title: Jiashi melon Infection by Alternaria alternata 18d, replicate 2

description:
fpkm.txt
JA18P_2


title: D14-VP64-library-control

status: Public on Mar 01 2024

type: SRA

city: Melbourne

first: Charles

middle: C

last: Bell

state: VICTORIA

address: VCCC, Gate 1, 14 Flemington Road

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

library_source: genomic

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were trimmed to remove adapter with fastx clipper or cutadapt
Trimmed reads were aligned to the reference sgRNA library with bowtie2
After filtering to remove multi-aligning reads, the read counts were computed for each sgRNA.
Supplementary files format and content: Guide Counts file

molecule: genomic DNA

organism: Homo sapiens

source_name: K562 cells

growth_protocol: K562 cells were cultured in RPMI-1640 supplemented with 20% FCS, streptomycin (100ug/ml), penicillin (100 units/ml) and glutamax, under standard culture conditions (5% CO2, 37C).

extract_protocol:
Genomic DNA was extracted using Monarch Genomic DNA purification kit
PCR was conducted to maintain guide representation, using Q5 High Fidelity DNA Polymerase

treatment_protocol: K562 cells containing Cas9 were infected with a sgRNA library. For the transcription screens, GFP negative, guide positive cells were sorted on D5, D6 and D7 after guide infection. For dropout screen, cells were grown until D14, before being isolated for sequencing.

tag: cell line


title: iLIN28AGFP_clone A3_b_dox_3hrs

city: London

first: Jernej

last: Ule

address: 10-12 Russell sq

department: Neuromuscular Diseases

country: United Kingdom

institute: UCL Institute of Neurology

description:
iLIN28AGFP inducible overexpression, More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A3_b_dox_3

library_source: transcriptomic

data_processing:
To calculate mRNA T>C conversion the pipeline was enclosed in Snakemake5.3.0 (Koster and Rahmann, 2012). For analysis of mRNA 3’ end sequencing data, reads were demultiplexed with Cutadapt 1.18 prohibiting mismatches in the barcode (Martin, 2011).
Then, sequencing reads quality was assessed (-q 20), barcode trimmed (--cut 12) discarding short reads (--length 16). Poly-adenylated stretches (>4) at the 3’ end were removed up to 20 tandems without indels nor mismatches. Trimmed reads were aligned with Slamdunk map0.3.3 (Neumann et al., 2019) to reference mouse genome (mm10) using local alignment and allowing up to 100 multi-mapping reads (-n 100). Aligned reads were subject to a filtering step retaining only alignments with a minimum identity of 95% and a minimum of 50% of the read bases mapped. Reads ambiguously mapping to more than one 3’UTR were discarded (https://github.com/AmeresLab/UTRannotation).
SNPs were called using VarScan 2.4.1with default parameter and establishing 10 fold coverage cut off and a variant fraction cut off 0.8 (-c 10 -f 0.8). SNPs overlapping T> C conversions need to present at least >26 base quality Phred score. T> C conversions were counted with rolling windows and normalised by T content, coverage of each position and average per possible transcript 3’UTR. Finally, the T> C conversion quality was assessed by Slamdunk alleyoop0.3.3 (Neumann et al., 2019).
To calculate half-life, T> C conversion were background-subtracted and normalised to the chase S4U treatment. T> C conversions were fit to exponential decay non-linear function using the R minpack.lm 1.2 (Bates and Chambers, 2017). Only 3’UTR half-life that correlated to the model R2 > 0.6 in all the experimental conditions were retrained.
Genome_build: mm10
Supplementary_files_format_and_content: T>C S4U Conversions

molecule: polyA RNA

organism: Mus musculus

source_name: ESC

growth_protocol: All mouse ESC lines e.g., J1 IDG3.2 and V6.5, were maintained in 1:1 Neurobasal (21103049) DMEM (11320033) medium containing N2 (17502048) and B27 (17504044) supplements, 1% Glutamax (35050), 1% nonessential amino acids (1140050), 0.1 mM 2-mercaptoethanol (31350-010) (all Thermo Fisher Scientific), 1 mM MEK inhibitor PD0325901 (1408, Axon Medchem), 3 mM GSK3 inhibitor CHIR99021 (4953/50 Tocris), and 1,000 U/ml LIF (ESGRO ESG1107, Merck), a condition named 2iLIF. Cells were passaged using Stempro-Accutase (A1110501, Thermo Fisher Scientific). Cells were grown on gelatin coated plates which were prepared by first incubating the wells 0.1% gelatin (EmbryoMax® ES-006-B, Merck) with 1% FBS (EmbryoMax® ES Cell Qualified FBS, ES-009-B, Merck) for 1 h at 37 °C followed by a rinse with PBS. To transit from naive ESC to priming ESC cells, accutased naive ESCs were seeded onto gelatine and FBS-coated plates in N2B27 medium supplemented with recombinant 20 ng ml–1activin A (338-AC-050, R&D Systems) and 12 ng ml–1 bFGF (100-18B, Peprotech) for 12 hours.

