title: WBGS_KO_72h_rep2

first: Maximilian

last: Stötzel

address: Ihnestraße 65

institute: Max-Planck-Institute for molecular genetics

data_processing:
Bisulfite-converted reads were quality filtered and adapter trimmed using cutadapt (v2.4), followed by alignment to the mm9 reference genome with bsmap using the following parameter: -v 0.01 -s 16 -w 100 -S 1 -R -u -q 20. Duplicate reads were removed using GATK MarkDuplicates (v4.1.0.0).
Methylation rates were called using mcall using default parameter and subsequently filtered for coverage (min 10 reads).
Assembly: mm10
Supplementary files format and content: bigWig file of 10X coverage filtered methylation rate BED file (<chr> <start> <end> <methylation rate>)

source_name: E14 TET1/2 DKO, 72 hours

extract_protocol:
Purelink Genomic DNA mini kit (Invitrogen)
Accel-NGS Methyl-Seq DNA Library Kit (manufacturer's recommendation)

value: embryonic stem cell

value: E14 TET1/2 DKO

value: mTORi


title: HIO Mut-No Dox TXP Rep 3

status: Public on Mar 19 2024

type: SRA

city: Cincinnati

first: Jim

middle: M

last: Wells

state: Ohio

address: 3333 Burnet Ave

department: Developmental Biology

country: USA

institute: Cincinnati Childrens Hospital

library_source: transcriptomic

data_processing:
RNA-seq data was analyzed using Computational Suite for Bioinformaticians and Biologists (CSBB – v3.0.0) using the Process-RNASeq_PairedEnd and Generate-TPM_Counts_Matrix modules (https://github.com/praneet1988/Computational-Suite-For-Bioinformaticians-and-Biologists).
Assembly: hg38 iPSC RNA-seq
Supplementary files format and content: tab-delimited text files including TPM per sample

molecule: total RNA

organism: Homo sapiens

source_name: hPSC-derived intestinal organoid

extract_protocol:
RNA was extracted using RNA NucleoSpin kit (Macherey-Nagel) according to manufacturer's instructions. >300 ng/sample of RNA used to make RNA library.
Library construction was performed by CCHMC DNA sequencing core using standard Illumina mRNA Stranded Library Preperation protocol.

tag: tissue

value: hPSC-derived intestinal organoid

tag: cell line

tag: cell type

value: Pooled organoids epithelium and mesenchyme

tag: age

value: 35 days post-hPSC + 10wk transplant

tag: treatment

value: No Treatment


title: WBGS_KO_24h_rep2

city: Berlin

state: Berlin

department: Meissner

country: Germany

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: E14 TET1/2 DKO, 24 hours

treatment_protocol: Cells were cultured without (0h) or in presence of the mTOR inhibitor Ink128 (24h, 72h, 144h)


title: 119133_ATTACTCG-CTTCGCCT

city: SAN FRANCISCO

first: Hanrui

last: Zhang

state: California

address: 148 Locksley Ave Apt2

institute: University of Michigan

description:
8w-BS-a587-9
Sample_119133

data_processing:
The RNAseq data were processed as previously described. Briefly, reads were pseudo-aligned to the ENSEMBL 108 mouse reference cDNA sequences (June 2020, GRCm39) using Kallisto 0.45 and quantified transcripts aggregated by their gene were fed to Sleuth 0.30.1 for differential expression analysis.
Assembly: mm39
Supplementary files format and content: tar archives include abundance.h5, abundance.tsv, and run_info.json files.
Supplementary files format and content: Tab-delimited text files include est_counts and tpm values.

source_name: Brain Stem

growth_protocol: Homozygous YACMJD84.2Q-C57BL/6 transgenic mice (referred to in this study as “Q84 mice”) and wild type (WT) sex- and age-matched controls were used. Genotyping was completed via tail biopsy DNA isolation prior to weaning and confirmed postmortem.

extract_protocol:
RNA was extracted from PBS-perfused, flash-frozen BS/Dien, spinal cord, and cerebellum samples from the left hemisphere. Using the Next Advance Bullet Blender, samples were homogenized in radioimmunoprecipitation assay (RIPA, by Sigma, St. Louis, MO) buffer (750 µL for BS/Dien and 500 µL for cerebellum and spinal cord samples) with added proteinase inhibitor (BioRad, Hercules, CA). A 250 µL aliquot of this lysate was reserved for Western blot analysis and the remaining sample was used for RNA extraction.
RNA extraction was conducted using the QIAshredder (Qiagen Hilden, Germany), RNeasy Mini Kit (Qiagen, Hilden, Germany), and DNase I kit (Qiagen, Hilden, Germany), then eluted in RNase-free water, according to manufacturer’s instructions. RNA samples were assessed by nanodrop to determine concentration and sample purity.
For library preparation, 1 μg of total BS/Dien RNA was submitted to the University of Michigan Sequencing Core for Illumina HiSeq library preparation, quality control, and RNA sequencing. WT and Q84 RNA samples were chosen for RNA sequencing based on RIN number (>7 RIN) and, if applicable, CAG repeat expansion size (>average 72Q) as determined by Laragen, Inc. The University of Michigan Bioinformatics Core generated libraries (Illumina TruSeq) from purified brain RNA samples, completed quality control analysis, and ran 75x75 paired end sequencing on Illumina HiSeq 4000.

treatment_protocol:
4-6 mice (equal numbers of males and females) per genotype were collected for tissue analysis at 4, 12, or 16 weeks of age. Left hemisphere brain tissue was macrodissected into brainstem and diencephalon tissue (BS/Dien - includes whole of brainstem, striatum, and thalamus), cerebellum, and cervical spinal cord for biochemical analysis.
Premanifest mice used in this study received a post-natal day 0 injection of either ASO-5 or PBS into both lateral ventricles. Pups were placed on ice for cryo-anesthetization before performing a bilateral intracerebroventricular (ICV) injection of either ASO-5 or PBS (2 µL per hemisphere, 5 µg/µL ASO-5). Immediately following injection, pups were placed on a heating pad before returning to their cage. Pups were monitored and weighed weekly following treatment. Brain and peripheral tissue were collected from mice at 4 weeks of age for biochemical and histological assessment. Symptomatic ASO treatment was completed as previously described,9,18,53 with 700 µg of ASO-5 injected in a total volume of 10 µL at 8 weeks of age. Post-operative care was performed for at least 7 days following treatment.

value: Brain Stem

tag: time

value: 8 weeks

tag: genotype

value: WT


title: WBGS_KO_72h_rep1


title: 30-Smoking-Anhui-5 US84403582_252800518908_S01_GE1_107_Sep09_2_1

type: RNA

city: Minato

first: Yoshihiro

last: Kawaoka

state: Tokyo

address: Shirokanedai 4-6-1

department: ERATO Influenza-induced Host Responses Project

country: Japan

institute: Japanese Science and Technology Agency

hyb_protocol: Using Agilents Gene Expression Hybridizatoin kit #4 and Gene Expression wash pack #5, Cy3-labeled cRNA preparations were hybridized with mouse arrays (Agilent Microarray Design Identification Number 028005) for 17 h at 65°C.

scan_protocol: Immediately after washing, Feature Extraction Software, version 7 (Agilent Technologies) was used for image analysis and data extraction.

data_processing: Per chip and per gene normalization was performed using the LIMMA package in R.

source_name: lung

label_protocol: Using the Quick Amp Labeling Kit, T7 RNA polymerase was used to simultaneously amplify target material and incorporate cyanine 3-labeled CTP to prepare Cy3-labeled cRNA.

extract_protocol: Total RNA was extracted from lung samples by using the RNeasy Mini Kit (Qiagen), according to the manufacturer’s protocol.

treatment_protocol: Seven-week-old female C57BL/6j mice were purchased from Charles River Japan Inc. Mice were exposed to cigarette smoke (Peace®, 28 mg of tar, 2.3 mg of nicotine/cigarette, Japan Tobacco Inc., Tokyo, Japan) or to air (as a control) for 20‒30 min per time by using a mainstream smoke-generating apparatus for period of 30, 90, or 180 days. Following smoke exposure, mice were intranasally inoculated with A(H7N9) virus (refered to as the Anhiu strain). For controls, mice were mock-infected with sterile PBS-solution. Lungs were harvested at days 2 or 5 post infection.

tag: animal #

tag: Sex

value: female

tag: exposure days

tag: smoking or air

value: Smoking

tag: strain

value: Anhui

tag: day

value: C57BL/6j mouse


title: 30-Smoking-Anhui-5 US84403582_252800518907_S01_GE1_107_Sep09_2_1


title: HIO Mut-No Dox TXP Rep 1


title: HIO Mut-RFX6 Ind D7 Rep 4

source_name: hPSC-derived hindgut

value: hPSC-derived hindgut

value: 7 days post-hPSC

value: Doxycycline D4-7


title: 30-Air-PBS-2 US84403582_252800518909_S01_GE1_107_Sep09_1_4

value: Air

value: PBS


title: WBGS_KO_24h_rep1

value: embryonic stem cell

value: E14 TET1/2 DKO

value: mTORi


title: 119132_ATTACTCG-TCAGAGCC

description:
8w-BS-a590-0
Sample_119132


title: WBGS_KO_N_rep2

source_name: E14 TET1/2 DKO, 0 hours

value: control


title: 119131_ATTACTCG-AGGATAGG

description:
8w-BS-a594-3
Sample_119131


title: HIO Mut-RFX6 Ind D7 Rep 3

value: Pooled organoids epithelium and mesenchyme


title: HIO Mut-RFX6 Ind D7 Rep 2


title: 119134_ATTACTCG-TAAGATTA

description:
8w-BS-a591-7
Sample_119134

value: Brain Stem


title: WBGS_KO_N_rep1


title: 119130_ATTACTCG-GCCTCTAT

description:
8w-BS-a588-2
Sample_119130

value: 8 weeks


title: 30-Air-PBS-2 US84403582_252800518908_S01_GE1_107_Sep09_1_4


title: WBGS_WT_144h_rep2

source_name: E14 wild-type, 144 hours

value: E14 wild-type


title: HIO Mut-PDX1 Ind D7 Rep 3


title: 119129_ATTACTCG-AGGCTATA

description:
8w-BS-a592-0
Sample_119129

value: WT


title: HIO Mut-RFX6 Ind D7 Rep 1


title: Week-10 wild-type replicate5

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

data_processing:
Transcript abundance was estimated with Salmon(v1.1.0) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.6.2) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.26.0).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

source_name: Brain

growth_protocol: ES cells containing the Katnal2-targeted allele were received from EUCOMM (MAE-4330; Katnal2tm1a(EUCOMM)Wtsi) and used to generate transgenic mice. The first-generation mice were backcrossed with mice in the C57BL/6J background for more than 5 generations before conducting experiments. Mating with Protamine-Flp mice was used to generate Katnal2fl/+ mice. Fertilized eggs (from the breeding with C57BL/6J WT mice) at the two-cell embryo stage were treated with purified HTNC, a cell-permeable Cre recombinase, at a final concentration of 0.3 μM for 30–40 min. All mice were housed and bred at the mouse facility of Korea Advanced Institute of Science and Technology (KAIST) and maintained according to the Animal Research Requirements of KAIST. All animals were fed ad libitum and housed under 12 h light/dark cycle (light phase during 1 am to 1 pm). Mice were weaned at around the age of postnatal day 21, and mixed-genotype littermate mice with same gender were housed together until experiments. All procedures were approved by the Committee of Animal Research at KAIST (KAIST; KA2020-80).

