and_content: The processed data file is in txt format, and contains readcounts.

molecule: total RNA

organism: Homo sapiens

source_name: human breast

extract_protocol:
RNA was isolated from samples with a tumor percentage > 50%, from thirty 30-μm cryosections. A 5-μm section halfway through the biopsy was stained for hematoxylin and eosin and analyzed by a pathologist for tumor percentage. Total RNA was isolated with RNA-Bee (Bio-Connect, Huissen, The Netherlands, Cat No. CS-100B), DNase-treated by using the Qiagen RNase-free DNase Set (Qiagen, Venlo, The Netherlands, Cat No. 79254) and RNeasy spin columns (Qiagen, Cat No. 74104) and dissolved in RNase-free H2O. Quality and quantity of the total RNA was assessed by the 2100 Bioanalyzer using a Nano chip (Agilent, Santa Clara, CA); samples having RIN>6.4 were subjected to library generation.
mRNA libraries were generated using the TruSeq RNA Library Preparation Kit v2 (Illumina Inc., San Diego, Cat.No RS-122-2001/2) according to the manufacturer's instruction (Part # 15026495 Rev. B). The libraries were analyzed on a 2100 Bioanalyzer using a 7500 chip (Agilent, Santa Clara, CA), diluted and pooled equimolar into a 10nM sequencing pool containing 9 libraries each, and sequenced with 50 basepair single reads (pre-treatment samples only) or 65 basepair single reads (pre-post treatment set) on a HiSeq2000 using V3 chemistry (Illumina Inc., San Diego).

tag: tissue type

value: biopsy

tag: chemotherapy

value: 6x ddAC

tag: neoadjuvant response index (nri)

tag: grade

tag: t-stage

tag: n-stage

tag: subtype

value: LUM

tag: recurrence


title: Huh7_NC1_E3_R1

type: RNA

city: Rotterdam

first: Rute

last: Marques

address: Dr Molewaterplein 50

institute: Erasmus MC

hyb_protocol: 750 ng of labelled cRNA were hybridized overnight onto Illumina HT-12 v3 BeadChip arrays, according to Illumina's protocols

scan_protocol: Following hybridization, the arrays were washed, blocked, stained and scanned on an Illumina BeadStation 500GX, following the manufacturer's protocols. Illumina GenomeStudio v1.5 software was used to generate signal intensity values from the scanned pictures.

data_processing: The Limma and Lumi packages for R were used for the normalization and statistical analysis of the microarray data. Data analysis started with background subtraction, followed by VST transformation and quartile normalization, using the LumiExpresso command. After normalization, VST transformation was inversed to extract the normalized signal intensity values.

label: biotin

source_name: Huh7, Negative Control1, Experiment3, Replicate1

label_protocol: 250ng of total RNA was reverse transcribed, amplified and biotinylated using Illumina TotalPrep RNA Amplification Kit (Ambion), according to manufacturer's instructions

growth_protocol: Huh7 and THP1 cells were grown in RPMI medium containing L-glutamine and HEPES, supplemented with 10% FCS and penicillin/streptomycin antibiotics, at 37C and 5% CO2

extract_protocol: Total RNA was extracted using the RNeasy Mini kit from Qiagen, including an on-column DNAse digestion step, according to the manufacturer's manual

treatment_protocol: For the siRNA knockdown we used the Silencer Select Negative Controls #1 and #2 from Ambion, and the intergenic transcript specific siRNA against target sequence AACTACGTGAAGAGGCCTCTG. Cells (300000 per well) were transfected in 6-well plates, in 2.5 ml Optimem medium (Invitrogen) supplemented with 2.5% FCS.  Per well, 250 ul transfection mix was added containing 5ul Lipofectamine 2000 (Invitrogen) and 50 pmol siRNA(Ambion/Applied Biosystems), according to the manufacturer’s protocol. Cells were incubated for 2 days at 37C under 5% CO2 before sample collection.

tag: tissue

value: Liver

tag: cell line

tag: treatment


title: shScr+ IR_2

city: Hangzhou

first: Pan

last: Liu

state: Zhejiang

address: Yuhangtang road 866

country: China

institute: Zhejiang university school of medicine

data_processing:
Clustering and sequencing (Novogene Experimental Department) The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Quality control Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: HUVECs

growth_protocol: HUVECs (passages 2-6) were cultured in 53% M199 (Corning, USA)/37% human endothelial serum-free mixed medium (Gibco, USA) with 10% FBS (Biowest, France) and endothelial cell growth supplement (Millipore, USA).

extract_protocol:
RNA were extracted 24 h after irradiation
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Cells were exposed to different doses of radiation using an X-ray linear accelerator (Rad Source Technologies, USA) at a dose rate of 1.201 Gy/min. Lentiviral particles were directly delivered into cells in OPTI-MEM (Gibco, USA).

value: umbilical vein

tag: shRNA

value: shScr

tag: protocol

value: irradiated cells


title: shShp2+ IR_1


title: shShp2+ IR_2


title: shScr+ IR_3


title: shShp2+ IR_3


title: 2677_S

description:
2677_S
3597_16_2677_S_AAGACGGA


title: Huh7_INTG_E2_R2

source_name: Huh7, C5_TRAF1_Intergenic siRNA, Experiment2, Replicate2


title: 2677_B

description:
2677_B
3597_15_2677_B_AACGCTTA


title: shScr+ IR_1


title: 2661_S

description:
2661S
3597_14_2661_S_AACCGAGA


title: 2661_B

description:
2661_B
3597_13_2661_B_AACAACCA


title: 2653_S

description:
2653_S
3597_12_2653_S_AGTACAAG

value: 3x ddAC, 2x CD, 2x D


title: Huh7_NC2_E3_R1

source_name: Huh7, Negative Control2, Experiment3, Replicate1

value: Negative Control siRNA #2


title: pr_RNA_dexab_5dpi_ha2

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description:
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina
adapter sequence: GATCGGAAGAGCACACGT

data_processing:
For bulk RNA-sequencing, alignments were done using hisat2 (Kim et al, 2015)
Syrian hamster: Sequencing reads were aligned to the MesAur 1.0 version of the Mesocricetus auratus genome using standard parameter, using the Refseq gtf file described in GEO accession number GSE162208
Roborovski hamster: Sequencing reads were aligned to the draft assembly and gtf file described previously (doi: 10.1101/2021.10.02.462569)
For single-cell RNA-sequencing data, fastq files were processed using a merged Roborvski hamster/SARS-CoV-2 genome by applying CellRanger 6.0.2 with standard parameters
Seurat R and loom objects were processed as described on the github page https://github.com/Berlin-Hamster-Single-Cell-Consortium/Dwarf-Hamster-Dexamethasone-Antibody
Genome_build: MesAur 1.0
Genome_build: Phodopus roborvskii draft assembly
Genome_build: SARS-CoV-2 MN908947
Supplementary_files_format_and_content: tab-separated values
Supplementary_files_format_and_content: h5 matrix
Supplementary_files_format_and_content: Seurat R object
Supplementary_files_format_and_content: loom object

molecule: polyA RNA

organism: Phodopus roborovskii

source_name: Antibody+Dexamethasone treated animal 2, 5dpi, lung sample for bulk RNA-seq

growth_protocol:
Hamsters were weighted daily and monitored for signs of disease twice-daily. Severely sick animals were euthanized according to defined humane endpoints including body temperature <33 °C, acute respiratory distress or weight loss >20%. Hamsters were selected randomly for all scheduled take-out time points (day 3 and 5 for Roborovski hamsters, day 5 and 7 for Syrian hamsters).
Euthanasia prior analysis occurred by exsanguination under anesthesia as previously described (PMID 32698441, 33271063). Peripheral blood was collected in EDTA-coated syringes and lung lobes were collected for follow-up analyses, in which the left lobe was used for histopathology, the right caudal lobe for single-cell analysis, the right cranial lobe for virological assessments and the right medial as backup to repeat virological analyses as needed.

