title: AD-04-3

city: Atlanta

first: Janise

middle: Nichole

last: Kuehner

state: GA

address: 615 Michael St NE

institute: Emory University

data_processing:
Library strategy: 5hmC Capture
RNA-seq reads were aligned to hg19 using tophat v1.3.3 and differential RPKM expression values were extracted using cuffdiff v2.2.1
5hmC-IP-seq paired-end reads were mapped to the hg19 reference genome using bowtie2 (v2.2.6) (Langmead et al., 2009) with the parameters --no-discordant --no-mixed to prevent discordant alignments and alignments for the individual mates. Flags -F 4 and -q 10 were used in samtools (v 1.9) (Li et al., 2009) to exclude unmapped reads and reads with Mapping Quality (MAPQ) values less than 10 for each replicate in all stages.
Peaks were called using MACS version 1v 2.1.0 with the following setting: macsBW 200, macs_qvalue 0.01, peaks narrow.
Peak regions were annotated to their corresponding nearby genes using HOMER v4.9 with an additional flag -annStats to also annotate genomic features to these peak regions.
Genome_build: hg19

source_name: Organoid

extract_protocol:
The human iPSC lines (provided by Dr. Chadwick Hales’ laboratory at Emory University) were cultured on irradiated MEFs in human iPSC medium consisting of D-MEM/F12 (Invitrogen), 20% Knockout Serum Replacement (KSR, Invitrogen), 1X Glutamax (Invitrogen), 1X MEM Non-essential Amino Acids (NEAA, Invitrogen), 100 µM β- Mercaptoenthanol (Invitrogen), and 10 ng/ml human basic FGF (bFGF, PeproTech) as described (Wen et al., 2014b). Forebrain-specific organoids were generated as previously described(Qian et al., 2016). Briefly, human iPSC colonies were detached from the feeder layer with 1 mg/ml collagenase treatment for 1 hour and suspended in embryonic body (EB) medium, consisting of FGF-2-free iPSC medium supplemented with 2 µM Dorsomorphin and 2 µM A-83 in non-treated polystyrene plates for 4 days with a daily medium change. On days 5-6, half of the medium was replaced with induction medium consisting of DMEM/F12, 1X N2 Supplement (Invitrogen), 10 μg/ml Heparin (Sigma), 1X Penicillin/Streptomycin, 1X Non-essential Amino Acids, 1X Glutamax, 4 ng/ml WNT-3A (R&D Systems), 1 μM CHIR99021 (Tocris), and 1 μM SB-431542 (Tocris). On day 7, organoids were embedded in Matrigel (BD Biosciences) and continued to grow in induction medium for 6 more days. On day 14, embedded organoids were mechanically dissociated from Matrigel by pipetting up and down onto the plate with a 5ml pipette tip. Typically, 10 - 20 organoids were transferred to each well of a 12-well spinning bioreactor (SpinΩ) containing differentiation medium, consisting of DMEM/F12, 1X N2 and B27 Supplements (Invitrogen), 1X Penicillin/Streptomycin, 100 µM β- Mercaptoenthanol (Invitrogen), 1X MEM NEAA, 2.5 μg/ml Insulin (Sigma). At day 71, differentiation medium was exchanged with maturation medium, consisting of Neurobasal (Gibco), 1X B27 Supplement, 1X Penicillin/Streptomycin, 1X β-Mercaptoenthanol, 0.2 mM Ascorbic Acid, 20 ng/ml BDNF (Peprotech), 20 ng/ml GDNF (Peprotech), 1 ng/ml TFGβ (Peprotech), and 0.5 mM cAMP (Sigma). All media were changed every other day.
5hmC Capture: Five ug of genomic DNA was sonicated to 300-400 base pair (bp) using a Covaris focused ultrasonicator. 5hmC capture was performed according to the method described in (Song et al., 2011).First, a glucosyltransfer reaction was performed using 2.5µl of T4 phage ß-glucosyltransferase enzyme (10,000U/ml; New England BioLabs) and 100µM UDP-6-N3-glucose (Jena Biosciences) and incubated at 37 degrees C for 2 hours. After purification with AMPure XP beads (Beckman Coulter), the glucosylated 5hmC-containing DNA fragments were biotinylated with 150µM disulfide biotin linker (Click Chemistry Tools) at 37 degrees C for 2 hours. After purification with AMPure XP beads, the biotinylated 5hmc-containing DNA fragments were pulled down using Dynabeads MyOne Streptavidin C1 beads (ThermoFisher Scientific) and were washed three times with Binding/Washing buffer (20mM Tris pH 7.5, 1mM EDTA, 2M NaCl, 0.01% Tween-20). The 5hmC-containing DNA fragments were then removed from the beads with fresh 100mM dithiothreitol for 2 hours with rotation at room temperature. After final purification with AMPureXP beads, the 5hmC-enriched DNA fragments were eluted in nuclease-free water and quantified by Qubit. Library Preparation adn High-throughput Sequencing: Enriched DNA from 5hmC capture were subjected to library construction using the NEBNext Ultra II DNA Library Prep kit for Illumina (New England BioLabs) according to manufacturer’s protocol. Briefly, 1-7ng of 5hmC-enriched DNA or un-enriched genomic DNA was utilized for each library construction. An Agilent 2100 Bioanalyzer was used to confirm purity and fragmentation size of the final libraries. RNAseq libraries were generated using TruSeq RNA Sample Prep V2 kit (New England BioLabs) with 1g of RNA to first obtain poly-A-enriched RNA and synthesize cDNA, and then the same library construction protocol was followed using 5ng of cDNA. Libraries were sequenced pair-end (150bp) on an Illumina HiSeq platform.

tag: disease state

value: Alzheimer's Disease

value: hiPSC-derived organoid

tag: seq type


title: Granulosa_ZT0_1

status: Public on Apr 27 2021

type: SRA

city: Chengdu

first: Liang

last: Li

state: Sichuan

address: Wenjiangqu huiminlu211hao sichuan nongyedaxue

country: China

institute: Sichuan agricultural university

library_source: transcriptomic

data_processing:
Clean reads were mapped against chicken reference genome using STAR v2.6.0c and merged with Cuffmerge (Cufflinks v2.2.1).
Assemblyline and TACO to filter transcripts and merge all expressed transcripts
Remove transcripts of coding gene while comparing to annotated genome by Cuffcompare
The prediction and calculation of the coding potential of the remaining transcripts by CPC2
Comparing with the Pfam-31A database and trimming out transcripts with a p-value < 10-4 by Hmmscan
Genome_build: STAR v2.6.0c
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

molecule: total RNA

organism: Gallus gallus

source_name: Granulosa cells

extract_protocol:
Granulosa cells were collected and put into liquid nitrogen immediately from preovulatory follicles (F1). For total RNA sequencing, about 4 μg total RNA was isolated from the granulosa cells (a total of 9 samples) by using TRIzol reagent (Invitrogen, USA) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Chicken follicle

tag: cell type

value: Granulosa cells

tag: time


title: Flowthrough, high density, stress, fish 3

type: RNA

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Arrays were scanned with GenePix 4100 microarray scanner

data_processing: Images were processed using GenePix Pro 6.0. After removal of flagged spots, lowess normalization was performed

organism: Salmo salar

source_name: Skin

label_protocol: Amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Salmon was fed with commercial feed

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen)

value: Skin

tag: culture method

value: flowthrough

tag: condition

value: crowding stress

tag: density

value: high


title: AD-04-2

department: Human Genetics

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens


title: Sample14.Killer whale.202897220080_R03C01

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

institute: University of California, Los Angeles

description: genomic DNA methylation from tissue=Muscle species=Killer whale

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

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

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

organism: Orcinus orca

source_name: Muscle

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from tissues

extract_protocol: genomic DNA was extracted

treatment_protocol: Standard Illumina Protocol

tag: basename

tag: canbeusedforagingstudies

value: yes

tag: Sex

value: Female

value: Muscle


title: Sample13.Killer whale.202897220080_R02C01

description: genomic DNA methylation from tissue=Heart species=Killer whale

source_name: Heart

value: Male

value: Heart


title: Sample12.Killer whale.202897220080_R01C01

description: genomic DNA methylation from tissue=Blubber species=Killer whale

source_name: Blubber

value: Blubber


title: HCC38-siCIP2A#3

city: Turku

first: Jukka

last: Westermarck

address: Tykistokatu 6

department: Turku Bioscience Centre

country: Finland

institute: University of Turku

data_processing:
The base calling was done using bcl2fastq (v. 2.17)
Read alignment was done using Star (v. 2.5.4b)
Genewise read counts were calculated using subreads package (v. 1.5.1)
Genome_build: human genome hg38
Supplementary_files_format_and_content: Processed data file GeneCounts.csv is tab delimited text file containing the genewise read counts for each sample.

molecule: polyA RNA

source_name: Basal like breast cancer cell line

growth_protocol: Cells were cultured using RPMI media supplemented with 10% FBS, 1% Glutamine and 1% antibiotics (Penicillin/Streptomycin)

extract_protocol:
RNA was isolated using NucleoSpin RNA Mini kit for RNA purification (Macherey-Nagel)
Library preparation was done according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide

treatment_protocol: CIP2A was silenced using 3 unique CIP2A siRNAs. Oligofectamine was used as the transfection reagent and standard manufacturer's protocols were followed. Non transfection control (Mock) and two nontargeting control siRNAs were used as controls.

tag: lineage

value: Breast ductal adenocarcinoma

value: Triple negative breast cancer (Basal-like)

tag: cell line

tag: treatment

value: Transfected with CIP2A targeted siRNA sequence siCIP2A#3


title: Sample10.Killer whale.202897220022_R05C02

description: genomic DNA methylation from tissue=Lung species=Killer whale

source_name: Lung

value: Lung


title: AD-04-1

value: Alzheimer's Disease

value: hiPSC-derived organoid


title: Sample11.Killer whale.202897220022_R06C02

description: genomic DNA methylation from tissue=LymphNode species=Killer whale

source_name: LymphNode

value: LymphNode


title: HAP1_PDCL3P4_NULL1_2

city: Wooloongabba

first: Seth

last: Cheetham

state: QLD

address: Level 4, 37 Kent St

country: Australia

institute: Mater Research Institute-University of Queensland

description:
Null1_2
rnaseq_counts.txt

data_processing:
STAR 2.7.3a was used to align RNA-seq reads to GRCh38.3.
htseq-count 0.11.2 was used to quantify read counts against Ensembl genes GRCh38.8.
Genome_build: GRCh38.3
Supplementary_files_format_and_content: rnaseq_counts.txt: Tab-delimited text file containing counts for each replicate.

source_name: HAP1 cells

growth_protocol: Low passage (≤ p10) HAP1 cells (Horizon) were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM) (Gibco cat # 12440-053) supplemented with 10% Fetal Bovine Serum (Sigma Aldrich cat # F2442) and 1% Penicillin / Streptomycin (Gibco cat # 15140-122) and grown in a tissue culture incubator (37ºC, 5% CO2).

extract_protocol:
RNA was extracted from validated clones and wild-type HAP1 cells using the RNeasy Mini Kit (Qiagen cat # 74104) following the manufacturer’s instructions and then treated with TURBO DNA-free™ Kit (Life Technologies cat # AM1907) to remove genomic DNA.
Paired-end 150bp.

tag: genotype/variation

value: PDCL3P4 null


title: HAP1_PDCL3P4_NULL2_1

description:
Null2_1
rnaseq_counts.txt


title: AD-03-3


title: HAP1_PDCL3P4_NULL2_4

description:
Null2_4
rnaseq_counts.txt


title: HAP1_PDCL3P4_NULL1_1

description:
Null1_1
rnaseq_counts.txt


title: HAP1_wildtype_4

description:
WT_4
rnaseq_counts.txt

value: wildtype


title: Sample9.Killer whale.202897220022_R04C02

description: genomic DNA methylation from tissue=Pancreas species=Killer whale

source_name: Pancreas

value: Pancreas


title: HCC38-siCIP2A#2

value: Transfected with CIP2A targeted siRNA sequence siCIP2A#2


title: Sample8.Killer whale.202897220022_R03C02

description: genomic DNA methylation from tissue=Skin species=Killer whale

value: yes

value: Skin


title: AD-03-2


title: HCC38-SCR#3

value: Transfected with non targeting control sequence - SCR3


title: AD-01-3


title: HCC38-SCR#2

value: Transfected with non targeting control sequence - SCR2


title: HAP1_wildtype_3

description:
WT_3
rnaseq_counts.txt


title: AD-03-1


title: HCC38-Mock

value: Only transfection reagent (Mock)


title: HCC38-siCIP2A#1

value: Transfected with CIP2A targeted siRNA sequence siCIP2A#1


title: HAP1_wildtype_1

description:
WT_1
rnaseq_counts.txt


title: KO_Polysome_associated_Bio_Rep2

city: HONG KONG

first: Jie

last: Yuan

state: HONG KONG

address: Prince of Wales Hospital

department: Orthopaedics and Traumatology

institute: The Chinese University of Hong Kong

description: Polysome-associated RNA

data_processing:
Library strategy: Polysome profiling
Adaptor sequence trimming, quality filtering (i.e. quality<38 and length<22) and duplication removal were first conducted.
Remaining reads were aligned to the mouse genome mm9 using Tophat2 (v2.0.13) software with the following parameters: --no-coverage-search; --mate-std-dev 60.
Expression levels were quantified using Cufflinks with default parameters and annotated gene model (refGene for mm9) from UCSC.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.fpkm_tracking: Tab-delimited files from Cufflinks containing FPKM values.

organism: Mus musculus

source_name: C2C12 myoblasts

growth_protocol: C2C12 myoblasts were grown in growth medium containing DMEM, 10% FBS and 1% pen/strep.