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole brain

value: 10 week

value: male

value: wildtype


title: HIO Mut-PDX1 Ind D7 Rep 2

value: hPSC-derived hindgut

value: 7 days post-hPSC


title: WBGS_WT_72h_rep2

source_name: E14 wild-type, 72 hours


title: Week-10 wild-type replicate4


title: 30-Air-PBS-2 US84403582_252800518907_S01_GE1_107_Sep09_1_4

value: female

value: Air

value: C57BL/6j mouse


title: HIO Mut-PDX1 Ind D7 Rep 1

value: Doxycycline D4-7


title: 30-Air-Anhui-2 US84403582_252800518909_S01_GE1_107_Sep09_1_3

value: Anhui


title: WBGS_WT_72h_rep1

value: embryonic stem cell

value: mTORi


title: 30-Air-Anhui-2 US84403582_252800518908_S01_GE1_107_Sep09_1_3


title: Week-10 wild-type replicate3


title: 30-Smoking-PBS-2 US84403582_252800518909_S01_GE1_107_Sep09_1_2

value: Smoking

value: PBS


title: 30-Air-Anhui-2 US84403582_252800518907_S01_GE1_107_Sep09_1_3


title: WBGS_WT_24h_rep2

source_name: E14 wild-type, 24 hours

value: E14 wild-type


title: HIO Mut-CRISPR-Corr D7 Rep 4

value: hiPSC 95b_1

value: Pooled organoids epithelium and mesenchyme

value: No Treatment


title: 30-Smoking-PBS-2 US84403582_252800518908_S01_GE1_107_Sep09_1_2


title: HIO Mut-CRISPR-Corr D7 Rep 3


title: Week-10 wild-type replicate2

value: whole brain

value: 10 week

value: male


title: WBGS_WT_144h_rep1


title: 30-Smoking-PBS-2 US84403582_252800518907_S01_GE1_107_Sep09_1_2


title: WBGS_WT_24h_rep1


title: Week-10 Katnal2 knock-out replicate5

value: Katnal2 Knock-out


title: Week-10 wild-type replicate1

value: wildtype


title: 30-Smoking-Anhui-2 US84403582_252800518909_S01_GE1_107_Sep09_1_1

value: female


title: HIO Mut-CRISPR-Corr D7 Rep 2

value: hPSC-derived hindgut

value: 7 days post-hPSC


title: HIO Mut-CRISPR-Corr D7 Rep 1


title: 30-Smoking-Anhui-2 US84403582_252800518908_S01_GE1_107_Sep09_1_1

value: Anhui

value: C57BL/6j mouse


title: WBGS_WT_N_rep2

source_name: E14 wild-type, 0 hours

value: embryonic stem cell

value: control


title: 30-Smoking-Anhui-2 US84403582_252800518907_S01_GE1_107_Sep09_1_1

value: Smoking


title: PTET2

data_processing:
Assembly: mm10
bigWig coverage files

extract_protocol:
Cells are crosslinked with 0.15mJ/cm2 UV-C irradiation, lysed with 1xNLB and homogenized by waterbath-sonication. Target protein of interest is pulled-down with paramagnetic beads pre-coupled to antibodies against the protein of interest.  After a brief RNAseI-digestion, RNA 3'-ends are healed with T4 PNK. Custom-made, barcoded adapters are ligated using T4 RNA Ligase 1 or T4 RNA Ligase 2KQ (if pre-adenylated adapters are used) for 1 hr at 25˚C. Custom FLASH adapters contained two barcodes and random nucleotides adjacent to the 3'-adapters according to the pattern NNBBNTTTTTTNN (N: random tag nucleotide, T: tag nucleotide, B: RY-space tag nucleotide). Random tags are used to merge PCR-duplicates, regular tags are used to specify the pulldown condition, and semi-random RY-space tags are used to distinguish the biological replicates (RR: replicate A, YY: replicate B, R: purine, Y: pyrimidine). Excess adapters are washed away, negative controls (IgG) are mixed with experimental controls and RNA is isolated with Proteinase K treatment and column purification. Isolated RNA is reverse-transcribed and RNaseH-treated. cDNA is column-purified and circularized with CircLigase for 2-16hrs. Circularized cDNA is directly PCR amplified, quantified with Qubit / Bioanalyzer and sequenced on Illumina NextSeq 500 in paired-end mode (Ilik et al. 2020).
cDNA is column-purified and circularized with CircLigase for 2-16hrs. Circularized cDNA is directly PCR amplified, quantified with Qubit / Bioanalyzer and sequenced on Illumina NextSeq 500 in paired-end mode.

value: mTORi


title: WBGS_WT_N_rep1

value: E14 wild-type


title: HIO Mut D7 Rep 2

value: Pooled organoids epithelium and mesenchyme


title: Week-10 Katnal2 knock-out replicate3


title: Week-10 Katnal2 knock-out replicate2


title: PTET1


title: Week-10 Katnal2 knock-out replicate4


title: human T_ALL PDX from mouse 8 treated with Teplizumab mAb

city: Orsay

first: Sabine

last: Druillennec

address: Bat 110 centre universitaire

country: France

institute: Institut Curie

hyb_protocol: 3 μg of cDNAs were hybridized for 16 hours at 45C on GeneChip Human Gene 2.0 ST arrays (Affymetrix).

scan_protocol: The chips were stained in the GeneChip Fluidics Station 450 (Affymetrix) and scanned with the GeneChip Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing:
Raw data were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2.  CEL files were further processed with Affymetrix Expression Console software to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.
RMA expression estimated from expression Console software version 1.4.1. RMA algorithms with default settings.

label: biotin

source_name: T_ALL tumor from human patient

label_protocol: Single-stranded cDNA were labeled with the Affymetrix GeneChip WT Terminal Labeling Kit according to Affymetrix recommendations.

growth_protocol: NSG female mice were tail vein injected (1 million cells/mouse) with human T-ALL cells (hCD45+; hCD7+) and treated when tumor burden reached around 1% in blood.

extract_protocol: Single strand cDNA targets were prepared starting from 200 ng of total RNA (Rneasy kit QIAGEN) using the Ambion WT Expression Kit according to Affymetrix recommendations.

treatment_protocol: T-ALL xenografted mice were treated for 6h with either 40µg control IgG2a, or OKT3 or Teplizumab. Mice were killed and  leukemic cells were flow cytometry-sorted (hCD45+; hCD7+).

value: CD45+ CD7+ tumor cell sorted from bone marrow

value: Teplizumab mAb

tag: mouse id


title: HIO Mut D7 Rep 1

value: No Treatment


title: HIO  WT D7 Rep 4


title: NTET2


title: Week-03 wild-type replicate4

value: whole brain

value: 3 week

value: male


title: HIO  WT D7 Rep 3


title: 72hTET2


title: human T_ALL PDX from mouse 7 treated with Teplizumab mAb


title: human T_ALL PDX from mouse 9 treated with Teplizumab mAb


title: HIO Mut D7 Rep 4


title: NTET1


title: Week-10 Katnal2 knock-out replicate1

value: 10 week

value: Katnal2 Knock-out


title: human T_ALL PDX from mouse 6 treated with OKT3 mAb

value: OKT3 mAb


title: Week-03 wild-type replicate5

value: wildtype


title: condDMSO_dko_reprep1_time0

city: Heidelberg

first: Alessia

last: Ruggieri

address: Im Neuenheimer Feld 344

department: Dpt. of Infectious Diseases, Molecular Virology

institute: Heidelberg University

data_processing:
Reads were mapped to the human genome (hg38, using Gencode V27 as downloaded from the UCSC Genome browser wgEncodeGencodeBasic27 table as transcriptome annotation) and the ERCC92 spike-in mix with STAR v2.5.3a, allowing up to 2 mismatches.
Read counts were summarized at the gene level with the featureCounts function of the subread package v1.6.3. A read was only counted when it was completely contained within an exon.
Read counts were normalized to library size using the median of ratios method of the DESeq2 package.
Assembly: hg38
Supplementary files format and content: csv file containing raw read counts per gene

source_name: Huh7 cells

growth_protocol: Huh7 control cell clone #1 and Brf1/TTP DKO cell clone #18 were cultivated in complete Dulbecco’s modified Eagle medium (DMEM) supplemented with 10 % fetal calf serum (Capricorn), 2 mM L-glutamine, non-essential amino acids, 100 U/ml penicillin and 100 µg/ml streptomycin (all from Gibco).

extract_protocol:
RNA was extracted with the NucleoSpin RNA Plus kit (Macherey Nagel) following the manufacturer’s protocol.
Prior to rRNA depletion using the  NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat, E7400L), 1 μg total RNA was mixed with 2 μl 1:100 diluted ERCC RNA Spike-In Mix (Thermo Fisher Scientific). Libraries were prepared with the NEBNext Ultra II Directional RNA Kit (NEB). Libraries were equimolarly pooled and sequenced on a NextSeq550 system (Illumina) with 80 bases single-end.

treatment_protocol: Cells were seeded one day prior to treatment (1.5 x 10^5 cells).  Cells were treated with DMSO for 3h prior to a 10-min treatment with 5 µg/ml actinomycin D in DMSO and sample harvesting.

value: Huh7 cells

value: Brf1/TTP DKO


title: condDMSO_dko_reprep2_time0

value: DMSO for 3h prior to a 10-min treatment with 5 µg/ml actinomycin D in DMSO


title: human T_ALL PDX from mouse 5 treated with OKT3 mAb


title: control

value: embryonic stem cell

value: control


title: HIO Mut D7 Rep 3

value: hPSC-derived hindgut

value: 7 days post-hPSC


title: 72hTET1

value: mTORi


title: human T_ALL PDX from mouse 3 treated with control IgG2a

value: CD45+ CD7+ tumor cell sorted from bone marrow

value: control antibody IgG2a


title: HIO  WT D7 Rep 2

value: Pooled organoids epithelium and mesenchyme

value: No Treatment


title: human T_ALL PDX from mouse 2 treated with control IgG2a


title: Week-03 wild-type replicate1

value: whole brain

value: 3 week

value: male


title: condDMSO_ctrl_reprep2_time0

value: WT


title: human T_ALL PDX from mouse 1 treated with control IgG2a


title: Week-03 wild-type replicate2

value: wildtype


title: condDMSO_ctrl_reprep1_time0

value: Huh7 cells


title: HIO Mut-CRISPR-Corr TXP Rep 3

value: hPSC-derived intestinal organoid

value: hiPSC 95b_1

value: 35 days post-hPSC + 10wk transplant


title: crz1_KCl_48_3

city: Worcester

first: Jennifer

last: Benanti

state: MA

address: 364 Plantation St., LRB 525

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

data_processing:
Paired-end reads were aligned to Saccharomyces_cerevisiae.R64-1-1, with star_2.5.3a, annotated with Saccharomyces_cerevisiae.R64-1-1.90.gtf.
Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts. Differential expression (DE) analysis was performed with DESeq2. Within DE analysis, 'ashr' was used to create log2 Fold Change (LFC) shrinkage for each comparison. Significant DE genes (DEGs) were filtered with the criteria FDR < 0.05.
Assembly: Saccharomyces_cerevisiae.R64-1-1,
Supplementary files format and content: csv, raw count and TPM

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: haploid yeast

growth_protocol: All strains are in the BY4741 background and were grown in synthetic media with ammonium chloride as a nitrogen source.

extract_protocol:
Total RNA was purified using an acid-phenol extraction protocol.
poyA enrichment and library construction were performed by BGI Americas

treatment_protocol: Yeast cells were grown in 400mM KCl and diluted every 12 hours to maintain logarithmic growth. Samples were collected after 48 hours of KCl treatment for RNA isolation.