extract_protocol:
For isolation of single cells lobus caudalis of the right lung was removed and placed in storage medium (1× PBS, 0.5 % BSA) until further processing. Storage and isolation media contained 2 µg/mL ActinomycinD. Tissues and cells were always spun at 350 x g for 6 minutes at 4 °C. Mechanical dissociation of lung lobes was achieved by clapping motions with tweezers for 2 minutes in enzymatic digestion medium (3,4 mg/mL Collagenase Cls II (Merck), 1 mg/mL DNase I (PanReac AppliChem), in 2 mL Dispase medium per lung lobe (Corning), 50 Caseinolytic Units/mL followed by 30 minutes incubation at 37°C and 5 % CO2.
Further tissue dissociation was achieved by repeated pipetting of digested lung tissue with 5 mL pipettes and passing of cell suspension with plungers through 70 µm cell strainers. Cells were pelleted from suspension by centrifugation and resuspended in red blood cell lysis buffer (BioLegend). Lysis reaction was stopped and cells washed with excessive volumes of PBS/BSA. Cells were centrifuged, resuspended in low-BSA buffer (1× PBS, 0.04 % BSA) and counted via hemocytometer and trypan blue.
Then, 1,000,000 lung cells per sample were subjected to Cell Multiplexing Oligo (CMO) labeling according to the manufacturers’ instructions (3ʹ-CellPlex-Kit-Set-A, 10x Genomics). Labelled cells from 12 samples were pooled, filtered (40 µm) and counted. Pooled cells were adjusted to a final concentration of ~1,600 cells / μL and filtered with 40 µm FloMi filters (Merck) suitable for low volumes prior subjection to scRNA sequencing.
For Lung RNA Bulk sequencing the lobus medialis of the right lung lobe was removed carefully and homogenzied in Trizol reagent using a bead mill procedure (Speedmill, Analytic Jena), RNA was extracted according to the manufacturer’s instructions.
Bulk and single-cell RNA-sequencing libraries were constructed using commercial kits (New England Biolabs, 10xGenomics), see column "library construction protocol" in the SAMPLES section.

treatment_protocol: At 6-10 weeks of age hamsters were infected intranasally as previously described (PMID 32698441, 33271063). Briefly, hamster received 1 x 105 pfu SARS-CoV-2 Variant B1 (BavPat1) intranasally under anesthesia.

value: Lung

value: antibody+dexamethasone

tag: sampling timepoint


title: pr_RNA_dexab_5dpi_ha3

source_name: Antibody+Dexamethasone treated animal 3, 5dpi, lung sample for bulk RNA-seq


title: 2653_B

description:
2653_B
3597_11_2653_B_CTGTAGCC


title: Huh7_NC2_E2_R2

source_name: Huh7, Negative Control2, Experiment2, Replicate2


title: Huh7_INTG_E2_R1

source_name: Huh7, C5_TRAF1_Intergenic siRNA, Experiment2, Replicate1


title: 2492_S

description:
2492_S
3597_10_2492_S_ACAAGCTA

value: TN


title: Huh7_NC1_E2_R2

source_name: Huh7, Negative Control1, Experiment2, Replicate2


title: Huh7_INTG_E1_R2

source_name: Huh7, C5_TRAF1_Intergenic siRNA, Experiment1, Replicate2


title: pr_RNA_dexab_3dpi_ha3

source_name: Antibody+Dexamethasone treated animal 3, 3dpi, lung sample for bulk RNA-seq


title: pr_RNA_dexab_5dpi_ha1

source_name: Antibody+Dexamethasone treated animal 1, 5dpi, lung sample for bulk RNA-seq


title: Huh7_NC2_E1_R2

source_name: Huh7, Negative Control2, Experiment1, Replicate2


title: Huh7_NC2_E2_R1

source_name: Huh7, Negative Control2, Experiment2, Replicate1


title: 3dA_P1

city: Athens

first: Brian

middle: H

last: Kvitko

state: GA - Georgia

address: 120 Carlton St

department: Plant Pathology

country: USA

institute: University of Georgia

data_processing:
Illumina BaseSpace Sequence Hub used for base-calling
FastQC/0.11.8-Java-1.8.0_144 for quality checking
Trimmomatic/0.36-Java-1.8.0_144 to trim the read
EDGE-pro/1.3.1 for read alignment to the Pto genome
Bowtie2/2.3.5.1-GCC-8.2.0-2.31.1 to check plant RNA contamination
DESeq2 for differential expression assessment using data from EDGE-pro
Genome_build: NC_004278.1, NC_004632.1, NC_004633.1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each gene for each sample

organism: Pseudomonas syringae pv. tomato str. DC3000

source_name: A. thaliana leaf physical seperation

growth_protocol: Inoculum was prepared in 0.25mM MgCl2 from overnight grown lawn on KB agar plates to OD600=0.8.

extract_protocol:
After 5hrs of infection, Leaves from each treatment (“M” or “F”)  were vacuum infiltrated with a RNAlater-like RNA stabilizing buffer pH 5.2 at 95 kPa for 2 min followed by a slow release of the vacuum.  Then they were frozen in liquid nitrogen until RNA extraction. RNA was extracted by grinding under frozen conditions in Trizol then purified using either the Zymo RNA miniprep kit, or the NEB Monarch RNA isolation kit. All samples were DNAse- treated using the Ambion TurboDNAse kit, then cleaned up with the NEB RNA Cleanup kit.
RNA transcriptome libraries were prepared with the Illumina Tru-Seq stranded total RNA kit as per instructions, using the rRNA-Removal Beads for both bacteria and plants (or just bacteria in the case of P-samples) to remove ribosomal RNAs.
Enriched and amplified libraries were given to the GGBC for quantification, QC analysis and RNA sequencing. Samples were divided into two runs on two different dates. All runs were performed on the Illumina NextSeq sequencer using three Single-End 75-High Flowcells

treatment_protocol: 5-week old A. thaliana were pre-treated 20hr in advance of inoculation with either Flg22 (“F”) or mock (water+DMSO, “M”). Four marked leaves each on plants (24-31 per time point per treatment) were treated with either 1 mM flg22 in 0.1% DMSO or with 0.1% DMSO (mock) by infiltration with a 1 mL blunt syringe on the abaxial surface.  Plants were kept uncovered in the growth room for 20 hours prior to bacterial inoculation.

tag: genotype

value: algUmucAB deletion, pEM53-AlgU

value: cell pellet (innoculum)

tag: time point

value: 5 hpi


title: 3dA_P3


title: Huh7_NC2_E1_R1

source_name: Huh7, Negative Control2, Experiment1, Replicate1


title: 3dA_P2


title: 3dA_F3


title: 2492_B

description:
2492_B
3597_9_2492_B_CGCTGATC

source_name: human breast


title: 3dA_F2


title: pr_RNA_dexab_3dpi_ha1

source_name: Antibody+Dexamethasone treated animal 1, 3dpi, lung sample for bulk RNA-seq


title: 2472_B

description:
2472_B
3597_7_2472_B_CAGATCTG

value: 4x ddAC, 2x CTC + PSCT


title: 2472_S

description:
2472_S
3597_8_2472_S_CATCAAGT


title: Huh7_NC1_E1_R1

source_name: Huh7, Negative Control1, Experiment1, Replicate1

value: Negative Control siRNA #1


title: Huh7_NC1_E2_R1

source_name: Huh7, Negative Control1, Experiment2, Replicate1


title: Huh7_INTG_E1_R1

source_name: Huh7, C5_TRAF1_Intergenic siRNA, Experiment1, Replicate1


title: Huh7_NC1_E1_R2

source_name: Huh7, Negative Control1, Experiment1, Replicate2


title: Huh7_INTG_E3_R1

source_name: Huh7, C5_TRAF1_Intergenic siRNA, Experiment3, Replicate1


title: active, UNICAMP 13

city: Campinas

first: Juliana

middle: Albano de

last: Guimarães

state: SP

address: Tessália Vieira de Camargo, 126, Cidade Universitária

department: Ophthalmology

country: Brazil

institute: School of Medical Sciences of University of Campinas

description: Gene expression data from pterygium surgically excised

hyb_protocol: ss c-DNA was hybridized on Human Clariom D Assay gene chip (Affymetrix)

scan_protocol: The normalization of the transcriptomic data of 9 samples from our cohort was performed by SST-RMA summarization to generate gene level expression signals using Transcriptome Analysis Console (TAC 4.0, Applied Biosystems) software after the evaluation of quality control metrics.