extract_protocol:
Total cytoplasmic RNA or RNA bound by more than 4 ribosomes were extracted using TRIzol LS reagent (Invitogen) following the manufacturer's instructions and then subjected to poly(A) selection by using mRNA purification beads (Ambion, 61006).
RNA libraries were prepared by using NEBNext® Ultra™ II RNA Library Preparation Kit (NEB, E7770S) and barcoded libraries were pooled at equal concentration and sequenced on the HiSeq1500 platform.

treatment_protocol: C2C12 myoblasts were treated by 100 μg/ml of cycloheximide in culture medium and incubated at 37℃ for 10 min.

tag: developmental stage

value: GM 48 hours

tag: genotype

value: Dhx36 KO


title: KO_Polysome_associated_Bio_Rep1

description: Polysome-associated RNA


title: Sample5.Killer whale.202897220022_R05C01

description: genomic DNA methylation from tissue=Thyroid species=Killer whale

source_name: Thyroid

value: Male

value: Thyroid


title: HAP1_controlclone_2

description:
Control_2
rnaseq_counts.txt

value: control


title: Sample6.Killer whale.202897220022_R01C02


title: Sample3.Killer whale.202897220022_R03C01

description: genomic DNA methylation from tissue=Kidney species=Killer whale

source_name: Kidney

value: Kidney


title: AD-01-2

tag: disease state

value: Alzheimer's Disease

value: hiPSC-derived organoid


title: HAP1_controlclone_3

description:
Control_3
rnaseq_counts.txt


title: Sample4.Killer whale.202897220022_R04C01

description: genomic DNA methylation from tissue=Spleen species=Killer whale

source_name: Spleen

value: Spleen


title: AD-01-1

tag: seq type


title: C-21-3

value: Healthy/ Control


title: Dhx36_KO_Total_mRNA

description: Total cytoplasmic RNA


title: HAP1_controlclone_1

description:
Control_1
rnaseq_counts.txt


title: WT_Polysome_associated_Bio_Rep2

description: Polysome-associated RNA

value: Wild Type


title: C-21-1


title: HypIL-6 stimulation_24h_biorep3

city: Dundee

first: Stephan

last: Wilmes

address: Dow Street

department: School of Life Sciences

country: United Kingdom

institute: University of Dundee

data_processing:
Primary data analysis for quality control, mapping to reference genome and quantification was conducted by Novogene as follows. Quality control: Raw data (raw reads) of FASTQ format were firstly processed through in-house scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Genome_build: Mapping to reference genome: Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome using HISAT2 software. HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. Quantification: HTSeq was used to count the read numbers mapped of each gene, including known and novel genes. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, (Reads Per Kilobase of exon model per Million mapped reads), 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.
Supplementary_files_format_and_content: ENSG gene ID, stimulated value (RKPM), unstimulated value (RKPM), log2fold change(stimulated/unstimulated), p-value, p adjust, significance (yes/no), gene_name, gene_description

source_name: Human, Th-1 cells

extract_protocol:
Rneasy Mini Kit, Quiagen Cat#74104
Sequencing libraries were generated using NEBNext® UltraTM RNALibrary Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First StrandSynthesis 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, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp inlength, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. 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. The platform used was Novoseq6000 (GPL27804)

treatment_protocol: CD4 T cells isolated by positive selection from human buffy coats. Cells activated for three days with anti-CD3/antiCD28, IL-2, IL-12 and anti-IL-4 and expanded for a further five days with IL-2, IL-12 and anti-IL-4.

value: Th-1 cells

tag: stimulation

value: stimulated with HypIL-6 (10nM) for 24h


title: Sample1.Killer whale.202897220022_R01C01

value: yes

tag: tissue

value: Muscle


title: C-09-3

tag: cell type


title: Sample2.Killer whale.202897220022_R02C01

description: genomic DNA methylation from tissue=Testis species=Killer whale

source_name: Testis

value: Testis


title: HypIL-6 stimulation_6h_biorep3

value: stimulated with HypIL-6 (10nM) for 6h


title: Sample7.Killer whale.202897220022_R02C02

value: Skin


title: HAP1_wildtype_2

description:
WT_2
rnaseq_counts.txt

value: wildtype


title: C-09-1

source_name: Organoid


title: WT_Polysome_associated_Bio_Rep1

description: Polysome-associated RNA

value: GM 48 hours


title: C-21-2


title: WT_Total_mRNA

description: Total cytoplasmic RNA


title: HypIL-6 stimulation_1h_biorep3

value: stimulated with HypIL-6 (10nM) for 1h


title: Mu1_H_3

city: Portland

first: Alexey

last: Danilov

state: Oregon

address: 3681 SW Sam Jackson Rd

department: Knight Cancer Institute

institute: Oregon Health and Science University

description: Patient derived xenograft implanted into SCID mice treated with CG806, replicate 3

data_processing:
Trimming of Fastq files was performed with Trimmomatic
QC was performed with FASTQC
mapping to GRCh38 was performed with STAR
DGE was performed using edgeR filtering for genes that were expressed in at least one sample
Genome_build: GRCh38
Supplementary_files_format_and_content: normalized counts were calculated using edgeR

source_name: Patient Derived Xenograft

growth_protocol: All animal studies were carried out in accordance with institutional guidelines. Five-week-old nonobese diabetic/severe combined immunodeficiency/γCnull (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ [NSG]) mice (The Jackson Laboratory) received 25 mg/kg busulfan via intraperitoneal injection. The following day, MCL cells (3x106 in 200 µL PBS) were inoculated via tail vein injection. aggressive patient derived xenograft (PDX) model were used: MCL96069 (BIRC3L548fs; further referred to as MCL-A) Circulating MCL cells are detected within 4 weeks (MCL-A) and 2 weeks of inoculation (MCL-B). If left untreated, mice succumb to disease within 9-10 and 6 weeks, respectively.   Mice were bled weekly; red cells were lysed using ACK lysis buffer (Life Technologies), and the remaining cells were washed and stained with 0.5 µL LIVE/DEAD Fixable Aqua (Invitrogen), 20 µL CD19 (Becton Dickinson), 2 µL CD5, and 10 µL CD45 (Miltenyi Biotech) in 150 µL PBS to detect circulating MCL cells.

extract_protocol:
Total RNA was isolated using the E.Z.N.A. HP Total RNA Isolation Kit (Omega Bio-tek). RNA concentration was determined using the Qubit RNA HS Assay Kit (Invitrogen). 2500ng of Total RNA (100 ng/µL) per sample was submitted to Novogene Corporation. RNA integrity was determined using the 2100 Bioanalyzer Instrument (Agilent).
Library preparation and sequencing was carried out by Novogene Corporation. Samples were sequenced 12 per lane on a NovaSeq 6000 (Illumina).

treatment_protocol: Upon detection of  circulating cells, mice were separated into groups and received treatment with CG-806 at either 30.8 or 308 mg/kg diluted in sodium lauryl sulfate (SLS) 8 mg/kg, or vehicle control (SLS 8 mg/kg), daily via oral gavage

value: MCL Xenograft


title: C-03-2


title: C-03-3


title: Mu1_H_2

description: Patient derived xenograft implanted into SCID mice treated with CG806, replicate 2


title: 4C-Seq MUTZ-3 olaparib

city: Heidelberg

first: Stefan

last: Gröschel

address: Im Neuenheimer Feld 581

country: Germany

institute: DKFZ German Cancer Research Center

data_processing:
demulitplexing was done using HTSeq version 0.9.1 with mismatches = 0
trimming, in our case with custom made barcodes 4 bp, the restriction enzyme site was kept for alignment, was performed using the R package FourCSeq
bwa version 0.7.17 was used for alignment
running mean smoothed tracks with a window size of 21 were generated using the R package FourCSeq
finally bigWig files were generated from these smoothed tracks using the R package FourCSeq
Genome_build: hg19
Supplementary_files_format_and_content: running mean smoothed bigWig files generated from alignment files (.bam)

source_name: myeloid leukemia

growth_protocol: MUTZ-3 cells were grown in MEMalpha with 20% FBS, 20% conditioned medium of 5637 cells, 10 ng/mL GM-CSF and 1x Pen/Strep

extract_protocol:
Sample preparation was carried out as described previously (van de Werken et al., 2012). DpnII was used as first cutter and Csp6I as second cutter.
PCR amplification was done using custom barcoded primers specific for the EVI1 promoter region.

treatment_protocol: Cells were treated with DMSO, 10 µM olaparib oder 1 µM talazoparib for 24 h

tag: view point

value: EVI1 promoter

tag: primers

value: 10 µM olaparib


title: IL27 stimulation_24h_biorep3

value: stimulated with IL-27 (2nM) for 24h


title: 4C-Seq MUTZ-3 talazoparib

value: 1 µM talazoparib


title: 4C-Seq MUTZ-3 DMSO

value: DMSO


title: IL27 stimulation_6h_biorep3

value: stimulated with IL-27 (2nM) for 6h


title: Mu1_H_1

description: Patient derived xenograft implanted into SCID mice treated with CG806, replicate 1


title: Mu1_S_3

description: Patient derived xenograft implanted into SCID mice treated with control, replicate 3

value: SLS 8mg/kg (control)


title: HypIL-6 stimulation_24h_biorep2

value: Th-1 cells

value: stimulated with HypIL-6 (10nM) for 24h


title: IL27 stimulation_1h_biorep3

value: stimulated with IL-27 (2nM) for 1h


title: unstim_control_biorep3

value: unstimulated


title: HypIL-6 stimulation_6h_biorep2

value: stimulated with HypIL-6 (10nM) for 6h


title: MOLM-1 input

data_processing:
quality check was performed using FastQC version 0.11
trimming of adaptor sequences and quality filtering (minimum Phred quality score of 30 was used) was done by using trimgalore version 0.4
Bowtie 2 version 2.3 was used for single end read alignment
background correction was done by using an input sample and the tool samtools version 1.9
sorting, indexing and converting to bam was done by using samtools version 1.9
bigWig files were generated using deeptools version 3.0 with a binsize of 40
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files generated from sequencing alignment files (.bam)
Supplementary_files_format_and_content: adaptor sequence cleanded and for sequencing read quality filtered fastq files as zip format

growth_protocol: MOLM-1 cells were grown in RPMI 1640 with 20% FBS and 1x Pen/Strep

extract_protocol:
Cells were fixed, chromatin was extracted and sheard by sonication, and CEBPA-DNA complexes were isolated with a specific antibody.
Library preparation was performed using the NEBNext system for Illumina (NEB)

tag: chip antibody


title: Cebpd_sgRNA2_IFNgamma_Rep1

city: Boston

first: Xiaoqing

last: Wang

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR v2.4.0 with parameters --outFilterMultimapNmax 1 --outFilterMatchNmin 35
Primary aligned reads were counted using htseq-count -m union -s no -t exon
The DESeq2 R package version 1.10 was used for differential gene expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: raw_count.csv  (Matrix table with raw gene counts for every gene and every sample)

source_name: 4T1 mouse breast cancer cells

extract_protocol:
Cancer cell were collected, flash frozen on dry ice, and RNA was harvested using QIAGEN DAN/RNA mini kit (Cat#80204). Illumina TruSeq RNA Library Prep Kit (Cat#RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: IFNgamma, 20ng/ml, 24 hours

tag: strain

value: BALB/c

value: Cebpd knockout

value: IFNgamma


title: CJ_CG84-21_CoIP_Cas9-3xF_R3

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

institute: University of Wuerzburg

description: eluted after co-immunoprecipitation with anti-FLAG antibody.

data_processing:
Base calling with Illumina NextSeq RTA v2.4.11
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) version 1.16 (cutadapt parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Alignment of reads longer than 11 nt to reference genome using segemehl version 0.2.0 with minimum accuracy 95% (parameters for reademption align: -l 12 -a 95 ) (READemption 0.4.5, Förstner et al., 2014)
Coverage calculation via reademption coverage based on all aligned reads (full-length); Normalization: coverage-tnoar_mil_normalized (counts divided by total number of aligned reads and multiplied by 1,000,000) (READemption 0.4.5, Förstner et al., 2014)
Genome_build: Campylobacter jejuni CG84-21 (Assembly acc.: GCF_000171795.2, Sequence ID: NZ_CP005388.1)
Supplementary_files_format_and_content: wiggle files containing positional read coverage values

organism: Campylobacter jejuni subsp. jejuni CG8421

source_name: Campylobacter jejuni CG84-21 cells

growth_protocol: Bacterial cells grown to exponential phase in Brucella Broth media at 37° C, 140 rpm agitation in microaerobic environment (10% CO2, 5% O2, 85% N2) of HERAcell 150i incubator.

extract_protocol:
Cas9-bound RNAs (eluted RNA) were extracted from beads harboring anti-FLAG immunoprecipitated proteins. For both, untagged and Cas9-3xFLAG co-immunoprecipitated samples, RNA was purified from the bound complexes using Phenol:Chloroform:Isoamylalcohol extraction. Eluted RNA was precipitated overnight at -20°C.
Eluted RNA from co-immunoprecipitation experiments was used as such. At first, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The first-strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/µl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis.
RIP-seq library prepared using adapter ligation protocol.

treatment_protocol: No treatment applied during growth, bacterial lysates used for coIP.