value: haploid yeast

value: MATa his3delta1 ura3delta0 leu2delta0 lys2delta0 crz1delta::LEU2 ChrVI181901-182001::HYG-TEFp-GFP(Y66F)

value: 400mM KCl

tag: time point

value: 48 hours


title: 24hTET2

value: embryonic stem cell

value: mTORi


title: HIO  WT D7 Rep 1

value: hPSC-derived hindgut

value: Pooled organoids epithelium and mesenchyme

value: 7 days post-hPSC


title: Week-03 wild-type replicate3

value: whole brain

value: 3 week


title: human T_ALL PDX from mouse 4 treated with OKT3 mAb

value: CD45+ CD7+ tumor cell sorted from bone marrow

value: OKT3 mAb


title: 24hTET1


title: Week-03 Katnal2 knock-out replicate4

value: male

value: Katnal2 Knock-out


title: HIO Mut-CRISPR-Corr TXP Rep 1

value: hPSC-derived intestinal organoid

value: hiPSC 95b_1

value: No Treatment


title: crz1_KCl_48_1

value: haploid yeast

value: MATa his3delta1 ura3delta0 leu2delta0 lys2delta0 crz1delta::LEU2 ChrVI181901-182001::HYG-TEFp-GFP(Y66F)


title: crz1_control_3

value: 0 hours


title: Week-03 Katnal2 knock-out replicate2


title: HIO Mut Ile TXP Rep 3

value: 35 days post-hPSC + 10wk transplant


title: Week-03 Katnal2 knock-out replicate3


title: crz1_control_2


title: HIO Mut Ile TXP Rep 1


title: Week-03 Katnal2 knock-out replicate1


title: HIO Mut Ile TXP Rep 2


title: crz1_control_1


title: Week-03 Katnal2 knock-out replicate5


title: HIO Mut Duod TXP Rep 3


title: HIO Mut-CRISPR-Corr TXP Rep 2


title: crz1_KCl_48_2

value: 400mM KCl

value: 48 hours


title: HIO Mut Duod TXP Rep 2

value: Pooled organoids epithelium and mesenchyme


title: crz1cnb1_KCl_48_3

value: MATa his3delta1 ura3delta0 leu2delta0 lys2delta0 crz1delta::LEU2 cnb1delta::KanMx ChrVI181901-182001::HYG-TEFp-GFP(Y66F)


title: HIO WT Ile TXP Rep 2


title: VANCO_RECIPIENT7

city: Safed

first: Shai

last: Bel

address: 8 Henrietta Szold St, P.O. Box 1589

department: The Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

data_processing:
The RNA sequencing data were analyzed using the RASflow pipeline mapping the reads to the transcriptome (Mus_musculus.GRCm39.cdna) using the hisat2 aligner and counting features using featureCounts. For the genome and transcriptome datasets, any missing gene names (using mmusculus_gene_ensembl) are replaced with gene IDs and unnecessary columns like 'gene_id' are dropped. We filtered out sparse genes, which we defined as those with over 50% zero values, to concentrate on genes with meaningful expression levels and to decrease computational complexity. We started with 35453 genes and removed 14981 sparse genes, leaving us with 20472 genes. Following this, we normalized the data with a scaling factor of 10^6. The purpose of this normalization was to make the samples comparable by compensating for variations in library sizes.
Assembly: Mus_musculus.GRCm39.cdna
Supplementary files format and content: Xlsx file includes RPKM values for each Sample

source_name: Colon

growth_protocol: Mice grown under SPF or germ-free conditions

extract_protocol:
RNA from frozen colonic tissues was extracted using Qiagen RNeasy Universal kit. Integrity of the isolated RNA was analysed using the Agilent TS HS RNA Kit and TapeStation 4200
1000ng of total RNA was treated with the NEBNext poly (A) mRNA Magnetic Isolation Module (NEB, #E7490L). RNA sequencing libraries were produced by using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770L). Quantification of the library was performed using a dsDNA HS Assay Kit and Qubit (Molecular Probes, Life Technologies) and qualification was done using the Agilent TS D1000 kit and TapeStation 4200. 250nM of each library was pooled together and diluted to 4nM according to the NextSeq manufacturer’s instructions. 1.6pM was loaded onto the Flow Cell with 1% PhiX library control. Libraries were sequenced with the Illumina NextSeq 550 platform with single-end reads of 75 cycles according to the manufacturer's instructions.

treatment_protocol: 8 to 14-week-old mice were treated twice a day for 3 days with 2.5 mg  vancomycin dissolved in 100µl drinking water or PBS. Feces collected from vancomycin-treated mice housed at the SPF barrier facility were immediately transferred into an anaerobic chamber. Feces were vortexed in sterile PBS, debris allowed to settle by gravity, and supernatant transferred to new tubes. Sealed tubes were then removed from the anaerobic chamber and orally administered to germ-free Swiss Webster mice via gavage. Inoculated mice were then transferred to Tecniplast IsoCages to prevent outside contamination.

value: Colon

value: WT

value: 2.5mg of vancomycin


title: crz1cnb1_control_2


title: crz1cnb1_KCl_48_2


title: VANCO_RECIPIENT6


title: crz1cnb1_control_3


title: VANCO_RECIPIENT5


title: VANCO_RECIPIENT4


title: HIO Mut Duod TXP Rep 1


title: crz1_ctrl_3

treatment_protocol: Yeast cells were grown in 200mM CaCl2 and diluted every 12 hours to maintain logarithmic growth. Samples were collected after 12, 48 and 72 hours of CaCl2 treatment for RNA isolation.


title: VANCO_RECIPIENT3


title: HIO WT Ile TXP Rep 3


title: crz1cnb1_control_1


title: HIO WT Ile TXP Rep 1


title: PBS_RECIPIENT6

value: PBS


title: VANCO_RECIPIENT2


title: crz1cnb1_KCl_48_1


title: PBS_RECIPIENT7


title: crz1_ctrl_1


title: VANCO_RECIPIENT1


title: crz1_ctrl_2


title: HIO WT Duod TXP Rep 1


title: HIO WT Duod TXP Rep 2


title: PBS_RECIPIENT5


title: dTAG-RBBP6_plus_rep2

city: Exeter

first: Steven

last: West

state: Devon

address: Stocker Rd

department: Living Systems Institute

country: United Kingdom

institute: University of Exeter

data_processing:
Processed using usegalaxy.org
Adapters removed from sequencing reads using Trim Galore
Alignment with Hisat2 to ensembl GRCh38 (default settings)
Removal of unmapped, multimapped and discordant mapped reads (MAPQ <30) using SAMTools
Merge biological replicates using BamTools
Split reads by strand using SAMTools
Bigwig files were generated from split strand BAM files using the bamCoverage of Deeptools v3.5.0
Log2FC bigwigs files were generated using bamCompare of split strand BAM files
Assembly: GRCh38
Supplementary files format and content: Single nucleotide resolution RPKM bigwig coverage was generated from split strand merged replicates
Supplementary files format and content: Log2FC split strand bigwig RPKM coverage of merged replicates at single nucleotide resolution

growth_protocol: HCT116 cell lines were maintained in DMEM with 10% fetal bovine serum, pen/strep at 37 °C and 5% CO2.

extract_protocol:
RNA for POINT-Seq was extracted using a protocol designed by Sousa-Luis et al., 2021.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB)

value: colorectal carcinoma

value: plus dTAGv-1


title: crz1cnb1_ctrl_3


title: PBS_RECIPIENT4


title: HIO WT Duod TXP Rep 3

value: hPSC-derived intestinal organoid


title: dTAG-RBBP6_minus_rep2

value: minus dTAGv-1


title: dTAG-RBBP6_plus_rep1


title: PBS_RECIPIENT3


title: crz1cnb1_ctrl_2


title: TFE3_WT_144h_rep2

data_processing:
The CUT&TAG data were aligned to the mouse mm10 reference genome using BWA mem using the default parameter. Duplicate reads were removed using GATK MarkDuplicates (v4.1.0.0).
Peaks were called using the MACS2 peakcall (2.1.2_dev) function with default parameters.
Assembly: mm10
Supplementary files format and content: bigWig coverage files
Library strategy: CUT&TAG

extract_protocol:
Cleavage Under Targets and Tagmentation (CUT&Tag) on cryopreserved nuclei was performed as described previously in Kaya-Okur et al. (2019) Nature Communications
CUT&Tag libraries were generated by amplifying the CUT&Tag DNA fragments with i5- and i7- barcoded HPLC-grade primers (Buenrostro et al., 2015)

value: embryonic stem cell

value: E14 wild-type

value: mTORi


title: crz1cnb1_ctrl_1

value: haploid yeast

value: 0 hours


title: crz1cnb1_CaCl2_72_3

value: 200mM CaCl2

value: 72 hours


title: PBS_RECIPIENT1


title: IgG_WT_144h


title: dTAG-RBBP6_minus_rep1


title: PBS_RECIPIENT2


title: Rep2 Short POINT-Seq INTS11 plus dTAGv-1 plus TEXO

data_processing:
Processed using usegalaxy.org
Adapters removed from sequencing reads using Trim Galore
Alignment with Hisat2 to ensembl GRCh38 (default settings)
Removal of unmapped, multimapped and discordant mapped reads (MAPQ <30) using SAMTools
Merge biological replicates using BamTools
Split reads by strand using SAMTools
Normalised to Drosophila spike-in
Bigwig files generated from split strand BAM files using the bamCoverage of Deeptools
Assembly: GRCh38
Supplementary files format and content: Single nucleotide resolution RPKM bigwig coverage was generated from split strand merged, Drosophila spike-in normalised, replicates

extract_protocol:
RNA for POINT-Seq was extracted using a protocol designed by Sousa-Luis et al., 2021.
SMARTer smRNA-seq kit for Illumina (Takara Bio)

value: plus dTAGv-1 plus TEXO


title: crz1cnb1_CaCl2_72_2

value: MATa his3delta1 ura3delta0 leu2delta0 lys2delta0 crz1delta::LEU2 cnb1delta::KanMx ChrVI181901-182001::HYG-TEFp-GFP(Y66F)


title: VANCO_DONOR7

value: Colon


title: crz1cnb1_CaCl2_72_1


title: TFE3_WT_N_rep1

value: control


title: Rep1 Short POINT-Seq INTS11 plus dTAGv-1 plus TEXO


title: TFE3_WT_N_rep2


title: Rep2 Short POINT-Seq INTS11 plus dTAGv-1 minus TEXO

value: plus dTAGv-1 minus TEXO


title: VANCO_DONOR6

value: WT

value: 2.5mg of vancomycin


title: VANCO_DONOR5


title: Rep1 Short POINT-Seq INTS11 plus dTAGv-1 minus TEXO

value: colorectal carcinoma


title: crz1cnb1_CaCl2_48_3

value: 48 hours


title: TFE3_WT_72h_rep1


title: crz1cnb1_CaCl2_48_2


title: VANCO_DONOR4


title: TFE3_DKO_N_rep2

value: E14 TET1/2 DKO


title: TFE3_WT_144h_rep1

value: embryonic stem cell


title: Rep1 Short POINT-Seq INTS11 minus dTAGv-1 plus TEXO

value: minus dTAGv-1 plus TEXO


title: VANCO_DONOR3


title: crz1cnb1_CaCl2_12_3

value: 12 hours


title: Rep2 Short POINT-Seq INTS11 minus dTAGv-1 plus TEXO


title: IgG_WT_N

value: E14 wild-type


title: crz1cnb1_CaCl2_12_2

value: haploid yeast


title: TFE3_DKO_72h_rep2

value: mTORi


title: VANCO_DONOR2


title: TFE3_DKO_N_rep1


title: Rep2 Short POINT-Seq INTS11 minus dTAGv-1 minus TEXO

value: minus dTAGv-1 minus TEXO


title: Rep1 Short POINT-Seq INTS11 minus dTAGv-1 minus TEXO


title: VANCO_DONOR1


title: crz1_CaCl2_72_3

value: MATa his3delta1 ura3delta0 leu2delta0 lys2delta0 crz1delta::LEU2 ChrVI181901-182001::HYG-TEFp-GFP(Y66F)

value: 200mM CaCl2

value: 72 hours


title: Rep3 POINT-Seq INTS11 plus dTAGv-1

value: plus dTAGv-1


title: crz1cnb1_CaCl2_12_1

value: MATa his3delta1 ura3delta0 leu2delta0 lys2delta0 crz1delta::LEU2 cnb1delta::KanMx ChrVI181901-182001::HYG-TEFp-GFP(Y66F)


title: TFE3_DKO_72h_rep1


title: PBS_DONOR6

value: Colon

value: WT

value: PBS


title: TFE3_WT_72h_rep2


title: TET2_WT_N_rep2

value: control


title: crz1_CaCl2_72_2


title: PBS_DONOR5


title: TET2_WT_N_rep1


title: Rep3 POINT-Seq INTS11 minus dTAGv-1

value: colorectal carcinoma

value: minus dTAGv-1


title: crz1cnb1_CaCl2_48_1

value: 48 hours


title: Rep2 POINT-Seq INTS11 plus dTAGv-1


title: TET2_WT_72h_rep2

value: embryonic stem cell


title: crz1_CaCl2_48_3


title: PBS_DONOR4


title: Rep2 POINT-Seq INTS11 minus dTAGv-1


title: PBS_DONOR3


title: Rep1 POINT-Seq INTS11 minus dTAGv-1


title: PBS_DONOR2


title: TET2_WT_72h_rep1

value: E14 wild-type


title: TET2_WT_24h_rep2


title: crz1_CaCl2_48_2

value: haploid yeast


title: PBS_DONOR7


title: PBS_DONOR1


title: Rep3 POINT-Seq NVP2 INTS11 plus dTAGv-3 and plus NVP2

value: plus dTAGv-1, plus NVP2


title: Rep1 POINT-Seq INTS11 plus dTAGv-1


title: TET2_WT_144h_rep2

value: mTORi


title: TET2_WT_24h_rep1


title: Rep3 POINT-Seq NVP2 INTS11 plus NVP2

value: minus dTAGv-1, plus NVP2


title: TET2_WT_144h_rep1


title: crz1_CaCl2_48_1

value: MATa his3delta1 ura3delta0 leu2delta0 lys2delta0 crz1delta::LEU2 ChrVI181901-182001::HYG-TEFp-GFP(Y66F)