data_processing:
Affymetrix probes were annotated to human genome hg38 version using TAC software and the Clariom D annotation file Clariom_D_Human.r1.na36.hg38.a1.transcript.csv. Probes mapped to more than one gene were removed.
To identify the divergent gene expression pattern between active and atrophic pterygium, a differential gene expression analysis was performed using a linear model fitted in limma package37 after adjusting variables by age. We also applied the Empirical Bayes framework to estimate the more precise expression of each gene to discriminate DE genes. DE genes were identified based on the adjusted p-valor < 0.05 and filtered with the fold change values.

source_name: pterygium of a 35 year-old male

label_protocol: Fifty nanograms of total RNA were used to generate ss-cDNA.

growth_protocol: Surgery to excise pterygia was performed. The entire pterygium tissue was collected, and the samples were immediately stored in RNAlater stabilization solution (Invitrogen) until RNA extraction

extract_protocol: Total RNA extraction was performed using TRIzol Reagent (Invitrogen) and purified with RNeasy RNA extraction kit (Qiagen) according to the manufacturer's protocol. RNA concentration and purity were assessed through NanoDrop 2000 spectrophotometer (Thermo Scientific) whereas RNA integrity was measured in the Bioanalyzer 2100 System (Agilent Technologies). Samples with an RNA integrity number ≥ 7 were subjected to microarray analysis.   Total RNA extraction was performed using TRIzol Reagent (Invitrogen) and purified with RNeasy RNA extraction kit (Qiagen) according to the manufacturer's protocol. RNA concentration and purity were assessed through NanoDrop 2000 spectrophotometer (Thermo Scientific) whereas RNA integrity was measured in the Bioanalyzer 2100 System (Agilent Technologies). Samples with an RNA integrity number ≥ 7 were subjected to microarray analysis.   Total RNA extraction was performed using TRIzol Reagent (Invitrogen) and purified with RNeasy RNA extraction kit (Qiagen) according to the manufacturer's protocol. RNA concentration and purity were assessed through NanoDrop 2000 spectrophotometer (Thermo Scientific) whereas RNA integrity was measured in the Bioanalyzer 2100 System (Agilent Technologies). Samples with an RNA integrity number ≥ 7 were subjected to microarray analysis.   Total RNA extraction was performed using TRIzol Reagent (Invitrogen) and purified with RNeasy RNA extraction kit (Qiagen) according to the manufacturer's protocol.

treatment_protocol: Tissue samples were transferred to liquid nitrogen and ground into powder.

value: pterygium

tag: classification

value: active

value: grade 2


title: active, UNICAMP 12

source_name: pterygium of a 48 year-old female

value: grade 3


title: active, UNICAMP 14

source_name: pterygium of a 51 year-old male

value: grade 4


title: active, UNICAMP 15

source_name: pterygium of a 29 year-old male


title: active, UNICAMP 11

source_name: pterygium of a 27 year-old female


title: pr_RNA_dexab_3dpi_ha2

source_name: Antibody+Dexamethasone treated animal 2, 3dpi, lung sample for bulk RNA-seq


title: 3dA_F1


title: 2046_B

description:
2046_B
3597_3_2046_B_ATGCCTAA

tag: tissue type

value: biopsy

value: 6x ddAC


title: pr_RNA_dex_5dpi_ha3

source_name: Dexamethasone treated animal 2, 5dpi, lung sample for bulk RNA-seq

value: dexamethasone


title: 2271_S

description:
2217_S
3597_6_2271_S_ACATTGGC

tag: chemotherapy


title: 3d_P3

value: algUmucAB deletion


title: pr_RNA_dex_5dpi_ha1

source_name: Dexamethasone treated animal 1, 5dpi, lung sample for bulk RNA-seq

value: Lung


title: 2046_S

description:
2046_S
3597_4_2046_S_AGTGGTCA

tag: neoadjuvant response index (nri)


title: D_CLIP_PC2_3_S21_R1_001

city: Loughborough

first: Nathan

last: Archer

state: East Midlands

address: Sutton Bonington

department: School of Veterinary Medicine and Sciences

country: United Kingdom

institute: University of Nottingham

data_processing:
BCL2FASTQ --with-failed-reads --no-lane-splitting
bbduk for adapter trimming from read 2
STAR alignment of read 2
HTSEQCOUNT for gene counts
DESEQ2 for differential expression analysis
Genome_build: dmel:r6
Supplementary_files_format_and_content: .csv for read counts (matrix, normalised counts from DESEQ2 for both CLIP experiments), .tsv for differential expression output

organism: Drosophila melanogaster

source_name: drosophila whole fly total RNA CLIP, PC2/CMTR2 pulldown RNA

extract_protocol:
trizol extraction of RNA from wildtype flies followed by formaldehyde crosslinking to recombinant drosophila melanogaster CMTR1 or CMTR2, protein-bound RNA was proteinase K treated and Trizol-extracted.
Lexogen's quant-seq 3'FWD kit was used, using a random nonamer tagged partial p7 sequence (i.e. CACGACGCTCTTCCGATCTNNNNNNNNN) in place of the partial p7 sequence containing anchored oligoDT primer found in the manufacturer's protocol. The remainder of the protocol was performed as prescribed by Lexogen (Vienna). Size selection of libraries were carried out with PAGE.

value: whole fly

tag: target

value: PC2-bound RNA


title: pr_RNA_dex_5dpi_ha2


title: 3dA_M2

source_name: A. thaliana leaf physical seperation

value: algUmucAB deletion, pEM53-AlgU

value: mock (water + DMSO)


title: 3dA_M3

value: 5 hpi


title: 3d_P2

value: cell pellet (innoculum)


title: 2271_B

description:
2271_B
3597_5_2271_B_ACCACTGT

source_name: human breast

tag: grade

tag: t-stage

value: TN


title: pr_RNA_dex_3dpi_ha1

source_name: Dexamethasone treated animal 1, 3dpi, lung sample for bulk RNA-seq


title: 97_S

description:
97_S
3597_2_97_S_AAACATCG

tag: n-stage

tag: subtype

value: LUM


title: pr_RNA_dex_3dpi_ha3

source_name: Dexamethasone treated animal 3, 3dpi, lung sample for bulk RNA-seq

tag: tissue


title: 3dA_M1


title: 97_B

description:
97_B
3597_1_97_B_AACGTGAT

tag: recurrence


title: b6_cast_cd4_cd8_scATAC

city: Shanghai

first: Yi

last: Zhong

address: 227 South Chongqing Rd.

institute: SJTU

library_source: genomic

data_processing:
scATAC-seq data processing: cellranger-atac v1.2.0
scATAC-seq analysis: ArchR v1.0.1
Genome_build: GRCm38 and CAST/EiJ
Supplementary_files_format_and_content: count data for peaks in cell subpopulation: text format

molecule: genomic DNA

organism: Mus musculus

source_name: B6/Cast F1 Spleen  CD4 and CD8 T cell

extract_protocol:
Nuclei were diluted to 5 μl with 1× nuclei buffer (10x Genomics) and mixed with ATAC buffer (10x Genomics) and ATAC enzyme (10x Genomics) for tagmentation.
Libraries were generated using the Chromium Chip E Single Cell ATAC kit. Final libraries were quantified using a Qubit fluorimeter.