tag: replicate

value: replicate 3

tag: antibody for coip

value: ANTI-FLAG M2 (Sigma, cat. #F 1804)

tag: molecule subtype

value: RNA bound to Cas9-3xFLAG


title: IL27 stimulation_24h_biorep2


title: Cebpd_sgRNA2_IFNgamma_Rep2

tag: cell line


title: HypIL-6 stimulation_1h_biorep2

value: stimulated with HypIL-6 (10nM) for 1h


title: paAD84.3

data_processing:
RNA-seq reads were aligned to hg19 using tophat v1.3.3 and differential RPKM expression values were extracted using cuffdiff v2.2.1
5hmC-IP-seq paired-end reads were mapped to the hg19 reference genome using bowtie2 (v2.2.6) (Langmead et al., 2009) with the parameters --no-discordant --no-mixed to prevent discordant alignments and alignments for the individual mates. Flags -F 4 and -q 10 were used in samtools (v 1.9) (Li et al., 2009) to exclude unmapped reads and reads with Mapping Quality (MAPQ) values less than 10 for each replicate in all stages.
Peaks were called using MACS version 1v 2.1.0 with the following setting: macsBW 200, macs_qvalue 0.01, peaks narrow.
Peak regions were annotated to their corresponding nearby genes using HOMER v4.9 with an additional flag -annStats to also annotate genomic features to these peak regions.

value: hiPSC-derived organoid

value: Alzheimer's Disease


title: paAD84.2


title: Cebpd_sgRNA1_IFNgamma_Rep2

tag: treatment


title: CJ_CG84-21_CoIP_WT_R3

value: RNA bound non-specifically


title: Cebpd_sgRNA1_IFNgamma_Rep1


title: Mu1_S_2

description: Patient derived xenograft implanted into SCID mice treated with control, replicate 2

value: MCL Xenograft


title: IL27 stimulation_1h_biorep2


title: IL27 stimulation_6h_biorep2

value: stimulated with IL-27 (2nM) for 6h


title: CJ_CG84-21_CoIP_WT_R2

value: replicate 2


title: Mu1_S_1

description: Patient derived xenograft implanted into SCID mice treated with control, replicate 1

value: SLS 8mg/kg (control)


title: unstim_control_biorep2

value: Th-1 cells


title: Rosa26_sgRNA_IFNgamma_Rep2

value: control


title: paAD84.1


title: Rosa26_sgRNA_IFNgamma_Rep1


title: MOLM-1 CEBPA ChIP-Seq

value: C/EBPα (D56F10); Cell Signaling


title: paD112.2

value: Healthy/ Control


title: paD112.1


title: CJ_CG84-21_CoIP_Cas9-3xF_R1

value: replicate 1


title: paD112.3


title: Cebpd_sgRNA2_Rep1

value: BALB/c

value: Cebpd knockout

value: vehicle


title: paD84.3


title: Cebpd_sgRNA2_Rep2


title: HypIL-6 stimulation_1h_biorep1


title: HypIL-6 stimulation_6h_biorep1

value: stimulated with HypIL-6 (10nM) for 6h


title: paD84.2


title: Jul_MII_6

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

data_processing:
IMultiplexed sequencing reads that passed filters were trimmed to remove low quality reads and adaptors. The quality of reads after filtering was examined using fastQC, followed by alignment to the bovine genome UMD3.1.1 by STAR (2.5.3a) with default parameters. Individual mapped reads were quantified to calculate FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) values using RefSeq genes as reference. Differential gene expression analysis was performed using Partek Flow GSA algorithm with default parameters. The genes are deemed differentially expressed if a false discovery rate (FDR) of < 0.05. DAVID (https://david.ncifcrf.gov) and IPA (Ingenuity Pathway Analysis) were used to reveal the Gene Ontology (GO) and pathways, respectively.
Genome_build: UMD3.1.1
Supplementary_files_format_and_content: normalize_counts

organism: Bos taurus

source_name: oocytes

extract_protocol:
The RNA-seq libraries were generated from individually cells using Smart-seq2 with minor modification. Briefly, individually cells were lysed and mRNA was captured and amplified by using Smart-seq2 v4 kit (Clontech). After pre-amplification and AMPure XP beads purification, amplified RNAs were quality checked using Agilent High Sensitivity D5000 kit (Agilent Technologies).
High quality of amplified RNAs were subject to library preparation using Nextera XT DNA Library Preparation Kit (Illumina) and multiplexed by Nextera XT Indexes (Illumina). The quality and quantity of sequencing libraries were determined using Qubit 3.0 assay (Life Technologies) and Agilent High Sensitivity kit at Tapestation 4200 system (Agilent), respectively. All sequencing libraries were pooled and then sequenced on the Illumina NextSeq 500 with 100 bp pair-end reads.

value: MII oocytes

tag: collection time

value: July


title: Cebpd_sgRNA1_Rep2


title: paD84.1

value: hiPSC-derived organoid


title: IL27 stimulation_24h_biorep1

value: stimulated with IL-27 (2nM) for 24h


title: paD56.3


title: Jul_MII_4


title: Rosa26_sgRNA_Rep1


title: CJ_CG84-21_CoIP_WT_R1

value: ANTI-FLAG M2 (Sigma, cat. #F 1804)

value: RNA bound non-specifically


title: Rosa26_sgRNA_Rep2


title: unstim_control_biorep1

value: unstimulated


title: paD56.2


title: Jul_MII_3


title: Cebpd_sgRNA1_Rep1


title: Jul_MII_2


title: paEB.3

source_name: Embryoid body

value: hiPSC-derived embryoid body


title: IL27 stimulation_1h_biorep1

value: Th-1 cells

value: stimulated with IL-27 (2nM) for 1h


title: Jul_MII_1


title: paD56.1


title: N1AcSpd CD34+ rep.4

city: Koln

first: Jorge

last: Boucas

address: Joseph-Stelzmann-Str. 9b

department: Bioinformatics

institute: Max Planck Institute for Biology of Ageing

data_processing:
Quality check: FastQC 0.11.7
raw reads were demultiplexed and the UMI-tag was added to each read name using flexbar 3.5.0. flexbar -r R1.fastq.gz -p R2.fastq.gz -b barcodes.fa --umi-tags -n 4 -t sample -u 5 -q TAIL -qt 25 -qf i1.8 -z GZ
only the second end of read-pairs were pseudo mapped to mm10 using kallisto 0.45.0 kallisto quant -t 18 -i kallisto_index fr-secondstrand --genomebam -g mm10.gtf -c mm10.chromosomes -o sample -b 100 --single -l 75-s 10 sample_R2.fastq.gz
bedtools intersect together with some bash re-formatting was used assign umi-tags to genes bedtools intersect -a pseudoalignments.bam -b ${ind}gene.model.bed -bed -wo > tmp.bed sed 's/_/\t/' tmp.bed |awk '{print $umi_tag "\t" $gene_name}' |sort -u > gene_reads.bed
An R script was used to count unique umi-tags per gene
The R package DESeq2 was used to calculate the differential gene expression
Genome_build: mm10
Supplementary_files_format_and_content: tab-separated values or excel table of gene expression

source_name: HFSC organoid culture

growth_protocol: 3D-3C organoid cultures were cultured for 2 weeks and sorted to obtain alpha6+CD34- and alpha6+CD34+ cells

extract_protocol:
Sorted cells were frozen in QIAzol and frozen in liquid nitrogen. Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to manufacturer's instruction.
cDNA synthesis was performed using Maxima H Minus reverse transcriptase (ThermoFisher). During reverse transcription, unique barcodes were attached to each sample. cDNA of all samples was pooled and purified using Ampure XP beads (Beckman Coulter). Eluted cDNA was subjected to Exonuclease I (NEB) treatment. cDNA was PCR-amplified and tagmented using the Illumina tagmentation mix. Nextrea Index PCR primers were attached to the libraries during PCR amplification. cDNA was purified and library concentration and size were validated.

treatment_protocol: w/ or w/o 72h N1-acetylspermidine

value: hair follicle stem cell (HFSC) organoid

tag: mouse

tag: cell markers


title: May_MII_6

value: May


title: paEB.2

tag: disease state

value: Healthy/ Control


title: N1AcSpd CD34- rep.4


title: paEB.1


title: WT CD34+ rep.4

value: control


title: Jul_MII_5


title: IL27 stimulation_6h_biorep1

value: stimulated with IL-27 (2nM) for 6h


title: May_MII_4


title: N1AcSpd CD34+ rep.3


title: May_MII_3


title: N1AcSpd CD34- rep.3


title: D112_3

data_processing:
Library strategy: 5hmC Capture
RNA-seq reads were aligned to hg19 using tophat v1.3.3 and differential RPKM expression values were extracted using cuffdiff v2.2.1
5hmC-IP-seq paired-end reads were mapped to the hg19 reference genome using bowtie2 (v2.2.6) (Langmead et al., 2009) with the parameters --no-discordant --no-mixed to prevent discordant alignments and alignments for the individual mates. Flags -F 4 and -q 10 were used in samtools (v 1.9) (Li et al., 2009) to exclude unmapped reads and reads with Mapping Quality (MAPQ) values less than 10 for each replicate in all stages.
Peaks were called using MACS version 1v 2.1.0 with the following setting: macsBW 200, macs_qvalue 0.01, peaks narrow.
Peak regions were annotated to their corresponding nearby genes using HOMER v4.9 with an additional flag -annStats to also annotate genomic features to these peak regions.


title: May_MII_2


title: D112.3


title: D84Input


title: iMAC tolerance RAJ6744A15

city: Melbourne

first: Jarny

last: Choi

state: Victoria

address: The University of Melbourne

department: Anatomy and Neuroscience

institute: Centre for Stem Cell Systems

description: iMAC tolerance

data_processing:
Individual fastq files were aligned to the reference genome (GRCh38 assembly and ENSEMBL version 91) with Rsubread 1.20.6 with default settings in R version 3.2.2.
Reads were summarised from bam files to counts with the featureCounts library within Rsubread 1.20.6.
Genome_build: HG38
Supplementary_files_format_and_content: raw counts and abundance measures as tab delimited text files

source_name: macrophage

growth_protocol: Monocytes/pluripotent stem cell-derived progenitor cells were cultured in tissue-culture treated 6 well plates. Cells were cultured in RPMI-1640 medium containing L-Glutamine (Life Technologies) with 10% Fetal Bovine Serum and 100ng/ml recombinant Human M-CSF (R&D Systems; 216-MC) for 5 days. Media changes were carried out on day 4.

extract_protocol:
Total RNA was isolated using the RNeasyⓇ Plus Mini Kit (Qiagen) according to manufacturer’s instructions.
Illumina Novaseq

treatment_protocol: On day 4 of differentiation, one well containing PBMC- or hPSC-Macrophages were stimulated with 10ng/ml LPS for 18 hours. After 18 hours, media was aspirated from all wells and were washed twice using PBS (Ca2+Mg2+ free). Fresh media was added into all wells and cells were left for 2 hours. After 2 hours, two wells were stimulated or re-stimulated with 10ng/ml LPS for acute and tolerance response, respectively, for 2 hours.

value: human induced pluripotent stem cell-derived macrophage

value: 10ng/mL LPS for 18 hours and restimulated with 10ng/mL LPS for 2 hours


title: WT CD34- rep.3


title: May_MII_5

value: MII oocytes


title: May_MII_1


title: D112.2


title: D112.1


title: Jul_GV_5

value: GV oocytes

value: July


title: WT CD34- rep.4


title: iMAC tolerance RAJ6744A12

description: iMAC tolerance


title: D84_3

value: hiPSC-derived organoid


title: iMAC acute response RAJ6744A14

description: iMAC acute response

value: 10ng/mL LPS for 2 hours


title: N1AcSpd CD34+ rep.2


title: iMAC control RAJ6744A13

description: iMAC control

value: control untreated


title: iMAC acute response RAJ6744A11

description: iMAC acute response


title: N1AcSpd CD34- rep.2


title: HypIL-6 stimulation_24h_biorep1

value: stimulated with HypIL-6 (10nM) for 24h


title: WT CD34+ rep.2


title: D84.3


title: WT CD34+ rep.3


title: Jul_GV_3


title: Jul_GV_6


title: iMAC control RAJ6744A10

description: iMAC control


title: D84.2


title: WT CD34- rep.2


title: Jul_GV_2


title: MDM acute response RAJ6744A8

description: MDM acute response

value: peripheral blood monocyte-derived macrophage


title: MDM control RAJ6744A7

description: MDM control


title: N1AcSpd CD34+ rep.1


title: Jul_GV_1


title: N1AcSpd CD34- rep.1


title: D84_2


title: MDM tolerance RAJ6744A9

description: MDM tolerance


title: MDM acute response RAJ6744A5

description: MDM acute response


title: D84.1


title: May_GV_5


title: WT CD34+ rep.1


title: May_GV_6


title: MDM control RAJ6744A4

description: MDM control


title: May_GV_4


title: Jul_GV_4


title: MDM tolerance RAJ6744A6

description: MDM tolerance


title: May_GV_3


title: MDM acute response RAJ6744A2

description: MDM acute response


title: May_GV_2


title: D84_1


title: May_GV_1


title: MDM control RAJ6744A1

description: MDM control


title: EB_5

value: hiPSC-derived embryoid body


title: D56.2


title: D56_1


title: EB_4


title: D56.3


title: WT CD34- rep.1


title: CJ_CG84-21_CoIP_Cas9-3xF_R2

value: replicate 2

value: ANTI-FLAG M2 (Sigma, cat. #F 1804)

value: RNA bound to Cas9-3xFLAG


title: 29_CSF_uns_5pGEX

status: Public on Apr 26 2021

city: San Francisco

first: Akshaya

last: Ramesh

address: 675 Nelson Rising Lane

institute: UCSF

data_processing:
Seurat (v3.1.2)
Spliced Transcripts Alignment to a Reference (STAR) algorithm (v2.5.1)
SingleR (v1.1.7)
DoubletFinder (v2.0.2)
Genome_build: GRCh38.v93
Supplementary_files_format_and_content: filtered single-cell gene count matrices

extract_protocol:
CSF and blood were obtained during diagnostic and research procedures after subjects had provided informed consent; 20 to 30 mL of CSF was centrifuged immediately after collection at 400 × g for 15 min at 4 °C. The pellet was resuspended in ∼80 µL of residual supernatant, and lymphocytes were counted using a hemocytometer. Peripheral blood mononuclear cells (PBMCs) were isolated using cell preparation tubes and resuspended in 2% fetal bovine serum. All experiments were performed immediately with freshly collected, unsorted cells.
Sequencing libraries were prepared using 3′ or 5′ library preparation kits (10x Genomics).

