title: Tet_WT_NSC_pcHiC

city: New York

first: Meelad

middle: M

last: Dawlaty

address: 1301 Morris Park Ave, Price 419, Bronx

department: Genetics

institute: Albert Einstein College of Medicine

data_processing:
For pcHiC, libraries were sequenced at Arima Genomics and reads from each sample were processed with the Arima Capture-HiC v1.5 pipeline. Reads were aligned to the mm10 reference genome using HiCUP and chromatin loop calling was performed using CHiCAGO.
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files. Bigwig files were generated using bamCoverage from deepTools, and bigwig files were analyzed using plotProfile and plotHeatmap. Peaks annotation were implemented by R package "ChIPseeker".
Assembly: mm10
Library strategy: pcHiC

source_name: Neural stem cells

growth_protocol: ESCs preplated and cultured on gelatin in serum/LIF for 24 hours before harvest for high-throughput sequencing. NSCs were generated following the protocol of Okabe et al. (1996) as modified by Lee et al. (2000), passaged once, and then harvested for high-throughput sequencing.

extract_protocol: pcHiC libraries were prepared by Arima Genomics (https://arimagenomics.com/)

treatment_protocol: For pcHiC, NSCs were crosslinked with 4% PFA.

tag: cell line

value: Neural stem cells

tag: genotype

value: Tet wildtype


title: WT_LT-HSC2

status: Public on Jul 25 2024

type: SRA

city: Guangzhou

first: Fangshu

last: Liu

address: he First Affiliated Hospital of Jinan University, 613W Huangpu Rd, Guangzhou, Guangdong,

country: China

institute: Department of Hematology, the First Affiliated Hospital of Jinan University

library_source: transcriptomic

data_processing:
Raw reads were pre-processed using fastp filtering low-quality reads.
Clean reads were mapped to the the reference genome using HISAT2.
Quantification of gene expression levels were performed using Stringtie and RSEM.
Assembly: Ensembl_release104
Supplementary files format and content: processed counts was uploaded as xls file

molecule: polyA RNA

organism: Mus musculus

source_name: bone marrow

extract_protocol:
500-800 sorted LT-HSC cells (Lin-Sca-1+c-Kit+CD135-CD150+CD48-) were used for sequencing.
Sequencing libraries were prepared using TruePrep DNA Library Prep Kit V2 for Illumina according to the manufacturer’s protocol (Vazyme, TD503-01)

tag: tissue

value: bone marrow

tag: cell type

value: Long-term Hematopoietic stem cells

tag: surface markers

value: WT

tag: age

value: 6-8 weeks olds

tag: strain


title: WT_LT-HSC3


title: E1_hap_5_none_none_none_DHFR_cj_2

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

country: USA

institute: Stanford University

library_source: genomic

data_processing:
*library strategy: Targeted deep sequencing of an amplicon
Fastq files were analyzed with CRISPResso2 to yield an allele frequency table of repair outcomes for each sample.
Assembly: A custom reference was created for each amplicon which consisted of the two Cas9 cut sites for the amplicon being directly ligated together.
Supplementary files format and content: The processed data file is a csv file containing a merged allele frequency table for all the samples. It has every repair outcome, its frequency, and metadata, merged across all samples.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: (C631) and Hap1 knockout cell lines (PRKDC-KO: HZGHC024034c011, LIG4-KO: HZGHC000759c014; POLQ-KO: HZGHC000647c003, Horizon Discovery) were maintained in IMDM supplemented with GlutaMAX and 10% FCS (Gibco). K562 cells (ATCC) were maintained in RPMI supplemented with 10% FCS. Cell lines were used as received without authentication. Cells regularly tested negative for mycoplasma contamination. The FTE5 organoid line was generated from phenotypically normal fresh surgical discards of a patient undergoing salpingectomy at Stanford University Hospital via Stanford University Hospital’s Tissue Procurement Shared Resource Facility. Isolation of fallopian tube epithelial cells followed previously established protocols. Isolated fallopian tube cells were resuspended in matrigel (R&D Systems: Basement Membrane Extract type 2 #3533-005-02) and plated in a 24 well plate as individual domes. Following solidification, organoid media supplemented with 10 uM Y-27632 (PeproTech: #1293823) was added to each well. After 2 days, Y-27632 was removed from the media and changed every 3-4 days. Organoids were passaged every 14 days by dissolving Matrigel and dissociating fallopian tube organoids to single cells using TrypLE (Invitrogen: #12604-012) at 37°C for 15 minutes inverting 2-3 times every 5 mins. TrypLE was quenched with FBS and removed following centrifugation for 3 minutes at 600g. The single cells were resuspended in matrigel and plated in a 24 well plate.

extract_protocol:
gDNA was isolated using DNeasy columns (QIAGEN) according to the manufacturer’s instructions, including a 10-min incubation at 56 °C during the proteinase K digestion step; DNA was eluted with 100 μl EB buffer.
20 cycles of primary PCR to amplify the region of interest was performed using ~200ng µL of genomic DNA in a 10 µL Platinum SuperFi II polymerase reaction (Thermo Fisher Scientific; for primers see Supplementary Data Set 1). Illumina adapters and indexing sequences were added via 15 cycles of secondary PCR with 1 µL of primary PCR product in a 10 µL Platinum SuperFi II polymerase reaction. The final amplicons were run on a TAE-agarose gel (0.7%); and the product band was excised and extracted using the Freeze and Squeeze Kit according to the manufacturer’s instructions (Bio-Rad). Gel-purified amplicons were quantified with a dsDNA HS Assay kit on a Qubit fluorometer (ThermoFisher Scientific). Then, amplicons were pooled and sequenced on the NextSeq 550 platform (Nextseq 500/550 Mid Output Kit v2.5, Illumina, for primers see Supplementary Data Set 1). DHFR CRISPR-C time course samples in Fig. 3D were reported previously described, and subsequently sequenced for this study

treatment_protocol: Hap1 cells were trypsinized, quenched with IMDM (GlutaMAX, 10% FCS), counted and centrifuged at 300g for 5 min. Cells were washed once with PBS before resuspension in Neon Resuspension Buffer to 1.1 × 107 cells per mL for Hap1 cells and 2.67 × 107 cells per mL for K562 cells. Ribonucleoprotein (RNP) complexes were formed as follows: Cas9 (IDT) was diluted to 36 μM in Neon Resuspension Buffer. Equal volumes of diluted Cas9 and sgRNA (44 μM in TE, pH 8.0) were mixed and incubated at room temperature for 10–20 min. Left and right sgRNA RNPs were assembled separately. Then, 5.5 μl of each RNP, 5.5 22 μl of electroporation enhancer (10.8 μM; IDT) and 99 μl of cells were mixed and electroporated according to the manufacturer’s instructions using a 100-μl Neon pipet tip and electroporated with the Neon Transfection System (Thermo Fisher Scientific) using the following settings: Hap1 (1,575 V, 10 ms pulse width, 3 pulses); K562 (1,700 V, 20 ms, 1 pulse). Single-guide controls were prepared as above except 11 μl of the appropriate sgRNA was used. Volumes were scaled down for 10 uL electroporations. Cells were collected at the 24 hours post-electroporation as follows: cells were washed with 1 ml per well prewarmed PBS (Gibco), followed by the addition of 100 μl TrypLE Express (Thermo Fisher Scientific) and incubation at 37 °C for 5–10 min. TrypLE was quenched with 800 μl IMDM (GlutaMAX, 10% FCS) and the cell suspension was pelleted at 300 g for 5 min at 4 °C. The supernatant was discarded and the cell pellets were stored at −80 °C.  For experiments including inhibition of DDR proteins, after electroporation, cells were plated in media containing either AZD7648 (1 μM), SCR7 (1 μM,), Berzosertib (80 nM), KU-55933 (10 μM) Talazoparib (10 nM), or DMSO. Samples were harvested 24 hours after electroporation. All compounds were obtained from Selleck Chemicals. Final DMSO concentration in all wells was 0.2%. Final drug concentrations were selected based on effective doses for cell culture reported in the literature(50–54). For ecDNA generation vía CRISPR-C in FTE5 organoids, organoid media was supplemented with Y-27632 one day prior to electroporation. RNP complexes were made by incubating (per reaction) 10uL Opti-MEM (Gibco #31985062), 0.6ul 10ug/mL Cas9 (IDT #1081059), and 44umol sgRNA for each sgRNA and incubated at room temperature for 15 minutes before combining. FTE5 organoids were dissociated as above and 2x10^5 cells were resuspended 10ul Opti-MEM per reaction. Cells and RNP complexes were combined and 20ul was added per well of a Nucleocuvette strip (Lonza #NC0828118) and electroporated using a Lonza 4D Nucleofactor-x with protocol “Primary Cell P3 code CA137. Cells were collected from the cassette and resuspended in matrigel before plating in a 24 well plate and given organoid media containing Y-27632 for 3 days before removing. 3 reactions were performed per replicate. 24 hours post electroporation, organoids were dissociated as before and DNA was harvested from the organoids using a Qiagen DNAeasy Blood and Tissue kit (Qiagen #69506).

tag: day

tag: drug

tag: ko

tag: grna

value: DHFR_gL, DHFR_gR

tag: replicate

tag: amplicon name

value: DHFRcj

tag: group


title: WT_LT-HSC1


title: E1_hap_5_none_none_none_DHFR_cj_1


title: E1_hap_5_none_none_none_DHFR_sj_1

value: DHFRsj


title: Cxcr3_LT-HSC1


title: E1_hap_15_none_none_none_DHFR_sj_3


title: GJ20

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

description: OTU genus read count

library_source: other

data_processing:
*library strategy: AmpliSeq
QIIME 2
Assembly: COBS, minHash and pp_sketch indices are available from: ftp.ebi.ac.uk/pub/databases/ENA2018-bacteria-661k
Supplementary files format and content: raw_count.txt

molecule: other

organism: Bacteria

source_name: faeces

extract_protocol:
microbial DNA extraction using QIAsymphony DSP Virus/Pathogen Midi Kit
16S metagenomics ION (ThermoFisher)

value: faeces

tag: cohort

value: discovery

tag: bmi

tag: smoke

value: Smoker

tag: diabetes

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

value: Prostatectomy

tag: appendectomy

value: No appendectomy

tag: rt technique

value: VMAT

tag: rt intent

value: Radical

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: Yes

tag: physical activity_status

value: undeclared

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype

value: microbial DNA


title: Cxcr3_LT-HSC2

tag: tissue

value: bone marrow

tag: cell type

value: Long-term Hematopoietic stem cells

tag: surface markers

tag: genotype

tag: age

tag: strain


title: E1_hap_15_none_none_none_DHFR_sj_2

tag: day

tag: drug

tag: ko

tag: grna

tag: replicate

tag: amplicon name

tag: group


title: E1_hap_15_none_none_none_DHFR_sj_1


title: Tet_TKO_NSC_pcHiC

state: New York

tag: cell line

value: Neural stem cells

value: Tet triple knockout


title: Cxcl10_LT-HSC1

value: 6-8 weeks olds


title: Cxcl10_LT-HSC2


title: E1_hap_15_none_none_none_DHFR_cj_1

value: DHFR_gL, DHFR_gR

value: DHFRcj


title: E1_hap_1_none_none_none_DHFR_sj_3

value: DHFRsj


title: siYTH1_2_3_nuc_2

city: Rehovot

first: David

last: Dierks

state: Central District

address: Herzl St 234, Weizmann Institute of Science to the Department of Biomolecular Sciences, Laboratory of Dr. Scherz-Shouval