tag: strain

value: B6/Cast F1

value: Spleen

tag: cell type

value: CD4 and CD8 T cells


title: pr_RNA_dex_3dpi_ha2

source_name: Dexamethasone treated animal 2, 3dpi, lung sample for bulk RNA-seq

tag: treatment


title: D_CLIP_PC2_2_S20_R1_001


title: 3d_F3


title: CMTR1_pd_2

description:
Drosophila melanogaster embryo CMTR1_pulldown_RNA_REP2
CMTR1_pulldown_normalised_counts.txt
CMTR1_pulldown_readcounts_matrix.xlsx
CMTR1_pulldown_DiffE.csv

data_processing:
BCL2FASTQ  --no-lane-splitting
UMI sequencing trimmed and added to read identifiers
cutadapt
FASTQC
STAR
UMI_tools(lexogen) reads with identical map coordinated and UMI sequences are collapsed to remove PCR duplicates
Aligned bam files of UMI-deduplicated reads produced
Htseq-count
DESEQ2 for read normalisation
Genome_build: dmel BDGP6.32.104.
Supplementary_files_format_and_content: CMTR1_pulldown_DiffE.csv
Supplementary_files_format_and_content: CMTR1_pulldown_readcounts_matrix.xlsx - raw readcounts matrix
Supplementary_files_format_and_content: CMTR1_pulldown_normalised_counts.txt - normalised readcount matrix

source_name: embryo

extract_protocol:
Trizol extraction of RNA from wildtype flies followed by formaldehyde crosslinking to recombinant Drosophila melanogaster CMTR1 or CMTR2, protein-bound RNA was proteinase K treated and Trizol-extracted. Following this, Lexogen Corall-seq was carried out following the manufacturer's instructions, including UMI.
Lexogen Corall-seq

tag: fraction

tag: developmental stage

value: embryo


title: pr_RNA_ab_5dpi_ha1

source_name: Antibody treated animal 1, 5dpi, lung sample for bulk RNA-seq

value: antibody

tag: sampling timepoint


title: 3d_F2

tag: genotype

tag: time point


title: 3d_P1


title: D_CLIP_I_3_S15_R1_001

source_name: drosophila whole fly total RNA CLIP, input RNA

value: input RNA


title: pr_RNA_ab_3dpi_ha3

source_name: Antibody treated animal 3, 3dpi, lung sample for bulk RNA-seq


title: D_CLIP_PC2_1_S19_R1_001


title: pr_RNA_ab_3dpi_ha2

source_name: Antibody treated animal 2, 3dpi, lung sample for bulk RNA-seq


title: CMTR1_pd_1

description:
Drosophila melanogaster embryo CMTR1_pulldown_RNA_REP1
CMTR1_pulldown_normalised_counts.txt
CMTR1_pulldown_readcounts_matrix.xlsx
CMTR1_pulldown_DiffE.csv


title: pr_RNA_ab_3dpi_ha1

source_name: Antibody treated animal 1, 3dpi, lung sample for bulk RNA-seq


title: active, UNICAMP 5

source_name: pterygium of a 45 year-old female

value: pterygium

tag: classification

value: active

value: grade 2


title: D_CLIP_I_1_S13_R1_001

value: whole fly


title: pr_RNA_ab_2dpi_ha1

source_name: Antibody treated animal 1, 2dpi, lung sample for bulk RNA-seq

value: Lung


title: 3d_M3

value: algUmucAB deletion


title: 3d_M2

value: mock (water + DMSO)


title: CMTR1_in_2

description:
Drosophila melanogaster embryo input_RNA_REP2
CMTR1_pulldown_normalised_counts.txt
CMTR1_pulldown_readcounts_matrix.xlsx
CMTR1_pulldown_DiffE.csv

value: input_RNA (control)


title: CMTR1_in_1

description:
Drosophila melanogaster embryo input_RNA_REP1
CMTR1_pulldown_normalised_counts.txt
CMTR1_pulldown_readcounts_matrix.xlsx
CMTR1_pulldown_DiffE.csv


title: MH7A cell line_Tub B Treat_rep_2

city: Shenzhen

first: Yuyang

last: Miao

state: Guangdong

address: Longguan Road 101

department: Longhua Branch

institute: Shenzhen Peoples‘s Hospital

data_processing:
Illumina RTA software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR 2.7.0 with default parameters
The gene expression level was calculated by featureCounts with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: MH7A cell line

extract_protocol:
Total RNA was extracted by using EASYspin RNA Mini Kit (Aidlab RN07).
RNA-seq libraries were constructed by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111).

value: human rheumatoid arthritis synovial cells

tag: cell line

value: treated with 60 uM Tub B for 24 h


title: MH7A cell line_Tub B Treat_rep_1


title: 3d_M1

value: 5 hpi


title: 3d_F1


title: KO_br4_Input

description:
Drosophila Melanogaster Cmtr1/Cmtr2 Knockout whole fly input
KO4_Input_S8

data_processing:
bcl2fastq with the option --no-lane-splitting
trimming with Bbduk (bluebee genomics) for low quality poly(A) tails and adapter sequences
STAR with the settings: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD  --outSAMtype BAM SortedByCoordinate
HTSeq-count
R studio and DESEQ2 with the following command: DESeqDataSetFromHTSeqCount(sampleTable=Book1, design= ~ assay + treatment + assay:treatment
generating the final comparisson table with "Reduce= ~ assay:treatment" for "knockout polysomes" also output normalised read count data for all samples for TE calculations using "counts(dds, normalized=TRUE)"
Bluebee genomics platform to generate DEseq2 perturbations for QC. E.g. Control vs Control, Knockout vs Knockout and to normalise all read counts within one "experiment" for the monosome-to-polysome ratios.
Genome_build: dmel_r6.02
Supplementary_files_format_and_content: .txt, raw read counts. "Control"= wildtype, "Knockout"= Cap1 and Cap2 methyltransferase double knockout, [0-4] = biological replicate,
Supplementary_files_format_and_content: .txt and .csv files of differential expression results

source_name: whole fly

extract_protocol:
Whole fly frozen with liquid nitrogen and ground in presence of lysis buffer containing heparin sulphate. Polysome profiling carried out as described with aliquot of initial loading material saved as "input" samples. After fractionation, fractions for monosome and polysome were identified and pooled appropriately.
quant-seq 3' fwd kit was used to generate cDNA libraries from Input, Monosome, and Polysome fractions, with the addition of heparinase I in the early steps.

treatment_protocol: Double knockout of cap-adjacent methyltransferases AFT and CG6379

tag: genotype/variation

value: Cmtr1/Cmtr2 Knockout

tag: polysome profiling location

value: input

tag: replicate type

value: biological


title: atrophic, UNICAMP 6

source_name: pterygium of a 53 year-old male

value: atrophic

tag: grade


title: active, UNICAMP 8

source_name: pterygium of a 34 year-old male

value: grade 1


title: atrophic, UNICAMP 9

source_name: pterygium of a 70 year-old male

value: grade 3


title: pr_RNA_ab_2dpi_ha2

source_name: Antibody treated animal 2, 2dpi, lung sample for bulk RNA-seq

value: antibody


title: pr_RNA_aaUntr_5dpi_ha2

source_name: Untreated animal 2, 5dpi, lung sample for bulk RNA-seq


title: MH7A cell line_TNF+Tub B-treat_rep_2

value: treated with 20 ng/u TNFa+60 uM Tub B for 24 h


title: KO_br3_Input

description:
Drosophila Melanogaster Cmtr1/Cmtr2 Knockout whole fly input
KO3_Input_S7


title: D_CLIP_I_2_S14_R1_001

tag: target

value: input RNA


title: pr_RNA_aaUntr_5dpi_ha1

source_name: Untreated animal 1, 5dpi, lung sample for bulk RNA-seq

tag: tissue


title: MH7A cell line_TNF+Tub B-treat_rep_1


title: MH7A cell line_TNF_treat_rep_2

value: treated with 20 ng/ul TNFa for 24h


title: KO_br2_Input

description:
Drosophila Melanogaster Cmtr1/Cmtr2 Knockout whole fly input
KO2_Input_S6


title: pr_RNA_aaUntr_3dpi_ha3

source_name: Untreated animal 3, 3dpi, lung sample for bulk RNA-seq

value: Lung


title: Hamster3_GEX

description:
Processed data files include  DexAb*rds and DexAb.loom files on series record.
10xGenomics Chromium v3.1 single cell 3' gene expression kit

source_name: multiplexed sample

value: Multiplexed sample (mixed treatments)