value: 200mM CaCl2


title: crz1_CaCl2_12_1

value: 12 hours


title: Rep2 POINT-Seq NVP2 INTS11 plus dTAGv-3 and plus NVP2


title: KO4

city: Zhengzhou

first: Jiqi

last: Shan

state: Henan

address: 1 Jianshe East Road, Erqi District, Zhengzhou City, Henan Province

country: China

institute: The First Affiliated Hospital of Zhengzhou University, Zhengzhou,

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed
clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster.
Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster.
Deduplicated Reads were mapped to the reference genome ofMus_musculus.GRCm38 using STRA software (version 2.5.3a) with default parameters.Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited excel file includes RPKM values for each Sample

source_name: B16 tumor

extract_protocol:
Total RNAs were extracted using TRIzol reagent(Invitrogen, cat. NO 15596026) following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999).
2 μg total RNAs were used for stranded RNA sequencing library preparation KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

value: B16 tumor

value: T cell


title: crz1_CaCl2_72_1

value: 72 hours


title: TET1_WT_N_rep2


title: WT_ctrl_3

value: MATa his3delta1 ura3delta0 leu2delta0 lys2delta0 ChrVI181901-182001::HYG-TEFp-GFP(Y66F)

value: 0 hours


title: Rep2 POINT-Seq NVP2 INTS11 plus NVP2

value: colorectal carcinoma


title: KO3


title: TET1_WT_N_rep1

value: control


title: KO1


title: Rep2 POINT-Seq NVP2 INTS11 plus dTAGv-1

value: plus dTAGv-1


title: WT_ctrl_2


title: TET1_WT_24h_rep2

value: embryonic stem cell


title: WT2


title: crz1_CaCl2_12_3


title: TET1_WT_72h_rep1

value: E14 wild-type


title: WT4


title: WT3


title: Rep1 POINT-Seq NVP2 INTS11 minus dTAGv-1

value: minus dTAGv-1


title: TET1_WT_72h_rep2


title: crz1_CaCl2_12_2

value: haploid yeast


title: Rep2 POINT-Seq NVP2 INTS11 minus dTAGv-1


title: KO2


title: Rep1 POINT-Seq NVP2 INTS11 plus NVP2


title: Rep1 POINT-Seq NVP2 INTS11 plus dTAGv-3 and plus NVP2

value: plus dTAGv-1, plus NVP2


title: WT1


title: WT_CaCl2_72_3


title: WT_CaCl2_72_2


title: Rep1 POINT-Seq NVP2 INTS11 plus dTAGv-1


title: WT_CaCl2_48_3

value: 48 hours


title: TET1_WT_144h_rep1

value: mTORi


title: WT_CaCl2_72_1

value: 200mM CaCl2


title: KO_AA3

source_name: Spleen

value: Spleen


title: WT_CaCl2_48_2


title: RNA Pol II ChIP-Seq INTS11-dTAG plus rep 2

data_processing:
Adapters removed from sequencing reads using Trim Galore 0.6.5dev (Cutadapt v2.9)
Alignment with Hisat2 v2.0.0-beta to ensembl GRCh38 (default settings) with splice awareness disabled
Removal of unmapped, multimapped, discordant mapped and PCR duplicate reads (MAPQ <30) using SAMTools v.1.13
Convert BAM to BEDPE using bedtools v2.30.0 and perform MACS2 v2.2.7.1 peak calling
MACS2 output -log10 qvalue coverage was scaled to Drosophila S2 spike-in reads and converted from bedgraph to bigwig. Scaled biological replicates were merged
Assembly: GRCh38
Supplementary files format and content: Single nucleotide resolution S2 spike-in scaled merged replicate bigwig coverage was generated from MACS2 called peak coverage (-log10 qvalue)

extract_protocol:
SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling Technologies) using the above mentioned antibody
NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB)

tag: chip antibody

value: total RNA Pol II


title: KO_AA4

value: T cell


title: ATAC_KO_72h_rep2

data_processing:
The ATAC-seq data were aligned to the mouse mm10 reference genome using BWA mem using the default parameter. Duplicate reads were removed using GATK MarkDuplicates (v4.1.0.0).
Peaks were called using the MACS2 peakcall (2.1.2_dev) function with default parameters.
Assembly: mm10
Supplementary files format and content: bigWig coverage files

source_name: E14 TET1/2 DKO, 72 hours

extract_protocol:
The Omni-ATAC protocol was followed (Corces et al. Nature Methods 2017)
genomic DNA

value: E14 TET1/2 DKO


title: WT_ctrl_1

value: MATa his3delta1 ura3delta0 leu2delta0 lys2delta0 ChrVI181901-182001::HYG-TEFp-GFP(Y66F)


title: TET1_WT_144h_rep2


title: RNA Pol II ChIP-Seq INTS11-dTAG plus rep 1


title: TET1_WT_24h_rep1


title: KO_AA1


title: ATAC_KO_72h_rep1


title: WT_CaCl2_12_3

value: 12 hours


title: ATAC_KO_24h_rep1

source_name: E14 TET1/2 DKO, 24 hours


title: KO_OA3


title: RNA Pol II ChIP-Seq INTS11-dTAG minus rep 2

value: colorectal carcinoma


title: RNA Pol II ChIP-Seq INTS11-dTAG minus rep 1


title: WT_CaCl2_12_1


title: T_ALL PDX-OKT3-5

data_processing:
Raw sequencing reads were first checked for quality with Fastqc (0.11.9) and trimmed for adapter sequences with cutadapt (1.12) using the TrimGalore (0.6.2) wrapper.
Trimmed reads were subsequently aligned to the complete human ribosomal RNA sequence with bowtie (2.4.2).
Reads that did not align to rRNA were then mapped to the human reference genome GRCh37/hg19 and read counts per gene were generated with with STAR mapper (2.7.6a).
The bioinformatics pipelines used for these tasks are available online (RNAseq v4.0.0: https://gitlab.curie.fr/data-analysis/RNA-seq , doi: 10.5281/zenodo.7443721).
Assembly: hg19
Supplementary files format and content: csv file includes raw counts for each sample

source_name: CD45+ CD7+ tumor cell sorted from bone marrow

extract_protocol:
RNA was harvested using RNAeasy mini kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing librairies.
RNA libraries were prepared using the Illumina Stranded mRNA Prep Ligation kit following manufacturer's protocols.

treatment_protocol: T-ALL xenografted mice were treated for 6h with either 40µg control IgG2a or OKT3. Mice were sacrified and  leukemic cells were flow cytometry-sorted (hCD45+; hCD7+).

value: OKT3 mAb


title: KO4


title: T_ALL PDX-OKT3-6

value: CD45+ CD7+ tumor cell sorted from bone marrow


title: KO_OA2


title: WT_CaCl2_12_2


title: ATAC_KO_N_rep2

value: embryonic stem cell

value: control


title: ATAC_KO_N_rep1


title: T_ALL PDX-cont-6

value: control antibody IgG2a


title: cnb1_ctrl_3

value: haploid yeast

value: MATa his3delta1 ura3delta0 leu2delta0 lys2delta0 cnb1delta::KanMx ChrVI181901-182001::HYG-TEFp-GFP(Y66F)

value: 0 hours


title: cnb1_ctrl_2


title: WT_CaCl2_48_1

value: 48 hours


title: KO3


title: cnb1_ctrl_1


title: KO_AA2


title: ATAC_WT_144h_rep2

value: E14 wild-type

value: mTORi


title: KO2

value: Spleen


title: ATAC_WT_72h_rep2


title: KO_OA1

value: T cell


title: ATAC_KO_24h_rep2

value: E14 TET1/2 DKO


title: ATAC_WT_144h_rep1


title: KO1


title: T_ALL PDX-OKT3-4


title: cnb1_CaCl2_72_3

value: 200mM CaCl2

value: 72 hours


title: T_ALL PDX-cont-5


title: WT_AA4


title: T_ALL PDX-OKT3-3


title: cnb1_CaCl2_72_1


title: cnb1_CaCl2_72_2


title: ATAC_WT_72h_rep1


title: ATAC_WT_24h_rep2


title: cnb1_CaCl2_48_3


title: WT_AA3


title: T_ALL PDX-cont-3


title: ATAC_WT_24h_rep1


title: WT_AA2


title: T_ALL PDX-OKT3-2


title: cnb1_CaCl2_48_2


title: ATAC_WT_N_rep1


title: WT_OA4


title: WT_AA1


title: ATAC_WT_N_rep2


title: WT_OA3


title: T_ALL PDX-OKT3-1


title: cnb1_CaCl2_48_1


title: cnb1_CaCl2_12_3

value: 12 hours


title: T_ALL PDX-cont-2


title: cnb1_CaCl2_12_2


title: T_ALL PDX-cont-1


title: WT_OA2


title: T_ALL PDX-cont-4


title: MNase TDG-null P19 ECCs +RA, rep2

city: Rennes

first: Gilles

last: Salbert

address: 263 Av. Gal. Leclerc

department: IGDR UMR6290

institute: University Rennes 1

data_processing:
Sequencing reads were mapped to mm8 using Bowtie and processed by SAMtools to generate bam files followed by wig file generation with MACS
Assembly: mm8
Supplementary files format and content: Wig

growth_protocol: wt and TDG-null P19 mouse embryonal carcinoma cells (ECCs) were grown in cell culture plastic dishes in 10% FCS DMEM containing penicillin and streptomycin.

extract_protocol:
For MNase-seq assays, 10-20.106 cells were incubated for 10 min in 1% formaldehyde in PBS, washed twice and scraped in ice cold PBS and spun down at 100g for 10min at 4°C. Cells were re-suspended in digestion buffer (50 mM Tris-HCl pH7.6, 2 mM CaCl2, 0.2% NP40) containing protease inhibitors (complete EDTA-free, Roche) and warm-up to 37°C for 2min. 4U of MNase were added to wt ECC chromatin and the reaction mixture was incubated at 37°C for 5 min. For TDG-null ECCs, 2U of MNase were added, due to the limited amount of recovered mono-nucleosomal DNA when using 2U of MNase. The reaction was stopped by adding EDTA to a final concentration of 10mM. Cells were then incubated for 10 min on ice in SDS lysis buffer (1% SDS, 50 mM Tris pH8, 10 mM EDTA pH8). An equal volume of TE/RNase (10 mM Tris pH8, 0.1 mM EDTA pH8, 0.4 µg/ml RNase A) was added before incubating at 37°C for 2 hours. A Proteinase K digestion (1 mg/ml) was then performed at 55°C overnight. The mixture was then extracted twice with Phenol/chloroform and the DNA was precipitated 1 hour at -20°C in the presence of glycogen (20µg).  After centrifugation, DNA pellets were washed by ethanol, dissolved in TE buffer (10 mM Tris pH8, 1 mM EDTA pH8) and purified using NucleoSpin Gel and PCR clean-up (Macherey-Nagel). DNA was loaded on a 2% agarose gel. The mono-nucleosome band was excised and the corresponding DNA was purified using MinElute Gel Extraction kit (Qiagen). Mono-nucleosomal DNA was further analyzed by deep sequencing.
MNase-seq libraries were prepared using the TrueSeq ChIP Sample Prep kit (Illumina) and single-end sequenced using a HiSeq 1500 sequencing system.

treatment_protocol: To induce cell differentiation, cells were treated with 1 micromolar retinoic acid (RA) for 48 hours.

value: Embryonal carcinoma

value: Tdg knock out

value: retinoic acid, 48hrs


title: cnb1_CaCl2_12_1


title: WT_OA1


title: PC3_RNA_siSIX2_rep3

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Basecalls performed using CASAVA
Alignment of RNA-seq data to human reference genome version hg38 was done with STAR. Differential expression of genes was analyzed using DESeq2 using HOMER.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

growth_protocol: PC-3 cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum, 2 mM L-Glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin, kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
The isolation of RNA was conducted using TriPure Isolation Reagent (Roche, cat. no. 11667165001) following manufacturer’s protocol.
mRNA was enriched using oligo(dT) beads and fragmented randomly by adding fragmentation buffer. The cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. After a series of terminal repair, ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.