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
mRNA samples from human and mouse were aligned to the mm9/hg19 genome using STAR v.2.5.3a with default settings (‘--alignIntronMax 1000000’) (Dobin et al., 2013). For gene expression (TPM) and read counts, rsem-calculate-expression (rsem/1.3.3) was employed (Li and Dewey, 2011). m6A-GI and m6A-SI metrics were derived using the bam2ReadEnds.R script (Garcia-Campos et al., 2019) as per Dierks et al. 2021, calculating m6A IP enrichment against input coverage.
Assembly: mm9 & hg19
Supplementary files format and content: RSEM hg19 counted reads and tpm tables

growth_protocol: Mammalian cell lines were grown at 37°C and 5 % CO2 in DMEM (10% FBS, with Antibiotics Penn/Strep)

extract_protocol:
Nucleozol total RNA extraction protocol according to the manufacturers protocol.
All libraries were conducted according to the libraray preparation protocol in Dierks et al. 2021. For RNA-seq, the protocol was performed as in Dierks 2021, excluding the m6A IP step, (performed as if only is the input sample.
m6A-seq2 & RNA-seq (m6A-seq2 protocol exluding the m6A IP section)

value: cell line

tag: library type

value: RNA-seq


title: siYTH1_2_3_nuc_1


title: E1_hap_1_none_none_none_DHFR_sj_2


title: E1_hap_15_none_none_none_DHFR_cj_3


title: E1_hap_1_none_none_none_DHFR_cj_3


title: siCtrl_nuc_2


title: siCtrl_nuc_1


title: E1_hap_1_none_none_none_DHFR_cj_2


title: siYTH1_2_3_cyt_2


title: E1_hap_1_none_none_none_DHFR_sj_1


title: E1_hap_1_none_none_none_DHFR_cj_1


title: E1_hap_1_none_none_sg14_MYCsg14_cj_1

value: MYC_sg1, MYC sg4


title: siCtrl_cyt_2


title: siYTH1_2_3_cyt_1


title: Cxcr3_LT-HSC3


title: E2_hap_none_dmso_none_none_MYCec2_sj_3

value: dmso

value: MYCec2_gL, MYCec2_gR


title: Cxcl10_LT-HSC3


title: E1_hap_15_none_none_none_DHFR_cj_2


title: siCtrl_cyt_1


title: E2_hap_none_dmso_none_none_MYCec2_sj_1


title: E2_hap_none_ku_none_none_MYCec2_sj_3


title: siCtrl_wholecell_ip_1


title: siYTH1_2_3_wholecell_ip_2


title: E2_hap_none_ku_none_none_MYCec2_sj_2


title: siYTH1_2_3_wholecell_ip_1


title: siCtrl_wholecell_ip_2


title: E2_hap_none_dmso_none_none_MYCec2_sj_2


title: E2_hap_none_azd_none_none_MYCec2_sj_2


title: siYTH1_2_3_wholecell_input_2


title: E2_hap_none_azd_none_none_MYCec2_sj_1


title: E2_hap_none_azd_none_none_MYCec2_sj_3


title: E2_hap_none_ku_none_none_MYCec2_sj_1


title: siCtrl_wholecell_input_1


title: siCtrl_wholecell_input_2


title: siYTH1_2_3_wholecell_input_1


title: E2_hap_none_dmso_none_none_MYCec2_cj_3


title: E2_hap_none_dmso_none_none_MYCec2_cj_2


title: HSTC_pmef_KO_m6Aseq2_r4_3_ip

source_name: pMEF

value: pMEF

value: primary cells


title: HSTC_pmef_KO_m6Aseq2_r4_2_ip


title: E2_hap_none_dmso_none_none_MYCec2_cj_1


title: HSTC_pmef_KO_m6Aseq2_hs90_2_ip


title: E2_hap_none_ku_none_none_MYCec2_cj_3


title: HSTC_pmef_KO_m6Aseq2_r4_1_ip


title: HSTC_pmef_KO_m6Aseq2_hs90_3_ip


title: E2_hap_none_ku_none_none_MYCec2_cj_2


title: E2_hap_none_ku_none_none_MYCec2_cj_1


title: HSTC_pmef_KO_m6Aseq2_hs90_1_ip


title: HSTC_pmef_KO_m6Aseq2_c3_ip


title: E2_hap_none_azd_none_none_MYCec2_cj_3


title: HSTC_pmef_KO_m6Aseq2_c2_ip


title: E2_hap_none_azd_none_none_MYCec2_cj_1


title: E2_hap_none_azd_none_none_MYCec2_cj_2


title: E2_hap_none_dmso_none_none_KRAS_sj_3

value: KRAS_gL, KRAS_gR


title: HSTC_pmef_KO_m6Aseq2_r4_3_input


title: HSTC_pmef_KO_m6Aseq2_r4_2_input


title: E2_hap_none_dmso_none_none_KRAS_sj_2


title: E2_hap_none_ku_none_none_KRAS_sj_3


title: E2_hap_none_ku_none_none_KRAS_sj_2


title: HSTC_pmef_KO_m6Aseq2_hs90_3_input


title: HSTC_pmef_KO_m6Aseq2_r4_1_input


title: E2_hap_none_dmso_none_none_KRAS_sj_1


title: E2_hap_none_ku_none_none_KRAS_sj_1


title: E2_hap_none_azd_none_none_KRAS_sj_3


title: HSTC_pmef_KO_m6Aseq2_hs90_2_input


title: HSTC_pmef_KO_m6Aseq2_hs90_1_input


title: HSTC_pmef_KO_m6Aseq2_c3_input


title: E2_hap_none_azd_none_none_KRAS_sj_2


title: HSTC_pmef_KO_m6Aseq2_c2_input


title: E2_hap_none_dmso_none_none_KRAS_cj_3


title: HSTC_pmef_KO_m6Aseq2_c1_input


title: E2_hap_none_dmso_none_none_KRAS_cj_2


title: HSTC_pMEF_KO_frac_nuc_hs90


title: HSTC_pMEF_KO_frac_cyt_hs90


title: E2_hap_none_azd_none_none_KRAS_sj_1


title: HSTC_pmef_KO_m6Aseq2_c1_ip


title: E2_hap_none_dmso_none_none_KRAS_cj_1


title: E2_hap_none_ku_none_none_KRAS_cj_2


title: E2_hap_none_ku_none_none_KRAS_cj_3


title: HSTC_pMEF_KO_frac_cyt_ctrl


title: E2_hap_none_ku_none_none_KRAS_cj_1


title: HSTC_pMEF_KO_frac_nuc_ctrl


title: HSTC_pmef_wt_frac_rna_seq_nuc_r4


title: HSTC_pmef_wt_frac_rna_seq_nuc_r1


title: E2_hap_none_azd_none_none_KRAS_cj_3


title: HSTC_pmef_wt_frac_rna_seq_nuc_hs90


title: E2_hap_none_azd_none_none_KRAS_cj_1


title: HSTC_pmef_wt_frac_rna_seq_cyt_r4


title: E2_hap_none_dmso_none_none_EGFR_sj_2

value: EGFR_gL, EGFR_gR


title: HSTC_pmef_wt_frac_rna_seq_cyt_r1


title: HSTC_pmef_wt_frac_rna_seq_cyt_ctrl


title: E2_hap_none_ku_none_none_EGFR_sj_2


title: HSTC_pmef_wt_frac_rna_seq_cyt_hs90


title: E2_hap_none_ku_none_none_EGFR_sj_3


title: HSTC_pmef_wt_frac_rna_seq_nuc_ctrl


title: E2_hap_none_ku_none_none_EGFR_sj_1


title: HSTC_pmef_wt_m6Aseq2_r4_2_ip


title: HSTC_pmef_wt_m6Aseq2_r4_1_ip


title: E2_hap_none_azd_none_none_EGFR_sj_3


title: E2_hap_none_azd_none_none_EGFR_sj_2


title: E2_hap_none_azd_none_none_EGFR_sj_1


title: HSTC_pmef_wt_m6Aseq2_r1_3_ip


title: HSTC_pmef_wt_m6Aseq2_r1_1_ip


title: HSTC_pmef_wt_m6Aseq2_hs90_3_ip


title: HSTC_pmef_wt_m6Aseq2_hs90_1_ip


title: HSTC_pmef_wt_m6Aseq2_r1_2_ip


title: E2_hap_none_dmso_none_none_EGFR_cj_2


title: E2_hap_none_azd_none_none_KRAS_cj_2


title: E2_hap_none_dmso_none_none_EGFR_sj_1


title: E2_hap_none_dmso_none_none_EGFR_sj_3


title: HSTC_pmef_wt_m6Aseq2_hs90_2_ip


title: E2_hap_none_dmso_none_none_EGFR_cj_1


title: E2_hap_none_ku_none_none_EGFR_cj_3


title: HSTC_pmef_wt_m6Aseq2_hs45_2_ip


title: E2_hap_none_ku_none_none_EGFR_cj_2


title: HSTC_pmef_wt_m6Aseq2_hs45_3_ip


title: HSTC_pmef_wt_m6Aseq2_r4_3_ip


title: E2_hap_none_ku_none_none_EGFR_cj_1


title: E2_hap_none_azd_none_none_EGFR_cj_3


title: E2_hap_none_azd_none_none_EGFR_cj_2


title: HSTC_pmef_wt_m6Aseq2_c2_ip


title: E2_hap_none_dmso_none_none_EGFR_cj_3


title: HSTC_pmef_wt_m6Aseq2_c1_ip


title: E2_fallop_none_none_p53_none_MYC_sj_3

value: MYC_sg2, MYC_sg4


title: HSTC_pmef_wt_m6Aseq2_r4_3_input


title: E2_hap_none_azd_none_none_EGFR_cj_1


title: E2_fallop_none_none_p53_none_MYC_sj_2


title: HSTC_pmef_wt_m6Aseq2_r4_2_input


title: E2_fallop_none_none_p53_none_MYC_sj_1


title: E2_hap_none_dmso_none_none_BRAF_sj_2

value: BRAF_gL, BRAF_gR


title: HSTC_pmef_wt_m6Aseq2_r1_2_input


title: E2_hap_none_dmso_none_none_BRAF_sj_1


title: E2_hap_none_dmso_none_none_BRAF_sj_3


title: HSTC_pmef_wt_m6Aseq2_r4_1_input


title: HSTC_pmef_wt_m6Aseq2_r1_3_input


title: E2_hap_none_ku_none_none_BRAF_sj_2


title: E2_hap_none_ku_none_none_BRAF_sj_3


title: HSTC_pmef_wt_m6Aseq2_hs90_3_input


title: HSTC_pmef_wt_m6Aseq2_hs45_1_ip


title: E2_hap_none_ku_none_none_BRAF_sj_1


title: HSTC_pmef_wt_m6Aseq2_hs90_1_input


title: E2_hap_none_azd_none_none_BRAF_sj_3


title: HSTC_pmef_wt_m6Aseq2_r1_1_input


title: HSTC_pmef_wt_m6Aseq2_hs45_3_input


title: E2_hap_none_azd_none_none_BRAF_sj_2


title: E2_hap_none_azd_none_none_BRAF_sj_1


title: HSTC_pmef_wt_m6Aseq2_hs45_1_input


title: HSTC_pmef_wt_m6Aseq2_c3_ip


title: HSTC_pmef_wt_m6Aseq2_c3_input


title: E2_hap_none_dmso_none_none_BRAF_cj_3


title: E2_hap_none_dmso_none_none_BRAF_cj_2


title: HSTC_pmef_wt_m6Aseq2_c2_input


title: E2_hap_none_dmso_none_none_BRAF_cj_1


title: 3t3_IP_nuc_2


title: E2_hap_none_ku_none_none_BRAF_cj_2


title: E2_hap_none_ku_none_none_BRAF_cj_1


title: HSTC_pmef_wt_m6Aseq2_hs90_2_input


title: 3t3_IP_nuc_1


title: 3t3_IP_cyto_2


title: E2_hap_none_azd_none_none_BRAF_cj_2


title: 3t3_IP_cyto_1


title: E2_hap_none_azd_none_none_BRAF_cj_3


title: E2_hap_none_none_prkdc_none_MYC_sj_3

value: prkdc


title: 3t3_Input_cyto_2


title: 3t3_Input_nuc_2


title: E2_hap_none_azd_none_none_BRAF_cj_1


title: E2_hap_none_none_prkdc_none_MYC_sj_2


title: 3t3_Input_cyto_1


title: 3t3_Input_nuc_1


title: E2_hap_none_none_prkdc_none_MYC_sj_1


title: m_KO_3

city: Dresden

first: Ben

last: Wielockx

address: Fetscherstrasse 74

country: Germany

institute: IKL, Carl Gustav Carus Universitätklinikum Dresden

data_processing:
Low quality nucleotides were removed Illumina fastq filter (http://cancan.cshl.edu/labmembers/gordon/fastq_illumina_filter/).
Reads were further subjected adaptor trimming using cutadapt.
Alignment of the reads to the Mouse genome was done using STAR Aligner  using the parameters: “--runMode alignReads --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat”. Mouse Genome version GRCm38 (release M12 GENC
HTSeq-0.6.1p1  was used to count the reads that map to the genes in the aligned sample files. Read Quantification was performed using the parameters: 'htseq-count -f bam -s reverse -m union -a 20'. The GTF file (gencode.vM12.annotation.gtf) used for read
mm10
Assembly: Tab-Delimited Gene-Wise Raw read counts text file

molecule: total RNA

source_name: Bone marrow

extract_protocol:
Bone marrow cells were isolated by crushing long bones in 2% FCS using a mortar and then filtering the suspension through a 40 µm filter. Following centrifugation, the resulting pellet was resuspended in ACK lysis buffer for 30-40 seconds to lyse red blood cells, and the lysis was subsequently stopped with a 2% FCS solution. After centrifuging the solution, cells were stained for specific cell markers using fluorophore-conjugated antibodies for 30 minutes at +4. For RNAseq analysis, endothelial cells (ECs) from the bone marrow of mice were isolated directly into the lysis buffer of the RNeasy Plus Micro Kit ECs from the BM were defined as CD45-, Ter119- and CD31+, Sca1+. RNA was isolated according to manufacturer’s instructions, and SmartSeq2 sequencing was performed.
Illumina DNA Tagmentation followed by mRNA enrichment by poly-dT