title: Hamster2_GEX


title: pr_RNA_aaUntr_3dpi_ha2

source_name: Untreated animal 2, 3dpi, lung sample for bulk RNA-seq


title: MH7A cell line_TNF_treat_rep_1


title: Hamster2_CELLPLEX


title: MH7A cell line_Mock_rep_2

value: DMSO


title: pr_RNA_aaUntr_2dpi_ha1

source_name: Untreated animal 1, 2dpi, lung sample for bulk RNA-seq


title: WT_br1_Input

description:
Drosophila Melanogaster Wildtype whole fly input
C1_Input_S1

value: Wildtype


title: Hamster1_CELLPLEX


title: MH7A cell line_Mock_rep_1

value: human rheumatoid arthritis synovial cells


title: WT_br2_Input

description:
Drosophila Melanogaster Wildtype whole fly input
C2_Input_S2


title: WT_br3_Input

description:
Drosophila Melanogaster Wildtype whole fly input
C3_Input_S4


title: Hamster1_GEX


title: 10d_0min_A

status: Public on Dec 17 2021

city: Riverside

first: Christi Ann

last: Scott

state: CA

address: 3401 Watkins Drive

department: Molecular, Cell, and Systems Biology

institute: University of California, Riverside

data_processing:
For HiSeq2000: RTA v1.7, CASAVA v1.7 used for basecalling. For NextSeq500: RTA 2.0 used for basecalling.
Reads aligned to the latest release of each of the genomes used (dm6 for the Drosophila genome, GRCm38 for the Mus Musculus genome, and Araport11 for the Arabidopsis genome) and quantified with kallisto (Version: kallisto 0.43.1, Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification, Nature Biotechnology 34, 525-527(2016), doi:10.1038/nbt.3519) . Only libraries for which we obtained >75 % alignment were used for downstream analysis.
Transcript counts were summarized to gene-level using tximport package (version 1.4.0).
For any instances of detected batch effects, we removed unwanted variation using RuvR in the RuvSeq package (version_1.10.0).
Differentially expressed gene (DEG) analysis was performed with the edgeR package (version 3.18.1), using low count filtering (cpm >0.5) and TMM normalization.
Genome_build: dm6 for the Drosophila genome, GRCm38 for the Mus Musculus genome, and Araport11 for the Arabidopsis genome
Supplementary_files_format_and_content: tab-delimited .tsv files including counts TPM normalized read counts for each sample

source_name: Brain

extract_protocol:
RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit v2 was used with total RNA for the construction of sequencing libraries.

value: OreR

value: wild type

tag: age

value: 10 days

tag: Sex

value: male

value: 0 min (control) sensory deprived

value: brain


title: 25d_30min_A

tag: strain

value: 25 days

value: 30 min :Odor and light stimulated


title: Hamster3_CELLPLEX

tag: treatment


title: KO_br1_Input

description:
Drosophila Melanogaster Cmtr1/Cmtr2 Knockout whole fly input
KO1_Input_S5

value: Cmtr1/Cmtr2 Knockout

value: input

value: biological


title: 5d_45min_B

value: 4-5 days

value: 45 min :Odor and light stimulated


title: 25d_0min_A


title: 5d_45min_A


title: 5d_30min_B


title: 5d_10min_B

value: 10 min :Odor and light stimulated


title: 5d_20min_A

value: 20 min :Odor and light stimulated


title: 5d_0min_B


title: 5d_20min_B


title: pr_RNA_aaUntr_3dpi_ha1

source_name: Untreated animal 1, 3dpi, lung sample for bulk RNA-seq

value: Lung


title: WT rep1

city: Guangzhou

first: Mei

last: Wu

address: Waihuan Dong Road

department: School of Medicine

institute: South China University of Technology

data_processing:
Sequenced reads were mapping using STAR
Genome_build: GRCz11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Danio rerio

source_name: Whole embryos

extract_protocol:
The gfi1aa-/-gfi1ab-/- mutant and the gfi1aa-/-gfi1b-/-gfi1ab-/- mutant were generated from gfi1aa+/-gfi1ab-/- intercross embryos and gfi1aa-/-gfi1b-/-gfi1ab+/- intercross embryos by genotyping. Then, RNA from gfi1-related single, double, and triple mutants as well as WT embryos was extracted with TRIzol reagent.
Sequencing libraries were generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® RNA according to the manufacturer’s instructions.

value: Whole embryos

value: 15 hpf


title: 10d_30min_A

value: OreR

value: wild type


title: gfi1aagfi1ab double mutant rep2


title: gfi1aagfi1bgfi1ab triple mutant rep2


title: gfi1bgfi1ab double mutant rep2


title: WT rep2


title: gfi1aagfi1bgfi1ab triple mutant rep1


title: gfi1aagfi1b double mutant rep2


title: gfi1b mutant rep2


title: 5d_10min_A

value: male


title: gfi1b mutant rep1


title: HO28_Hiva_OA

type: genomic

city: Tartu

first: Tuuli

last: Reisberg

address: Riia 23

country: Estonia

institute: University of Tartu

description: Genomic DNA extracted from blood was genotyped using HumanOmniExpress 24 v1.2 BeadChip (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing:
Image data was analyzed using Genomestudio v2.0 with GT module 2.0.4 (Illumina).
Genotype: AA,AB,BB,or NC (no call)

label: Cy3, Cy5

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: population

tag: region

value: Oceania

value: blood


title: gfi1aa mutant rep1

tag: developmental stage


title: gfi1aa mutant rep2

tag: genotype


title: gfi1ab mutant rep2


title: gfi1aagfi1ab double mutant rep1


title: gfi1ab mutant rep1


title: HO24_Hiva_OA


title: gfi1aagfi1b double mutant rep1


title: HO23_Hiva_OA


title: 5d_30min_A

value: brain


title: 5d_0min_A

value: 0 min (control) sensory deprived


title: HO21_Hiva_OA


title: HO22_Hiva_OA


title: HO19_Hiva_OA


title: Rpb3-HA (subunit of RNAPol2) ChIP 32min after release from G1 dye flip

city: Montpellier

first: Marta

last: Radman-Livaja

address: 1919 route de Mende

department: IGMM

country: France

institute: CNRS

hyb_protocol: Labeled probes (a mixture of Cy3 labeled Rpb3-HA_ChIP_DNA|sonicated_chromatin_genomic DNA and Cy5sonicated_chromatin_genomic DNA|labeled Rpb3-HA_ChIP_DNA) were hybridized onto an Agilent yeast 4x44K whole genome DNA array (ref. G4810A-14810).

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an InnoScan 710 MicroArray scanner (Innopsys) at 5 micron resolution and processed with the Mapix software.

data_processing: After background correction and removal of flagged values, data was block normalized by dilation and log base 2 ratios (Cy3/Cy5) were calculated to produce the values given in the data table.

organism: Saccharomyces cerevisiae

source_name: Rpb3-HA ChIP DNA from S-phase 32min after release from G1 arrest

label_protocol: ChIPed DNA samples and their corresponding input samples were amplified, with a starting amount of up to 30 ng, using the DNA linear amplification method described previously (Liu et al., 2005; Liu et al., 2003). 2.5 µg of aRNA from each sample produced from the linear amplification was transformed into cDNA by reverse transcription in the presence of amino-allyl dUTP. The resulting cDNA was dye-coupled with Cy5 or Cy3 NHS-esters and purified as described previously (Liu et al., 2005).

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 into preheated (SCD-URA) + 10 μM EdU.