treatment_protocol: PC-3 cells were transfected with siRNA using Opti-MEM and Lipofectamine RNAiMAX reagent 48 h before extraction of RNA.

value: Bone Metastasis Prostate Cancer 3

tag: sirna treatment

value: SIX2 silencing RNA (siSIX2, Dharmacon, cat.no. L-017024-00-0005)

tag: sirna concentration

value: 25 nM

tag: sirna time


title: PC3_RNA_siSIX2_rep2

tag: cell type

tag: cell line


title: WT4

tag: tissue


title: MNase TDG-null P19 ECCs +RA, rep1

tag: treatment


title: PC3_RNA_siSIX2_rep1


title: R248W#1-LSKs

city: Chicago

first: Yan

last: Liu

state: IL

address: 303 E. Superior Street, Lurie 5-107, Northwestern University

department: Department of Medicine

institute: Northwestern University

data_processing:
Paired-end 42bp sequencing reads were mapped to the mouse reference genome. Only uniquely mapped reads were used for further analysis, and duplicate reads were removed.
MACS 1.4.2 was used for peak calling
Assembly: mm10
Supplementary files format and content: bigwig files
Supplementary files format and content: peak files in excel formt

source_name: Bone marrow

extract_protocol:
Murine LSK cells were purified using FACS. 1. Prepare nuclei. To prepare nuclei, we spun 50,000 cells at 500g for 5 min, which was followed by a wash using 50 μL of cold 1× PBS and centrifugation at 500g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge. To avoid losing cells during the nuclei prep, we used a fixed-angle centrifuge and carefully pipetted away from the pellet after centrifugations. 2. Transpose and purify. Immediately following the nuclei prep, the pellet was resuspended in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase (Illumina) and 22.5 μL nuclease-free water). The transposition reaction was carried out for 30 min at 37 °C. Directly following transposition the sample was purified using a Qiagen MinElute kit.
3. PCR. Following purification, we amplified library fragments using 1× NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2, using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. To reduce GC and size bias in our PCR, we monitored the PCR reaction using qPCR in order to stop amplification before saturation. To do this, we amplified the full libraries for five cycles, after which we took an aliquot of the PCR reaction and added 10 μl of the PCR cocktail with Sybr Green at a final concentration of 0.6×. We ran this reaction for 20 cycles to determine the additional number of cycles needed for the remaining 45-μL reaction. The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ∼30 nM in 20 μL. Libraries were amplified for a total of 10–12 cycles.

value: Bone marrow

value: LSKs

value: hematopoietic stem and progenitor cells

tag: genotype


title: R248W#2-LSKs


title: PC3_RNA_siNON_rep3

value: non-targeting siRNA (siNON, Dharmacon, cat. no. D-001810-01-05)


title: MNase TDG-null P19 ECCs, rep1


title: WT#2-LSKs


title: WT3


title: MNase wt P19 ECCs +RA, rep1

value: WT


title: WT2

value: Spleen


title: MNase wt P19 ECCs, rep2


title: PC3_RNA_siNON_rep2


title: WT1

value: T cell


title: WT#1-LSKs


title: PC3_RNA_siNON_rep1


title: MNase wt P19 ECCs, rep1


title: MNase TDG-null P19 ECCs, rep2


title: CB-HSPC, scRNAseq

city: Guangzhou

first: Fei

last: Li

address: 190 Kai Yuan Avenue,Science Park

institute: Guangzhou Institutes of Biomedicine and Health

library_source: transcriptomic single cell

data_processing:
10X sequencing data were processed with Cellranger (version 6.1.2) with default parameters based on the human reference genome GRCh38
The read1 data of pooled cells were split into single-cell data using the barcode sequences contained in the first 16 bp. The next 10 bp were recorded as unique molecular identifiers (UMIs). Read2 with 98 bp were aligned to the hg38 genome.
Assembly: hg38
Supplementary files format and content: file include UMI values for each cell
Supplementary files format and content: file include matrix table with raw gene counts
Supplementary files format and content: file inculde features information

source_name: umbilical cord blood

extract_protocol:
After removal of red blood cells using ACK lysis buffer, the remaining cells were separated by CD34 Microbead kit and magnetic-activated cell-sorting separation columns (Miltenyi Biotec) according to the manufacturer’s instruction. Human hematopoietic lineage FITC cocktail (CD4, CD8, CD11b, CD14, CD19, CD20, CD56, CD235a, and CD10), anti-human CD34-Percp- Cy5.5 and anti-human CD38-APC were used to sort CD34+ fraction.
The single-cell libraries were prepared following the Chromium Single Cell 3′ Reagent Kits User Guide

value: hematopoietic stem/progenitor cells

value: umbilical cord blood


title: Orc1_delBP3_Orc4mut_rep1

status: Public on Mar 18 2024

city: Somerville

first: Michal

last: Chappleboim

address: 73A Bartlett

department: Systems Biology

institute: Harvard Medical School

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase-Del-320-340 ORC4-F485A-Y486A
ChEC-seq

data_processing:
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt
genome coverage with bedtools (-5 -fs 1 -d)
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: be
Library strategy: ChEC-seq

extract_protocol:
Overnight cultures from fresh colonies were diluted (>1:10000) and grown to exponential growth in YPD medium
ChEC-Seq protocol as described in Zentner et al. MNase-seq modified from Yaakov et al. 2021
ChEC-seq: phenol chloroform
One tube library construction based on Skeene et al. 2017 as described in Gera 2021

tag: background

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase-Del-320-340 ORC4-F485A-Y486A


title: Orc1_delBP3_Orc4mut_rep2_seq2


title: Orc4mutant_rep4

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1∆ ORC1_N'-3xFlag-MNase ORC4-F485A-Y486A
ChEC-seq

source_name: Orc1-MNase, Orc4-F485A-Y486A

value: Orc1-MNase, Orc4-F485A-Y486A

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1delta ORC1_N'-3xFlag-MNase ORC4-F485A-Y486A


title: Orc1_delBP3_Orc4mut_rep2


title: Orc4mutant_rep5_seq2


title: Orc1_delBP3_Orc4mut_rep1_seq2


title: MNase wt P19 ECCs +RA, rep2

value: Embryonal carcinoma


title: Orc1-del357-375_Orc1synCopy_rep5

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase-del357-375
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase-del357-375


title: Orc4mutant_rep5


title: Orc1-del357-375_Orc1synCopy_rep6


title: Orc1-del357-375_Orc1synCopy_rep3


title: Orc1-delBP3_rep2

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase-Del-320-340
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase-Del-320-340


title: Orc1-delBP3_BP4_rep1

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase-Del-320-375
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase-Del-320-375


title: Orc1-delBP3_rep1


title: Orc1-del357-375_Orc1synCopy_rep4


title: Orc4mutant_rep4_seq2


title: Orc1-delBP3_BP4_rep2


title: Orc1-delBP3_rep3


title: Orc1-trunc320_Orc1synCopy_rep2

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase-Truncation-320
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase-Truncation-320


title: Orc1-trunc340_Orc1synCopy_rep2

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase-Truncation-340
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase-Truncation-340


title: Orc1-trunc340_Orc1synCopy_rep1


title: Orc1-trunc320_Orc1synCopy_rep1


title: Orc1-delBAH_Orc1synCopy_rep2

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase-Truncation-188
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase-Truncation-188


title: Orc1-delBAH_Orc1synCopy_rep1


title: Orc1-trunc290_Orc1synCopy_rep1

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase-Truncation-290
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase-Truncation-290


title: Orc1_Orc1synCopy_rep13

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase


title: Orc1_Orc1synCopy_rep12


title: Orc1_Orc1synCopy_rep10


title: Orc1_Orc1synCopy_rep11


title: Orc1_Orc1synCopy_rep8


title: Orc1_Orc1synCopy_rep9


title: Orc1-rep21_seq2

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1∆ ORC1_N'-3xFlag-MNase
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1delta ORC1_N'-3xFlag-MNase


title: Orc1-del340-375_Orc1synCopy_rep3

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase-del340-375
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase-del340-375


title: Orc1-rep20


title: Orc1-del340-375_Orc1synCopy_rep3_seq2


title: Orc1-rep21


title: Orc1-del357-375_Orc1synCopy_rep2


title: Orc1-del340-375_Orc1synCopy_rep2


title: Orc1_Orc1synCopy_rep5


title: Orc1-del357-375_Orc1synCopy_rep1


title: Orc1-K380A_Orc1synCopy_rep1

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-K380A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-K380A


title: Orc1_Orc1synCopy_rep7


title: Orc1_Orc1synCopy_rep6


title: Orc1-K380A_Orc1synCopy_rep2


title: Orc1-K380A_rep4

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1∆ ORC1_N'-3xFlag-MNase-K380A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1delta ORC1_N'-3xFlag-MNase-K380A


title: Orc1-K380A_rep2


title: Orc1-del340-375_Orc1synCopy_rep1


title: Orc1-trunc290_Orc1synCopy_rep2


title: Orc1-K380A_rep3


title: Orc1-F379A_Orc1synCopy_rep2

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-F379A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-F379A


title: Orc1-K380A_rep1


title: Orc1-F379A_Orc1synCopy_rep1


title: Orc1-F379A_rep3

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1∆ ORC1_N'-3xFlag-MNase-F379A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1delta ORC1_N'-3xFlag-MNase-F379A


title: Orc1-F379A_rep2


title: Orc1-F379A_rep4


title: Orc1-R378A_Orc1synCopy_rep4

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-R378A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-R378A


title: Orc1-K380A_Orc1synCopy_rep3


title: Orc1-R378A_Orc1synCopy_rep2


title: Orc1-R378A_Orc1synCopy_rep3


title: Orc1-R378A_Orc1synCopy_rep1


title: Orc1-R378A_rep3

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1∆ ORC1_N'-3xFlag-MNase-R378A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1delta ORC1_N'-3xFlag-MNase-R378A


title: Orc1-R378A_rep1


title: Orc1-R378A_rep2


title: Orc1-F379A_Orc1synCopy_rep3


title: Orc1-K377A_Orc1synCopy_rep3_seq2

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-K377A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-K377A


title: Orc1-K377A_Orc1synCopy_rep2


title: Orc1-K377A_Orc1synCopy_rep1


title: Orc1-K377A_rep3

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1∆ ORC1_N'-3xFlag-MNase-K377A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1delta ORC1_N'-3xFlag-MNase-K377A


title: Orc1-F379A_rep1


title: Orc1-K377A_rep2


title: Orc1-S376A_Orc1synCopy_rep4

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-S376A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-S376A


title: Orc1-K377A_rep1


title: Orc1-S376A_Orc1synCopy_rep3_seq2


title: Orc1-S376A_Orc1synCopy_rep2


title: Orc1-S376A_rep3

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1∆ ORC1_N'-3xFlag-MNase-S376A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1delta ORC1_N'-3xFlag-MNase-S376A


title: Orc1-S376A_rep2


title: Orc1-S376A_Orc1synCopy_rep1


title: Orc1-S376A_rep1


title: Orc1-F375A_rep3

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1∆ ORC1_N'-3xFlag-MNase-F375A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1delta ORC1_N'-3xFlag-MNase-F375A


title: Orc1-F375A_rep4


title: Orc1-F375A_rep2


title: Orc1-F375A_rep1


title: Orc1-K377A_Orc1synCopy_rep3


title: Orc1-R378A_rep4


title: Orc1-P374A_Orc1synCopy_rep4

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-P374A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-P374A


title: Orc1-P374A_Orc1synCopy_rep3


title: Orc1-P374A_Orc1synCopy_rep2


title: Orc1-S376A_Orc1synCopy_rep3


title: Orc1-P374A_Orc1synCopy_rep1


title: Orc1-P374A_rep3

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1∆ ORC1_N'-3xFlag-MNase-P374A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1delta ORC1_N'-3xFlag-MNase-P374A


title: Orc1-T373A_Orc1synCopy_rep3

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-T373A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-T373A