value: Bone marrow

value: Endothelial cell

value: KO

tag: Sex

value: male

tag: treatment

value: Tamoxifen injections

tag: time

value: 2 weeks


title: HSTC_pmef_wt_m6Aseq2_hs45_2_input

tag: cell type

value: RNA-seq


title: E2_hap_none_none_polq_none_MYC_sj_2

value: polq


title: E2_hap_none_none_polq_none_MYC_sj_3


title: m_KO_2

tag: tissue


title: f_KO_4

tag: genotype

value: female


title: E2_hap_none_none_lig4_none_MYC_sj_3


title: E2_hap_none_ku_none_none_BRAF_cj_3


title: f_KO_1


title: m_WT_3

value: WT


title: HSTC_pmef_wt_m6Aseq2_c1_input

value: pMEF


title: E2_hap_none_none_lig4_none_MYC_sj_2


title: E2_hap_none_none_polq_none_MYC_sj_1


title: E2_hap_none_none_lig4_none_MYC_sj_1


title: f_WT_4


title: E2_hap_none_none_wt_none_MYC_sj_3

value: wt


title: KO_m3

value: 4 weeks


title: f_WT_1


title: E2_hap_none_none_wt_none_MYC_sj_2


title: E2_hap_none_none_wt_none_MYC_sj_1


title: E2_k562_none_dmso_none_none_MYC_sj_3

value: dmso


title: KO_m1


title: E2_k562_none_dmso_none_none_MYC_sj_2

value: MYC_sg2, MYC_sg4


title: E2_k562_none_dmso_none_none_MYC_sj_1


title: WT_m3


title: E2_k562_none_ku_none_none_MYC_sj_3


title: E2_k562_none_ku_none_none_MYC_sj_2


title: WT_m1


title: KO_f2


title: WT_m2


title: E2_k562_none_ku_none_none_MYC_sj_1


title: WT_f


title: E2_k562_none_azd_none_none_MYC_sj_2


title: E2_k562_none_azd_none_none_MYC_sj_1


title: m_WT_2


title: WT_f3


title: E2_hap_none_dmso_none_none_MYC_sj_3


title: wild type, scRNA-seq

first: Yinshan

last: Fang

address: 650W 168th Street

institute: Columbia University Medical Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software v7.1.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: matrix files

source_name: esophagus

extract_protocol:
To obtain single cell suspension, esophagus tissues from p63-KO and littermate control at E18.5 were dissected, washed with PBS and then the muscle layer was removed using fine forceps. The tissues were treated with dispase (Corning 354235) for 5 min at room temperature. DMEM containing 10% FBS was added to stop digestion and then the epithelial layers were treated with 0.1% Trypsin for 10 min at 37°C. DMEM containing 10% FBS was added to stop digestion and then the cells were filtered through 40-μm strainers, and then centrifuged at 300g for 5 min to obtain cell pellet.
Single Cell 3’ V2 chemistry kit (10x Genomics) was used to produce single-cell barcoded droplets and libraries according to the manufacturer's protocol.

value: esophagus

tag: developmental stage

value: epithelium


title: p63-KO, scRNA-seq

description: 10x Genomics

tag: strain


title: E2_hap_none_dmso_none_none_MYC_sj_2

tag: day


title: TAM_CP4

city: Hangzhou

first: Xiaonan

last: Xiang

address: No.866, Yuhangtang road Road

department: School of Medicine

institute: Zhejiang University

description: RNAseq for TAM

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platformand 150 bppaired-endreadswere generated. About 40 million raw reads for each sample were generated. Rawreads of fastqformatwere firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT. FPKM of each gene was calculatedandthe read counts of each gene were obtained by HTSeq-count.
PCA analysis were performedusingR(v 3.2.0) to evaluate the biological duplication of samples
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for all samples

source_name: liver cancer

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) accordingtothemanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop2000spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed usingtheAgilent2100Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructedusingVAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. Thetranscriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: liver cancer

value: Tumor-infiltrating Macrophages


title: E2_hap_none_dmso_none_none_MYC_sj_1

tag: drug


title: E2_hap_none_ku_none_none_MYC_sj_3

tag: ko


title: KO_m2

value: Bone marrow

value: Endothelial cell

value: KO


title: E2_hap_none_ku_none_none_MYC_sj_1

tag: grna


title: TAM_CP2

description: RNAseq for TAM


title: TAM_CP1

description: RNAseq for TAM


title: E2_hap_none_ku_none_none_MYC_sj_2

tag: replicate


title: E2_hap_none_azd_none_none_MYC_sj_3

tag: amplicon name


title: TAM_C2

description: RNAseq for TAM


title: E2_k562_none_azd_none_none_MYC_sj_3

tag: group


title: TAM_C1

description: RNAseq for TAM


title: E2_hap_none_azd_none_none_MYC_sj_2


title: E2_hap_none_azd_none_none_MYC_sj_1


title: TAM_PD4

description: RNAseq for TAM


title: TAM_PD3

description: RNAseq for TAM


title: E2_hap_none_none_lig4_none_MYC_cj_3


title: E2_hap_none_none_lig4_none_MYC_cj_2


title: TAM_PD1

description: RNAseq for TAM


title: E2_hap_none_none_wt_none_MYC_cj_3


title: TAM_PD2

description: RNAseq for TAM


title: TAM_IgG4

description: RNAseq for TAM

value: IgG


title: E2_hap_none_none_wt_none_MYC_cj_2


title: E2_hap_none_none_wt_none_MYC_cj_1


title: TAM_C4

description: RNAseq for TAM


title: TAM_IgG2

description: RNAseq for TAM


title: TAM_IgG3

description: RNAseq for TAM


title: E2_hap_none_none_lig4_none_MYC_cj_1


title: TAM_IgG1

description: RNAseq for TAM


title: TAM_C3

description: RNAseq for TAM


title: TAM_CP3

description: RNAseq for TAM


title: E2_k562_none_ku_none_none_MYC_cj_2


title: E2_k562_none_ku_none_none_MYC_cj_1


title: NB_GEX

city: West haven

first: Antariksh

last: Tyagi

state: CT

address: 830 West Campus Dr

institute: Yale University

data_processing:
alignment, filtering, counting barcodes, quantifying unique molecular identifiers (UMIs), and conducting antibody capture analysis to determine the gene transcript counts per cell was executed using the “multi” function of Cell Ranger (v7.1.0; 10x Genomics)
Assembly: GRCm39
Supplementary files format and content: Tab-seperated values files, comma-seperated values files and matrix files

source_name: mesenteric lymph node

extract_protocol:
For single cell sequencing of all CD4+ T cells, sorted CD3+B220-Tcrb+CD4+ cells from 3 SPF and 3 N.b- infected mice were each labeled with TotalSeq™-C0301,C0302 and C0303 anti-mouse Hashtag antibodies (Biolegend) so that cells from individual mice had unique hashtag-oligos. Antibody cocktail was prepared according to manufacturer’s protocol and labeling was performed by incubating cells with each oligo-tagged antibody for 30 minutes at 4C at 1:50 Ab dilution.
Gene expression, TCR, and barcode libraries were created and sequenced using the ChromiumSingle Cell 5ʹ GEM, Library, TCR & Gel Bead Kit v2 (10x Genomics).

value: mesenteric lymph node

value: T cells

value: Nippostrongylus brasiliensis infection (1week)


title: NB_VDJ


title: NB_Antibody


title: E2_k562_none_azd_none_none_MYC_cj_2


title: SPF_VDJ

value: no infection


title: E2_k562_none_azd_none_none_MYC_cj_3


title: SPF_Antibody


title: E2_k562_none_azd_none_none_MYC_cj_1


title: mESC_Dhx9_cuttag_rep1

city: Chengdu

first: Zhihong

last: Xue

state: Sichuan

address: No. 20, 3rd section, South Renmin Road

institute: Sichuan University

data_processing:
Untrimmed sequencing reads were first analyzed for quality control by fastqc software(v0.11.9).
The adaptor sequence and low-quality reads were then trimmed off using fastp software(v0.22.0)
Reads were then aligned to the UCSC hg38 genome or the UCSC mm10 genome  using bowtie2. Only uniquely mapping reads (quality score > 40) were retained.
Bam files were converted to bigwig files using Deeptool.
Assembly: hg38 or mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

growth_protocol: DMEM, 10% FBS, 1× non-essential amino acid solution, 1× GlutaMAX, 1 mM sodium pyruvate, 0.1 mM β-mercaptoethanol, 100 U/mL Penicillin-Streptomycin. Cells were cultured at 37℃ at 5% CO2

extract_protocol:
Live cells were conjugated to concanavalin A–coated magnetic beads. The antibody was bound to the cell and fragmented with Tn5.Genomic DNA was extracted by ethanol precipitation.
To generate libraries, purified genomic DNA was amplified with the barcoded i5 and i7 primer using VAHTS HiFi Amplification Mix. The library PCR products were cleaned up with VAHTS DNA Clean Beads and size selected at 200-500bp in length.

treatment_protocol: HEK293 cells were exposed to DMSO (as a control) or 25 μM ML216 or 3 μM NSC 617145 for 16 hrs.

tag: cell line

value: Mouse embryonic stem cell

value: WT


title: mESC_Dhx9_cuttag_rep2


title: E2_fallop_none_none_p53_none_MYC_cj_1


title: E2_fallop_none_none_p53_none_MYC_cj_2


title: E2_hap_none_ku_none_none_MYC_cj_3


title: E2_hap_none_ku_none_none_MYC_cj_2


title: mESC_Dhx9KO_HBD-seq_1


title: mESC_Dhx9KO_HBD-seq_2


title: E2_hap_none_ku_none_none_MYC_cj_1


title: E2_k562_none_ku_none_none_MYC_cj_3


title: E2_hap_none_azd_none_none_MYC_cj_3


title: mESC_Dhx9KO_HepG4-seq_1


title: E2_hap_none_azd_none_none_MYC_cj_2


title: mESC_Dhx9KO_HepG4-seq_2


title: E2_hap_none_azd_none_none_MYC_cj_1


title: mESC_HBD-seq_RNase_1


title: mESC_HBD-seq_RNase_2


title: mESC_HBD-seq_2


title: E2_hap_none_none_prkdc_none_MYC_cj_3

value: prkdc


title: E2_hap_none_none_polq_none_MYC_cj_3

value: polq


title: E2_fallop_none_none_p53_none_MYC_cj_3

value: MYC_sg2, MYC_sg4


title: SPF_GEX


title: E2_hap_none_none_polq_none_MYC_cj_2


title: mESC_HBD-seq_1


title: E2_hap_none_none_prkdc_none_MYC_cj_2


title: E2_hap_none_none_prkdc_none_MYC_cj_1


title: mESC_HepG4-seq_Non-label_Ctrl_2


title: E2_k562_none_dmso_none_none_MYC_cj_3

value: dmso


title: mESC_HepG4-seq_2


title: E2_hap_none_none_polq_none_MYC_cj_1


title: mESC_Dhx9KO_3

data_processing:
Untrimmed sequencing reads were analyzed for quality control by fastp software(v0.22.0). The adaptor sequence and low-quality reads were trimmed off at the same time.
Ribosome RNAs were removed from trimmed reads using SortMeRNA software.
Reads without ribosome RNAs were mapped to hg38 or mm10 reference genome using STAR software(v2.7.1a) as default parameters
Raw readcounts were calculated using RSEM software（v1.2.28）.The raw readcounts were normalized by the FPKM method.
Assembly: hg38 or mm10
Supplementary files format and content: Comma-Separated Values CSV files include FPKM values for each Sample

growth_protocol: HEK293 cells were maintained in the medium (DMEM, 10% FBS, 1× NEAA, 1× GlutaMAX, 1mM sodium pyruvate, 0.1mM β-mercaptoethanol, 100U/ml penicillin, 100 mg/ml streptomycin) in humidified atmosphere with 5% CO2 at 37oC. V6.5 ESC cells were maintained in the medium (DMEM, 10% FBS, 2,000U/ml LIF, 1× NEAA, 1×GlutaMAX, 1mM sodium pyruvate, 0.1mM β-mercaptoethanol, 100U/ml penicillin, 100 mg/ml streptomycin) in humidified atmosphere with 5% CO2 at 37oC.

extract_protocol:
Total RNAs were isolated using the Trizol Reagent.
Libraries were prepared from 1 µg total RNAs. We purified the mRNA using ABclonal mRNA capture Module. The libraries were generated using ABclonal Fast RNA-seq Lib Prep Kit V2, and evaluated using Qsep with S2 Cartridge.
Strand-specific RNA-seq, the RNA strand is the same direction as R2.