tag: subject status

value: Relapsing MS

tag: subject id

value: CSF


title: 27_PB_uns_5pGEX

tag: tissue

value: PB


title: 32_PB_uns_5pGEX

value: Healthy


title: 31_CSF_uns_5pGEX

value: Clinically isolated syndrome


title: 32_CSF_uns_5pGEX


title: 28_CSF_uns_5pGEX


title: 24_PB_uns_5pGEX


title: 25_PB_uns_5pGEX


title: 24_CSF_uns_5pGEX


title: 28_PB_uns_5pGEX


title: 31_PB_uns_5pGEX


title: 22_CSF_uns_5pGEX


title: 22_PB_uns_5pGEX


title: 29_PB_uns_5pGEX


title: 21_PB_uns_5pGEX

value: Uveitis


title: 21_CSF_uns_5pGEX


title: 18_PB_uns_3pGEX


title: 18_CSF_uns_3pGEX


title: 16_PB_uns_3pGEX


title: 16_CSF_uns_3pGEX


title: C-09-2

data_processing:
Library strategy: 5hmC Capture
RNA-seq reads were aligned to hg19 using tophat v1.3.3 and differential RPKM expression values were extracted using cuffdiff v2.2.1
5hmC-IP-seq paired-end reads were mapped to the hg19 reference genome using bowtie2 (v2.2.6) (Langmead et al., 2009) with the parameters --no-discordant --no-mixed to prevent discordant alignments and alignments for the individual mates. Flags -F 4 and -q 10 were used in samtools (v 1.9) (Li et al., 2009) to exclude unmapped reads and reads with Mapping Quality (MAPQ) values less than 10 for each replicate in all stages.
Peaks were called using MACS version 1v 2.1.0 with the following setting: macsBW 200, macs_qvalue 0.01, peaks narrow.
Peak regions were annotated to their corresponding nearby genes using HOMER v4.9 with an additional flag -annStats to also annotate genomic features to these peak regions.
Genome_build: hg19

extract_protocol:
The human iPSC lines (provided by Dr. Chadwick Hales’ laboratory at Emory University) were cultured on irradiated MEFs in human iPSC medium consisting of D-MEM/F12 (Invitrogen), 20% Knockout Serum Replacement (KSR, Invitrogen), 1X Glutamax (Invitrogen), 1X MEM Non-essential Amino Acids (NEAA, Invitrogen), 100 µM β- Mercaptoenthanol (Invitrogen), and 10 ng/ml human basic FGF (bFGF, PeproTech) as described (Wen et al., 2014b). Forebrain-specific organoids were generated as previously described(Qian et al., 2016). Briefly, human iPSC colonies were detached from the feeder layer with 1 mg/ml collagenase treatment for 1 hour and suspended in embryonic body (EB) medium, consisting of FGF-2-free iPSC medium supplemented with 2 µM Dorsomorphin and 2 µM A-83 in non-treated polystyrene plates for 4 days with a daily medium change. On days 5-6, half of the medium was replaced with induction medium consisting of DMEM/F12, 1X N2 Supplement (Invitrogen), 10 μg/ml Heparin (Sigma), 1X Penicillin/Streptomycin, 1X Non-essential Amino Acids, 1X Glutamax, 4 ng/ml WNT-3A (R&D Systems), 1 μM CHIR99021 (Tocris), and 1 μM SB-431542 (Tocris). On day 7, organoids were embedded in Matrigel (BD Biosciences) and continued to grow in induction medium for 6 more days. On day 14, embedded organoids were mechanically dissociated from Matrigel by pipetting up and down onto the plate with a 5ml pipette tip. Typically, 10 - 20 organoids were transferred to each well of a 12-well spinning bioreactor (SpinΩ) containing differentiation medium, consisting of DMEM/F12, 1X N2 and B27 Supplements (Invitrogen), 1X Penicillin/Streptomycin, 100 µM β- Mercaptoenthanol (Invitrogen), 1X MEM NEAA, 2.5 μg/ml Insulin (Sigma). At day 71, differentiation medium was exchanged with maturation medium, consisting of Neurobasal (Gibco), 1X B27 Supplement, 1X Penicillin/Streptomycin, 1X β-Mercaptoenthanol, 0.2 mM Ascorbic Acid, 20 ng/ml BDNF (Peprotech), 20 ng/ml GDNF (Peprotech), 1 ng/ml TFGβ (Peprotech), and 0.5 mM cAMP (Sigma). All media were changed every other day.
5hmC Capture: Five ug of genomic DNA was sonicated to 300-400 base pair (bp) using a Covaris focused ultrasonicator. 5hmC capture was performed according to the method described in (Song et al., 2011).First, a glucosyltransfer reaction was performed using 2.5µl of T4 phage ß-glucosyltransferase enzyme (10,000U/ml; New England BioLabs) and 100µM UDP-6-N3-glucose (Jena Biosciences) and incubated at 37 degrees C for 2 hours. After purification with AMPure XP beads (Beckman Coulter), the glucosylated 5hmC-containing DNA fragments were biotinylated with 150µM disulfide biotin linker (Click Chemistry Tools) at 37 degrees C for 2 hours. After purification with AMPure XP beads, the biotinylated 5hmc-containing DNA fragments were pulled down using Dynabeads MyOne Streptavidin C1 beads (ThermoFisher Scientific) and were washed three times with Binding/Washing buffer (20mM Tris pH 7.5, 1mM EDTA, 2M NaCl, 0.01% Tween-20). The 5hmC-containing DNA fragments were then removed from the beads with fresh 100mM dithiothreitol for 2 hours with rotation at room temperature. After final purification with AMPureXP beads, the 5hmC-enriched DNA fragments were eluted in nuclease-free water and quantified by Qubit. Library Preparation adn High-throughput Sequencing: Enriched DNA from 5hmC capture were subjected to library construction using the NEBNext Ultra II DNA Library Prep kit for Illumina (New England BioLabs) according to manufacturer’s protocol. Briefly, 1-7ng of 5hmC-enriched DNA or un-enriched genomic DNA was utilized for each library construction. An Agilent 2100 Bioanalyzer was used to confirm purity and fragmentation size of the final libraries. RNAseq libraries were generated using TruSeq RNA Sample Prep V2 kit (New England BioLabs) with 1g of RNA to first obtain poly-A-enriched RNA and synthesize cDNA, and then the same library construction protocol was followed using 5ng of cDNA. Libraries were sequenced pair-end (150bp) on an Illumina HiSeq platform.

value: Healthy/ Control

tag: cell type

tag: seq type


title: 31_PB_uns_5pGEX_2


title: 10_CSF_uns_5pGEX


title: 9_CSF_uns_5pGEX_2


title: 27_CSF_uns_5pGEX


title: 9_PB_uns_5pGEX_2


title: 25_CSF_uns_5pGEX


title: 8_CSF_uns_5pGEX


title: 10_PB_uns_5pGEX


title: 7_CSF_uns_5pGEX


title: 6_PB_uns_5pGEX


title: 2_CSF_uns_5pGEX


title: 6_CSF_uns_5pGEX


title: Rep3 CD4 TN TKO [ATAC-Seq]

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

country: France

institute: IGBMC (CNRS/INSERM/UDS)

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Data analysis was performed using the Encode ATAC-seq pipeline v1.4.2.  Adapter sequences were removed and low-quality ends were trimmed. Sequence alignment was performed into the mm10 assembly of Mus musculus genome using Bowtie2 (version 2.2.6) choosing the zero multi-mapping option. Mitochondrial reads were removed.
Genome_build: mm10
Supplementary_files_format_and_content: Fold-enrichment bigwig files generated with the MACS2 bdgcmp command

source_name: sorted CD4+ naive T cells (DAPI-CD4+CD8-CD44-/lowCD25-NK1.1-TCRgd-) from lymph nodes and spleen (day 0)

growth_protocol: Naive CD4+ T cells (DAPI-CD4+CD8-CD44-/lowCD25-NK1.1-TCRgd-) from lymph nodes and spleen were either left untreated (day 0) or cultured for 1 or 2 days under Th0 condition with plate-coated anti-CD3, anti-CD28 Abs (2μg/ml) in the presence of neutralizing anti-IL-4 and anti-IFNγ Abs (10μg/ml).

extract_protocol:
FACS sorted naive CD4+ T cells were sorted from lymph nodes and spleen of WT and Ikaros TKO mice. Naive CD4+ T cells were directly used for the ATAC-seq protocol for the day 0 condition, while the remaining naive CD4+ T cells were activated in Th0 culture condition for 1 or 2 days. At day 1 and 2, live cells (DAPI-) were sorted and used for the ATAC-seq protocol.
Libraries were prepared as described in Buenrostro et al., 2013.

tag: age

value: 4,7 weeks

tag: genotype

value: Ikaros f/f CD4-Cre +


title: 5_PB_uns_5pGEX

value: Neuromyelitis optica


title: Rep2 CD4 TN TKO [ATAC-Seq]


title: Rep2 TH0 d2 TKO [ATAC-Seq]

source_name: sorted CD4+ naive T cells from lymph nodes and spleen, activated with anti-CD3+anti-CD28 Abs for 2 days


title: 3_PB_uns_5pGEX


title: Rep3 TH0 d2 TKO [ATAC-Seq]


title: Rep2 TH0 d1 TKO [ATAC-Seq]

source_name: sorted CD4+ naive T cells from lymph nodes and spleen, activated with anti-CD3+anti-CD28 Abs for 1 day


title: Rep3 TH0 d2 WT [ATAC-Seq]

value: Ikaros f/f CD4-Cre -


title: 3_CSF_uns_5pGEX


title: Rep1 CD4 TN TKO [ATAC-Seq]

value: 5,3 weeks


title: Rep1 TH0 d2 TKO [ATAC-Seq]


title: Rep3 TH0 d1 WT [ATAC-Seq]


title: Rep2 CD4 TN WT [ATAC-Seq]


title: Rep1 TH0 d1 WT [ATAC-Seq]


title: 8_PB_uns_5pGEX


title: 7_PB_uns_5pGEX


title: Rep3 CD4 TN WT [ATAC-Seq]


title: Rep1 TH0 d2 WT [ATAC-Seq]


title: Rep3 TH0 d1 TKO [ATAC-Seq]


title: maize_input

city: Athens

first: Robert

middle: J

last: Schmitz

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

description: input

data_processing:
Reads were trimmed using trimmomatic, and aligned to the genome using bowtie2, `--very-sensitive`. Only uniquely mapping reads were used for downstream analysism, with duplicates being removed using the picard MarkDuplicates command.
 Peak calling was done for histone modifications known to have broad peaks (H3K36me3, and H3K4me1) using the software epic2 with the parameters “--false-discovery-rate-cutoff .1 --keep-duplicates”, as well as MACS2 to identify smaller regions of enrichment using the parameters `callpeak --keep-dup all -g 1.6e9 -q .1`. Narrow peaks (H3K56ac and H3K4me3) were called using MACS2 with the parameters “ --keep-dup all --extsize 147 -g 1.6e9 -p .05’ (Stovner and Sætrom, 2019, p. 2; Zhang et al., 2008). Peaks which were within 480 bps, or roughly two nucleosomes of each other were merged. Intersection between replicates of the same histone modification were taken, and the total length of the two overlapping segments were taken.
Genome_build: Z. mays genome and gene annotation AGPv4
Supplementary_files_format_and_content: bed files. Column1: Chromosome; Column2: Start of Peak; Column3: End of peak

organism: Zea mays

source_name: ear

growth_protocol: Glycine max (accession William82) were grown in the soil for approximately 10 days under 25°C and photoperiodic lighting (16 hours of light:8 hours of dark). The 2nd and 3rd leaves were collected for the experiments. For Zea mays Ear primordia protocol: Plants were grown in greenhouse or field conditions. Plants were harvested approximately one month after sowing and ear primordia were dissected from shoots. Ear primordia were harvested from any node of the shoot if they were within the desired size range: between 3 to 8 millimeters from the base to the apical tip of the ear.

extract_protocol:
ChiP-seq was performed following the methods of (Zang et al. 2007). Tissues were cross-linked with 1% formaldehyde and chromatin was sonicated, followed by immunoprecipitation
Antibidies Used: Anti-trimethyl-Histone H3 (Lys4) [EMD Millipore, Cat#:07-473],   Anti-Histone H3 (tri methyl K36) [Abcam, Cat#:ab9050], Anti-acetyl-Histone H3 (Lys56) [EMD Millipore, Cat#:07-677-I]

treatment_protocol: No Treatmant

value: ear

tag: strain

tag: chip antibody

value: none (input)


title: Rep1 CD4 TN WT [ATAC-Seq]


title: Rep2 TH0 d1 WT [ATAC-Seq]


title: Rep1 TH0 d1 TKO [ATAC-Seq]


title: WT CD4TN d0 Input

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated using Homer software makeUCSCfile script with default parameters.