title: Orc1-P374A_rep1


title: Orc1-T373A_Orc1synCopy_rep2


title: Orc1-T373A_rep4

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1∆ ORC1_N'-3xFlag-MNase-T373A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1delta ORC1_N'-3xFlag-MNase-T373A


title: Orc1-S376A_rep4


title: Orc1-P374A_rep2


title: Orc1-T373A_Orc1synCopy_rep3_seq2


title: Orc1-T373A_Orc1synCopy_rep1


title: Orc1-T373A_rep1


title: Orc1-Y372A_Orc1synCopy_rep2

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-Y372A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-Y372A


title: Orc1-T373A_rep3


title: Orc1-Y372A_Orc1synCopy_rep3


title: Orc1-K371A_Orc1synCopy_rep4

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-K371A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-K371A


title: Orc1-Y372A_Orc1synCopy_rep1_seq2


title: Orc1-Y372A_Orc1synCopy_rep1


title: Orc1-K371A_Orc1synCopy_rep2


title: Orc1-K371A_Orc1synCopy_rep1


title: Orc1-K371A_Orc1synCopy_rep4_seq2


title: Orc1-K371A_Orc1synCopy_rep3


title: Orc1-K371A_rep4

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1∆ ORC1_N'-3xFlag-MNase-K371A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1delta ORC1_N'-3xFlag-MNase-K371A


title: Orc1-K371A_rep3


title: Orc1-K371A_rep2


title: Orc1-K371A_rep1


title: Orc1-K370A_Orc1synCopy_rep3

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-K370A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-K370A


title: Orc1-K370A_Orc1synCopy_rep4


title: Orc1-K370A_Orc1synCopy_rep1


title: Orc1-K370A_rep3

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1∆ ORC1_N'-3xFlag-MNase-K370A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1delta ORC1_N'-3xFlag-MNase-K370A


title: Orc1-K370A_rep1


title: Orc1-K369A_Orc1synCopy_rep2

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-K369A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-K369A


title: Orc1-K370A_Orc1synCopy_rep2


title: Orc1-K369A_rep4

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1∆ ORC1_N'-3xFlag-MNase-K369A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1delta ORC1_N'-3xFlag-MNase-K369A


title: Orc1-K369A_rep2_seq2


title: Orc1-K369A_rep3


title: Orc1-K369A_Orc1synCopy_rep1


title: Orc1-T373A_rep2


title: Orc1-K369A_rep2


title: Orc1-K370A_rep2


title: Orc1-R367A_Orc1synCopy_rep5

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-R367A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-R367A


title: Orc1-R367A_Orc1synCopy_rep4


title: Orc1-R367A_Orc1synCopy_rep2


title: Orc1-V365A_Orc1synCopy_rep3

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-V365A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-V365A


title: Orc1-K369A_rep1


title: Orc1-V365A_Orc1synCopy_rep2


title: Orc1-R367A_Orc1synCopy_rep3


title: Orc1-R367A_Orc1synCopy_rep1


title: Orc1-V365A_Orc1synCopy_rep1


title: Orc1-V365A_rep4

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1∆ ORC1_N'-3xFlag-MNase-V365A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1delta ORC1_N'-3xFlag-MNase-V365A


title: Orc1-V365A_rep3


title: Orc1-V365A_rep2


title: Orc1-V365A_rep1


title: Orc1-N364A_Orc1synCopy_rep4_seq2

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-N364A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-N364A


title: Orc1-N364A_Orc1synCopy_rep4


title: Orc1-N364A_Orc1synCopy_rep2_seq2


title: Orc1-N364A_Orc1synCopy_rep2


title: Orc1-K369A_Orc1synCopy_rep3


title: Orc1-N364A_Orc1synCopy_rep1_seq2


title: Orc1-N364A_Orc1synCopy_rep1


title: Orc1-N364A_rep3

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1∆ ORC1_N'-3xFlag-MNase-N364A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1delta ORC1_N'-3xFlag-MNase-N364A


title: Orc1-N364A_rep1


title: Orc1-K363A_Orc1synCopy_rep3_seq2

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-K363A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-K363A


title: Orc1-N364A_rep2


title: Orc1-N364A_rep4


title: Orc1-K363A_Orc1synCopy_rep2


title: Orc1-K363A_Orc1synCopy_rep1


title: Orc1-K363A_Orc1synCopy_rep3


title: immune cells, HSV, rep2

city: Hamilton

first: Clayton

last: Winkler

state: MT

address: 903 S. 4th St

institute: Rocky Mountain Laboratories/NIAID/NIH

data_processing:
Raw fastq files were trimmed to remove adapters and low-quality bases using Cutadapt v1.18
Alignment to the GRCh38 reference genome and the Gencode v30 genome annotation using STAR v2.7.9a
PCR duplicates were marked using the MarkDuplicates tool from the Picard v3.1.0
Raw gene counts were generated using RSEM v1.3.3 and differential expression was evaluated using DESeq2
Assembly: GRCm39/Gencode 30
Supplementary files format and content: rawcounts.txt contains raw expected counts from RSEM
Supplementary files format and content: fpkm.txt contains FPKM normalized expression

extract_protocol:
RNA was extracted from ½ brains, and inguinal lymph nodes following a Trizol and chloroform protocol
Starting with 200 pg of high-quality total RNA for each sample, volumes were concentrated via speed-vacuum to 9.5 ul. Sequencing libraries were constructed following the Takara SMART-Seq v4 PLUS protocol 011820 (Takara, Mountain View, CA) beginning with oligo(dT) priming/cDNA synthesis and following the manufacturers recommendations.  Modifications during cDNA amplification included the use of SeqAmp CB PCR Buffer with 14 cycles of PCR. After AmPure XP bead purification (Agencourt Biosciences, Beverly, MA), cDNA quality was visualized and quantity assessed on a BioAnalyzer HS chip (Agilent Technologies, Inc., Santa Clara, CA). Purified cDNA for each sample was normalized to 1.5 ng in 8 ul volume going into library preparation with the Stem-Loop Adaptor mix. Following 15 cycles of library amplification using balanced SMARTer RNA unique-dual index primers from 96U SetA kit 042121 for Illumina sequencing (Takara, Mountain View, CA), individual libraries were cleaned using an 80% vol of AmPure XP beads

treatment_protocol: B6 mice were infected with either 103 LACV or 107 HSV IP and brain immune cells isolated as described above

value: Brain

value: Immune cells isolated from brain

value: Herpes Simplex Virus 1 Infected


title: immune cells, HSV, rep1


title: immune cells, LACV, rep2

value: LaCrosse Virus Infected


title: immune cells, LACV, rep3


title: immune cells, LACV, rep1


title: Orc1-K362A_Orc1synCopy_rep4

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-K362A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-K362A


title: Trailer_B_WT.fastq

city: Bethesda

first: Markus

last: Hafner

state: MD

address: 50 South Drive

department: NIAMS

institute: NIH

description: tRNA Sequencing

data_processing:
demultiplexing cutadapt v2.4
alignment using bowtie v1.1.2
Assembly: artificial genome with MASC constracts
Supplementary files format and content: txt with counts

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS), maintained at 37 ◦C in a humidified atmosphere of 5% CO2

extract_protocol:
Cells were lysed using TRIzol Reagent (Invitrogen) and total RNA fractions were isolated using the Direct-zol RNA Miniprep (Zymo Research)
tRNA-Seq

treatment_protocol: Cells were transfected using Lipofectamine 2000 (Invitrogen) according to manufacturer’s recommendations


title: Orc1-K363A_rep1

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1∆ ORC1_N'-3xFlag-MNase-K363A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1delta ORC1_N'-3xFlag-MNase-K363A


title: Orc1-K363A_rep2


title: Orc1-K362A_Orc1synCopy_rep3


title: Orc1-N364A_Orc1synCopy_rep3


title: Trailer_B_G11U.fastq

description: tRNA Sequencing


title: Trailer_A_WT.fastq

description: tRNA Sequencing


title: Orc1-K362A_Orc1synCopy_rep1


title: Orc1-K362A_Orc1synCopy_rep2


title: Orc1-T361A_Orc1synCopy_rep4

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-T361A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-T361A


title: Trailer_A_G14CG15C.fastq

description: tRNA Sequencing


title: Trailer_A_G11U.fastq

description: tRNA Sequencing


title: immune cells, HSV, rep3


title: Orc1-T361A_Orc1synCopy_rep3


title: Adaptor_B_G11U.fastq

description: tRNA Sequencing


title: Orc1-T361A_Orc1synCopy_rep2


title: Adaptor_B_G14CG15C.fastq

description: tRNA Sequencing


title: Adaptor_B_WT.fastq

description: tRNA Sequencing


title: Orc1-T361A_Orc1synCopy_rep1


title: Orc1-K362A_Orc1synCopy_rep5


title: Adaptor_A_WT.fastq

description: tRNA Sequencing


title: Orc1-T361A_rep3

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1∆ ORC1_N'-3xFlag-MNase-T361A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1delta ORC1_N'-3xFlag-MNase-T361A


title: Orc1-F360A_Orc1synCopy_rep1

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-F360A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-F360A


title: Adaptor_A_G14CG15C.fastq

description: tRNA Sequencing


title: Orc1-F360A_Orc1synCopy_rep2


title: NT_mitoriboIP_rep1

city: Sherbrooke

first: Karine

last: Choquet

state: Québec

address: 3201 rue Jean-Mignault

department: Biochemistry and Functional Genomics

country: Canada

institute: Université de Sherbrooke

data_processing:
Basecalling (live with MinKNOW v20.10.3 or later)
Alignment (minimap2)
Poly(A) tail length estimation (nanopolish v0.13.3)
Determination of transcript abundance and processing levels (custom scripts available at https://github.com/churchmanlab)
Assembly: GRCh38
Supplementary files format and content: *_read_processing_status.txt: 5' and 3' ends processing status for each mitochondrial read

extract_protocol:
IP of mitochondrial ribosome + phenol chloroform extraction
Direct RNA nanopore sequencing; Poly(A) tailing, 3'-end ligation or poly(A) selection followed by direct RNA sequencing library preparation (SQK-RNA002)


title: FASTKD5_KO_mitoriboIP_rep1


title: Orc1-T361A_rep2


title: HeLa_polyA+

data_processing:
Basecalling (live with MinKNOW v20.10.3 or later)
Alignment (minimap2)
Poly(A) tail length estimation (nanopolish v0.13.3)
Determination of transcript abundance and processing levels (custom scripts available at https://github.com/churchmanlab)
Assembly: GRCh38
Supplementary files format and content: *_gene_counts.txt: number of reads mapping to each mitochondrial transcript (whole gene or 100/200 nt window at 3'-end of gene)
Supplementary files format and content: *_polyA_length.txt or *_polyA_estimates.tsv: poly(A) tail length estimated by nanopolish
Supplementary files format and content: *_read_processing_status.txt: 5' and 3' ends processing status for each mitochondrial read
Library strategy: Direct RNA nanopore sequencing

source_name: HeLa

extract_protocol:
total RNA Trizol extraction
Poly(A) tailing, 3'-end ligation or poly(A) selection followed by direct RNA sequencing library preparation (SQK-RNA002)

value: HeLa


title: Orc1-F360A_Orc1synCopy_rep3


title: Orc1-F360A_Orc1synCopy_rep5


title: Orc1-T361A_rep1


title: FASTKD5_KO_mitoriboIP_rep2


title: FASTKD5_KO_totalRNA_rep2

extract_protocol:
total RNA Trizol extraction
Direct RNA nanopore sequencing; Poly(A) tailing, 3'-end ligation or poly(A) selection followed by direct RNA sequencing library preparation (SQK-RNA002)


title: Adaptor_A_G11U.fastq

description: tRNA Sequencing


title: Orc1-F360A_Orc1synCopy_rep4


title: Orc1-K359A_Orc1synCopy_rep4

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-K359A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-K359A


title: Orc1-K359A_Orc1synCopy_rep5


title: FASTKD5_KO_totalRNA_rep1


title: Orc1-K359A_Orc1synCopy_rep1


title: total_RNA_ligation_rep2


title: NT_totalRNA_rep1


title: Orc1-K359A_Orc1synCopy_rep2


title: total_RNA_ligation_rep1


title: myoblasts_D0_polyA_enriched

source_name: myoblasts

extract_protocol:
total RNA Qiazol extraction
Poly(A) tailing, 3'-end ligation or poly(A) selection followed by direct RNA sequencing library preparation (SQK-RNA002)