title: E2_hap_none_dmso_none_none_MYC_cj_3


title: mESC_WT_1


title: mESC_WT_3


title: E2_hap_none_dmso_none_none_MYC_cj_1


title: E2_hap_none_dmso_none_none_MYC_cj_2


title: E2_k562_none_dmso_none_none_MYC_cj_2


title: mESC_Dhx9KO_1


title: E2_k562_none_dmso_none_none_MYC_cj_1


title: mESC_WT_2


title: mESC_HepG4-seq_Non-label_Ctrl_1


title: E2_fallop_none_none_p53_none_DHFR_sj_2

value: DHFR_gL, DHFR_gR

value: DHFRsj


title: FoxO3, Pten KO 2i, rep2, ChIP

city: Vienna

first: Martin

last: Leeb

address: Dr.-Bohr-Gasse 9/3

department: Max Perutz Labs

country: Austria

institute: University of Vienna

data_processing:
Quality control of fastq files was performed using fastQC (v0.11.9) before and after trimming the sequencing adapter fragments with trim-galore (v0.6.7) and cutadapt (v3.5). Additional 2 bp at the 3’ end were removed with the parameters --three_prime_clip_R1 2 (--three_prime_clip_R2 2 in case of paired end reads).
The trimmed reads were aligned to the mm10 assembly mouse reference genome with bowtie2 (v2.4.4).
The obtained sam files were converted to bam files with samtools (v1.13), and uniquely mapping reads were extracted by removing duplicate reads (as potential PCR artefacts) with samtools markdup.
Peak calling was performed on bam files with macs2 (v2.2.7.1) on combined ChIP duplicates, using all Input samples as control files.
Potential artifactual regions listed in the mm10 blacklist were removed from the obtained bed files using bedtools (v2.31.0).
Assembly: mm10
Supplementary files format and content: bed
Supplementary files format and content: peaks

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured on gelatin-coated plates in DMEM high-glucose medium supplemented with 10% FBS, 2 mM L-Glutamine, 0.1 mM NEAA, 1 mM Sodium Pyruvate, 10 µg/ml penicillin-streptomycin , 55 µM β-mercaptoethanol, 10 ng/ml LIF and 2i (1.5 μM PD0325901 and 3 μM CHIR99021). mESCs were cultured at 37°C and 5%CO2.

extract_protocol:
mESCs were fixed with 1% formaldehyde for 10 minutes, and cross-linking was then quenched with glycine. After cell lysis, chromatin was sonicated in Bioruptor® Pico Tubes (diagenode).
ChIP-seq libraries were prepared using the Ligation Sequencing kit and the Unique NEB adaptors from 1-50 ng of DNA as starting material. Libraries size was measured with the Agilent High Sensitivity DNA kit (median of 350-450 bp), and their qPCR-based quantification was performed with the KAPA Library Quantification kit.

treatment_protocol: mESCs were plated on gelatin-coated plates at a final density of 1 × 104 cells/cm2 in N2B27 medium (1:1 mix of DMEM/F12 ) and Neurobasal medium supplemented with  N2, B27 Serum-Free Supplement, 2 mM L-Glutamine,  0.1 mM NEAA, 10 µg/ml penicillin-streptomycin, 55 µM β-mercaptoethanol) and 2i (1 μM PD0325901 and 3 μM CHIR99021). The following day, cells were washed with PBS and medium was exchanged to either N2B27 without 2i to induce differentiation for the indicated time, or to fresh N2B27-2i for the undifferentiated controls.

value: embryonic stem cell

value: Pten KO

tag: timepoint

tag: chip antibody


title: FoxO3, WT N24, rep2, ChIP


title: E2_fallop_none_none_p53_none_DHFR_sj_1


title: E2_fallop_none_none_p53_none_DHFR_sj_3


title: FoxO3, Pten KO N24, rep2,ChIP


title: E2_hap_none_none_prkdc_none_DHFR_sj_3


title: mESC_HepG4-seq_1


title: FoxO3, WT N24, rep1, ChIP


title: E2_hap_none_none_polq_none_DHFR_sj_3


title: E2_hap_none_none_prkdc_none_DHFR_sj_2


title: FoxO3, WT 2i, rep2, ChIP


title: FoxO3, Pten KO 2i, rep1, ChIP


title: mESC_Dhx9KO_2


title: E2_hap_none_none_polq_none_DHFR_sj_2


title: FoxO3, WT 2i, rep1, ChIP


title: E2_hap_none_none_polq_none_DHFR_sj_1


title: FoxO3, Pten KO N24, rep2, input


title: E2_hap_none_none_lig4_none_DHFR_sj_3


title: E2_hap_none_none_lig4_none_DHFR_sj_2


title: E2_hap_none_none_lig4_none_DHFR_sj_1


title: FoxO3, Pten KO N24, rep1, input


title: FoxO3, Pten KO 2i, rep2, input


title: E2_hap_none_none_wt_none_DHFR_sj_2

value: wt


title: E2_hap_none_none_wt_none_DHFR_sj_3


title: FoxO3, WT 2i, rep2, input


title: FoxO3, Pten KO 2i, rep1, input


title: FoxO3, WT N24, rep1, input


title: FoxO3, Pten KO N24, rep1, ChIP


title: E2_hap_none_none_prkdc_none_DHFR_sj_1


title: FoxO1, Pten KO N24, rep2,ChIP


title: E2_hap_none_none_wt_none_DHFR_sj_1


title: FoxO1, WT N24, rep2, ChIP


title: E2_hap_none_none_prkdc_none_DHFR_cj_2

value: DHFRcj


title: FoxO1, Pten KO N24, rep1, ChIP


title: E2_hap_none_none_polq_none_DHFR_cj_3


title: E2_hap_none_none_polq_none_DHFR_cj_2


title: FoxO1, WT N24, rep1, ChIP


title: FoxO1, Pten KO 2i, rep2, ChIP


title: E2_hap_none_none_polq_none_DHFR_cj_1


title: E2_k562_none_dmso_none_none_DHFR_sj_3


title: FoxO1, WT 2i, rep2, ChIP


title: FoxO1, Pten KO 2i, rep1, ChIP


title: FoxO3, WT N24, rep2, input


title: E2_k562_none_dmso_none_none_DHFR_sj_2


title: E2_k562_none_dmso_none_none_DHFR_sj_1


title: E2_hap_none_none_prkdc_none_DHFR_cj_3


title: FoxO3, WT 2i, rep1, input


title: FoxO1, WT 2i, rep1, ChIP


title: FoxO1, Pten KO N24, rep2, input


title: E2_k562_none_ku_none_none_DHFR_sj_3


title: FoxO1, WT N24, rep2, input


title: E2_k562_none_ku_none_none_DHFR_sj_2


title: E2_hap_none_none_prkdc_none_DHFR_cj_1


title: E2_k562_none_ku_none_none_DHFR_sj_1


title: E2_k562_none_azd_none_none_DHFR_sj_3


title: E2_k562_none_azd_none_none_DHFR_sj_1


title: FoxO1, Pten KO N24, rep1, input


title: FoxO1, Pten KO 2i, rep2, input


title: FoxO1, WT 2i, rep2, input


title: FoxO1, WT N24, rep1, input


title: E2_hap_none_none_lig4_none_DHFR_cj_2


title: FoxO1, Pten KO 2i, rep1, input


title: FoxO1, WT 2i, rep1, input


title: E2_hap_none_none_wt_none_DHFR_cj_3


title: E2_hap_none_none_lig4_none_DHFR_cj_3


title: E2_hap_none_none_wt_none_DHFR_cj_2


title: WT, N24, rep2

data_processing:
Fastq files were analysed with a Nextflow 23.04.1.5866 /nf-core/rnaseq v3.10.1 pipeline.
Quality control was performed using fastQC (v0.11.9), and transcripts were mapped to the mm10 assembly mouse reference genome using Salmon (v1.9.0) as a pseudoaligner and STAR (v2.7.10a) as an aligner.
DESeq2 (v1.38.3) was used to generate normalised count tables and to perform differential expression analyses (FDR-adjusted p-value ≤ 0.05; H0: log2FC = 0)
Assembly: mm10
Supplementary files format and content: comma-delimited text file include normalized counts for each Sample

extract_protocol:
RNA was extracted using the ExtractMe kit (Blirt, EM15) following the manufacturer's instructions.
200-500 ng of RNA were used as starting material for library preparation with the Lexogen 3' mRNA Seq Library Prep Kit. Libraries size was measured with the Agilent High Sensitivity DNA kit, and their qPCR-based quantification was performed with the KAPA Library Quantification kit.

treatment_protocol:
Rapamycin experiment: mESCs were plated on gelatin-coated plates in N2B27-2i + DMSO or N2B27-2i + 20 nM rapamycin. The following day, cells were washed with PBS and medium was exchanged to N2B27+DMSO or N2B27+ 20 nM rapamycin to induce differentiation for the indicated time.
RNAi experiment: mESCs were plated on gelatin-coated plates in N2B27-2i and transfected with FlexiTube siRNAs (Qiagen) using DharmaFECT 1 (Fisher Scientific, T-2001). The next day, cells were washed with PBS and medium was exchanged to either N2B27 without 2i to induce differentiation, or fresh N2B27-2i for the undifferentiated controls. Two siRNAs targeting FoxO1 (SI01005200, SI02694153) were used at a final concentration of 20 nM. As controls, siRNAs targeting GFP (siGFP) or scrambled siRNAs (siScr) were used.
MK-2206 experiment: mESCs were plated on gelatin-coated plates in N2B27-2i or N2B27-2i + 1 μM MK-2206. The following day, cells were washed with PBS and medium was exchanged to either N2B27 or N2B27+1 μM MK-2206 to induce differentiation for the indicated time, or to N2B27-2i or N2B27-2i+1 μM MK-2206 for the undifferentiated controls.

tag: treatment


title: E2_k562_none_azd_none_none_DHFR_sj_2


title: WT, N24, rep1


title: E2_k562_none_dmso_none_none_DHFR_cj_3


title: WT, 2i, MK, rep2


title: E2_hap_none_none_lig4_none_DHFR_cj_1


title: E2_hap_none_none_wt_none_DHFR_cj_1


title: E2_k562_none_dmso_none_none_DHFR_cj_2


title: WT, N24, MK, rep2


title: WT, 2i, rep2


title: WT, 2i, MK, rep1


title: E2_hap_none_dmso_none_none_DHFR_sj_3


title: WT, 2i, rep1


title: E2_hap_none_dmso_none_none_DHFR_sj_2


title: E2_hap_none_dmso_none_none_DHFR_sj_1


title: WT, N24, siFoxo1, rep3

value: Foxo1 KD


title: Pten KO N24, rep2

data_processing:
Fastq files were analysed with a Nextflow 23.04.1.5866 /nf-core/atacseq v2.0 pipeline. Quality control was performed using fastQC (v0.11.9).
Reads were mapped to the mm10 assembly mouse reference genome using bowtie2 (v2.4.4).
Peak calling was performed on the bam files generated by the nfcore pipeline with Genrich (v0.6.1).
Consensus peaks were defined as peaks with at least a 50% overlap between replicates and generated with samtools intersect. Bed files were filtered for the mm10 blacklist using bedtools. Peaks assigned to unidentified regions (chrUn) were manually removed.
Assembly: mm10
Supplementary files format and content: bed

extract_protocol:
250,000 cells were lysed with 0.5x lysis buffer, and nuclei were isolated.
Tagmentation reaction (Tn5 Illumina) was performed on 50,000 isolated nuclei, and libraries were prepared Libraries were prepared with the Nextera DNA Library Preparation kit. Libraries size was measured with the Agilent High Sensitivity DNA kit, and their qPCR-based quantification was performed with the KAPA Library Quantification kit.


title: Pten KO N24, rep1


title: E2_hap_none_ku_none_none_DHFR_sj_1


title: gamma delta control, scATAC-seq

city: Saint-Malo

first: Phuong

middle: Hang

last: PHAM

address: 7 allée Métis

department: Data science

country: France

institute: Parean Biotechnologies

description: 10x Genomics

library_source: genomic single cell

data_processing:
CellRanger arc count (v2.0.2) was used to process in parallel scATAC-Seq and scRNA-Seq fastq data.
The 10X Genomic pre-built reference refdata-cellranger-arc-mm10-2020-A-2.0.0 was used for alignment.
Assembly: mm10-2020-A
Supplementary files format and content: CellRanger arc output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CellRanger arc ouptut files: atac_fragments.tsv.gz

source_name: spleen

extract_protocol:
Nuclei isolation from gamma delta T cells from splenocytes
TCRa-/- mice (n=15) were infected with MCMV for 3 months. Splenocytes were pooled and γd T lymphocytes isolated using the TCR gd T cell Isolation kit (Miltenyi Biotec). gd TCM and TEM from infected mice were stained and sorted using FACSAria II Sorter (BD Biosciences). Purity was > 95%.  Whole gd T cells were also prepared from the spleen of age-matched TCR-/- mice (n=9). Nuclei were isolated following the 10x Genomics protocol for use with the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (GEX) protocol. 4 libraries were prepared for scRNASeq (1= gd TCM, 2= gd TEM, 3= gd  infected and 4=gd  control) and 4 for scATACSeq (5= gd TCM, 6= gd TEM, 7= gd infected and 8= gd  control).