source_name: sorted CD4+ naive T cells (DAPI-CD4+CD8-CD44-/lowCD25-NK1.1-TCRgd-) from lymph nodes (day 0)

growth_protocol: Naive CD4+ T cells (DAPI-CD4+CD8-CD44-/lowCD25-NK1.1-TCRgd-) from lymph nodes were either left untreated (day 0) or cultured for 1 day under Th0 condition with plate-coated anti-CD3, anti-CD28 Abs (2μg/ml) in the presence of neutralizing anti-IL-4 and anti-IFNγ Abs (10μg/ml).

extract_protocol:
FACS sorted naive CD4+ T cells were sorted from lymph nodes. Naive CD4+ T cells were directly used for the ChIP-seq protocol for the day 0 condition, while the remaining naive CD4+ T cells were activated in Th0 culture condition for 1 day. At day 1 activated CD4+ T cells were used for the ChIP-seq protocol.  Lysed nuclei were sonicated using the Covaris E220 sonicator (Peak incident power 100, Duty factor 50, 200 cycles/burst) for 10 min. DNA fragment between 150-300bp were immunoprecipitated with anti-Ikaros antibody (#Ct, 3072, Rabbit Ab), purified and sequenced using Illumina Genome Analyzer as recommanded by the manufacturer.
Library were prepared following the Diagenode MicroPlex Library Preparation Kit (C05010014) using the manifacturer instructions.

value: 4 weeks

value: WT


title: WT CD4Th0d1 IP Ikaros

source_name: sorted CD4+ naive T cells from lymph nodes, activated with anti-CD3+anti-CD28 Abs for 1 day


title: Rep 3 TH0 d1 TKO [RNA-Seq]

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were preprocessed in order to remove adapters, polyA and low-quality sequences (Phred quality score below 20). After this preprocessing, reads shorter than 40 bases were discarded for further analysis. These preprocessing steps were performed using Cutadapt version 1.10.
Reads were mapped into the mm10 assembly of Mus musculus genome using STAR version 2.5.3a. The reads were aligned across exonic, intronic and intergenic genomic region using annotations from Ensembl 94.
Gene expression quantification was performed from uniquely aligned reads using Htseq-count version 0.6.1p1, with annotations from Ensembl version 94 and “union" mode. Only non-ambiguously assigned reads have been retained for further analyses.
In order to make these counts comparable between samples, read counts have been normalized across samples with the median-of-ratios method proposed by Anders and Huber.
Comparisons of interest were performed using the test for differential expression, proposed by Love et al. and implemented in the Bioconductor package DESeq2 version 1.16.1
Genome_build: mm10
Supplementary_files_format_and_content: A TSV (tab-separated values) file provides raw read counts and normalized read counts for each gene together with gene annotations and the p-value, adjusted p-value and log2 fold-change for each performed comparison. This file contains only genes with at least one read count in one sample.

extract_protocol:
FACS sorted naive CD4+ T cells were sorted from lymph nodes and spleen. Naive CD4+ T cells were directly used for the RNA-seq protocol for the day 0 condition, while the remaining naive CD4+ T cells were activated in Th0 culture condition for 1 or 2 days. At day 1 and 2, live cells (DAPI-) were sorted and used for the RNA-seq protocol.  Total RNA extractions were performed using the RNeasy Plus Micro Kit (Qiagen 74034).
Full length cDNA were generated from 5 ng of total RNA using Clontech SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 9 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, CA) followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.

value: 4,6 weeks


title: WT CD4Th0d1 input


title: WT CD4TN d0 IP Ikaros


title: Rep 2 TH0 d1 TKO [RNA-Seq]

value: 4,9 weeks


title: Rep 1 TH0 d2 TKO [RNA-Seq]

value: 4,7 weks


title: Rep 3 CD4 TN TKO [RNA-Seq]


title: Rep 2 TH0 d2 TKO [RNA-Seq]


title: Rep1 TH0 d1 TKO [RNA-Seq]


title: Rep 2 CD4 TN TKO [RNA-Seq]


title: Rep 3 TH0 d2 TKO [RNA-Seq]


title: Rep 3 TH0 d1 WT [RNA-Seq]


title: Rep 3 TH0 d2 WT [RNA-Seq]


title: Rep 3 CD4 TN WT [RNA-Seq]


title: Rep 2 TH0 d1 WT [RNA-Seq]


title: Rep 2 TH0 d2 WT [RNA-Seq]


title: Rep 2 CD4 TN WT [RNA-Seq]


title: Rep 1 TH0 d2 WT [RNA-Seq]


title: Rep 1 TH0 d1 WT [RNA-Seq]


title: Rep 1 CD4 TN WT [RNA-Seq]


title: RRBS_MEFs_Crispr_Ex3KO2

first: Michael

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

institute: CNRS

data_processing:
Reads were cleaned with Trim Galore v0.4.2 using the parameters --rrbs --paired -r1 30 -r2 30 -q 20 --length 20 --stringency 5 --retain_unpaired.
Reads were aligned to the mouse mm10 genome with BSMAP v2.74 using the parameters -v 2 -w 100 -r 1 -x 400 -m 30 -D C-CGG -n 1.
Methylation percent values were extracted with methratio.py from BSMAP v2.74 using the parameters -z -u -g.
CGs were filtered to have a minimum sequencing depth of 8X using a custom developped script in R v3.0.0.
Genome_build: mm10
Supplementary_files_format_and_content: We provide bigWig files for visualization of ChIP-seq tracks.
Supplementary_files_format_and_content: We provide bigWig files for visualization of RNA-seq tracks.
Supplementary_files_format_and_content: We provide IGV files containing methylation scores for all CGs with at least 5X sequencing depth.
Supplementary_files_format_and_content: We provide IGV files containing methylation scores for all CGs with at least 8X sequencing depth.

source_name: Mouse Embryonic Fibroblasts

extract_protocol:
Genomic DNA samples were extracted with the AllPrep DNA/RNA Mini Kit (Qiagen).
RRBS libraries were prepared as described in Auclair et al., Genome Biol 15:545 (2014). Briefly, we digested 50-100 ng genomic DNA 5 hours with MspI (Thermo Scientific), followed by end-repair and A-tailing (Klenow fragment, Thermo Scientific) and ligation to methylated adapters (T4 DNA ligase, Thermo Scientific) in Tango 1X buffer. Fragments between 150 and 400 bp were excised from a 3% agarose 0.5X TBE gel with the MinElute kit (Qiagen) and bisulfite-converted with the EpiTect Bisulfite kit (Qiagen) using two consecutive rounds of conversion. Final RRBS libraries were amplified with 14-16 cycles of PCR. The libraries were purified using Ampure XP beads (Beckman Coulter).

tag: developmental stage

tag: genetic background


title: RRBS_MEFs_Crispr_Ex4KO1


title: RRBS_MEFs_Crispr_Ex4KO2


title: RRBS_MEFs_Crispr_Ex3KO1


title: Rep2 TH0 d2 WT [ATAC-Seq]


title: RRBS_MEFs_Crispr_WT2

value: wild type


title: RRBS_MEFs_Crispr_WT1


title: RRBS_pMEFs_E2f6KO_rep2


title: RRBS_pMEFs_E2f6KO_rep1


title: RRBS_pMEFs_WT_rep1


title: RRBS_pMEFs_WT_rep2


title: RRBS_Muscle_E2f6KO_rep3

source_name: Skeletal muscle

value: Adult


title: RRBS_Muscle_WT_rep3


title: Rep 1 CD4 TN TKO [RNA-Seq]


title: RRBS_Muscle_E2f6KO_rep2


title: RRBS_Muscle_WT_rep2


title: RRBS_Muscle_WT_rep1


title: RRBS_Kidney_E2f6KO_rep3

source_name: Kidney


title: RRBS_Kidney_E2f6KO_rep2


title: RRBS_Kidney_WT_rep2


title: RRBS_Kidney_WT_rep3


title: RRBS_Kidney_E2f6KO_rep1


title: RRBS_Kidney_WT_rep1


title: RRBS_Brain_E2f6KO_rep3

source_name: Brain


title: RRBS_Brain_E2f6KO_rep1


title: RRBS_Brain_E2f6KO_rep2


title: RRBS_Brain_WT_rep3


title: RRBS_Brain_WT_rep2


title: RRBS_ESCs_E2f6KO

source_name: ES cells


title: RRBS_ESCs_WT


title: RRBS_E8.5_E2f6KO_rep1

source_name: E8.5 whole embryos


title: RRBS_E8.5_E2f6KO_rep2


title: RRBS_Brain_WT_rep1


title: RRBS_E8.5_WT_rep2


title: RRBS_E8.5_WT_rep1


title: RRBS_Muscle_E2f6KO_rep1


title: RNA-seq_E8.5_E2f6KO_rep3

data_processing:
Reads were aligned to the mouse mm10 genome with TopHat2 v2.0.13 using default parameters and a RefSeq transcriptome index.
For data visualization, bigWig files were generated using bam2wig.py from the RSeQC package v2.6.4 using the parameters -u -t 5000000000.
Genome_build: mm10
Supplementary_files_format_and_content: We provide bigWig files for visualization of ChIP-seq tracks.
Supplementary_files_format_and_content: We provide bigWig files for visualization of RNA-seq tracks.
Supplementary_files_format_and_content: We provide IGV files containing methylation scores for all CGs with at least 5X sequencing depth.
Supplementary_files_format_and_content: We provide IGV files containing methylation scores for all CGs with at least 8X sequencing depth.

extract_protocol:
RNA samples were prepared using the RNeasy kit (Qiagen) or the AllPrep DNA/RNA Mini Kit (Qiagen).
RNA-Seq libraries were prepared from 250 ng of total RNA using the TruSeq Stranded Total RNA Library Preparation kit with Ribo-Zero depletion (Illumina), according to the manufacturer's instructions.


title: WGBS_E8.5_E2f6KO

data_processing:
Reads were cleaned to remove low quality bases as well as the first five bases of reads R1 and ten bases of reads R2 with Trim Galore v0.4.2 using the parameters --paired -q 20 --stringency 2 --clip_R1 5 --clip_R2 10.
Reads were aligned to the mouse mm10 genome and methylation calls were extracted with Bismark v0.18.2 using default parameters.
CGs were filtered to have a minimum sequencing depth of 5X using a custom developped script in R v3.0.0.
Genome_build: mm10
Supplementary_files_format_and_content: We provide bigWig files for visualization of ChIP-seq tracks.
Supplementary_files_format_and_content: We provide bigWig files for visualization of RNA-seq tracks.
Supplementary_files_format_and_content: We provide IGV files containing methylation scores for all CGs with at least 5X sequencing depth.
Supplementary_files_format_and_content: We provide IGV files containing methylation scores for all CGs with at least 8X sequencing depth.

extract_protocol:
Genomic DNA was extracted from single embryos with the AllPrep DNA/RNA Mini Kit (Qiagen).
101 ng genomic DNA was fragmented to 350 bp using a Covaris E220 sonicator, and bisulfite-converted with the EZ DNA Methylation-Gold kit (Zymo Research). WGBS librairies were prepared using the Accel-NGS Methyl-Seq DNA Library Kit and the Methyl-Seq Set A Indexing Kit (Swift Biosciences) according to the manufacturer's instructions with 6 PCR cycles for the final amplification. The libraries were purified using Ampure XP beads (Beckman Coulter).


title: RNA-seq_E8.5_E2f6KO_rep1


title: RNA-seq_E8.5_WT_rep2


title: WGBS_E8.5_WT

extract_protocol:
Genomic DNA was extracted from single embryos with the AllPrep DNA/RNA Mini Kit (Qiagen).
100 ng genomic DNA was fragmented to 350 bp using a Covaris E220 sonicator, and bisulfite-converted with the EZ DNA Methylation-Gold kit (Zymo Research). WGBS librairies were prepared using the Accel-NGS Methyl-Seq DNA Library Kit and the Methyl-Seq Set A Indexing Kit (Swift Biosciences) according to the manufacturer's instructions with 6 PCR cycles for the final amplification. The libraries were purified using Ampure XP beads (Beckman Coulter).


title: RNA-seq_E8.5_E2f6KO_rep2


title: RNA-seq_ESCs_E2f6KO_rep1


title: RNA-seq_E8.5_WT_rep1


title: RNA-seq_ESCs_E2f6KO_rep3


title: RNA-seq_E8.5_WT_rep3


title: RNA-seq_ESCs_E2f6KO_rep2


title: RNA-seq_ESCs_WT_rep1


title: RNA-seq_411 Kihet_Rep3

first: Anna

last: Niewiadomska-Cimicka

institute: IGBMC

data_processing:
Base calling : Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment : Reads were mapped onto mm10 assembly of mouse genome using Tophat v2.0.14 with bowtie v2.1.0.
Quantification : Gene expression was quantified using HTSeq v0.6.1 (intersection-nonempty mode) and Ensembl release 86 annotations.
Genome_build: mm10
Supplementary_files_format_and_content: Tabulated text file containing raw read counts in each sample.

source_name: SCA7 KI cerebellum

extract_protocol:
Cerebella were flash frozen in liquid nitrogen and stored at -800C. The total RNA was obtained using Qiagen Mini Kit.
Libraries were generated using Biomek FXP (Beckman Coulter) from 300 ng of total RNA according to TruSeq Stranded mRNA Sample Preparation Guide (Illumina, PN 15031047 Rev.E) with 12 cycles library PCR amplification.