value: myoblasts


title: Orc1-R358A_Orc1synCopy_rep4

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-R358A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-R358A


title: myoblasts_D7_polyA_enriched


title: Orc1-T361A_rep4


title: Trailer_B_G14CG15C.fastq

description: tRNA Sequencing


title: NT_totalRNA_rep2


title: Orc1-R358A_Orc1synCopy_rep3


title: Orc1-K359A_Orc1synCopy_rep3


title: Orc1-R358A_Orc1synCopy_rep1


title: Orc1-R358A_Orc1synCopy_rep2


title: total_RNA_polyA_tailing_rep1


title: total_RNA_polyA_tailing_rep2


title: bovine_elongation_D18_B

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

data_processing:
To analyze 10X Genomics single-cell data, the base call files (BCL) were transferred to FASTQ files by using CellRanger (v.7.1.0) mkfastq with default parameters, followed by aligning to the most recent bovine reference genome downloaded from Ensembl database (UCD1.2.109), then the doublets were detected and removed from single cells by using Scrublet (0.2.3) with default parameters.
Assembly: UCD1.2.109
Supplementary files format and content: Tab-separated values files and matrix files

organism: Bos taurus

source_name: Peri-implatation embryo

extract_protocol:
After embryo collection, fresh embryos were washed with PBS and placed in a 3% FBS in ice cold PBS. Embryos were centrifuged for 5 minutes at 400xg at 4ºC. After supernatant aspiration, embryos were resuspended in 200mL of TrypLE and minced by scissors. 500mL of TrypLE were added and then embryos were incubated at 37°C in a shaker at 150rpm for 4-7 minutes depending on size of embryos. Dissociation was stopped with same volume of 3% FBS (700L), and the suspensions were pass through 70m cell strainer and centrifuged for 5 min at 400xg at 4ºC. The cell pellet was resuspended with 0.04% BSA (volume depended on the size of cell pellet). Cell suspensions were filtered through 40m cell strainer into a new 1.5mL Eppendorf tube. Cell viability and concentration were measured using a Countess Automated Cell Counter.
Library was performed following manufacter's instructions (10x Chromium Next GEM Single Cel 3' Reagent Kit v3.1 Dual Index) and  was target of 10,000 cells per sample.

treatment_protocol: Cows were synchronized starting on day 0 with dominant follicle removal (DFR) followed by insertion of standard 7-day vaginal controlled internal drug release of progesterone (CIDR, Zoetis). On day 2 ovulation-inducing gonadotropin-release hormone (GnRH, Fertagyl, Merk Animal Health) was administered intramuscular (IM) injection. From day 4-7, follicle stimulating hormone (FSH, Folltropin, Vetoquinol) was administered twice a day in a decreasing dose. Upon CIDR removal on day 7, one dose of prostaglandin (Lutalyse, Zoetis) was administered in the morning and afternoon. 48 hours after CIDR removal another dose of GnRH was administered via IM injection and artificial insemination was procedure twice in a 12-hour interval. Bovine peri-implantation embryos were collected at day 12, 14, 16 18 days after artificial insemination. Embryos were recovered by standard non-surgical flush with lactated ringer solution supplemented with 1% fetal bovine serum and washed with PBS before processing for single cell isolation. All cows were treated with prostaglandin (Lutalyse, Zoetis) after flushing.

value: Peri-implatation embryo

value: Early embryonic lineages

value: In vivo

tag: time


title: Orc1-R358A_rep1

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1∆ ORC1_N'-3xFlag-MNase-R358A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1delta ORC1_N'-3xFlag-MNase-R358A


title: bovine_elongation_D14_B


title: Orc1-I357A_Orc1synCopy_rep1

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-I357A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-I357A


title: Orc1-R358A_rep3


title: Orc1-R358A_rep2


title: Orc1-I357A_rep4

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1∆ ORC1_N'-3xFlag-MNase-I357A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1delta ORC1_N'-3xFlag-MNase-I357A


title: bovine_elongation_D16_B


title: Orc1-I357A_Orc1synCopy_rep2


title: bovine_elongation_D12_B


title: Orc1-I357A_rep3


title: bovine_elongation_D16_A


title: Orc1-I357A_rep2


title: bovine_elongation_D14_A


title: bovine_elongation_D12_A


title: B16-F10 WT cells rep 2

city: Pittsburgh

first: Saumendra

middle: N

last: Sarkar

state: Pennsylvania

address: UPMC Hillman Cancer Center, 5117 Centre Avenue

department: UPMC Hillman Cancer Center

institute: University of Pittsburgh

data_processing:
CLC Genomics Workbench v 12.0.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomics workbench (parameter – Quality limit: 0.05)
Trimmed sequence reads were mapped to GRCm38/mm19 using CLC genomics workbench (parameter – mismatch cost = 2, insertion cost = 3, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8)
Read count extraction and normalization were performed using CLC genomics workbench
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes RPKM values for each sample

extract_protocol:
RNA was extracted using Qiagen Rneasy Plus mini kit
RNA library for RNA-seq were prepared by Illumina TruSeq mRNA seq following manufacturers' instructions

value: melanoma cells

value: WT

value: day 12 post-injectin


title: B16-F10 IRF1-KO cells rep 2

value: IRF1 knockout


title: Orc1-V356A_Orc1synCopy_rep2

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-V356A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1_N'-3xFlag-MNase-V356A


title: Orc1-I357A_rep1


title: B16-F10 IRF1-KO cells rep1


title: B16-F10 WT cells rep 1


title: Orc1-I357A_Orc1synCopy_rep3


title: bovine_elongation_D18_A


title: Orc1-R358A_rep4


title: Orc1-V356A_Orc1synCopy_rep1


title: mito_enriched_polyA_tailing

extract_protocol:
mitochondria isolation + Trizol extraction
Poly(A) tailing, 3'-end ligation or poly(A) selection followed by direct RNA sequencing library preparation (SQK-RNA002)


title: Orc1-V356A_rep3

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1∆ ORC1_N'-3xFlag-MNase-V356A
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1delta ORC1_N'-3xFlag-MNase-V356A


title: Drip-seq-untreated-rnaseh-rep1

first: Pei-Chi

last: Wei

state: Baden-Württemberg

address: Im Neuenheim Feld 280

department: Structural and functional genomics

institute: German Cancer Research Center

data_processing:
DRIPc-seq: Illumina adaptor sequences were trimed by trip-glaore, and the sequences were aligned with Bowtie2. same files were sorted, marjedup, and DRIP signal enrichment were determined by MACS2 callpeak (parameter: --nomodel --slocal 1000000 --llocal 10000000 --extsize 100000)
Hi-resolution repli-seq: a sigularity package https://github.com/brainbreaks/HighRes_RepliSeq
Assembly: mm10
Supplementary files format and content: bedgraph and bw: display of continuous-valued data in track format
Library strategy: DRIPc-seq

source_name: neural progenitor cells

growth_protocol: The Xrcc4/p53-deficient mouse embryonic stem cells were cultured in DMEM medium supplemented with 15% ESC-grade fetal bovine serum, 20mM HEPES, non-essential amino acids, 100 U/ml Pen/Strep and glutamine mixture, 0.1mM beta-mercaptoethanol and 1000 U/mL ESGRO recombinant mouse leukemia inhibitory factor (LIF) on a monolayer of confluent irradiated mouse fibroblasts. The CAST x 129 hybrid mouse ES cells were cultured in 2i medium (50% DMEM/F12, 50% NeuralBasal, 0.5X N2 supplement, 0.5X B27 supplement, BSA, 10 mM PD03259010, 10 mM CHIR99021, 200 mM Glutamine, 11.9M Monothioglycerol, and 1x10^6 U/ml LIF). To induce mouse neural progenitor cells, Xrcc4/p53-deficient mouse ES cells were plated on laminine/poly-L-ornithine-coated plates and cultured in N2B27 medium (50% DMEM/F12, 50% NeuralBasal, 1% modified N2 supplement, 2% B27 supplement without RA, 1X Glutamax) for seven days. Cells were then passaged to laminin-coated plates and culture in NBBG medium (NeralBasalA, 2% B27 supplement without RA, 0.5 mM Glutamax, 10ng/ml human EGF, 10ng/ml mouse FGFb) for another five to six days. Neural progenitor cells were then collected for nucleofection, DRIP-seq, or Repli-seq experiments.

extract_protocol:
Genomic DNA for Repliseq: cells were lyzed in proteinase K digestion buffer, and genomic DNA were extraced by using a Zymo DNA extractin kit. RNA for DRIPc-seq: cells were lyzed in proteinase K digestion buffer, and genomic DNA/RNA complex were extraced with a standard phenol/chlorofomr protocol. DNA was degraded during the library prep procedure, and the RNA molecules were prerved.
We follow the published protocol, as indicated below, to construct the libraries. DRIPc-seq: https://www.nature.com/articles/s41596-019-0159-1 Repli-seq: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-01983-8

treatment_protocol: Cells were treated with indicated concentration of aphidicolin or the veichle control DMSO for the indicated period.

value: neural progenitor cells

value: untreated


title: Drip-seq-untreated-rnaseh-rep2


title: Orc1-V356A_rep2


title: Drip-c-seq-untreated-rep1

molecule: cytoplasmic RNA


title: Orc4mutant_rep2

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1∆ ORC1_N'-3xFlag-MNase ORC4-F485A-Y486A
ChEC-seq

value: Orc1-MNase, Orc4-F485A-Y486A

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1delta ORC1_N'-3xFlag-MNase ORC4-F485A-Y486A


title: Drip-c-seq-untreated-rep2


title: Orc4mutant_rep1


title: Orc4mutant_rep3


title: Repliseq-aph-s14-rep2

data_processing:
DRIPc-seq: Illumina adaptor sequences were trimed by trip-glaore, and the sequences were aligned with Bowtie2. same files were sorted, marjedup, and DRIP signal enrichment were determined by MACS2 callpeak (parameter: --nomodel --slocal 1000000 --llocal 10000000 --extsize 100000)
Hi-resolution repli-seq: a sigularity package https://github.com/brainbreaks/HighRes_RepliSeq
Assembly: mm10
Supplementary files format and content: bedgraph and bw: display of continuous-valued data in track format
Library strategy: Repli-seq

value: aphidicolin


title: Repliseq-aph-s13-rep2


title: rDDD7

city: New York

first: Ibrahim

last: Batal

state: NY

address: 630 W 168th street

department: Pathology & cell Biology

institute: Columbia University

description: Allograft rC3G

hyb_protocol: 100 ng of isolated RNA was hybridized to the 770 genes PanCancer Immune Profiling Panel (NanoString Technologies) for 20 h at 65 °C according to the manufacturer’s instructions

scan_protocol: Digital counting was used to determine gene expression using the maximum 555 fields of

data_processing:
nSolver Analysis Software (version 4.0), including the nCounter Advanced Analysis (version 2.0), which uses the geNorm algorithm to normalize the data.
nSolver Analysis 4.0 Normalized count

label: Biotin

source_name: Allograft kidney biopsy

label_protocol: Genes of interest is detected by a pair of reporter probe (contains unique color code at the 5ʹend form molecular barcoding) and capture probe (contains 35 to 50 base pairs of target gene specific sequences). The capture probes are all biotin labeled at the 3ʹendfor the attachment of the genes of interest during digital detection.

extract_protocol: 10 μm x10 FFPE curls were sectioned from each biopsy. Total RNA was isolated from sectioned material using miRNeasy FFPE Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions and quantified by NanoDrop (Thermo Scientific, Wilmington, DE), Bioanalyzer 2100 (Agilent, Santa Clara, CA), and Qubit RNA BR (Thermo Fisher Scientific, Waltham, MA).