treatment_protocol: Mice were infected or not (control) with mouse cytomegalovirus (CMV, Smith strain) for 3 months

value: spleen

value: gamma delta T

value: TCRalpha-/-

value: No


title: E2_hap_none_ku_none_none_DHFR_sj_2


title: gamma delta infected, scATAC-seq

description: 10x Genomics

value: CMV


title: E2_hap_none_azd_none_none_DHFR_sj_3


title: E2_hap_none_azd_none_none_DHFR_sj_2


title: WT N24, rep2

value: WT


title: E2_hap_none_azd_none_none_DHFR_sj_1


title: WT N24, rep1


title: gamma delta TCM, scATAC-seq

description: 10x Genomics

value: gamma delta T CD44+CD62L+


title: E2_k562_none_ku_none_none_DHFR_cj_3


title: gamma delta TEM, scATAC-seq

description: 10x Genomics

value: gamma delta T CD44+CD62L-


title: E2_k562_none_ku_none_none_DHFR_cj_2


title: gamma delta control, scRNA-seq

description: 10x Genomics


title: WT, N24, MK, rep1


title: E2_k562_none_ku_none_none_DHFR_cj_1


title: Pten KO 2i, rep2


title: E2_k562_none_azd_none_none_DHFR_cj_3


title: gamma delta infected, scRNA-seq

description: 10x Genomics


title: E2_hap_none_ku_none_none_DHFR_sj_3


title: E2_k562_none_azd_none_none_DHFR_cj_2


title: Pten KO 2i, rep1


title: E2_k562_none_azd_none_none_DHFR_cj_1


title: gamma delta TEM, scRNA-seq

description: 10x Genomics


title: E2_fallop_none_none_p53_none_DHFR_cj_3


title: E2_fallop_none_none_p53_none_DHFR_cj_2


title: WT 2i, rep2


title: gamma delta TCM, scRNA-seq

description: 10x Genomics


title: E2_fallop_none_none_p53_none_DHFR_cj_1


title: WT 2i, rep1


title: E2_hap_none_dmso_none_none_DHFR_cj_3


title: E2_hap_none_dmso_none_none_DHFR_cj_2


title: biol rep 4 YA Male him-5(e1490) strain of Caenorhabditis elegans exposed to PA14 for 6 hours

first: Rizwanul

last: Haque

state: Israel

address: Herzl St 234, Rehovot

department: Brain Sciences

data_processing:
Raw next-generation sequencing (NGS) data in the FASTQ format were analyzed using user-friendly transcriptome analysis pipeline (UTAP).
Briefly, reads were trimmed using “cutadapt” and mapped to the C. elegans reference genome WBcel235 using STAR v2.4.2a.
UMI counting was done using HTSeq-count after marking duplicates in union mode. Differential gene expression analysis and normalization of the counts was performed using DESeq2 using the rld (log2 normalized) gene expression values on OP50-PA14 exposed basis within sexes.
Assembly: C. elegans reference genome WBcel235
Supplementary files format and content: Tab-delimited file include raw counts for each sample
Supplementary files format and content: Tab-delimited file include processed counts for each sample

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: animals were grown at lab temperature (22C)

extract_protocol:
Worms pellet were collected in 500 µL of Trizol and flash frozen in liquid nitrogen and stored at -80oC until further processing. Total RNA was prepared from the frozen worm pellets following the instructions for the TRIzol LS (Invitrogen) protocol. After the isopropanol precipitation step, the RNA was re-suspended in the extraction buffer of the RNA isolation kit (PicoPure, Arcturus), and further isolation was carried out in accordance with the manufacturer's instructions.
RNA libraries for RNA seq were prepared using a bulk version of the MARS-Seq procedure was employed. Briefly, reverse transcription was used to barcode and pool 18 ng of input RNA from each sample. The pooled samples underwent second strand synthesis after Agencourt Ampure XP beads cleanup (Beckman Coulter), and they were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and then converted into final library by tagging the samples with Illumina sequences during ligation, RT, and PCR

treatment_protocol: YA animals were sex separated inot hermaphrodites and males and were exposed to OP50/PA14 for 6 hours.

value: Whole animal

value: exposed to PA14 for 6 hours


title: E2_hap_none_dmso_none_none_DHFR_cj_1

value: dmso

value: DHFR_gL, DHFR_gR


title: biol rep 3 YA Male him-5(e1490) strain of Caenorhabditis elegans exposed to PA14 for 6 hours


title: S24_P,PTEN

city: shanghai

first: jiaming

last: shen

address: SHANGHAI

institute: shanghai jiaotong university

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use fastp(0.22.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis
The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0)
we used HTSeq (v0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the exp
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Bone marrow-derived naive macrophages

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample preparations. Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was then sequenced on NovaSeq 6000 platform (Illumina)
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Bone marrow-derived naive macrophages

value: siPLXDC2#2,PTEN 24h


title: S24_C,PBS

value: siPLXDC2#2,PBS 24h


title: S23_P,PTEN


title: biol rep 1 YA Male him-5(e1490) strain of Caenorhabditis elegans exposed to PA14 for 6 hours


title: E2_hap_none_azd_none_none_DHFR_cj_3

value: DHFRcj


title: E2_hap_none_azd_none_none_DHFR_cj_2


title: E2_hap_none_ku_none_none_DHFR_cj_1


title: biol rep 2 YA Male him-5(e1490) strain of Caenorhabditis elegans exposed to PA14 for 6 hours


title: biol rep 4 YA Hermaphrodite him-5(e1490) strain of Caenorhabditis elegans exposed to PA14 for 6 hours


title: S22_P,PTEN


title: TYUC1_DNp63_D3_3

first: Dimitris

last: Karagiannis

state: NY

institute: Columbia University

description:
D23
RNAseq_ip63_counts.txt

data_processing:
Paired-end reads were mapped to the human genome assembly hg38 using HISAT2 (v2.1.0).
The mapped reads count of each gene was measured by featureCounts (v1.6.1).
Differential gene expression analysis was done by DEseq2
Assembly: hg38
Supplementary files format and content: single txt file containing matrix of read count for each gene and all samples

source_name: Neuroendocrine esophageal carcinoma

growth_protocol: in DMEM/F12 (Corning) plus 10% serum and 1% penicillin/streptomycin in suspension culture

extract_protocol:
total RNA was extracted in TRIzol (Invitrogen)
Libraries were prepared using NEBNext Ultra kit (New England Biolabs #E7490, #E7770, #E7335, #E7500) and sequenced using a Nextseq500/550 sequencer.

treatment_protocol: 1ug/ml doxycycline

value: Neuroendocrine esophageal carcinoma

value: cancer cell line

value: EPZ-6438 3 days

tag: induction

value: 3 days DMSO 3 days doxycycline


title: biol rep 3 YA Hermaphrodite him-5(e1490) strain of Caenorhabditis elegans exposed to PA14 for 6 hours


title: E2_hap_none_azd_none_none_DHFR_cj_1

tag: cell type


title: TYUC1_DNp63_D1_3

description:
D22
RNAseq_ip63_counts.txt

tag: tissue

value: EPZ-6438 1 day

value: 5 days DMSO 1 day doxycycline


title: TYUC1_DNp63_D0_3

description:
D21
RNAseq_ip63_counts.txt

tag: genotype

value: EPZ-6438 0 days

value: 6 days DMSO


title: TYUC1_DNp63_D6_3

description:
D24
RNAseq_ip63_counts.txt

value: EPZ-6438 6 days

value: 0 days DMSO 6 days doxycycline


title: TYUC1_TAp63_D6_3

description:
D20
RNAseq_ip63_counts.txt


title: E2_k562_none_dmso_none_none_DHFR_cj_1


title: S21_P,PTEN


title: TYUC1_TAp63_D3_3

description:
D19
RNAseq_ip63_counts.txt


title: E2_hap_none_ku_none_none_DHFR_cj_3


title: biol rep 1 YA Hermaphrodite him-5(e1490) strain of Caenorhabditis elegans exposed to PA14 for 6 hours

value: Whole animal

value: exposed to PA14 for 6 hours


title: E2_hap_none_ku_none_none_DHFR_cj_2

value: DHFR_gL, DHFR_gR


title: TYUC1_TAp63_D1_3

description:
D18
RNAseq_ip63_counts.txt


title: TYUC1_TAp63_D0_3

description:
D17
RNAseq_ip63_counts.txt


title: biol rep 4 YA Male him-5(e1490) strain of Caenorhabditis elegans exposed to OP50 for 6 hours

value: exposed to OP50 for 6 hours


title: S21_C,PBS

value: Bone marrow-derived naive macrophages


title: S23_C,PBS

value: siPLXDC2#2,PBS 24h


title: S14_P,PTEN

value: siPLXDC2#1,PTEN 24h


title: TYUC1_DNp63_D6_2

description:
D16
RNAseq_ip63_counts.txt

value: Neuroendocrine esophageal carcinoma


title: TYUC1_DNp63_D3_2

description:
D15
RNAseq_ip63_counts.txt

value: cancer cell line


title: S14_C,PBS

value: siPLXDC2#1,PBS 24h


title: biol rep 3 YA Male him-5(e1490) strain of Caenorhabditis elegans exposed to OP50 for 6 hours


title: TYUC1_DNp63_D1_2

description:
D14
RNAseq_ip63_counts.txt


title: biol rep 2 YA Male him-5(e1490) strain of Caenorhabditis elegans exposed to OP50 for 6 hours


title: S22_C,PBS


title: TYUC1_TAp63_D6_2

description:
D12
RNAseq_ip63_counts.txt


title: TYUC1_TAp63_D3_2

description:
D11
RNAseq_ip63_counts.txt

value: EPZ-6438 3 days

value: 3 days DMSO 3 days doxycycline


title: biol rep 2 YA Hermaphrodite him-5(e1490) strain of Caenorhabditis elegans exposed to PA14 for 6 hours


title: biol rep 1 YA Male him-5(e1490) strain of Caenorhabditis elegans exposed to OP50 for 6 hours


title: S13_C,PBS


title: TYUC1_TAp63_D0_2

description:
D9
RNAseq_ip63_counts.txt


title: TYUC1_TAp63_D1_2

description:
D10
RNAseq_ip63_counts.txt

value: EPZ-6438 1 day

value: 5 days DMSO 1 day doxycycline


title: biol rep 4 YA Hermaphrodite him-5(e1490) strain of Caenorhabditis elegans exposed to OP50 for 6 hours


title: TYUC1_DNp63_D6_1

description:
D8
RNAseq_ip63_counts.txt


title: S12_C,PBS


title: TYUC1_DNp63_D3_1

description:
D7
RNAseq_ip63_counts.txt


title: biol rep 2 YA Hermaphrodite him-5(e1490) strain of Caenorhabditis elegans exposed to OP50 for 6 hours


title: S12_P,PTEN


title: biol rep 3 YA Hermaphrodite him-5(e1490) strain of Caenorhabditis elegans exposed to OP50 for 6 hours


title: TYUC1_TAp63_D6_1

description:
D4
RNAseq_ip63_counts.txt


title: TYUC1_DNp63_D1_1

description:
D6
RNAseq_ip63_counts.txt


title: TYUC1_DNp63_D0_1

description:
D5
RNAseq_ip63_counts.txt

value: EPZ-6438 0 days

value: 6 days DMSO


title: TYUC1_TAp63_D1_1

description:
D2
RNAseq_ip63_counts.txt


title: S11_P,PTEN


title: TYUC1_TAp63_D3_1

description:
D3
RNAseq_ip63_counts.txt


title: biol rep 1 YA Hermaphrodite him-5(e1490) strain of Caenorhabditis elegans exposed to OP50 for 6 hours


title: TYUC1_DNp63_D0_2

description:
D13
RNAseq_ip63_counts.txt


title: S13_P,PTEN


title: TYUC1_p63_2

data_processing:
CUT&Tag reads of TYUC-1 cell samples were mapped to the mouse human assembly hg38 using hisat2.
Genomic enrichments of CUT&Tag signals were generated using deeptools (v3.3.2, parameters bamCoverage --normalizeUsing CPM).
Peaks were called using MACS2 and annotated by the R package ChIPSeeker (v1.28.3).
Tracks were visualized using IGV.
Assembly: hg38
Supplementary files format and content: bigwig - normalized genome-wide signal
Supplementary files format and content: narrowPeak - called peaks
Library strategy: CUT&Tag

growth_protocol: The cell line was maintained in DMEM/F12 (Corning) plus 10% serum and 1% penicillin/streptomycin in suspension culture