value: cerebellum

tag: genotype/variation

value: SCA7 140Q/5Q knock-in (Ki)

value: 40 weeks


title: RNA-seq_ESCs_WT_rep2


title: RNA-seq_408 Kihet_Rep2


title: RNA-seq_378 Kihet_Rep1


title: RNA-seq_392 WT_Rep2

source_name: WT cerebellum

value: wildtype


title: RNA-seq_390 WT_Rep1


title: RNA-seq_409 WT_Rep3


title: PVG_OM_treated_Virus_OVA_2_bone_marrow_rep6

city: Crawley, Perth

first: Emma

last: de Jong

state: WA

address: 35 Stirling Hwy

institute: University of Western Australia

description:
genecounts_bonemarrow.csv
RB94_HGMMWDMXX_CGTCTGCG.TTCACAAT_L001_R1.fastq.gz

data_processing:
Image analysis was performed in real time by the NovaSeq Control Software (NCS) v1.3.0 and Real Time Analysis (RTA) vv3.3.3, running on the instrument computer. RTA performs  real-time base calling on the NovaSeq instrument computer.
Then the Illumina bcl2fastq 2.20.0.422 pipeline was used to generate the sequence data
Read libraries were mapped to the rat genome (rn6) using HISAT2 (v2.0.4)
Gene-level quantitation (counts) of HISAT2 alignments was performed using SummarizeOverlaps
Genome_build: rn6
Supplementary_files_format_and_content: genecounts_lung.csv and genecounts_bonemarrow.csv files contain a matrix of raw gene counts (unfiltered and un-normalised data)

organism: Rattus norvegicus

source_name: bone marrow

extract_protocol:
Single-cell suspensions of bone marrow and lung tissue were resuspended in RNAlater (Ambion, Life Technologies, Mulgrave, VIC, Australia), and frozen at -80°C. Total RNA was extracted with TRIzol (Ambion) followed by RNAeasy (Qiagen Gmbh, Hilden, Germany). Total RNA libraries were prepared using TruSeq Stranded mRNA Library Prep Kit, Illumina Inc, San Diego, CA. Sequencing was performed by the Australian Genome Research Facility (Illumina HiSeq2500, 50bp single-end reads, v4 chemistry).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PVG

tag: treatment group

tag: experimental group

value: days post infection (dpi):2

tag: Sex

value: male

tag: rna integrity number


title: PVG_OM_treated_Virus_OVA_9_bone_marrow_rep6

description:
genecounts_bonemarrow.csv
RB95_HGMMWDMXX_TCGATATC.ACACGAGT_L001_R1.fastq.gz

value: days post infection (dpi):9


title: PVG_OM_treated_Control_Saline_0_bone_marrow_rep7

description:
genecounts_bonemarrow.csv
RB96_HGMMWDMXX_CTAGCGCT.GTGTAGAC_L001_R1.fastq.gz

value: days post infection (dpi):0


title: PVG_OM_treated_Virus_Saline_1_bone_marrow_rep6

description:
genecounts_bonemarrow.csv
RB93_HGMMWDMXX_TACTCATA.CCTGTGGC_L001_R1.fastq.gz

value: days post infection (dpi):1


title: PVG_Untreated_Virus_OVA_9_bone_marrow_rep6

description:
genecounts_bonemarrow.csv
RB91_HGMMWDMXX_GTATGTTC.AACAGGAA_L001_R1.fastq.gz

value: Untreated


title: PVG_Untreated_Virus_OVA_2_bone_marrow_rep6

description:
genecounts_bonemarrow.csv
RB90_HGMMWDMXX_CGCTATGT.TCCGACAC_L001_R1.fastq.gz


title: PVG_Untreated_Control_Saline_0_bone_marrow_rep6

description:
genecounts_bonemarrow.csv
RB88_HGMMWDMXX_TCTGTTGG.TCGAATGG_L001_R1.fastq.gz


title: PVG_Untreated_Virus_Saline_1_bone_marrow_rep6

description:
genecounts_bonemarrow.csv
RB89_HGMMWDMXX_TATCGCAC.CTTAGTGT_L001_R1.fastq.gz


title: PVG_OM_treated_Virus_OVA_2_bone_marrow_rep5

description:
genecounts_bonemarrow.csv
RB86_HGMMWDMXX_GAACCGCG.TGACCTTA_L001_R1.fastq.gz


title: PVG_OM_treated_Control_Saline_0_bone_marrow_rep6

description:
genecounts_bonemarrow.csv
RB92_HGMMWDMXX_ACGCACCT.GGTGAAGG_L001_R1.fastq.gz


title: RNA-seq_ESCs_WT_rep3


title: PVG_OM_treated_Control_Saline_0_bone_marrow_rep5

description:
genecounts_bonemarrow.csv
RB84_HGMMWDMXX_TCATCCTT.AGCGAGCT_L001_R1.fastq.gz


title: PVG_OM_treated_Virus_OVA_9_bone_marrow_rep5

description:
genecounts_bonemarrow.csv
RB87_HGMMWDMXX_CTCACCAA.CTAGGCAA_L001_R1.fastq.gz


title: PVG_Untreated_Virus_OVA_2_bone_marrow_rep5

description:
genecounts_bonemarrow.csv
RB82_HGMMWDMXX_GGTCACGA.GTATTATG_L001_R1.fastq.gz


title: PVG_Untreated_Virus_Saline_1_bone_marrow_rep5

description:
genecounts_bonemarrow.csv
RB81_HGMMWDMXX_AACTGTAG.ACGCCGCA_L001_R1.fastq.gz


title: PVG_OM_treated_Virus_Saline_1_bone_marrow_rep5

description:
genecounts_bonemarrow.csv
RB85_HGMMWDMXX_AGGTTATA.CAGTTCCG_L001_R1.fastq.gz


title: PVG_OM_treated_Virus_OVA_2_bone_marrow_rep4

description:
genecounts_bonemarrow.csv
RB78_HGMMWDMXX_CATAGAGT.TGCCACCA_L001_R1.fastq.gz


title: PVG_Untreated_Virus_OVA_2_bone_marrow_rep4

description:
genecounts_bonemarrow.csv
RB74_HGMMWDMXX_TGGCCGGT.TAGAGCGC_L001_R1.fastq.gz


title: PVG_OM_treated_Control_Saline_0_bone_marrow_rep4

description:
genecounts_bonemarrow.csv
RB76_HGMMWDMXX_GACGTCTT.GGTTCACC_L001_R1.fastq.gz


title: PVG_OM_treated_Virus_Saline_1_bone_marrow_rep4

description:
genecounts_bonemarrow.csv
RB77_HGMMWDMXX_TGCGAGAC.CATTGTTG_L001_R1.fastq.gz


title: PVG_Untreated_Virus_Saline_1_bone_marrow_rep4

description:
genecounts_bonemarrow.csv
RB73_HGMMWDMXX_CAATTAAC.CGAGATAT_L001_R1.fastq.gz


title: PVG_Untreated_Virus_OVA_9_bone_marrow_rep4

description:
genecounts_bonemarrow.csv
RB75_HGMMWDMXX_AGTACTCC.AACCTGTT_L001_R1.fastq.gz


title: PVG_OM_treated_Virus_OVA_9_bone_marrow_rep3

description:
genecounts_bonemarrow.csv
RB71_HGMMWDMXX_ACTCGTGT.ATTGGAAC_L001_R1.fastq.gz


title: PVG_OM_treated_Virus_Saline_1_bone_marrow_rep3

description:
genecounts_bonemarrow.csv
RB69_HGMMWDMXX_GCCACAGG.CATGCCAT_L001_R1.fastq.gz


title: PVG_OM_treated_Virus_OVA_2_bone_marrow_rep3

description:
genecounts_bonemarrow.csv
RB70_HGMMWDMXX_ATTGTGAA.TGCATTGC_L001_R1.fastq.gz


title: PVG_OM_treated_Control_Saline_0_bone_marrow_rep3

description:
genecounts_bonemarrow.csv
RB68_HGMMWDMXX_CCTTCACC.GACGCTCC_L001_R1.fastq.gz


title: PVG_Untreated_Virus_OVA_9_bone_marrow_rep3

description:
genecounts_bonemarrow.csv
RB67_HGMMWDMXX_TTCCTGTT.AGTATCTT_L001_R1.fastq.gz


title: PVG_Untreated_Virus_OVA_2_bone_marrow_rep3

description:
genecounts_bonemarrow.csv
RB66_HGMMWDMXX_GTGTCGGA.GCTTGCGC_L001_R1.fastq.gz


title: PVG_Untreated_Virus_Saline_1_bone_marrow_rep3

description:
genecounts_bonemarrow.csv
RB65_HGMMWDMXX_ACACTAAG.ATCCATAT_L001_R1.fastq.gz


title: PVG_OM_treated_Virus_OVA_9_bone_marrow_rep2

description:
genecounts_bonemarrow.csv
RB63_HGMMWDMXX_TTGCCTAG.ACCACTTA_L001_R1.fastq.gz


title: PVG_OM_treated_Virus_Saline_1_bone_marrow_rep2

description:
genecounts_bonemarrow.csv
RB61_HGMMWDMXX_CGGAACTG.CACTACGA_L001_R1.fastq.gz


title: PVG_OM_treated_Virus_OVA_2_bone_marrow_rep2

description:
genecounts_bonemarrow.csv
RB62_HGMMWDMXX_TAAGGTCA.TGTCGTAG_L001_R1.fastq.gz


title: PVG_Untreated_Virus_OVA_9_bone_marrow_rep5

description:
genecounts_bonemarrow.csv
RB83_HGMMWDMXX_CTGCTTCC.GATAGATC_L001_R1.fastq.gz


title: PVG_Untreated_Control_Saline_0_bone_marrow_rep5

description:
genecounts_bonemarrow.csv
RB80_HGMMWDMXX_GTGAATAT.TCTCATTC_L001_R1.fastq.gz


title: PVG_OM_treated_Control_Saline_0_bone_marrow_rep2

description:
genecounts_bonemarrow.csv
RB60_HGMMWDMXX_AGCTCGCT.GCAGAATC_L001_R1.fastq.gz


title: PVG_Untreated_Virus_OVA_9_bone_marrow_rep2

description:
genecounts_bonemarrow.csv
RB59_HGMMWDMXX_GATCTATC.ATGAGGCT_L001_R1.fastq.gz


title: PVG_Untreated_Virus_Saline_1_bone_marrow_rep2

description:
genecounts_bonemarrow.csv
RB57_HGMMWDMXX_TGCGGCGT.CCTCGGTA_L001_R1.fastq.gz


title: PVG_Untreated_Control_Saline_0_bone_marrow_rep2

description:
genecounts_bonemarrow.csv
RB56_HGMMWDMXX_GAATGAGA.GAGGCATT_L001_R1.fastq.gz


title: PVG_OM_treated_Virus_OVA_9_bone_marrow_rep4

description:
genecounts_bonemarrow.csv
RB79_HGMMWDMXX_ACAGGCGC.CTCTGCCT_L001_R1.fastq.gz


title: PVG_OM_treated_Virus_OVA_2_bone_marrow_rep1

description:
genecounts_bonemarrow.csv
RB54_HGMMWDMXX_TGGTGGCA.TCCTGTAA_L001_R1.fastq.gz


title: PVG_OM_treated_Control_Saline_0_bone_marrow_rep1

description:
genecounts_bonemarrow.csv
RB52_HGMMWDMXX_GGTGAACC.GCGTTGGA_L001_R1.fastq.gz


title: PVG_Untreated_Virus_OVA_2_bone_marrow_rep2

description:
genecounts_bonemarrow.csv
RB58_HGMMWDMXX_CATAATAC.TTCTAACG_L001_R1.fastq.gz


title: PVG_OM_treated_Virus_OVA_9_bone_marrow_rep1

description:
genecounts_bonemarrow.csv
RB55_HGMMWDMXX_AGGCAGAG.AGAATGCC_L001_R1.fastq.gz


title: PVG_Untreated_Virus_OVA_2_bone_marrow_rep1

description:
genecounts_bonemarrow.csv
RB50_HGMMWDMXX_GCGCTCTA.GCTCCGAC_L001_R1.fastq.gz


title: PVG_Untreated_Virus_OVA_9_bone_marrow_rep1

description:
genecounts_bonemarrow.csv
RB51_HGMMWDMXX_AACAGGTT.ATACCAAG_L001_R1.fastq.gz


title: PVG_Untreated_Control_Saline_0_bone_marrow_rep3

description:
genecounts_bonemarrow.csv
RB64_HGMMWDMXX_CCATTCGA.GTTGTCCG_L001_R1.fastq.gz


title: PVG_Untreated_Control_Saline_0_bone_marrow_rep4

description:
genecounts_bonemarrow.csv
RB72_HGMMWDMXX_GTCTACAC.GCCAAGGT_L001_R1.fastq.gz


title: PVG_Untreated_Control_Saline_0_bone_marrow_rep1

description:
genecounts_bonemarrow.csv
RB48_HGMMWDMXX_ACCTTGGC.GGCCTCAT_L001_R1.fastq.gz


title: PVG_Untreated_Virus_Saline_1_bone_marrow_rep1

description:
genecounts_bonemarrow.csv
RB49_HGMMWDMXX_ATATCTCG.ATCTTAGT_L001_R1.fastq.gz


title: PVG_OM_treated_Virus_Saline_1_bone_marrow_rep1

description:
genecounts_bonemarrow.csv
RB53_HGMMWDMXX_CAACAATG.CTTCACGG_L001_R1.fastq.gz


title: BN_OM_treated_Virus_OVA_2_bone_marrow_rep5

description:
genecounts_bonemarrow.csv
RB46_HGMMWDMXX_GCAATGCA.GGAACGTT_L001_R1.fastq.gz

value: BN


title: BN_Untreated_Virus_OVA_9_bone_marrow_rep6

description:
genecounts_bonemarrow.csv
RB43_HGMMWDMXX_AAGATACT.ACTTACAT_L001_R1.fastq.gz