extract_protocol:
The cells were lysed directly in Qiazol (Qiagen, 79306), followed by RNA preparation using miRNeasy Micro Kit (Qiagen, 217084) according to the manufacturer’s instructions.
0.5 μg of totalRNA was used per library prepared using Lexogen QuantSeq-FWD kit (Lexogen GmbH, 0.15) according to manufacturer’s instructions.
3'end mRNAseq (QuantSeqFWD)

treatment_protocol: Thiol(SH)-linked alkylation for the metabolic sequencing of RNA (SLAMseq) has been generated according to the published protocol (Ameres et al., 2017). Naïve or priming ESC were treated with 100 μM 4-thiouridine (s4U) (Sigma, T4509-25MG) for 24hours of pulse labeling. During the last 15hours of pulse labeling, fresh s4U-containing media has been exchanged every 3hours to enhance s4U incorporation in RNA species. Prior to initiation of the chase labeling with 10mM Uridine-containing (Sigma, U3750-25G) growth medium (100X excess of uridine compared to initial s4U concentrations), the media from the cells have been removed and washed twice with chase-labeling medium. The chase-labeling was initiated upon washing off pulse-labeling medium and upon indicated time-points, the media was taken off and cells were lysed directly in Qiazol (Qiagen, 79306), followed by RNA preparation.

tag: strain

value: mESC V6.5.

tag: developmental stage

value: naive embryonic stem cells

tag: treatment

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 3hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium

tag: genotype,

value: dooxycyclin treated

tag: 4su treatment hours


title: ChIP-seq_GATA3_WT_Naive_H3K4me3_rep2

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

country: USA

institute: NHLBI

data_processing:
Raw reads of RNA-seq data were mapped by STAR (v2.7.3a) (Dobin et al., 2013).   Raw reads of  ChIP-seq data were mapped by Bowtie2 (Langmead and Salzberg, 2012). Mapped unique paired-end reads with MAPQ 10 were used for the following analysis.  Raw reads of Hi-TrAC data were process by tracPre2.py in cLoops2 package (Cao et al., 2022).
Assembly: mm10
Supplementary files format and content: BigWig files for ChIP-seq were provided for visualization in genome browser.  TEXT files for RNA-seq gene expressions were provided. DIFF files for RNA-seq differential gene expression were provided. BEDPE files for Hi-TrAC or Hi-C data with high quality uniquely mapped paired-end tags (PETs) were provided.