extract_protocol:
In brief, 2x105 cells were washed once with 1 ml of wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine (Sigma-Aldrich), 1x Protease inhibitor cocktail (Roche). Concanavalin A-coated magnetic beads (Bangs Laboratories) were washed twice with binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM MnCl2, 1 mM CaCl2). 10 μl/sample of beads were added to cells in 400 μl of wash buffer and incubated at room temperature for 15 min. Beads-bound cells were resuspended in 100 μl of antibody buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.06% Digitonin (Sigma-Aldrich), 2 mM EDTA, 0.1% BSA, 1× Protease inhibitor cocktail and incubated with H3K27me3 antibody (Cell Signaling Technology #9733), H3K27ac antibody (Active Motif #39134), BRD4 antibody (Epicypher #13-2003) or normal rabbit IgG (Cell Signaling Technology #2729) at 4 ℃ overnight on nutator. After being washed once with Dig-wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.05% Digitonin, 1x Protease inhibitor cocktail), beads-bound cells were incubated with 1 μl Guinea pig anti-rabbit secondary antibody (Antibodies Online ABIN101961) and 2 μl Hyperactive pA-Tn5 Transposase adapter complex in 100 μl Dig-300 buffer (20 mM HEPES-NaOH, pH 7.5, 0.5 mM Spermidine, 1x Protease inhibitor cocktail, 300 mM NaCl, 0.01% Digitonin) at room temperature for 1 h. Cells were washed three times with Dig-300 buffer to remove unbound antibody and Tn5 and then resuspended in 300 μl of tagmentation buffer (10 mM MgCl2 in Dig-300 buffer) and incubated at 37 °C for 1 h. 10 μl of 0.5 M EDTA, 3 μl of 10% SDS and 5 μl of 10 mg ml−1 Proteinase K were added to each sample and incubated at 50 °C for 1 h to terminate tagmentation. DNA was purified using chloroform isoamyl alcohol (Sigma Aldrich) and eluted with 25 μl ddH2O.
For library amplification, 21 μl of DNA was mixed with 2µL i5 unique index primer (10 µM), 2 µL i7 unique index primer (10 µM) and 25 µL NEBNext® High-Fidelity 2X PCR Master Mix (NEB) and subjected to the following PCR program: 72 ℃, 5 min; 98 ℃, 30 sec; 13 cycles of 98 ℃, 10 sec and 63 ℃, 10 sec; 72 ℃, 1 min and hold at 10 ℃. To purify the PCR products, 1.1x volumes of pre-warmed Ampure XP beads (Beckman Coulter) were added and incubated at room temperature for 10 min. Libraries were washed twice with 80% ethanol and eluted in 20 μl of 10 mM Tris-HCl, pH 8

treatment_protocol: 1ug/ml dox for 16h

value: dox

tag: antibody


title: S11_C,PBS


title: TYUC1_TAp63_D0_1

description:
D1
RNAseq_ip63_counts.txt


title: TYUC1_p63_1


title: N4_P,PTEN

value: siNC,PTEN 24h


title: TYUC1_K27me3_D6

data_processing:
CUT&Tag reads of TYUC-1 cell samples were mapped to the mouse human assembly hg38 using Bowtie2 (v2.3.5.1, parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700)
Potential PCR duplicates were removed by the function "MarkDuplicates" (parameter: REMOVE_DUPLICATES=true) of Picard (v2.24.2).
Genomic enrichments of CUT&Tag signals were generated using deeptools (v3.3.2, parameters bamCoverage --normalizeUsing CPM --binSize 25 --smoothLength 100 --scaleFactor 1).
For H3K27me3 and H3K27ac the number of reads for each barcode was counted to determine the scaling factor.
Tracks were visualized using IGV.
Assembly: hg38
Supplementary files format and content: bigwig - normalized genome-wide signal
Library strategy: CUT&Tag

treatment_protocol: 2uM EPZ-6438 or DMSO

value: wild-type

tag: time


title: N4_C,PBS

value: siNC,PBS 24h


title: TYUC1_IgG

value: IgG


title: TYUC1_K27me3_D0


title: TYUC1_K27me3_D3


title: CPOP-tile5-37-MTX-rep2

city: Copenhagen

first: Sven

last: Larsen-Ledet

state: N

address: Ole Maaloes Vej 5

country: Denmark

institute: University of Copenhagen

data_processing:
Libraries were sequenced on a NextSeq 550 instrument (Illumina) and base called using the instrument's Real Time Analysis software.
Sequencing reads were converted to fastq format and demultiplexed using BaseSpace Sequence Hub.
Reads from each lane were merged and resulting R1 and R2 fastq files were trimmed to remove adapters and then merged. The merged fastq files were analysed using our in-house pipeline to count DHFR indel variants and calculate a score for each variant per condition.
Assembly: atggttggttctttgaactgtatcgttgctgtttcacaaaacatgggtatcggtaaaaatggtgacttgccatggccaccattaagaaacgaattcagatacttccaaagaatgactacaacttcttcagttgaaggtaaacaaaatttggttattatgggtaaaaagacttggttctctatcccagaaaagaatagaccattgaagggtagaattaatttggttttgtcaagagaattgaaagaaccaccacaaggtgctcatttcttgtctagatcattggatgatgcattgaagttgacagaacaaccagaattggctaataaggttgatatggtttggattgttggtggttcttcagtttacaaagaagcaatgaaccatccaggtcatttgaagttgttcgttactagaatcatgcaagatttcgaatctgatactttctttccagaaatcgatttggaaaagtacaagttgttgccagaatacccaggtgttttatcagatgttcaagaagaaaagggtattaaatacaagttcgaagtttacgaaaagaatgat
Supplementary files format and content: A csv file with a CPOP score for each mutation type (synonymous, stop codon, deletion and insertion) at each position for the four conditions (30 °C, 30 °C + MTX, 37 °C, 37 °C + MTX), including standard deviations.
Library strategy: Indel libraries in tiles

organism: synthetic construct

source_name: wild-type yeast strain (BY4741)

growth_protocol: Following library transformations, yeast cells were expanded in SC-LEU medium until saturation. Then, cells for the nonselect condition were harvested and stored at -20C prior to plasmid DNA extraction. In addition, yeast cells were washed and grown on solid SC-LEU-URA medium with and without 220 mM methotrexate and 1 mM sulfanilamide at 30C and 37C for two days. Following selection, the cells were harvested and stored at -20C prior to plasmid DNA extraction.

extract_protocol:
For all conditions, plasmid DNA was extracted from 9 OD units of yeast cells using the ChargeSwitch Plasmid Yeast Mini kit (Invitrogen).
Libraries comprising DHFR indel variants were prepared in each tile and cloned into pAG415 by Twist Bioscience.

treatment_protocol: For selection, yeast cells were grown on solid SC-LEU-URA medium with and without 220 mM methotrexate and 1 mM sulfanilamide at 30C and 37C for two days. Following selection, the cells were harvested and stored at -20C prior to plasmid DNA extraction.

tag: tile

value: human DHFR sequence

value: wild-type yeast strain (BY4741)

value: 37 °C + MTX


title: CPOP-tile5-37-MTX-rep1


title: CPOP-tile5-37-MTX-rep3


title: CPOP-tile5-37-rep3

value: 37 °C


title: N3_P,PTEN

value: Bone marrow-derived naive macrophages


title: TYUC1_K27ac_D3

value: Neuroendocrine esophageal carcinoma

value: cancer cell line


title: CPOP-tile5-37-rep2


title: N3_C,PBS


title: CPOP-tile5-37-rep1


title: N2_P,PTEN


title: TYUC1_BRD4_D3


title: N2_C,PBS


title: TYUC1_K27ac_D0


title: N1_P,PTEN


title: frac_mef_ip_nuc_ctrl_2

data_processing:
mRNA samples from human and mouse were aligned to the mm9/hg19 genome using STAR v.2.5.3a with default settings (‘--alignIntronMax 1000000’) (Dobin et al., 2013). For gene expression (TPM) and read counts, rsem-calculate-expression (rsem/1.3.3) was employed (Li and Dewey, 2011). m6A-GI and m6A-SI metrics were derived using the bam2ReadEnds.R script (Garcia-Campos et al., 2019) as per Dierks et al. 2021, calculating m6A IP enrichment against input coverage.
Assembly: mm9 & hg19
Supplementary files format and content: RSEM hg19 counted reads and tpm tables

value: pMEF

value: primary cells

tag: library type

value: RNA-seq


title: TYUC1_BRD4_D6


title: frac_mef_ip_nuc_ctrl_1


title: TYUC1_BRD4_D0


title: frac_mef_ip_cyt_ctrl_1


title: N1_C,PBS


title: CPOP-tile5-30-MTX-rep3

value: 30 °C + MTX


title: frac_mef_input_nuc_ctrl_2


title: TYUC1_K27ac_D6


title: CPOP-tile5-30-rep3

value: 30 °C


title: frac_mef_input_nuc_ctrl_1


title: F_PTEN_4


title: frac_mef_input_cyt_ctrl_1


title: CPOP-tile5-30-rep2


title: frac_mef_input_cyt_ctrl_2


title: F_PTEN_3


title: nuclear, mESC Mettl3 KO

source_name: mESC Mettl3 KO

value: mESC Mettl3 KO

value: cell line


title: cytosol, mESC Mettl3 KO


title: F_PTEN_1


title: CPOP-tile5-30-rep1


title: F_PTEN_2


title: cytosol, mESC WT

source_name: mESC WT

value: mESC WT


title: F_CON_4


title: CPOP-tile5-30-MTX-rep2


title: CPOP-tile5-no-sele-rep3

value: control


title: CD14+ monocyte Untreated Rep3

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

institute: University of Turin

data_processing:
Sequencing reads were preprocessed with fastp v0.21.0 (Chen et al., 2018) in default settings to remove reads associated with a low quality (phred quality <Q15), shorter than 15 nt reads, or with more than 5 Ns.
Reads passing the filtering step were aligned to the human Gencode v36 transcriptome using Salmon v1.4.0 (Patro et al., 2017) with option --validateMappings, --seqBias, and --gcBias.
Gene expression levels were normalized using tximport v.1.18 while DESeq2 v1.30.1 was applied for the differential expression analysis
Assembly: hg38
Supplementary files format and content: TPM-normalized gene expression levels

source_name: CD14+ monocyte

extract_protocol:
RNA was harvested using Maxwell RSC miRNA tissue kit on Maxwell RSC Instrument (Promega). The RNA concentration was assessed with a Qubit 4 fluorometer (ThermoFisher). RNA purity was assessed as 260/280 and 269/230 ratios by spectometric analysis and  RNA quality was verified on a 2100 bioanalyzer (Agilent Techn.).
200-800 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared with the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit (Illumina Inc.).

treatment_protocol: In vitro-derived FC were generated by culturing sorted CD14+ cells from PBMCs of healthy donors with M-CSF stimulating factor in absence or presence of oxLDL for 48h.

value: CD14+ monocyte

value: Untreated


title: CPOP-tile5-no-sele-rep2

value: human DHFR sequence

value: wild-type yeast strain (BY4741)


title: CD14+ monocyte oxLDL Rep3

value: oxLDL


title: frac_mef_ip_cyt_ctrl_2

extract_protocol:
Nucleozol total RNA extraction protocol according to the manufacturers protocol.
All libraries were conducted according to the libraray preparation protocol in Dierks et al. 2021. For RNA-seq, the protocol was performed as in Dierks 2021, excluding the m6A IP step, (performed as if only is the input sample.
m6A-seq2 & RNA-seq (m6A-seq2 protocol exluding the m6A IP section)


title: CD14+ monocyte Untreated Rep2


title: F_CON_3

value: Bone marrow-derived naive macrophages


title: CPOP-tile5-30-MTX-rep1


title: F_CON_2


title: CPOP-tile5-no-sele-rep1


title: CD14+ monocyte oxLDL Rep2


title: CD14+ monocyte Untreated Rep1


title: CPOP-tile4-37-MTX-rep3

value: 37 °C + MTX


title: TYUC1_K27me3

data_processing:
ChIP-seq reads were mapped to the human genome assembly hg38 using HISAT2 (v2.1.0, default parameters).
Genomic enrichments of CUT&Tag signals were generated using deeptools (v3.3.2).
Tracks were visualized using IGV.
Assembly: hg38
Supplementary files format and content: bigwig - normalized genome-wide signal

extract_protocol:
Cells were digested with MNase to generate mainly mononucleosomes with minor fraction of dinucleosomes for histone modification mapping. Chromatin from 2 × 107 cells was used for each ChIP experiment, which yielded approximately 200 ng of DNA. Immunoprecipitation was performed using antibody against H3K27me3 (table S1) and Protein A Dynabeads (Invitrogen). DNA was purified using QIAGEN DNA Purification Kit.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer’s instructions and single-end 75bp reads were obtained using an Illumina NextSeq 500 sequencer.   Tracks were visualized using IGV.