title: BN_OM_treated_Virus_Saline_1_bone_marrow_rep6

description:
genecounts_bonemarrow.csv
RB45_HGMMWDMXX_ATGGCATG.AAGGTACC_L001_R1.fastq.gz


title: BN_Untreated_Virus_Saline_1_bone_marrow_rep6

description:
genecounts_bonemarrow.csv
RB41_HGMMWDMXX_ATATGGAT.CTGTATTA_L001_R1.fastq.gz


title: BN_Untreated_Control_Saline_0_bone_marrow_rep6

description:
genecounts_bonemarrow.csv
RB40_HGMMWDMXX_CGGACAAC.TCCGGATT_L001_R1.fastq.gz


title: BN_Untreated_Virus_OVA_2_bone_marrow_rep6

description:
genecounts_bonemarrow.csv
RB42_HGMMWDMXX_GCGCAAGC.TCACGCCG_L001_R1.fastq.gz


title: BN_OM_treated_Virus_OVA_9_bone_marrow_rep5

description:
genecounts_bonemarrow.csv
RB39_HGMMWDMXX_TAAGTGGT.CTTAAGCC_L001_R1.fastq.gz


title: BN_OM_treated_Virus_OVA_2_bone_marrow_rep4

description:
genecounts_bonemarrow.csv
RB38_HGMMWDMXX_CTACGACA.GAGTCCAA_L001_R1.fastq.gz


title: BN_OM_treated_Virus_Saline_1_bone_marrow_rep5

description:
genecounts_bonemarrow.csv
RB37_HGMMWDMXX_TCGTAGTG.AGACTTGG_L001_R1.fastq.gz


title: BN_Untreated_Virus_OVA_9_bone_marrow_rep5

description:
genecounts_bonemarrow.csv
RB35_HGMMWDMXX_AGCCTCAT.AGTAGAGA_L001_R1.fastq.gz


title: BN_OM_treated_Control_Saline_0_bone_marrow_rep5

description:
genecounts_bonemarrow.csv
RB36_HGMMWDMXX_GATTCTGC.GACGAGAG_L001_R1.fastq.gz


title: BN_Untreated_Virus_Saline_1_bone_marrow_rep5

description:
genecounts_bonemarrow.csv
RB33_HGMMWDMXX_TACCGAGG.CCTGAACT_L001_R1.fastq.gz


title: BN_OM_treated_Control_Saline_0_bone_marrow_rep4

description:
genecounts_bonemarrow.csv
RB28_HGMMWDMXX_TCCAACGC.TTGGACTT_L001_R1.fastq.gz


title: BN_Untreated_Control_Saline_0_bone_marrow_rep5

description:
genecounts_bonemarrow.csv
RB32_HGMMWDMXX_AATGCCTC.TCGATCCA_L001_R1.fastq.gz


title: BN_OM_treated_Virus_OVA_9_bone_marrow_rep4

description:
genecounts_bonemarrow.csv
RB31_HGMMWDMXX_GGCATTCT.CTAGCTTG_L001_R1.fastq.gz


title: BN_OM_treated_Virus_OVA_2_bone_marrow_rep3

description:
genecounts_bonemarrow.csv
RB30_HGMMWDMXX_TTACAGGA.TGACAAGC_L001_R1.fastq.gz


title: BN_OM_treated_Virus_OVA_9_bone_marrow_rep6

description:
genecounts_bonemarrow.csv
RB47_HGMMWDMXX_GTTCCAAT.AATTCTGC_L001_R1.fastq.gz


title: BN_Untreated_Virus_OVA_9_bone_marrow_rep4

description:
genecounts_bonemarrow.csv
RB27_HGMMWDMXX_CTTGGTAT.CCAAGTCC_L001_R1.fastq.gz


title: BN_Untreated_Virus_Saline_1_bone_marrow_rep4

description:
genecounts_bonemarrow.csv
RB25_HGMMWDMXX_ACTAAGAT.AACCGCGG_L001_R1.fastq.gz


title: BN_Untreated_Virus_OVA_2_bone_marrow_rep4

description:
genecounts_bonemarrow.csv
RB26_HGMMWDMXX_GTCGGAGC.GGTTATAA_L001_R1.fastq.gz


title: BN_Untreated_Control_Saline_0_bone_marrow_rep4

description:
genecounts_bonemarrow.csv
RB24_HGMMWDMXX_ATGAGGCC.GTTAATTG_L001_R1.fastq.gz


title: BN_OM_treated_Virus_OVA_9_bone_marrow_rep3

description:
genecounts_bonemarrow.csv
RB23_HGMMWDMXX_GCAGAATT.ACCGGCCA_L001_R1.fastq.gz


title: BN_OM_treated_Virus_OVA_2_bone_marrow_rep2

description:
genecounts_bonemarrow.csv
RB22_HGMMWDMXX_AACGTTCC.GGAGTACT_L001_R1.fastq.gz


title: BN_OM_treated_Control_Saline_0_bone_marrow_rep6

description:
genecounts_bonemarrow.csv
RB44_HGMMWDMXX_GGAGCGTC.GTCCGTGC_L001_R1.fastq.gz


title: BN_OM_treated_Virus_Saline_1_bone_marrow_rep3

description:
genecounts_bonemarrow.csv
RB21_HGMMWDMXX_GGTACCTT.AAGACGTC_L001_R1.fastq.gz


title: BN_OM_treated_Control_Saline_0_bone_marrow_rep3

description:
genecounts_bonemarrow.csv
RB20_HGMMWDMXX_GCACGGAC.GTCTCGCA_L001_R1.fastq.gz


title: BN_Untreated_Control_Saline_0_bone_marrow_rep3

description:
genecounts_bonemarrow.csv
RB16_HGMMWDMXX_AATCCGGA.CTACAGTT_L001_R1.fastq.gz


title: BN_Untreated_Virus_OVA_9_bone_marrow_rep3

description:
genecounts_bonemarrow.csv
RB19_HGMMWDMXX_ATGTAAGT.ACTCTATG_L001_R1.fastq.gz


title: BN_Untreated_Virus_OVA_2_bone_marrow_rep3

description:
genecounts_bonemarrow.csv
RB18_HGMMWDMXX_CGGCGTGA.GCGCCTGT_L001_R1.fastq.gz


title: BN_Untreated_Virus_Saline_1_bone_marrow_rep3

description:
genecounts_bonemarrow.csv
RB17_HGMMWDMXX_TAATACAG.ATATTCAC_L001_R1.fastq.gz


title: BN_OM_treated_Virus_Saline_1_bone_marrow_rep2

description:
genecounts_bonemarrow.csv
RB14_HGMMWDMXX_TTGGACTC.GGAAGCAG_L001_R1.fastq.gz


title: BN_OM_treated_Control_Saline_0_bone_marrow_rep2

description:
genecounts_bonemarrow.csv
RB13_HGMMWDMXX_CCAAGTCT.AAGGATGA_L001_R1.fastq.gz


title: BN_Untreated_Virus_OVA_2_bone_marrow_rep2

description:
genecounts_bonemarrow.csv
RB11_HGMMWDMXX_TCTCTACT.CGCGGTTC_L001_R1.fastq.gz


title: BN_Untreated_Virus_OVA_9_bone_marrow_rep2

description:
genecounts_bonemarrow.csv
RB12_HGMMWDMXX_CTCTCGTC.TATAACCT_L001_R1.fastq.gz


title: BN_Untreated_Virus_OVA_2_bone_marrow_rep5

description:
genecounts_bonemarrow.csv
RB34_HGMMWDMXX_CGTTAGAA.TTCAGGTC_L001_R1.fastq.gz


title: BN_OM_treated_Virus_Saline_1_bone_marrow_rep4

description:
genecounts_bonemarrow.csv
RB29_HGMMWDMXX_CCGTGAAG.CAGTGGAT_L001_R1.fastq.gz


title: BN_OM_treated_Virus_OVA_9_bone_marrow_rep2

description:
genecounts_bonemarrow.csv
RB15_HGMMWDMXX_GGCTTAAG.TCGTGACC_L001_R1.fastq.gz


title: BN_Untreated_Virus_Saline_1_bone_marrow_rep2

description:
genecounts_bonemarrow.csv
RB10_HGMMWDMXX_GACCTGAA.TTGGTGAG_L001_R1.fastq.gz


title: BN_OM_treated_Virus_OVA_2_bone_marrow_rep1

description:
genecounts_bonemarrow.csv
RB07_HGMMWDMXX_CAAGCTAG.ACATAGCG_L001_R1.fastq.gz


title: BN_OM_treated_Virus_OVA_9_bone_marrow_rep1

description:
genecounts_bonemarrow.csv
RB08_HGMMWDMXX_TGGATCGA.GTGCGATA_L001_R1.fastq.gz


title: BN_OM_treated_Control_Saline_0_bone_marrow_rep1

description:
genecounts_bonemarrow.csv
RB05_HGMMWDMXX_ATCCACTG.AGGTGCGT_L001_R1.fastq.gz


title: BN_Untreated_Virus_OVA_9_bone_marrow_rep1

description:
genecounts_bonemarrow.csv
RB04_HGMMWDMXX_AAGTCCAA.TATGAGTA_L001_R1.fastq.gz


title: BN_Untreated_Control_Saline_0_bone_marrow_rep2

description:
genecounts_bonemarrow.csv
RB09_HGMMWDMXX_AGTTCAGG.CCAACAGA_L001_R1.fastq.gz


title: BN_OM_treated_Virus_Saline_1_bone_marrow_rep1

description:
genecounts_bonemarrow.csv
RB06_HGMMWDMXX_GCTTGTCA.GAACATAC_L001_R1.fastq.gz


title: BN_Untreated_Control_Saline_0_bone_marrow_rep1

description:
genecounts_bonemarrow.csv
RB01_HGMMWDMXX_CCGCGGTT.AGCGCTAG_L001_R1.fastq.gz


title: BN_Untreated_Virus_OVA_2_bone_marrow_rep1

description:
genecounts_bonemarrow.csv
RB03_HGMMWDMXX_GGACTTGG.CGCAGACG_L001_R1.fastq.gz


title: PVG_OM_treated_Virus_OVA_2_lung_rep6

description:
genecounts_lung.csv
RL95_HGMMWDMXX_TCGATATC.ACACGAGT_L002_R1.fastq.gz

source_name: lung


title: PVG_Untreated_Virus_OVA_9_lung_rep6

description:
genecounts_lung.csv
RL92_HGMMWDMXX_ACGCACCT.GGTGAAGG_L002_R1.fastq.gz


title: XpressRef Universal Iso-Seq

data_processing:
Transcripts were refined, adaptors removed and transcripts clustered with isoseq3
Reads were aligned with minimap2
Redundant isoforms were collapsed and 5' degraded transcripts removed with cDNA Cupcake
Transcripts were compared to Gencode.v29 with SQANTI2 and characterised
Genome_build: hg38
Supplementary_files_format_and_content: gff files representing full-length pseudogene transcripts, *csv files include cpm

source_name: Qiagen

extract_protocol:
RNA was extracted from HAP1 cells using the Qiagen RNA mini kit
Iso-Seq kit

value: commercial universal reference RNA


title: HAP1  Iso-Seq

source_name: HAP1 cells

tag: cell line


title: PVG_Untreated_Virus_OVA_2_lung_rep5

description:
genecounts_lung.csv
RL91_HGMMWDMXX_GTATGTTC.AACAGGAA_L002_R1.fastq.gz


title: Soybean_input

description: input

organism: Glycine max

source_name: leaf

value: leaf

value: none (input)


title: PVG_Untreated_Virus_Saline_1_lung_rep6

description:
genecounts_lung.csv
RL90_HGMMWDMXX_CGCTATGT.TCCGACAC_L002_R1.fastq.gz


title: PVG_Untreated_Control_Saline_0_lung_rep6

description:
genecounts_lung.csv
RL89_HGMMWDMXX_TATCGCAC.CTTAGTGT_L002_R1.fastq.gz


title: Soybean_10days_tis_leaf_H3K56ac

description: Chip sample


title: PVG_OM_treated_Virus_OVA_2_lung_rep5

description:
genecounts_lung.csv
RL87_HGMMWDMXX_CTCACCAA.CTAGGCAA_L002_R1.fastq.gz


title: Soybean_10days_tis_leaf_H3K36me3

description: Chip sample


title: PVG_OM_treated_Virus_Saline_1_lung_rep5

description:
genecounts_lung.csv
RL86_HGMMWDMXX_GAACCGCG.TGACCTTA_L002_R1.fastq.gz


title: PVG_OM_treated_Control_Saline_0_lung_rep5

description:
genecounts_lung.csv
RL85_HGMMWDMXX_AGGTTATA.CAGTTCCG_L002_R1.fastq.gz


title: THP-1 at 4 days post infection, HCMV

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine

description: RNA extracted from THP-1 cells after HCMV infection (Towne strain)

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the human Ensembl GRCh38.95 primary assembly and NCBI FJ616285.1 HCMV Towne genome with STAR version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in at least four samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights.
Genome_build: Human Ensembl GRCh38.95 primary assembly
Supplementary_files_format_and_content: Count   CPM     RPKM
Supplementary_files_format_and_content: raw counts at gene level

source_name: THP-1 cells

extract_protocol:
Total RNAs were extracted with the Trizol reagent (Invitrogen, USA).
cDNA libraries were constructed by using the Truseq™ RNA Sample Preparation Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: THP-1 cells were infected at a MOI of 5 with HCMV towne strain in culture medium.