source_name: CD4+ T cells

extract_protocol:
Detailed procedures for ChIP-Seq: 1. Three plates (15-cm) of HeLa or SW-13 cells cultured in 20 ml of DMEM containing 10% FCS and antibiotics were stimulated with 500 units/ml of IFN-α for 2 hrs. 2. Add HCHO to 1% of each plate and incubate at 37°C for 10 min; Stop the crosslinking by aspirating the medium. Wash the cells twice with 10 ml of 1xPBS. 3. Aspirate the buffer (keep 0.5 ml in the plate). Harvest cells by scraping. Wash the plate once with 0.5% BSA/PBS. Combine the cells from the three plates. 4. Spin down the cells at 3000rpm, 3 min, 4oC. 5. Remove supernatant and resuspend the cells in 2.5 ml of 1 x TE + 1 mM PMSF + 1 x proteinase inhibitor cocktail. For anti-AcH3 or anti-AcH4 CHIP, add sodium butyrate to 5 mM. Sonicate 20 x 20 seconds in ice-water bath with power setting at 5 with an Ultrasonic Processor XL (HEAT System) to break chromatin to about 0.3-05 kb. 6. Adjust to RIPA buffer + 200 mM NaCl by adding 0.28 ml of 10% TX100, 28 μl of 10% Na-Deoxycholate, 28 μl of 10% SDS, 110 μl of 5M NaCl. Mix well. Incubate for 5 min on ice. Spin in a microfuge, 13K rpm, 10 min, 4oC. 7. Collect supernatant. 8. Add 4 μg of the antibodies to 40 μl of Dynabeads protein A beads. Incubate at 4°C 4- 6hrs with rotation. Wash away antibody by 1xPBS. 9. Add 500 μl of the chromatin ( sup.) to the beads+antibody. Incubate at at 4°C overnight with rotation. 10. Wash the beads twice with RIPA buffer; twice with RIPA buffer (+0.3M NaCl); twice with LiCl buffer (1xTE, 0.25M LiCl, 0.5% NP40, 0.5% Na-Deoxycholate); and twice with 1xTE. 11. Resuspend the beads in 100 μl of 1xTE, 2.5 μl of 10% SDS, 5 μl of 10 mg/ml proteinase K, mix well, incubate at 65oC, overnight. Also treat 100 μl of the input chromatin in the same way. 12. Collect sup. Wash the beads once with 100 μl of 1xTE. Combine the supernatants. Extract 1 x with Phenol-CHCl3. 13. Precipitate DNA with 2 μl of 20mg/ml glycogen, 20 μl of 3M NaOAc pH5.2, 500 μl of ethanol. Incubate 10 min on dry ice. Spin 20 min at 4 °C in a microfuge. Remove sup, wash pellet 1 x with 70% ethanol, air dry, resuspend in 30 μl of 1 x TE. Use 3 μl for one PCR reaction. 14. The concentration of the input DNA is determined by spectrophotometer. RIPA buffer: 1X In 1X TE 0.1% SDS 0.1% Na deoxycholate 1% Triton X100.                                                                                For RNA-Seq, five thousand cells were sorted into 700μl of QIAzol Lysis Reagent (miRNAeasy Micro Kit (QIAGEN, Cat#217084). Total RNA was extracted and on-column digestion with DNase (QIAGEN, Cat#79254) was performed, followed by elution with 10μl of RNase-free water. Total RNA from 1K cells was reverse transcribed by SuperScript II (Invitrogen, Cat#18064-014) with oligo-dT and LNA-containing TSO primers in a final reaction volume of 10μl using the condition: 42°C for 90min, 10 cycles of 50°C 2min to 42°C 2min, 70°C for 15min and hold at 4°C. cDNA was pre-amplified by PCR using KAPA HiFi HotStart ReadyMix (KAPABIOSYSTEMS Cat#KK2602) with IS PCR for 12 cycles in 25μl. PCR products were purified by Ampure XP beads (Beckman Coulter, Cat#A63881) and eluted with 17.5μl Nuclease-free water as described for Smart-seq2 method (Picelli et al., 2014). PCR pre-amplified cDNA (40μl) was sonicated to 200~400bps by Bioruptor Pico (Diagenode) for 15 cycles (30″ on and 30″ off). Sonicted cDNA was blunt-ended by End-It DNA-Repair kit (Epicentre, Cat#ER81050), ligated to “Y” adaptor and PCR-amplified for 12 cycles and sequenced as described for the scDNase-seq libraries. For Hi-TrAC, cells were fixed with 1% Formaldehyde at room temperature for 10 minutes, and then incubated with the transposase complex to bridge interacting chromatin at 37 °C for 2 hours. Genomic DNA was purified after reverse cross-linking.
1. Repair DNA ends using the Epicentre DNA END-Repair kit (Cat. No. ER0720, Epicentre Biotechnologies, Tel 800-284-8474) This step generates blunt-ended DNA. 1-34 ul DNA (0.1 to 5 ug) 5 ul 10x End repair buffer (330 mM Tris-acetate, pH7.8, 660 mM potassium acetate, 100 mM magnesium acetate, 5 mM DTT) 5 ul 2.5 mM each dNTPs 5 ul 10 mM ATP x ul H2O to adjust the reaction volume to 49 ul 1 ul End-Repair Enzyme mix (T4 DNA Pol + T4 PNK) Incubate 45 min at room temperature. Purify the DNA using MinElute Reaction Cleanup Kit and protocol, eluting in 32 ul of EB. 2. Add “A” to 3’ ends 32 ul DNA from above 5 ul 10x Klenow buffer 10 ul 1 mM dATP 3 ul 5 U/ ul Klenow Exo- Incubate for 30 min at 37°C. Purify the DNA as before. Eluting in 22 ul of 1x EB. 3. Linker ligation (two mixed linkers). The oligo mix should contain 10x molar excess of the DNA templates. 23 ul DNA (300ng) 3 ul 10x T4 DNA ligase buffer 1 ul Index PE Adapter Oligo Mix (1:10 diluted) 3 ul T4 DNA ligase (400 units/ul) 2 Incubate for 30 min at room temperature. Purify the DNA as before. Eluting in 20 ul of 1x EB. 4. Size selection-2% E-Gel Load 20 ul linker ligated DNA onto a 2% E-Gel (Invitrogen). Cut the gel around 200-400 bp region (DNA will not be visible). Extract the DNA using MinElute gel extraction kit (every 900ul of QG Buffer add 400ul of 2-Propanol). Elute in 22 ul EB. (Note: (1) Dissolve gel slices at room temperature with frequent mixing, but not at elevated temperature. This helps to reserve AT-rich DNA that can be easily denatured at higher temperature and gets lost at column binding step. (2) NEVER run PCR-amplified samples of Step 7 with the linker-ligated products of Step 5 together on the same gel because the latter can be contaminated!). 5. Amplify the DNA using Solexa primers and enzyme mix (using half amount of the reagents and run a 25 ul reaction). 18 ul of DNA 20 ul of master mix 1 ul of PCR primer InPE1.0 (2x diluted) 1 ul of PCR Primer Index<#> (2x diluted) Total volume: 50 ul Denature at 98°C for 30 sec. 98°C, 10”; 65°C, 30”; 72°C, 30”. Try 18 cycles first, check 2.5 ul of product on 1.8% gel. If the band is not clearly visible, do 3 more cycles. Check again. 6. Purify the amplified products on 2.5% agarose gel. Excise the band near 220 bp and purify the DNA using QIAquick gel extraction kit. Measure the DNA concentration using Qubit fluorometer. (Note: Dissolve gel slices at room temperature with frequent mixing, but not at elevated temperature. This helps to reserve AT-rich DNA that can be easily denatured at higher temperature and gets lost at column binding step). For Hi-TrAC libraries, gaps in purified genomic DNA was repaired with T4 DNA polymerase. Genomic DNA was digested with MluCI and NlaIII restriction enzymes, and biotin labeled DNA fragments was enriched by streptavidin beads. Perform adapter ligation with T7 ligase on beads, and then run PCR to amplify and add index to libraries.