tag: age

tag: Sex

value: Male


title: Orc1Ntail-delBP4_rep4

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1:: 3xFlag-MNase-ORC1-AA1-357
ChEC-seq

tag: strain

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::3xFlag-MNase-ORC1-AA1-357


title: rC3GN9

description: Allograft rC3G


title: rIgAN2

description: Allograft GD control


title: rMN5

description: Allograft GD control


title: de novo MN1

description: Allograft GD control


title: Orc1Ntail-delBP4_rep3


title: PAβN_2

city: Chandigarh

first: Nisha

last: Mahey

state: Chandigarh

address: Sector 39A

department: BERPDC

country: India

institute: CSIR-Institute of Microbial Technology

data_processing:
Read alignment: The paired-end reads are aligned to the reference Pseudomonas aeruginosa genome (https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/765/GCF_000006765.1_A M676v1/). Alignment was performed using HISAT2 (2.1.0).
Expression estimation: The aligned reads are used to estimate the gene expression. The raw read counts were estimated using FeatureCount (1.5.2). Read count data were normalized using DESeq2.
Differential expression analysis: The raw read counts were normalized using DESeq2.The ratio of normalized read counts for treated over control was taken as the fold change. Genes were first filtered based on the p-value (<= 0.05). The distribution of these log2 (foldchange) values was found to be normally distributed. Those genes which were found to have -1 <= log2(foldchange) >= 1 were considered as statistically significant.
Assembly: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/765/GCF_000006765.1_A M676v1/
Supplementary files format and content: Microsoft excel files containing normalised read counts, Log2 fold change, Log2 scale values

organism: Pseudomonas aeruginosa

source_name: Bacterial cells

growth_protocol: The overnight culture of P. aeruginosa PAO1 propagated in LB was diluted 1:1000 in fresh media and incubated in the presence of Ar5 (16 µg/mL) and PAβN (16 µg/mL) for 17 h at 37 ºC.

extract_protocol:
After incubation, the 5 mL culture was centrifuged, and the pellet was stored overnight at -80 ºC. The pellet was removed from the freezer, mixed with 1 mL TRIzolTM reagent (Invitrogen), and immediately placed on ice. The solution was subject to bead beating for 45 sec, immediately placed on ice, and centrifuged at 13,000 ×g for 10 min at 4 ºC. The supernatant was transferred to another tube and gently mixed with an equal volume of absolute ethanol (molecular biology grade). Further, the total RNA was extracted using the RNeasy Mini Kit (QIAGEN).
NEB Ultra II directional RNA-Seq Library Prep kit (NEB, Cat# E7760L) protocol was used to prepare libraries for total RNA sequencing. An initial Concentration of 100 ng of total RNA was taken for the assay. First, the total RNA was hybridized with QIAseq® FastSelect™ –5S/16S/23S reagent mixture (Qiagen, Cat# 335927) by heat-fragmenting and cooling the reaction from 75°C to 25°C, followed by Bead clean-up. The cleaned-up ribo-depleted RNA fragments were copied into first-strand cDNA using reverse transcriptase. Second strand cDNA synthesis was performed using DNA Polymerase I and RNase H enzyme. The cDNA fragments were then subjected to a series of enzymatic steps that repair the ends, tails the 3' end with a single 'A' base, followed by ligation of the adapters. The adapter-ligated products were then purified and enriched using the following thermal conditions: initial denaturation of 98°C for 30sec; 13 cycles of - 98°C for 10sec, 65°C for 75sec; final extension of 65°C for 5 mins. The amplified libraries were purified and checked for fragment size distribution on Fragment Analyzer using HS NGS Fragment Kit (1-6000bp) (Agilent, Cat# DNF-474-1000).

value: Bacterial cells

value: Treated with PAβN (A known Efflux pump inhibitor)


title: rIgAN7

description: Allograft GD control


title: Orc1-V356A_rep4


title: Orc1Ntail-delBP4_rep2


title: Drip-seq-untreated-input

city: Heidelberg


title: Drip-seq-untreated-rep2


title: PAβN_1


title: Orc1-V356A_rep1


title: rDDD4

description: Allograft rC3G

value: Female


title: rMN3

description: Allograft GD control


title: Drip-seq-untreated-rep1


title: rMN4

description: Allograft GD control


title: Orc1Ntail-delBP4_rep1


title: rMN6

description: Allograft GD control


title: Orc1-delBP4_rep4

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase-del340-375
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase-del340-375


title: Ar5_2

value: Treated with Ar5 (our best Efflux pump inhibitor)


title: rIgAN8

description: Allograft GD control

value: male


title: de novo ICMGD NOS6

description: Allograft GD control


title: rMN10

description: Allograft GD control


title: Orc1-delBP4_rep3


title: rIgAN6

description: Allograft GD control


title: de novo MN2

description: Allograft GD control


title: Control_1

value: Control (Without treatment)


title: rMN2

description: Allograft GD control


title: rDP7

description: Allograft GD control


title: ALMOND_FRUIT_3

city: Cerdanyola del Vallès

first: Carlos

last: de Tomás

state: Barcelona

address: Carrer de la Vall Moronta

country: Spain

institute: CRAG

description: RNA-sequencing

data_processing:
For general gene expression analysis, we used the methology described in Vendrell-Mir et al., 2020, with minor modifications.
For Allele-specific expression, SNPS between P0 and P1 phases were detected using paftools.js call from Minimap2. RNA-seq reads were mapped to P0 using Hisat2 . Allele-specific counts were obtained using ASEReadCounter from GATK.
Assembly: Phased almond genome (v.3.0); FASTA with transcript sequences is available on the series record.
Supplementary files format and content: Matrix table with read counts for every gene per sample
Supplementary files format and content: Matrix table with rlog normalized expression values for every gene per sample
Supplementary files format and content: Matrix table with read counts for every allele of gene per sample
Supplementary files format and content: Matrix table with rlog normalized expression values for every gene per sample

organism: Prunus dulcis

source_name: Immature fruits

growth_protocol: Field conditions, normally watered trees.

extract_protocol:
Total RNA was extrated using the Maxwell RSC Plant RNA Kit and the Maxwell RSC instrument (Promega Corporation, Madison, WI, USA).
RNA libraries were prepared using TruSeq Stranded mRNA protocol and were sequenced on Illumina platform NewxSeq 500 (2x150 bp, Paired-end).

value: Immature fruits

tag: cultivar

value: Texas


title: Orc1-delBP4_rep1


title: Orc1-delBP4_rep2


title: PEACH_FRUIT_3

description: RNA-sequencing

organism: Prunus persica

value: Early Gold


title: ALMOND_FRUIT_2

description: RNA-sequencing


title: rDP6

description: Allograft GD control


title: PEACH_FRUIT_2

description: RNA-sequencing


title: rC3GN14

description: Allograft rC3G


title: ALMOND_FRUIT_1

description: RNA-sequencing


title: PEACH_FRUIT_1

description: RNA-sequencing


title: rDDD2

description: Allograft rC3G


title: ALMOND_FLOWER_3

description: RNA-sequencing

source_name: Flowers (pink stage)

value: Flowers (pink stage)


title: Orc1Ntail-delBAH_rep6

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1:: 3xFlag-MNase-ORC1-AA188-375
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::3xFlag-MNase-ORC1-AA188-375


title: Ar5_1


title: PEACH_FLOWER_3

description: RNA-sequencing


title: Orc1Ntail-delBAH_rep5


title: Orc1Ntail-delBAH_rep3


title: ALMOND_FLOWER_1

description: RNA-sequencing


title: PEACH_FLOWER_2

description: RNA-sequencing


title: Control_2


title: rIgAN5

description: Allograft GD control


title: rMN7

description: Allograft GD control


title: Orc1Ntail-delBAH_rep2


title: de novo MN3

description: Allograft GD control


title: ALMOND_FLOWER_2

description: RNA-sequencing


title: Orc1Ntail-delBAH_rep7


title: Wildtype3

city: Indianapolis

first: Luke

middle: Child

last: Dabin

state: Indiana

department: Medical and Molecular Genetics

institute: Indiana University

hyb_protocol: 75 ng of total RNA was hybridized for 16 hrs with capture probes and reporter probes from the AD-associated 770 standardized genes-targeted nCounter Gene Expression code set

scan_protocol: . After hybridization, the probe-target complexes were scanned by a fluorescence microscope and labeled barcodes were counted. Gene expression analysis was performed using the nCounter system (NanoString Technologies) according to the manufacturer's instructions

data_processing: Data were analyzed using nSolver Advanced analysis software (NanoString Technologies) with built-in quality control, normalization, and statistical analyses. Data were exported from nSolver and imported into R (v3.6.2) in RStudio (v1.2.5033). LIMMA (v3.40.6) was used to fit linear models of counts ~ Genotypes for WT (Pu.1+/+;APP/PS1) versus KD (Pu.1+/−;APP/PS1) and NTG (5XFAD) versus TG (Pu.1Tg/0;5XFAD) comparisons

source_name: cortex

extract_protocol: TRI-reagent

value: cortex

tag: ad model

tag: pu.1 genotype

value: Wildtype


title: Wildtype2


title: rC3GN2

description: Allograft rC3G


title: Orc1Ntail-delBAH_rep1


title: Wildtype1


title: de novo ICMGD NOS5

description: Allograft GD control


title: Liver, water, db/db, rep2

city: seoul

first: sungguan

last: hong

address: 84, Heukseok-ro, Dongjak-gu, Seoul, 104-407

department: Chemistry

institute: Chung-Ang

data_processing:
Raw sequencing data were processed using Illumina bcl2fastq conversion tool to generate FASTQ files
Sequences were aligned to GRCm39 genome to gene expression count using New Tuxedo Protocol's default settings
Gene expression level of Refseq coding genes were quantified using Ballgown tool which inspect the distribution of abundance estimates.
Assembly: GRCm39
Supplementary files format and content: gene_expression_fpkm.txt

source_name: Liver

extract_protocol:
Total RNA was isolated from tissue samples using the TRIzolTM Reagent. 1 mL of the reagent and a stainless-steel bead were added to the tissue samples, and tissues were fully homogenized by the TissueLyser LT homogenizer.
1000 ng of total RNA was processed to mRNA enrichment using NEBNext Poly(A) mRNA magnetic isolation module (New England BioLabs, MA, USA) and followed by fragmentation, cDNA synthesis, and library preparation with unique dual index using NEBNext Ultra II RNA library prep kit (New England BioLabs) according to the manufacturer’s manual.

value: Liver

value: db/db

value: 16 weeks


title: Liver, water, db/db, rep1

value: Male


title: Liver, sucrose, db/db, rep2


title: rMN9

description: Allograft GD control


title: Orc1Ntail_Orc1-delBAH_rep2

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 ORC1-Truncation-188 bar1:: 3xFlag-MNase-ORC1-AA1-375
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 ORC1-Truncation-188 bar1::3xFlag-MNase-ORC1-AA1-375


title: rDDD1

description: Allograft rC3G


title: Orc1Ntail_Orc1-delBAH_rep4


title: Orc1Ntail_Orc1-delBAH_rep3


title: Orc1Ntail-delBAH_rep4


title: Liver, sucrose, db/db, rep1


title: Knockdown3

value: Knockdown


title: de novo MN5

description: Allograft GD control

value: Female


title: Knockdown2


title: PEACH_FLOWER_1

description: RNA-sequencing


title: Orc1Ntail_Orc1-delBAH_rep1


title: Knockdown1


title: Liver, brazzein, db/db, rep2


title: Liver, brazzein, db/db, rep1


title: Orc1-delBAH_rep4

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1∆ ORC1-N'-3xFlag-MNase-Truncation-188
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1delta ORC1-N'-3xFlag-MNase-Truncation-188


title: Orc1-delBAH_rep3


title: Liver, water, db/+, rep2


title: de novo ICMGD  NOS4

description: Allograft GD control


title: rMN8

description: Allograft GD control


title: Non-Transgenic2


title: Non-Transgenic3


title: Liver, water, db/+, rep1


title: de novo ICMGD NOS3

description: Allograft GD control


title: Non-Transgenic1


title: de novo HCV1

description: Allograft GD control


title: Orc1-delBAH_rep2


title: Liver, sucrose, db/+, rep2


title: Orc1-delBAH_rep1


title: Transgenic3

value: Transgenic


title: Transgenic2


title: de novo ICMGD NOS2

description: Allograft GD control


title: Liver, sucrose, db/+, rep1


title: Liver, brazzein, db/+, rep2


title: Transgenic1


title: rDDD8

description: Allograft rC3G


title: rMN1

description: Allograft GD control


title: Orc1_Orc1synCopy_rep4

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase


title: Orc1_Orc1synCopy_rep3


title: Orc1_Orc1synCopy_rep2


title: Liver, brazzein, db/+, rep1


title: Brain, water, db/db, rep2

source_name: Brain

value: Brain

value: db/+