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). Zirconium beads were removed from the cell lysate by centrifugation and the entire cell lysate was subject to sonication using the Bioruptor-Pico (Diagenode) for 3x10 cycles of 30 seconds ON/OFF each resulting in a final median size of chromatin fragments of 200 bp. Cellular debris was then removed by centrifugation and 2 % of the total supernatant volume was kept for input fractions.The remainder of the sonicated chromatin was precleared using Protein A agarose beads (Repligen) for 1 hour (1h) at 4°C on the rotating wheel. The sonicated material was then pooled together and distributed into 500 µL aliquots (equivalent of 700 million cells per aliquot) and 25 µl of Protein G magnetic beads (Life Technologies-Invitrogen) pre-bound with 6µg of anti-HA (ab9110, abcam), was added to each tube. Aliquots were then incubated with rotation at 4°C overnight. The beads were then washed once with cold buffer L (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate), three times with cold Buffer W1 (Buffer L with 500mM NaCl), twice with cold Buffer W2 (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA), and once with cold TE buffer (10 mM Tris-HCl,pH 8.0, 1 mM EDTA). Chromatin was eluted in 2x125 μl elution buffer (25mM Tris-HCl pH 7.5, 5 mM EDTA, 0.5% SDS) after incubation for 2x10 min at 65°C. The eluates and reserved input samples were treated with RNase A (Qiagen) for 1h in 37°C and proteins were then digested with Proteinase K (Euromedex, final concentration 0.4 mg/ml) for 2h at 37°C and the temperature was then shifted to 65°C overnight to reverse cross-links. DNA was then purified with the QIAquick PCR purification kit (QIAGEN)

treatment_protocol: At  25, or 32 min after release, 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: antibody

value: anti-HA

value: MATa ade2-1::ADE2 his3-11 15 leu2-3 112 trp1-1 ura3-1 can1-100  Rpb3-3HA::TRP URA3::GDP-TK(7x) AUR1c::ADH-Hent1 ∆bar1::HIS6

source_name: sonicated chromatin from S-phase 32min after release from G1 arrest


title: Rpb3-HA (subunit of RNAPol2) ChIP 25min after release from G1

source_name: sonicated chromatin from S-phase 25min after release from G1 arrest

value: MATa ade2-1::ADE2 his3-11 15 leu2-3 112 trp1-1 ura3-1 can1-100  Rpb3-3HA::TRP URA3::GDP-TK(7x) AUR1c::ADH-Hent1 ∆bar1::HIS3

source_name: Rpb3-HA ChIP DNA from S-phase 25min after release from G1 arrest


title: Rpb3-HA (subunit of RNAPol2) ChIP 25min after release from G1 dye flip

value: MATa ade2-1::ADE2 his3-11 15 leu2-3 112 trp1-1 ura3-1 can1-100  Rpb3-3HA::TRP URA3::GDP-TK(7x) AUR1c::ADH-Hent1 ∆bar1::HIS5


title: HO16_Hiva_OA


title: HO14_Hiva_OA


title: NH5_Nuku_Hiva


title: NH30_Nuku_Hiva


title: NH48_Nuku_Hiva


title: NH25_Nuku_Hiva


title: NH20_Nuku_Hiva


title: NH10_Nuku_Hiva


title: NH09_Nuku_Hiva


title: NH01_Nuku_Hiva


title: gfi1bgfi1ab double mutant rep1


title: TA05_Tahuta

value: Tahuata


title: Rpb3-HA (subunit of RNAPol2) ChIP 32min after release from G1

value: MATa ade2-1::ADE2 his3-11 15 leu2-3 112 trp1-1 ura3-1 can1-100  Rpb3-3HA::TRP URA3::GDP-TK(7x) AUR1c::ADH-Hent1 ∆bar1::HIS4


title: TA08_Tahuta


title: TA03_Tahuta


title: TA04_Tahuta


title: TA07_Tahuta


title: Laos27

description: Genomic DNA extracted from blood was genotyped using HumanOmniExpress 24 v1.1 BeadChip (Illumina).

value: Lao

value: Southeast Asia


title: Laos19


title: mRNA+lncRNA-seq_HCT15-FR_2

first: Xuelong

last: Wang

address: No. 100 Banxia Road

institute: Chinese Academy of Sciences

data_processing:
Reads from all RNA-seq experiments were aligned to zebrafish genome build hg19 using STAR. All ATAC-Seq data sets were trimmed and aligned to zebrafish genome build hg19 genome using Bowtie2.
Duplicate reads of all RNA-seq and ATAC-seq data were removed with SAMtools.
The mRNA and lncRNA expression of a gene was quantified by FPKM based on RefSeq gene annotation using Cuffdiff. SPAR and DEseq2 were used to quantify small RNA expression. MACS2 was used to identify regions of ATAC-seq peaks.
The ATAC-seq peaks were used for known motif enrichment analysis of each sample, which were performed using HOMER (v4.9).
Genome_build: hg19
Supplementary_files_format_and_content: BigWig (bw) files were generated using deepTools.

source_name: colon cancer cell line

growth_protocol: The HCT15 and 5-fluorouracil-resistant HCT15 (HCT15-FR) cell lines were purchased from the iCell Bioscience Inc (Shanghai, China) and cultured in RPMI-1640 medium (KEL Biotech, China) with 10% fetal bovine serum (KEL Biotech, China), 2 mM L-Glutamine (Gibco, USA), 0.1 M sodium pyruvate (Gibco, USA), 50 units/mL penicillin and 50 µg/mL streptomycin (Sangon Biotech, China). All cells were grown to 80% confluence in 10 cm culture dishes in a humidified atmosphere with 5% CO2 at 37 °C, refreshing culture medium every 2-3 days.

extract_protocol:
Total RNA was isolated from samples using TRIzol Reagent (Invitrogen, USA) and purified using RNeasy Mini Kit (QIAGEN, Germany). Agilent Bioanalyzer 2100 was used to assess RNA integrity.
The mRNA and lncRNA‐seq library preparation from 3 μg of total RNA was performed with NEBNext UltraTM Directional RNA Library Prep Kit for Illumina (NEB, USA) according to the manufacturer's instructions. PE150 sequencing was performed on the Illumina HiSeq X Ten platform (Novogene Biotech, China). A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, USA) was used to generate the sequencing libraries following the manufacturer’s instructions. library quality was assessed on the Agilent Bioanalyzer 2100 system and then sequenced on an Illumina Hiseq 2500 platform (Novogene Biotech, China). 50bp single-end reads were generated for each sample. The ATAC-seq libraries were prepared using a total of 50,000 fresh cells were washed twice with 100 μl of cold PBS (KEL Biotech, China) and resuspended in 100 μl of lysis buffer [10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 0.1% IGEPAL CA-630 (Sigma-Aldrich) and 3 mM MgCl2] for 10 min on ice to prepare the nuclei. Immediately after lysis, the suspension of nuclei was spun at 500 g at 4°C for 5 min to remove the supernatant. Nuclei were then incubated with the 50 μl of Tn5 transposition reaction mix (DIATRE Biotech, China) at 37 °C for 30 min. The stop buffer was then added directly into the reaction to end the tagmentation. DNA was purified using the QIAquick PCR Purification Kit (QIAGEN, Germany). PCR was performed to amplify the library for 12 cycles. Libraries were purified with Agencourt Ampure XP beads (Beckman, USA) to remove contaminating primer dimmers.

treatment_protocol: The parental HCT15 cells were grown in a drug-free medium, resistant-derived cells were maintained in 5-FU at a concentration of 20 μg/mL.