value: mixed C57BL/6 and 129

tag: cell type

value: Naive CD4+ T cells

tag: tissue

value: lymph nodes

tag: genotype

value: GATA3 WT(CD4+CD8-CD62L+CD44-)


title: ChIP-seq_GATA3_WT_Naive_H3K27ac_rep1


title: D7-p53-library-control


title: Jiashi melon Infection by Alternaria alternata 18d, replicate 1

city: Urumqi

first: Bai

middle: Yu

last: jia

address: Nong Da Dong Lu No. 311, Urumqi, Xinjiang，China

country: China

institute: Xinjiang Agricultural University, College of Food Science and Pharmacy

description:
fpkm.txt
JA18P_1

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Cucumis_melo_L_CM3_6_1_MeloV4 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters  -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Cucumis_melo_L_CM3_6_1_MeloV4
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Cucumis melo

source_name: melon fruit(pulp)

extract_protocol:
In total, approximately 1 μg total RNA was initially used for BGISEQ-500 library construction. In general, DNase I was initially used to degrade double-stranded and single-stranded DNA contaminant in RNA samples. The mRNA molecules were then purified from total RNA using oligo(dT)-attached magnetic beads and fragmented into small pieces. First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The cDNA thus synthesized was subjected to end-repair and 3′ adenylation. Subsequently, adaptors were ligated to the ends of these 3′ adenylated cDNA fragments. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single stranded circular DNAs were formatted as the final library for Agilent Technologies 2100 bioanalyzer validation and subsequent SE50 sequencing.
RNA libraries were prepared for sequencing using BGISEQ-500 platform

value: Infection by Alternaria alternata


title: D7-NfKB-CMV-library-control


title: Jiashi melon Infection by Alternaria alternata 12d, replicate 2

description:
fpkm.txt
JA12P_2


title: ChIP-seq_GATA3_KO_Th2_72h_H3K4me3_rep2

value: Th2 CD4+ T cells

value: Cell culture

value: GATA3 KO(DAPI-)


title: iLIN28AGFP_clone A3_b_dox_1hrs

description:
iLIN28AGFP inducible overexpression, More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A3_b_dox_1