treatment_protocol: 1:1000 DMSO for 6 days

value: Neuroendocrine esophageal carcinoma

value: cancer cell line

value: wild-type

value: DMSO

value: antibody against H3K27me3


title: TYUC1_Input


title: CPOP-tile4-37-MTX-rep2


title: nuclear, mESC WT

value: RNA-seq


title: F_CON_1


title: biological replicate 3 irradiated

city: Essen

first: Bettina

last: Budeus

address: Virchowstrasse 173

department: Institute for Cell Biology

institute: University Hospital Essen

data_processing:
Reads were cleaned with TrimGalore-0.6.0
Aligned to hg38 with hisat2-2.2.1
And counted with summarizeOverlaps from the R-package with GenomicAlignments
Assembly: hg38
Supplementary files format and content: raw counts from summarizeOverlaps

source_name: thoracic aorta

extract_protocol:
Primary MSCs were cultured under standard conditions, irradiated and total RNA was isolated prior RNAseq
Libraries were constructed using Lexogens QuantSeq 3’ FWD kit

value: thoracic aorta

value: primary

value: MSC

value: unknown

value: RT


title: biological replicate 2 irradiated


title: CPOP-tile4-37-MTX-rep1


title: CPOP-tile4-37-rep3

value: 37 °C


title: biological replicate 3 non (control)  irradiated

value: control


title: biological replicate 2 non (control)  irradiated


title: CON_PTEN_3


title: biological replicate 1 non (control)  irradiated


title: CPOP-tile4-37-rep2

value: human DHFR sequence

value: wild-type yeast strain (BY4741)


title: CON_PTEN_1

value: Bone marrow-derived naive macrophages


title: CPOP-tile4-37-rep1


title: CD14+ monocyte oxLDL Rep1

value: CD14+ monocyte

value: oxLDL


title: Activated, anti-TNF-alpha Antibody Biological Replicate 5

city: Birmingham

first: Sarah

last: Dimeloe

address: Edgbaston

country: United Kingdom

institute: University of Birmingham

data_processing:
Basecalls by Illumina software on NextSeq500
Bbduk v37.99 from the bbmap suite was used for trimming low-quality read, poly(A) tails, rRNA and adapter contamination. STAR v2.7.2b aligner was used to align reads to the human genome.
HTSeq-count v0.13.5  was used to generate counts for mRNA species, raw read counts were then used for further analysis and generation of normalised counts by DESeq2 v1.30.160 in R v4.0.5
Assembly: STAR v2.7.2b aligner was used to align reads to the human genome.

source_name: Peripheral Blood

extract_protocol:
Live CD4+ T cells were sorted collected into eppendorfs. Cells were lysed in 100uL extraction buffer using Machery Nagel RNA extraction kit according to manufacturer's instructions. An on column DNase digest was performed.
Libraries were constructed using Lexogen Quantseq 3' mRNA Forward kits according to the manufacturer's instructions using a starting amount of 5ng of RNA and UMIs
3' mRNA-seq FWD UMI

value: Peripheral Blood

value: CD4+ T cell

value: anti-CD3 and anti-CD28, anti-TNF-alpha antibody


title: CON_CON_4


title: Activated, anti-TNF-alpha Antibody Biological Replicate 6


title: CPOP-tile4-30-MTX-rep3

value: 30 °C + MTX


title: Activated, anti-TNF-alpha Antibody Biological Replicate 4


title: Activated, anti-TNF-alpha Antibody Biological Replicate 3


title: CON_CON_3


title: Activated, anti-TNF-alpha Antibody Biological Replicate 2


title: CPOP-tile4-30-MTX-rep2


title: Activated, anti-TNF-alpha Antibody Biological Replicate 1


title: CON_PTEN_4


title: CON_CON_2


title: CON_CON_1


title: biological replicate 4 non (control)  irradiated


title: CPOP-tile4-30-MTX-rep1


title: Activated, Isotype Control Antibody Biological Replicate 4

value: anti-CD3 and anti-CD28, Isotype control antibody


title: biological replicate 1  irradiated

value: thoracic aorta


title: Activated, Isotype Control Antibody Biological Replicate 5


title: CPOP-tile4-30-rep3

value: 30 °C


title: CON_PTEN_2


title: P3,PTEN

value: 100 ng/mL PTEN, 24 h


title: Activated, Isotype Control Antibody Biological Replicate 2


title: Activated, Isotype Control Antibody Biological Replicate 3


title: CPOP-tile4-30-rep2


title: Activated, Isotype Control Antibody Biological Replicate 1


title: P2,PTEN


title: CPOP-tile4-30-rep1


title: Non-Activated Biological Replicate 5


title: Non-Activated Biological Replicate 6


title: P1,PTEN


title: Non-Activated Biological Replicate 3


title: CPOP-tile4-no-sele-rep3


title: Non-Activated Biological Replicate 4


title: CPOP-tile4-no-sele-rep2


title: Non-Activated Biological Replicate 2


title: C3,PBS

value: PBS,24 h


title: Non-Activated Biological Replicate 1


title: Activated, Isotype Control Antibody Biological Replicate 6


title: #2-IgG

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

institute: CGFL

data_processing:
Raw FASTQ files were trimmed for residual adapter sequences and quality filtered through Trimmomatic software.
Reads were pseudo-aligned against hg19 genome through Kallisto software.
Differential expression analysis was performed with DESeq2 R package.
Assembly: hg38

source_name: B-ALL cells

growth_protocol: hCD45+ leukemic cells were extracted with magnetic beads from the bone marrow of PDX mice following in vivo treatment with anti-CD40 agonist antibody (CD40) or isotype control antibody (IgG), there was no growth ex vivo. mRNA was freshly extracted.

extract_protocol:
Total mRNA were extracted (Trizol) from hCD45+ B-ALL cells purified with magnetic beads from the bone marrow of PDX mice
500 ng of total RNA were ribodepleted and used for library construction. Libraries were prepared thanks to NEBNext Ultra II Directional RNA Prep kit for Illumina according to manufacturer's instructions.

treatment_protocol: PDX mice developping B-ALL were intravenously (i.v.) treated with anti-CD40 agonist antibody (CD40) or isotype control antibody (IgG)

tag: strain

value: B-cell Acute leukemia

tag: in vitro polarization

value: Xenotransplanted in NSG

tag: sting activation

value: treated with Isotype antibody control


title: C2,PBS


title: CPOP-tile3-37-MTX-rep3

value: human DHFR sequence

value: 37 °C + MTX


title: #1-IgG


title: #1-anti-CD40

value: treated with CD40 agonist


title: WT, replicate 2, scRNAseq

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

data_processing:
We used 10X genomics CellRanger software (v6.0.1) to process the data after sequencing. CellRanger mkfastq pipeline to demultiplex raw base call (BCL) files generated by Illumina sequencers into FASTQ files.
CellRanger count pipeline was then used to perform alignment, filtering, barcode counting, and UMI counting for each sample. Alignment was performed using the mice reference genome GRCm38 with the gene set annotations from Ensembl release 97 (Ensembl.org) for gene quantification.
Assembly: GRCm38
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Gut

extract_protocol:
A 2 cm-long fragment of the proximal intestine was extracted from mice, washed with PBS and cut longitudinally. This fragment was incubated for 20 minutes at 4°C in a DPBS buffer supplemented with 30 mM EDTA and 1,5 mM DTT, then incubated for 10 minutes at 37°C in a DPBS-EDTA buffer (30mM). Cells were harvested, centrifuged at 300 g for 5 minutes at 4°C and washed with DPBS-FBS 10%. After centrifugation, samples were dissociated into single cell suspensions by incubation in HBSS-dispase (0,8 mg/mL) for 12 minutes at 37°C. Single cell solutions were sequentially passed through 70- and 40-mm strainers. Red blood cells were lysed (#130-094-183, Miltenyi Biotec) for 2 minutes at room temperature. Cells were counted and 10000 cells were sent for single cell RNA sequencing experiments.
For library preparation and sequencing, 10000 cells were injected for each sample in 4 different reactions into the Chromium Single Cell Controller following the protocol of the Chromium NextGEM Single Cell 3’ V3.1 Kit (10x Genomics). The protocol was followed according to the manufacturer’s guidelines.The quality control of DNA library was performed on Qiaxcel (QIAgen) and quantification by qPCR (KAPA SYBR Fast & LQ Stds+Primer (Illumina). All Single cell 3' Gene expression libraries were sequenced on a Novaseq 6000 System (Illumina) on a S1 flowcell.

treatment_protocol: IL-13-anti-IL-13 complexes were prepared by mixing 5 µg of recombinant mouse IL-13 (#575908, Biolegend) with 25 µg of IL-13 monoclonal antibody (eBio1316H,#16-7135-85, Invitrogen) in PBS. rIL-13 or vehicle (PBS) was injected intraperitoneally overnight before performing the Single Cell RNA-sequencing.

value: Gut

value: Intestinal epithelial cells

tag: age

value: 8-10 weeks

value: rIL-13 overnight


title: CPOP-tile4-no-sele-rep1

value: wild-type yeast strain (BY4741)

value: control


title: #2-anti-CD40


title: CPOP-tile3-37-MTX-rep2


title: Pancreatic islets, non-diabetic, biological replicate 14

city: New Orleans

first: Franck

last: Mauvais-Jarvis

state: LA

address: 1430 Tulane Avenue Lab# 2301

department: Department of Medicine - Section of Endocrinology and Metabolism

institute: Tulane University

description:
HP2132801
Single nuclei ATACseq Dataset containing FASTQ and Cellranger outputs

data_processing:
We utilized CellRanger ATAC v1.2.0 software using the [-mkfastq] command to de-multiplex FASTQ data. Reads were mapped and aligned to the human genome (10X genomics pre-built GRCh38-2020-A Homo sapiens reference transcriptome assembly) with STAR (70.70±11.46% of reads confidently mapped to the human genome). Cellranger identified 84,741 correctly annotated barcodes (cells), having an average transcriptional start site (TSS) enrichment score of 6.27±1.38 and 73.55±6.78% fragments overlapping peaks/sample. We then utilized Signac’s peak calling tool to call peaks on our dataset using MACS2. We utilize the [CallPeaks()] function to annotate accessible peaks using MACS2.
Assembly: GRCh38-2020-A
Supplementary files format and content: Cell Ranger Output
Supplementary files format and content: hm.integrated.dfree.macs2.chromvarmacs2.conns.qs.zip

source_name: Pancreas

growth_protocol: Human islets (500 IEQ per condition) were cultured overnight in a humidified incubator containing 5% CO2 at 37°C.

extract_protocol:
Islet cells were then dispersed using TrypLE (Thermofischer), and immediately evaluated for viability (90.61±3.04%) by Cellometer Automated Cell Counter (Nexcelom Bioscience) prior to single nuclei ATAC library preparation.
Nuclei were isolated based on the 10X genomics Nuclei isolation protocol (CG00169 Rev D) with some modifications. We observe that the usage of 0.5ml tubes yields superior nuclei collection. Furthermore, we optimize based on a sample-to-sample basis the time for cell lysis (3-5min). The final lysis buffer concentration for Nonidet P40 was 0.15% over the 0.1% recommendation. Finally, in addition to the final wash with wash buffer, we perform a final wash with the 10X Genomics Nuclei Buffer (PN-2000153/2000207). Nuclei are always kept < 0°C, visually inspected for integrity and quality using a viability dye, prior to library prep which was performed within 30min. Briefly, 5,000-6,500 isolated nuclei were incubated with a transposition mix to preferentially fragment and tag the DNA in open regions of the chromatin. The transposed nuclei were then partitioned into nanoliter-scale Gel Bead-In-emulsions (GEMs) with barcoded gel beads, a master mix, and partition oil on a chromium chip H. Upon GEM formation and PCR, 10x barcoded DNA fragments were generated with an Illumina P5 sequence, a 16nt 10x barcode, and a read 1 sequence. Following library construction, sequencing-ready libraries were generated with addition of P7, a sample index, and a read 2 sequence. Quality controls of these resulting single cell ATAC libraries were performed by using Agilent High Sensitive DNA kit with Agilent 2100 Bioanalyzer (Agilent) and quantified by Qubit 2.0 fluorometer (ThermoFisher). Pooled libraries at a final concentration of 750pM were sequenced with paired-end dual indexing configuration by Illumina NextSeq 2000 (Illumina) to achieve 40,000-30,000 read pairs per nucleus.

treatment_protocol: No treatments

value: Pancreas

value: Pancreatic Islets

tag: Sex

value: Female


title: CPOP-tile3-37-MTX-rep1


title: Pancreatic islets, non-diabetic, biological replicate 13

description:
HP2123201
Single nuclei ATACseq Dataset containing FASTQ and Cellranger outputs

value: Male


title: Pancreatic islets, non-diabetic, biological replicate 12

description:
HP2121601
Single nuclei ATACseq Dataset containing FASTQ and Cellranger outputs


title: CPOP-tile3-37-rep3

value: 37 °C


title: KO, replicate 1, scRNAseq


title: Pancreatic islets, non-diabetic, biological replicate 10

description:
HP2108901
Single nuclei ATACseq Dataset containing FASTQ and Cellranger outputs


title: Pancreatic islets, non-diabetic, biological replicate 11

description:
HP2110001
Single nuclei ATACseq Dataset containing FASTQ and Cellranger outputs


title: CPOP-tile3-37-rep2


title: Pancreatic islets, non-diabetic, biological replicate 8

description:
HP2107901
Single nuclei ATACseq Dataset containing FASTQ and Cellranger outputs


title: WT, replicate 1, scRNAseq


title: Hepa1-6 cells, IK_5

description: processed gene expression.xlsx

data_processing:
Eukaryotic RNA sequencing data processing protocol (Shanghai Biotechnology Corporation)
The raw data underwent a filtration process using SOAPnuke (v1.5.2) , incorporating the following steps: 1) Elimination of reads containing adapters to mitigate adapter contamination; 2) Exclusion of reads exhibiting a ratio of unknown bases ('N' bases) exceeding 10%; 3) Removal of reads with a low-quality base ratio (base quality less than or equal to 15) surpassing 50%. Subsequently, clean reads were obtained and stored in the FASTQ format.
The clean data obtained from the previous filtration step were aligned to the reference genome using HISAT (v2.1.0).
The clean data obtained after the filtration process were aligned to the assembled unique gene using Bowtie2 (v2.2.5). Subsequently, the expression levels of genes were quantified using RSEM (v1.2.8).
Annotating assembled Unigene with seven major functional databases (KEGG, GO, NR, NT, SwissProt, Pfam, and KOG), and predicting the transcription factors.
Assembly: According to the experimental operation instructions, the purified Total RNA was subjected to steps such as mRNA isolation, fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, addition of A to the 3' end, connection of adapters, and enrichment to complete the sequencing sample Library construction. The library was built using Qubit® 2.0 Fluorometer to detect the concentration, and Agilent4200 to detect the size of the library.
Supplementary files format and content: mm10
Supplementary files format and content: FPKM/count values for each Sample

growth_protocol: Hepa1-6 hepatoma cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics; Spleen CD8+T cells were isolated from spleens of 6-8 week-old male C57/BL6 mice using EasySep™ Mouse CD8+ T Cell Isolation Kit (Stemcell) and maintained in RPMI1640 supplemented with 10% FBS and antibiotics. All cells were keeped in humaidfied atmosphere with 5% CO2 at 37℃

extract_protocol:
After the treatment, cells were washed twice with pre-cooled PBS to remove any suspended cells and cell debris. RNA was then harvested using MJzol animal RNA Extraction Kit (MagBeads, Cat#T102096). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Vazyme, Cat# NR604-02) following manufacturer's protocols.