value: treated with 20microg/mL 5-FU

value: HCT15 cell line


title: mRNA+lncRNA-seq_HCT15-FR_1


title: HO05_Hiva_OA


title: ATAC-seq_HCT15_2

value: untreated

value: HCT17 cell line


title: Laos18


title: ATAC-seq_HCT15-FR_1

value: HCT18 cell line


title: ATAC-seq_HCT15_1

value: HCT16 cell line


title: Laos16

value: blood


title: ATAC-seq_HCT15-FR_2

value: HCT19 cell line


title: mRNA+lncRNA-seq_HCT15_2


title: Laos14


title: Laos5


title: mRNA+lncRNA-seq_HCT15_1


title: NH29_Nuku_Hiva

value: Oceania


title: TA02_Tahuta


title: Testis GMS rep2

city: Zhenjiang

first: Xinglin

last: Mei

state: Jiangsu

address: No.666, Changhui Road, Dantu New District, Zhenjiang city, Jiangsu Province

institute: Jiangsu University of Science and Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
The quality of the raw data was controlled by the FasQC. At the initial filtering step, we discarded poor quality reads using SOAPnuke , including reads that have adaptors, reads with more than 10% unknown bases, and reads that have more than 50% bases with quality value less than 5. The clean reads were mapped onto reference genome of silkworm independently by HISAT2 version 2.1.0 . The parameters were set to default values. And we used RSeQC packages (version 2.6.4) to process a comprehensively evaluation on RNA-Seq data after alignment.
Based on the HISAT2 alignment BAM file, featureCounts v1.6.2 was used to estimate and quantify gene expression with default parameters, yielding raw read counts for each gene. Gene expression was normalized by reads per kilobase of exon per million reads mapped (RPKM).
Genome_build: ASM15162v1 reference Annotation Release 102
Supplementary_files_format_and_content: Text files include RPKM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Bombyx mori

source_name: Testis

extract_protocol:
Total RNA was extracted from testes using TRIzol reagent according to the manufacturer’s protocol (Invitrogen, USA).The sequencing libraries were generated using the TruSeq RNA Sample Prep Kit v2 (Illumina, USA) following manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: GMS

value: testis

value: day 5 of fifth-instar larvae

value: mutant type


title: Testis GMS rep1


title: Testis WT rep2

value: wild type


title: Testis WT rep1


title: Testis WT rep3


title: 25d_30min_B

value: OreR

value: 25 days

value: male

value: 30 min :Odor and light stimulated

value: brain


title: Testis GMS rep3


title: 10d_30min_B

value: 10 days


title: 10d_0min_B

value: 0 min (control) sensory deprived


title: 5d_45min_C

value: 4-5 days

value: 45 min :Odor and light stimulated


title: 25d_0min_B


title: 5d_30min_C


title: 5d_20min_C

value: 20 min :Odor and light stimulated


title: 5d_0min_C


title: Laos4

value: Lao

value: Southeast Asia

value: blood


title: Orco2_ant_stim_C

source_name: Antenna

value: w*; TI{TI}Orco2

value: Orco mutant

value: stim:Odor and light stimulated (10,20,30 min)

value: 2nd and 3rd segment of the antenna


title: OreR_ant_stim_A

value: OreR

value: wild type


title: 5d_10min_C

value: male

value: 10 min :Odor and light stimulated


title: Orco2_ant_0min_C


title: Laos2


title: Orco2_ant_0min_B


title: OreR_ant_stim_B


title: Orco2_ant_stim_B


title: OreR_ant_0min_A


title: OreR_ant_0min_B


title: NKTL-primary sample #3

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

data_processing:
RNA-seq datasets of primary NKTL lymphoma samples and tonsil control samples were aligned to the hg19 human genome using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1.
featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation
Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 3 tonsil vs 3 NKTL samples (3 tonsil vs 3  NKTL samples).
Genome_build: hg19
Supplementary_files_format_and_content: txt files for differentially expressed genes, featureCount output

source_name: NKTL Sample

growth_protocol: Not applicable

extract_protocol:
Total RNA was harvested using the miRNeasy Mini Kit (Qiagen).
Library construction and sequencing of single-end 50bps long reads by the Illumina Hiseq4000 were performed at the BGI Biotech Solutions (Hong Kong) Co Ltd (Hong Kong).

treatment_protocol: No treatment

value: Primary NKTL tumor


title: NKTL-primary sample #1


title: Tonsil-primary sample #2

source_name: Tonsil Sample

value: Healthy Tonsil


title: Tonsil-primary sample #1


title: Tonsil-primary sample #3


title: NKTL-primary sample #2


title: NKYS_cellLine_ChIP_Input

data_processing:
ChIP-seq reads were mapped to human hg19 reference genome using bowtie2 program with default parameters.
Aligned ChIP-seq reads were remove duplicate with samtools rmdup package.
ChIP-Seq peaks were called with MACS2 software, version 2.1.1.2016030. Threshold for the peaks called is p-value < 1e-9, --keep-dup=1
Genome_build: hg19
Supplementary_files_format_and_content: broadPeak files called with MACS2

source_name: NKYS

growth_protocol: NKYS and HANK1 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.

extract_protocol:
Library construction from the H3K27ac ChIP-seq samples and sequencing of single-end 50bps long reads by the Illumina HiSeq 4000 were performed at BGI Biotech Solutions Co. Ltd (Hong Kong, China).
Single end ChIP-Seq sequencing

treatment_protocol: NKTL cell lines were cross-linked with formaldehyde for 10 min. Lysates were clarified from sonicated nuclei and H3K27ac-DNA complexes were isolated with antibody.  A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment.

value: NKYS

tag: chip antibody

value: none (WCE)


title: HANK1_cellLine_H3K27ac_ChIP-Seq

tag: cell line

value: anti-H3K27ac (Abcam, ab4729)


title: 25min-H3K36me3-ChIPNChAP-Mcm23A-2readsFigS7BGEO

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 2

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.

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 mcm38

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.

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: genotype/variation

value: Mcm23A mutant

tag: cell cycle

value: mid early S-phase (34% of the genome is unreplicated)

tag: edu incubation

value: from beginning of release from G1 arrest


title: 25min-H3K4me3-ChIPNChAP-Mcm23A-2readsFigS7BGEO

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 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 mcm40


title: 25min-Rpb3ChIPNChAP-Mcm23A-2readsFigS7BGEO

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 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 mcm48


title: 25min-H3ChIPNChAP-Mcm23A-2readsFigS7BGEO

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 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 mcm36


title: 25min-NChAP-Mcm2-3A-2readsFigS7BGEO

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 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 mcm46


title: 25min-Input-Mcm23A-2readsFigS7BGEO

description:
Input DNA from sonicated chromatin 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, 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 mcm44


title: 25min-ChIP-H3-Mcm23A-2readsFigS7BGEO

description:
H3 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, H3 on bulk 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 mcm32


title: NKYS_cellLine_H3K27ac_ChIP-Seq


title: 25min-ChIP-H3K56Ac-Mcm23A-2readsFigS7BGEO

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 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 mcm30


title: Tonsil_control#3_ChIP_Input

source_name: Healthy Tonsil


title: Tonsil_control#3_H3K27ac_ChIP-Seq


title: HANK1_cellLine_ChIP_Input


title: Tonsil_control#2_ChIP_Input


title: 25min-H3K56Ac-ChIPNChAP-Mcm23A-2readsFigS7BGEO

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 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 mcm42


title: 25min-ChIP-H3K4me3-Mcm23A-2readsFigS7BGEO

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 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 mcm28


title: 25min-ChIP-H3K36me3-Mcm23A-2readsFigS7BGEO

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 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 mcm26


title: 20min-Rpb3-ChIP-Mcm23A-2readsFigS7BGEO

description:
RNApol2 (Rpb3HA) 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, RNAPol2 on bulk 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 mcm22

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


title: 20min-Input-Mcm23A-2readsFigS7BGEO

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 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 mcm18


title: 20min-H3K56Ac-ChIP-Mcm23A-2readsFigS7BGEO

description:
H3K56Ac 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, H3K56Ac on bulk 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 mcm14


title: 20min-H3K4me3-McM23A-2readsFigS7BGEO

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 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 mcm12


title: 20min-NChAP-Mcm23A-2readsFigS7BGEO

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 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 mcm20


title: Tonsil_control#2_H3K27ac_ChIP-Seq


title: 20min-H3K36me3-McM23A-2readsFigS7BGEO

description:
H3K36me3 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, H3K36me3 on bulk 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 mcm8


title: Tonsil_control#1_ChIP_Input


title: 20min-H3-ChIP-McM23A-2readsFigS7GEO

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 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 mcm2


title: 25min-Input-WT-2readsFigS7GEO

description:
Input DNA from sonicated chromatin 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, input DNA.paired end reads, replicate 2