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 1hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: ChIP-seq_GATA3_KO_Th2_72h_H3K4me1_rep2


title: D7-GR-screen


title: iLIN28AGFP_clone A3_b_dox_0hrs

description:
iLIN28AGFP inducible overexpression, More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A3_b_dox_0

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.


title: Jiashi melon Infection by Alternaria alternata 12d, replicate 1

description:
fpkm.txt
JA12P_1


title: iLIN28AGFP_clone A3_a_dox_6hrs

description:
iLIN28AGFP inducible overexpression, More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A3_a_dox_6

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 6hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: ChIP-seq_GATA3_KO_Th2_72h_H3K4me1_rep1


title: D7-Notch-library-control


title: D7-Pu1-library-control


title: ChIP-seq_GATA3_KO_Th2_72h_H3K27ac_rep2


title: Jiashi melon Infection by Alternaria alternata 6d, replicate 3

description:
fpkm.txt
JA06P_3


title: iLIN28AGFP_clone A3_a_dox_4hrs

description:
iLIN28AGFP inducible overexpression, More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A3_a_dox_4

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 4hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: iLIN28AGFP_clone A3_b_dox_4hrs

description:
iLIN28AGFP inducible overexpression, More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A3_b_dox_4


title: Jiashi melon Infection by Alternaria alternata 6d, replicate 2

description:
fpkm.txt
JA06P_2


title: iLIN28AGFP_clone A3_b_dox_2hrs

description:
iLIN28AGFP inducible overexpression, More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A3_b_dox_2

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 2hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: D7-Irf1-library-control


title: Jiashi melon Infection by Alternaria alternata 12d, replicate 3

description:
fpkm.txt
JA12P_3


title: ChIP-seq_GATA3_KO_Th2_72h_H3K27ac_rep1


title: iLIN28AGFP_clone A3_a_dox_3hrs

description:
iLIN28AGFP inducible overexpression, More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A3_a_dox_3

value: mESC V6.5.


title: D7-VP64-screen


title: ChIP-seq_GATA3_KO_Th2_72h_H3K4me3_rep1


title: iLIN28AGFP_clone A3_a_dox_2hrs

description:
iLIN28AGFP inducible overexpression, More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A3_a_dox_2

value: naive embryonic stem cells


title: Jiashi melon Infection by Alternaria alternata 0d, replicate 3

description:
fpkm.txt
JA00P_3


title: D7-VP64-library-control


title: Jiashi melon Infection by Alternaria alternata 6d, replicate 1

description:
fpkm.txt
JA06P_1


title: ChIP-seq_GATA3_KO_Naive_H3K4me3_rep2

value: GATA3 KO(CD4+CD8-CD62L+CD44-)


title: ChIP-seq_GATA3_KO_Naive_H3K4me3_rep1


title: D7-Notch-screen


title: iLIN28AGFP_clone A3_a_dox_0hrs

description:
iLIN28AGFP inducible overexpression, More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A3_a_dox_0

value: dooxycyclin treated


title: Jiashi melon Infection by Alternaria alternata 0d, replicate 1

description:
fpkm.txt
JA00P_1


title: Jiashi melon Infection by Alternaria alternata 0d, replicate 2

description:
fpkm.txt
JA00P_2


title: D7-Myb-library-control


title: D7-EWS-screen


title: ChIP-seq_GATA3_KO_Naive_H3K4me1_rep1

value: mixed C57BL/6 and 129


title: ChIP-seq_GATA3_KO_Naive_H3K27ac_rep2

value: Naive CD4+ T cells


title: ChIP-seq_GATA3_KO_Naive_H3K4me1_rep2

value: lymph nodes


title: iLIN28AGFP_clone A1_b_dox_4hrs

description:
iLIN28AGFP inducible overexpression, More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A1_b_dox_4


title: batch5_hs_Guide-2

first: Guei-Sheung

last: Liu

address: 32 Gisborne Street

institute: Centre for Eye Research Australia

data_processing:
Raw data processing was performed using FASTQC to check the reads quality and Trimmomatic tool to further remove the bases and reads with low quality, adaptors and barcodes.  The clean reads were aligned to the reference human genome (version GRCh38), utilizing STAR v2.7 as the aligner. For RNA quantification, RSEM was employed to normalize raw read counts, transforming them into TPM (transcripts per million) values, providing a relative expression level that is theoretically comparable across samples. The magnitude (log2-transformed fold change) and significance (P-value) of differential expression between groups were then calculated.
Assembly: hg38
Supplementary files format and content: tab-delimited file includes FPKM and TPM values for each sample