treatment_protocol: Isolated murine spleen CD8+T cells were in vitro activated by anti-CD3 and anti-CD28 antibody (invitrogen) at 1:2000 for 5 days. Hepa1-6 Cells were seeded on 6-well plate with DMEM supplemented with 10% FBS overnight,  after which they co-cultured with pre-activated CD8+T cells for 48 hours in DMEM containing 10% FBS.

tag: cell line

value: Hepatoma cells

value: WT

value: CTL attack


title: Pancreatic islets, non-diabetic, biological replicate 6

description:
HP2106201
Single nuclei ATACseq Dataset containing FASTQ and Cellranger outputs


title: Hepa1-6 cells, IK_4

description: processed gene expression.xlsx


title: C1,PBS

value: Bone marrow-derived naive macrophages

value: PBS,24 h


title: CPOP-tile3-30-MTX-rep3

value: human DHFR sequence

value: 30 °C + MTX


title: Pancreatic islets, non-diabetic, biological replicate 5

description:
HP2105501
Single nuclei ATACseq Dataset containing FASTQ and Cellranger outputs


title: CPOP-tile3-30-MTX-rep2


title: Pancreatic islets, non-diabetic, biological replicate 4

description:
HP2031401
Single nuclei ATACseq Dataset containing FASTQ and Cellranger outputs


title: Pancreatic islets, non-diabetic, biological replicate 3

description:
HP2024001
Single nuclei ATACseq Dataset containing FASTQ and Cellranger outputs


title: KO, replicate 2, scRNAseq

value: Gut

value: Intestinal epithelial cells


title: Pancreatic islets, non-diabetic, biological replicate 15

description:
HP2202101
Single nuclei ATACseq Dataset containing FASTQ and Cellranger outputs


title: CPOP-tile3-30-MTX-rep1


title: Hepa1-6 cells, IK_3

description: processed gene expression.xlsx


title: Hepa1-6 cells, IK_2

description: processed gene expression.xlsx


title: CPOP-tile3-30-rep3

value: 30 °C


title: Pancreatic islets, non-diabetic, biological replicate 2

description:
SAMN15877725
Single nuclei ATACseq Dataset containing FASTQ and Cellranger outputs


title: Pancreatic islets, non-diabetic, biological replicate 1

description:
HP2022801
Single nuclei ATACseq Dataset containing FASTQ and Cellranger outputs


description: Single cell RNAseq Dataset containing FASTQ and Cellranger outputs

data_processing:
We utilized CellRanger v4.0.0 software using the [-mkfastq] command to de-multiplex FASTQ data. Reads were mapped and aligned to the human genome (10X genomics pre-built GRCh38-2020-A Homo sapiens reference transcriptome assembly) with STAR (95.33±0.75% of reads confidently mapped to the human genome).
Assembly: GRCh38-2020-A
Supplementary files format and content: Cell Ranger Output

extract_protocol:
Islet cells were then dispersed using TrypLE (Thermofischer), and immediately evaluated for viability (90.61±3.04%) by Cellometer Automated Cell Counter (Nexcelom Bioscience) prior to single cell RNAseq library preparation.
For 10x single cell RNAseq library preparation, 5000-6500 individual live cells per sample were targeted by using 10x Single Cell 3’ RNAseq technology provided by 10x Genomics (10X Genomics Inc). Briefly, viable single cell suspensions were partitioned into nanoliter-scale Gel Beads-In-EMulsion (GEMs). Full-length barcoded cDNAs were then generated and amplified by PCR to obtain sufficient mass for library construction. Following enzymatic fragmentation, end-repair, A-tailing, and adaptor ligation, single cell 3’ libraries comprising standard Illumina P5 and P7 paired-end constructs were generated. Library quality controls were performed by using Agilent High Sensitive DNA kit with Agilent 2100 Bioanalyzer (Agilent) and quantified by Qubit 2.0 fluorometer (ThermoFisher).

tag: disease state

value: non-diabetic

value: No treatment


title: Hepa1-6 cells, IK_1

description: processed gene expression.xlsx


title: Pancreatic islets, non-diabetic, biological replicate 9

description:
HP2108601
Single nuclei ATACseq Dataset containing FASTQ and Cellranger outputs

value: Pancreas


title: CPOP-tile3-30-rep2

value: wild-type yeast strain (BY4741)


value: Pancreatic Islets

value: Female


title: Hepa1-6 cells, Ctrl_5

description: processed gene expression.xlsx


value: Male


title: CPOP-tile3-30-rep1


title: Pancreatic islets, non-diabetic, biological replicate 7

description:
HP2107001
Single nuclei ATACseq Dataset containing FASTQ and Cellranger outputs


title: CPOP-tile3-no-sele-rep3

value: control


title: Hepa1-6 cells, Ctrl_3

description: processed gene expression.xlsx

value: Hepatoma cells

value: WT


title: CPOP-tile3-no-sele-rep1


title: Hepa1-6 cells, Ctrl_1

description: processed gene expression.xlsx


title: CPOP-tile2-37-MTX-rep3

value: 37 °C + MTX


title: isotype, replicate 1, scRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Orthotopic liver tumors (Hepa1-6)

extract_protocol:
Tumor samples were collected and placed in pre-cooled PBS to remove necrotic tissue, blood clots, and surrounding normal tissue. The samples were then cut into small pieces and added to a 6-well plate containing 2 mL of preheated tissue lysate (5 mg/mL collagenase IV and 1 mg/mL DNase, incubated at 37 °C on a shaker at 90-100rpm for 1 hour. Next, the cell suspension was filtered using a 70µm filter, and centrifuged at 300g, 4°C for 5 minutes. The supernatant was discarded, and the cell pellet was enriched by mouse CD45 MicroBeads (Miltenyi, Cat# 130-052-301) according to the manufacturer's instructions. Enriched cells were then stained with 7-AAD and APC-Cy7 anti-mouse CD45 antibody. Alive CD45+ cells were sorted using a BD FACSAria™ III cell sorter.  Sorted alive CD45+ cells were washed in HBSS-/- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, tumor-infiltrating CD45+ cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Orthotopic liver tumors (Hepa1-6)

value: tumor-infiltration CD45+ cells

value: isotype


title: BAT_CR-day-6h_CT44B

city: Dallas

first: Joseph

last: Takahashi

state: Texas

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: University of Texas Southwestern Medical Center

data_processing:
Sequencing libraries were constructed in house following Illumina single-stranded mRNA-seq protocol. RNA-sequencing of libraries was performed on the NextSeq 550 (Illumina) with 75 bp reads, according to the manufacturer’s instructions, by the UTSW McDermott Next Generation Sequencing Core. Read quality was assessed using the FASTQC quality control tool. Reads were mapped with STAR (Dobin et al., 2013) (with parameters:--runMode alignReads --genomeDir genomefolder --sjdbGTFfile gtf --readFilesIn sample_trim.gz --readFilesCommand zcat --outFileNamePrefix sample --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outSAMmapqUnique 255 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --alignIntronMax 1000000 --outFilterType BySJout --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 10 --outFilterMismatchNmax 3 --twopassMode Basic --quantMode GeneCounts) following Cutadapt trimming (with parameters: -g AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -m 30) to M14 GENCODE (protein coding only) version of mouse genome from www.gencodegenes.org. Raw reads were quantified using featureCounts tool from Rsubread package. Reads per kilobase per million (RPKM) was used to normalize uniquely mapped reads according to the sequencing depth and gene length. RPKM calculation was performed using in-house scripts. Downstream bioinformatic analysis after RPKM calculations was performed in R environment.
Assembly: M14 from GENCODE
Supplementary files format and content: excel file includes raw counts for all samples
Supplementary files format and content: excel file includes RPKM values for all samples

source_name: BAT

growth_protocol: C57BL/6J male mice (8 week-old) were individually housed in standard polycarbonate mouse cages (Fischer Scientific, Cat. Nos. 01-288-1B and 01-288-21) containing a 4.75 in diameter stainless steel running wheel inside isolation cabinets containing 12 cages each. Temperature and humidity levels were monitored, and the mice were housed under an LD12:12 cycle (green LEDs, ~100 lux at the level of the cage floor). Water was provided ad libitum throughout the study.

extract_protocol:
RNA from tissues was homogenized in 1mL of TRIzol and extracted according to manufacturer instructions. All RNA samples with RIN >7.5 were used; 260/280 ratio > 2; and 260/230 ratio > 2.
mRNA-Seq (polyA selection); mRNA-seq library preparation was done according to Illumina single-stranded mRNA-seq. Briefly, library was prepared with 25 ng of mRNA polyA-selected from 5ug total RNA, with 13 cycles of PCR amplification. Library size was confirmed by Tapestation 2200 (Agilent).

treatment_protocol: Mice were fed with a purified diet provided as round pellets of 300 mg each with 3.65 Kcal/g (Dustless Precision Pellets, Rodent, Purified, F0075, BioServ, Flemington, NJ, USA). Pellets composition is equivalent to regular chow, with 18.7% protein, 5.6% fat, 59.1% carbohydrates and 4.7% fiber (Acosta-Rodriguez et al., 2022). Food access was controlled by the automated feeder system designed in our lab with Phenome Technologies, Skokie, IL, USA (Acosta-Rodriguez et al., 2017). ClockLab Chamber Control Software v3.401 (Actimetrics Inc., Wilmette, IL, USA) was used to program feeding schedules and record food consumption. The feeders were monitored daily via remote access to detect and rectify any problems with the system (cages or feeder chute misalignments, motor errors, and sensor failures). A 10 min delay was programmed after each food pellet was taken before the next pellet was dropped to prevent hoarding behavior. Wheel-running behavior was recorded throughout the study using ClockLab Data Acquisition System v3.209 (Actimetrics Inc., Wilmette, IL, USA).  After three weeks of recording under ad libitum food access, mice were randomly assigned to one of 5 feeding conditions (n=72 per condition): 24h access ad libitum (AL); unlimited amount but temporally restricted to the first 6h during the dark (TR-night-6h), or light (TR-day-6h) phase; 6h access but calorically restricted (10 pellets distributed as 6:2:2 every 2h) pellets corresponding to 70% of baseline ad libitum levels fed at the start of the dark (CR-night-6h) or light (CR-day-6h) phase. Mice were weighed in the morning and cages were changed every 21 days, and bedding was checked for any evidence of food spillage.  Wheel-running behavior was recorded throughout the study using ClockLab Data Acquisition System v3.209 (Actimetrics Inc., Wilmette, IL, USA). All mice were monitored in real-time in these conditions  until the time points for the tissue collections (see tissue collection, n=24 per feeding). Samples were collected, snap frozen and stored at -80ºC until RNA extraction.

value: BAT

value: male

value: 6 months-old

tag: light condition

value: 12h light / 12h dark

tag: feeding

tag: collectiontime hours


value: non-diabetic

tag: cell type

tag: treatment

value: No treatment


title: CPOP-tile2-37-rep2

value: human DHFR sequence

value: wild-type yeast strain (BY4741)

value: 37 °C


title: BAT_CR-day-6h_CT36B

tag: tissue

tag: genotype


title: Hepa1-6 cells, Ctrl_4

description: processed gene expression.xlsx


title: CPOP-tile3-no-sele-rep2


title: BAT_CR-day-6h_CT32B


title: BAT_CR-day-6h_CT28B


title: CPOP-tile2-37-rep1


title: Hepa1-6 cells, Ctrl_2

description: processed gene expression.xlsx