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

value: wt

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


title: 25min-ChIP-Rpb3-Mcm23A-2readsFigS7BGEO

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 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 mcm34


title: 25min-H3K56ac-ChIP-WT-2readsFigS7GEO

description:
H3K56Ac ChIP 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 bulk DNA.paired end reads, replicate 2


title: Tonsil_control#1_H3K27ac_ChIP-Seq


title: NKTL_primary#3_ChIP_Input

source_name: Primary NKTL


title: NKTL_primary#2_ChIP_Input


title: NKTL_primary#2_H3K27ac_ChIP-Seq


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

description:
H3K4me3 ChIP 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 bulk DNA.paired end reads, replicate 2


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

description:
H3 ChIP 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 bulk DNA.paired end reads, replicate 2


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

description:
H3K36me3 ChIP 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 bulk DNA.paired end reads, replicate 2


title: NKTL_primary#1_ChIP_Input


title: NKTL_primary#3_H3K27ac_ChIP-Seq


title: NKTL_primary#1_H3K27ac_ChIP-Seq


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

description:
H3 ChIP 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 bulk DNA.paired end reads, replicate 2

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


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

description:
RNApol2 (Rpb3HA) ChIP 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 bulk DNA.paired end reads, replicate 2


title: 20min-H3K56ac-ChIP-WT-2readsFigS7GEO

description:
H3K56Ac ChIP 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 bulk DNA.paired end reads, replicate 2


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

description:
H3K4me3 ChIP 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 bulk DNA.paired end reads, replicate 2


title: 20min-Input-WT-2readsFigS7GEO

description:
Input DNA from sonicated chromatin 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, input DNA.paired end reads, replicate 2


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

description:
H3K36me3 ChIP 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 bulk DNA.paired end reads, replicate 2


title: Subject 101734 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

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.

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.

value: NT

value: Male

tag: diagnosis

value: Pervasive Developmental Disorder Not Otherwise Specified (PDDNOS) or Asperger

tag: subject age (ears)


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

description:
RNApol2 (Rpb3HA) 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, RNAPol2 on bulk DNA.paired end reads, replicate 1

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


title: 25min-H3-ChIP-McM23A-1readsFig6GEO

description:
H3 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, H3 on bulk DNA.paired end reads, replicate 1

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


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

description:
H3K56Ac 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, H3K56Ac on bulk DNA.paired end reads, replicate 1


title: Subject 101734 LPS

value: LPS


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

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 1


title: 25min-Input-McM23A-1readsFig6GEO

description:
Input DNA from sonicated chromatin 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, input DNA.paired end reads, replicate 1


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

description:
RNApol2 (Rpb3HA) ChIP 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 bulk DNA.paired end reads, replicate 2


title: 25min-Rpb3-ChIPNChAP-WT-1readsFig5GEO

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 1

value: mid early S-phase (25% of the genome is unreplicated)


title: Subject 101711 NT

value: Female


title: 25min-NChAP-WT-1readsFig5GEO

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 1


title: 25min-Inpt-WT-1readsFig5GEO

description:
Input DNA from sonicated chromatin 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, input DNA.paired end reads, replicate 1


title: 25min-H3K56ac-ChIPNChAP-WT-1readsFig5GEO

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 1


title: 25min-H3K56-ChIP-WT-1readsFig5GEO

description:
H3K56Ac ChIP 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 bulk DNA.paired end reads, replicate 1


title: 25min-H3K4me3-ChIP-WT-1readsFig5GEO

description:
H3K4me3 ChIP 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 bulk DNA.paired end reads, replicate 1


title: 25min-H3K36me3-ChIP-WT-1readsFig5GEO

description:
H3K36me3 ChIP 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 bulk DNA.paired end reads, replicate 1


title: 25min-H3K4me3-CHIP-NChAP-WT-1readsFig5GEO

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 1


title: 25min-H3-ChIP-WT-1readsFig5GEO

description:
H3 ChIP 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 bulk DNA.paired end reads, replicate 1


title: Subject 101711 LTA

value: LTA


title: 25min-H3-ChIPNChAP-WT-1readsFig5GEO

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 1


title: 25min-H3K36me3-ChIPNChAP-WT-1readsFig5GEO

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 1


title: 20min-H3K36me3-ChIP-McM23A-1readsFig6GEO

description:
H3K36me3 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, H3K36me3 on bulk DNA.paired end reads, replicate 1


title: 25min-Rpb3-ChIP-WT-1readsFig5GEO

description:
RNApol2 (Rpb3HA) ChIP 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 bulk DNA.paired end reads, replicate 1


title: 20min-Rpb3-ChIP-NChAP-WT-1readsFig5GEO

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 1

value: early S-phase (65% of the genome is unreplicated)


title: 20min-H3K56ac-ChIP-WT-1readsFig5GEO

description:
H3K56Ac ChIP 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 bulk DNA.paired end reads, replicate 1


title: 20min-Rpb3-ChIP-WT-1readsFig5GEO

description:
RNApol2 (Rpb3HA) ChIP 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 bulk DNA.paired end reads, replicate 1


title: Subject 101706 LTA


title: Subject 101706 NT


title: Subject 101711 LPS


title: 20min-H3K56ac-CHIP-NChAP-WT-1readsFig5GEO

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 1


title: Subject 101706 LPS


title: 20min-Input-WT-1readsFig5GEO

description:
Input DNA from sonicated chromatin 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, input DNA.paired end reads, replicate 1


title: Subject 101694 NT


title: Subject 101694 LPS


title: Subject 101694 LTA


title: 20min-H3K4me3-ChIP-WT-1readsFig5GEO

description:
H3K4me3 ChIP 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 bulk DNA.paired end reads, replicate 1


title: 20min-H3K4me3-ChIPNChAP-WT-1readsFig5GEO

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 1


title: 20min-H3K36me3-CHIP-NChAP-WT-1readsFig5GEO

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 1


title: 20min-H3K36me3-ChIP-WT-1readsFig5GEO

description:
H3K36me3 ChIP 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 bulk DNA.paired end reads, replicate 1


title: Subject 101692 NT


title: 20min-H3-ChIP-WT-1readsFig5GEO

description:
H3 ChIP 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 bulk DNA.paired end reads, replicate 1


title: Subject 101692 LPS


title: LW_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

value: L2HG followed by withdrawal


title: LW_rep2 [bulk RNA-seq]


title: 20min-NChAP-WT-1readsFig5GEO

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 1

value: from beginning of release from G1 arrest


title: 20min-H3-CHIP-NChAP-WT-1readsFig5GEO

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 1


title: LW_rep1 [bulk RNA-seq]


title: L+V_rep2 [bulk RNA-seq]

value: L2HG+vitamin C (A2P)


title: L+V_rep3 [bulk RNA-seq]


title: Subject 101334 NT

tag: Sex


title: L+V_rep1 [bulk RNA-seq]


title: Subject 101666 LPS


title: L2HG_rep3 [bulk RNA-seq]


title: L2HG_rep2 [bulk RNA-seq]


title: D+L_rep3 [bulk RNA-seq]


title: D+L_rep1 [bulk RNA-seq]


title: Subject 101334 LPS


title: L2HG_rep1 [bulk RNA-seq]


title: D2HG_rep1 [bulk RNA-seq]


title: D2HG_rep2 [bulk RNA-seq]


title: Ctrl_rep3 [bulk RNA-seq]

value: Untreated


title: Subject 101246 NT


title: Ctrl_rep2 [bulk RNA-seq]


title: Subject 101746 NT

tag: subject id

tag: tissue

value: PBMCs

tag: subject sex

value: Typical


title: Subject 101246 LTA

tag: treatment


title: D+L_rep2 [bulk RNA-seq]


title: Subject 101246 LPS


title: Ctrl_rep1 [bulk RNA-seq]


title: Subject 101746 LTA


title: Subject 101666 NT

value: NT


title: Subject 101334 LTA

value: Male


title: Subject 101739 NT


title: Subject 101746 LPS


title: Subject 101739 LPS


title: MWMSmmWTNM2: Normoxia WT #2

city: LA

first: Madhuri

last: Wadehra

address: 675 Charles Young Dr. South/ 4726 MRL

department: Pathology and Lab Medicine

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

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: age

value: Wild Type

value: Retina/coroid


title: MWMSmmWTNM4: Normoxia WT #4