tag: infection

value: HCMV


title: PVG_Untreated_Virus_OVA_2_lung_rep4

description:
genecounts_lung.csv
RL83_HGMMWDMXX_CTGCTTCC.GATAGATC_L002_R1.fastq.gz


title: PVG_Untreated_Virus_OVA_2_lung_rep6

description:
genecounts_lung.csv
RL97_HGMMWDMXX_TTCCTGTT.AGTATCTT_L002_R1.fastq.gz


title: PVG_Untreated_Virus_OVA_9_lung_rep5

description:
genecounts_lung.csv
RL84_HGMMWDMXX_TCATCCTT.AGCGAGCT_L002_R1.fastq.gz


title: PVG_OM_treated_Control_Saline_0_lung_rep6

description:
genecounts_lung.csv
RL93_HGMMWDMXX_TACTCATA.CCTGTGGC_L002_R1.fastq.gz


title: PVG_OM_treated_Virus_OVA_9_lung_rep6

description:
genecounts_lung.csv
RL96_HGMMWDMXX_CTAGCGCT.GTGTAGAC_L002_R1.fastq.gz


title: THP-1 at 4 days post infection, Mock

description: RNA extracted from THP-1 cells after Mock infection

value: Mock


title: PVG_Untreated_Control_Saline_0_lung_rep5

description:
genecounts_lung.csv
RL81_HGMMWDMXX_AACTGTAG.ACGCCGCA_L002_R1.fastq.gz


title: PVG_OM_treated_Virus_OVA_9_lung_rep4

description:
genecounts_lung.csv
RL80_HGMMWDMXX_GTGAATAT.TCTCATTC_L002_R1.fastq.gz


title: PVG_OM_treated_Virus_OVA_2_lung_rep4

description:
genecounts_lung.csv
RL79_HGMMWDMXX_ACAGGCGC.CTCTGCCT_L002_R1.fastq.gz


title: PVG_OM_treated_Virus_Saline_1_lung_rep4

description:
genecounts_lung.csv
RL78_HGMMWDMXX_CATAGAGT.TGCCACCA_L002_R1.fastq.gz


title: PVG_OM_treated_Virus_OVA_9_lung_rep5

description:
genecounts_lung.csv
RL88_HGMMWDMXX_TCTGTTGG.TCGAATGG_L002_R1.fastq.gz


title: PVG_OM_treated_Control_Saline_0_lung_rep4

description:
genecounts_lung.csv
RL77_HGMMWDMXX_TGCGAGAC.CATTGTTG_L002_R1.fastq.gz


title: control_rep2

city: Taipei

first: Yi-Shuian

last: Huang

address: 128 Sec. 2, Academia Rd. Nankang

country: Taiwan

institute: Institute of Biomedical Sciences, Academia Sinica

description: RNAs precipitated by control IgG

hyb_protocol: 0.6 ug Cy3-labled cRNA was fragmented to ~50-100 nt by incubation with fragmentation buffer at 60°C for 30 minutes, which were used for array (Agilent SurePrint G3 Mouse GE 8x60K Microarray) hybridization at 65°C for 17 h.

scan_protocol: Microarrays are scanned with an Agilent microarray scanner at 535 nm for Cy3.

data_processing:
The images were analyzed and quantified by using Feature extraction 10.5.1.1 software (Agilent).
ProcessedSignal(normalized by quantile)

source_name: control IgG RIP, replicate 2

label_protocol: RNA (0.2 ug per sample) was amplified by a Low Input Quick-Amp Labeling kit (Agilent) and labeled with Cy3 (CyDye, Agilent).

growth_protocol: 8-week-old male C57BL/6 mice from LASCO, Taiwan

extract_protocol: RNA was extracted using phenol:chloroform:isoamyl alcohol pH4.5.

treatment_protocol: corticohippocampal lysate incubated with either control or CPEB3 IgG-bound beads for 3 hours

value: corticohippocampal tissue

tag: gender

value: 8 weeks

tag: rip antibody

value: control


title: PVG_Untreated_Virus_OVA_9_lung_rep4

description:
genecounts_lung.csv
RL76_HGMMWDMXX_GACGTCTT.GGTTCACC_L002_R1.fastq.gz


title: HCT_CutnRun_input

city: Tallahassee

first: David

middle: M

last: Gilbert

address: 319 Stadium Drive

department: Department of Biological Science

institute: Florida State University

description:
Cut&Run
HCT116_RIF1_CutnRun_log2_FE_over_Input.bigwig

data_processing:
Repli-Seq experiments that are marked E and L were analysed according to (Marchal et al., 2018 PMID: 29599440). High-resolution Repli-Seq analysis was performed according to (Zhao et al., 2020 PMID: 32209126). Single-cell repli-seq reads were split according to the barcode list provided in the accompanying manuscript using awk. The subsequent analyses and construction of binarised arrays were performed according to (Dileep et al., 2018, PMID: 29382831). The Hi-C experiments were aligned and deduplicated using HiCUP (https://www.bioinformatics.babraham.ac.uk/projects/hicup/). The subsequent bam files were converted to pair text files using 4DN DCIC utility bam2pairs. Pairs were loaded into cooler at various bin sizes for downstream analyses. ChIP-seq reads were aligned using bowtie-2 to hg38 and PCR duplicates were removed using samtools markdup. Peak calling and fold enrichment over input were calculated using MACS2. In the cases where drosophila spike-in was used the datasets to be compared against each other (e.g. WT vs KO) were normalised according to (Orlando et al 2014, Cell Reports, PMID: 25437568).RNA-seq reads were aligned using STAR. The gene annotation for genome build GRCh38.p10 used for alignment was downloaded from Ensembl. Single cell RNA-seq was aligned to GRCh38 using 10X Genomics spaceranger v1.0.0. The gene count matrix output was used as input for Seurat v 4.0 for further downstream analyses.
Genome_build: hg38

source_name: HCT116 cells

growth_protocol: HCT116 cells were grown in McCoy’s 5A media plus 10% FBS and 1% Pen/Strep and passaged by trypsinization.

extract_protocol:
Cells were washed and bound to Concanavalin-A-coated magnetic beads, and permeabilized in wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and one Roche Complete protein inhibitor tablet per 50 mL) containing 0.03% digitonin and 20 mM EDTA (Dig-wash). Antibody was added to a final concentration of 1:100 and incubated overnight at 4°C. Cells were washed with Dig-wash buffer and incubated with Protein-A-MNase (pA-MN) for 1 hour at 4°C. Cells were washed three times with Dig-wash buffer to remove unbound pA-MN before placing cells in an ice-cold block and activating cleavage with the addition of CaCl2 to 2mM final concentration. Cleavage was stopped by the addition of 2x Stop Buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 0.05 mg/mL glycogen, 5 μg/mL RNase A), and fragments were released by 30 min incubation at 37°C. Supernatant was recovered and DNA was purified with phenol:chloroform extraction and precipitation with ethanol, before being used as input for library preparation.
Sequencing libraries were prepared from DNA fragments as described in (PMID: 28079019) but without size-selection, following the KAPA DNA polymerase library preparation kit protocol

tag: cell type

value: human colorectal cancer cell line

value: Wild type


title: E_fraction_H9_RIF1shRNA_Repliseq

description:
Repli-seq
H9_RIF1_shRNA_KD_log2EL_RT.bigwig

source_name: H9 hESCs

growth_protocol: H9 hESCs were grown in feeder free conditions on Geltrex matrix (Thermo Fisher A14133) coated dishes in StemPro (Thermo Fisher A100701) media according to manufacturer's specifications. hESCs were passaged with ReLeSR (StemCell Technologies 05872) according to manufacturer’s specifications.

extract_protocol:
gDNA was isolated with SDS-PK buffer containing 0.2 mg/ml proteinase K for 2 hours at 56C followed by purification with 800 µl of Genomic Lysis Buffer from the Zymo Quick-DNA Microprep Kit according to manufacturers instructions
DNA from was made into repli-seq library described in (PMID: 29599440)

treatment_protocol: Cells were transduced with lentivirus expressing RIF1 shRNA and selected with puromycin.

value: human embryonic stem cell line

value: RIF1 shRNA


title: CP3_rep1

description: RNAs precipitated by CPEB3 IgG

source_name: CP3 IgG RIP, replicate 1

tag: tissue

value: male

value: CPEB3 IgG


title: PVG_Untreated_Virus_OVA_2_lung_rep3

description:
genecounts_lung.csv
RL75_HGMMWDMXX_AGTACTCC.AACCTGTT_L002_R1.fastq.gz

value: PVG

value: days post infection (dpi):2


title: E_fraction_HCT_RIF1KO_control_siRNA_Repliseq

description:
Repli-seq
HCT_RIF1KO_H3K9me3KD_ctrlsiRNA_log2EL_RT.bigwig

treatment_protocol: Cells were transfected with scrambled control siRNAs and allowed to recover for 72hrs before a second transfection with the same siRNAs and 48hrs recovery. Cells were then labeled with 100uM BrdU for 2 hours before fixation.

value: RIF1 KO control siRNA


title: Rad21_H9_RIF1KO_ChIPSeq

description:
ChIP-seq
H9_RIF1KO_Rad21_tag_pileup.bigwig

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Drosophila S2 cells at a 2:1 ratio to human cells were used as spike in.
After washing with high salt buffer, LiCl buffer, and TE, chromatin was eluted and reverse crosslinked. Purified DNA was ethanol precipitated followed by Illumina Truseq library preparation. Libraries for Illumina sequencing were constructed using the following standard protocol. Fragment ends were repaired using the NEBNext End Repair Module and adenosine was added at the 3’ ends of fragments using Klenow fragment (3’ to 5’ exo minus, New England Biolabs), universal adaptors were ligated to the A-tailed DNA fragments at room temperature for 1 h with T4 DNA ligase (New England Biolabs) and amplified with Illumina barcoded primers using KAPA SYBR FAST qPCR Master Mix for 5~12 PCR cycles to obtain enough DNA for sequencing.

value: RIF1 KO

value: Rad21 Abcam (ab992)


title: control_rep1

description: RNAs precipitated by control IgG

source_name: control IgG RIP, replicate 1

tag: age


title: PVG_Untreated_Virus_Saline_1_lung_rep5

description:
genecounts_lung.csv
RL82_HGMMWDMXX_GGTCACGA.GTATTATG_L002_R1.fastq.gz

value: Untreated

value: days post infection (dpi):1


title: PVG_Untreated_Control_Saline_0_lung_rep4

description:
genecounts_lung.csv
RL73_HGMMWDMXX_CAATTAAC.CGAGATAT_L002_R1.fastq.gz

value: days post infection (dpi):0


title: PVG_Untreated_Virus_Saline_1_lung_rep4

description:
genecounts_lung.csv
RL74_HGMMWDMXX_TGGCCGGT.TAGAGCGC_L002_R1.fastq.gz


title: PVG_OM_treated_Virus_OVA_9_lung_rep3

description:
genecounts_lung.csv
RL72_HGMMWDMXX_GTCTACAC.GCCAAGGT_L002_R1.fastq.gz

value: days post infection (dpi):9


title: 2_PB_uns_5pGEX

extract_protocol:
CSF and blood were obtained during diagnostic and research procedures after subjects had provided informed consent; 20 to 30 mL of CSF was centrifuged immediately after collection at 400 × g for 15 min at 4 °C. The pellet was resuspended in ∼80 µL of residual supernatant, and lymphocytes were counted using a hemocytometer. Peripheral blood mononuclear cells (PBMCs) were isolated using cell preparation tubes and resuspended in 2% fetal bovine serum. All experiments were performed immediately with freshly collected, unsorted cells.
Sequencing libraries were prepared using 3′ or 5′ library preparation kits (10x Genomics).

tag: subject status

value: Healthy

tag: subject id

value: PB


title: L_fraction_HCT_RIF1KO_control_siRNA_Repliseq

value: human colorectal cancer cell line

tag: genotype

tag: chip antibody


title: H3K9me3_HCT_RIF1KO_Dm_spikein_ChIPseq

description:
ChIP-seq
HCT116_RIF1KO_H3K9me3_dm_normed_tag_count.bigwig

value: H3K9me3 Abcam (ab8898)


title: H3K27ac_HCT_WT_Dm_spikein_ChIPseq

description:
ChIP-seq
HCT116_WT_H3K27ac_dm_normed_tag_count.bigwig
HCT116_WT_H3K27ac_log2_FE_over_Input.bw

value: Wild type

value: H3K27ac Abcam (ab4729)


title: H3K9me3_H9_WT_Dm_spikein_ChIPseq

description:
ChIP-seq
H9_WT_H3K9me3_dm_normed_tag_count.bigwig

value: human embryonic stem cell line


title: L_fraction_H9_RIF1shRNA_Repliseq

value: RIF1 shRNA


title: H3K27ac_HCT_RIF1KO_Dm_spikein_ChIPseq

description:
ChIP-seq
HCT116_RIF1KO_H3K27ac_dm_normed_tag_count.bigwig
HCT116_RIF1KO_H3K27ac_log2_FE_over_input.bw


title: H3K27ac_H9_WT_Dm_spikein_ChIPseq

description:
ChIP-seq
H9_WT_H3K27ac_log2_foldenrichment_over_input.bw


title: PVG_OM_treated_Virus_Saline_1_lung_rep3

description:
genecounts_lung.csv
RL70_HGMMWDMXX_ATTGTGAA.TGCATTGC_L002_R1.fastq.gz

tag: strain

value: PVG

value: male


title: CP3_rep2

description: RNAs precipitated by CPEB3 IgG

source_name: CP3 IgG RIP, replicate 2

value: corticohippocampal tissue

value: 8 weeks

value: CPEB3 IgG


title: H3K9me3_HCT_WT_Dm_spikein_ChIPseq

description:
ChIP-seq
HCT116_WT_H3K9me3_dm_normed_tag_count.bigwig