source_name: Human embryonic kidney cells

extract_protocol:
RNA was extracted using Monarch Total RNA miniprep kit (New England Biolabs) and dried in RNA stabliistion tubes for sequencing.
Library was prepared using standard and optimised Genewiz's protocols

value: Human embryonic kidney cells

value: Retina

value: Guide


title: batch5_hs_Guide-3


title: D7-p53-screen


title: batch5_hs_Guide-1


title: D7-Irf1-screen


title: mESC_Firre_Rescue_firre_induced_120min_ATACseq

city: Boulder

first: John

last: Rinn

state: CO

address: 3415 Colorado Ave

department: Biochemistry

institute: CU Boulder

data_processing:
Quality control, read mapping, and peak calling were carried out using nf-core/atacseq v1.2.0. Reads were mapped to mm10 and the mm10 v2 blacklist from ENCODE was used.
Within the nf-core/atacseq pipeline MACS2 v2.2.7.1 (Feng et al. 2012; Zhang et al. 2008) was used to call peaks in each experiment separately.
Consensus peaks were called using the peak regions present in any single experiment. Reads within peaks were calculated using featureCounts.
Assembly: mm10
Supplementary files format and content: comma-separated text file with the consensus peak coordinates
Supplementary files format and content: comma-separated text file containing the peak counts in each Sample

source_name: mESC

growth_protocol: Cells were maintained on 0.1% gelatin in KnockOut DMEM (Thermo Fisher, 10829018) supplemented with 12.5% FCS (MilliporeSigma, ES-009-B), 1X GlutaMAX supplement (Thermo Fisher, 35050061), 1X non-essential amino acids (Thermo Fisher, 11140050), 100 U/mL penicillin/streptomycin (Thermo Fisher, 15140122), 100 μM 2-mercaptoethanol (Thermo Fisher, 31350010), 1 μM PD0325901 (MilliporeSigma, PZ0162-5MG), 3 μM CHIR99021 (MilliporeSigma, SML1046-5MG), and 100 U/mL LIF (MilliporeSigma, ESG1107) at 37°C and 7.5% CO2. Cells were routinely tested for mycoplasma contamination by PCR.

extract_protocol:
Genomic DNA was isolated using the Tagment DNA Enzyme and Buffer Kit (Illumina).
ATAC-seq libraries were prepared from 25,000 cells following the Omni-ATAC protocol (Corces et al., 2017) and using the Tagment DNA Enzyme and Buffer Kit (Illumina).

treatment_protocol: Cells were treated with 1 ng/μL dox (MilliporeSigma, D9891-5G) the day after they were seeded and one hour after medium was changed to reduce cell stress.

value: mESC

value: embryonic stem cells

value: Firre KO / Firre inducible transgene

value: doxycycline

tag: time

value: 120 minutes


title: iLIN28AGFP_clone A1_b_dox_2hrs

description:
iLIN28AGFP inducible overexpression, More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A1_b_dox_2


title: Hi-TrAC_HSS3_WT_Th2_72h_rep2

data_processing:
Raw reads of RNA-seq data were mapped by STAR (v2.7.3a) (Dobin et al., 2013).   Raw reads of  ChIP-seq data were mapped by Bowtie2 (Langmead and Salzberg, 2012). Mapped unique paired-end reads with MAPQ 10 were used for the following analysis.  Raw reads of Hi-TrAC data were process by tracPre2.py in cLoops2 package (Cao et al., 2022).
Assembly: mm10
Supplementary files format and content: BigWig files for ChIP-seq were provided for visualization in genome browser.  TEXT files for RNA-seq gene expressions were provided. DIFF files for RNA-seq differential gene expression were provided. BEDPE files for Hi-TrAC or Hi-C data with high quality uniquely mapped paired-end tags (PETs) were provided.
Library strategy: Hi-TrAC

value: Th2 CD4+ T cells

value: Cell culture

value: HSS3 WT(DAPI-)


title: batch5_hs_Control-3

value: Control


title: ChIP-seq_GATA3_KO_Naive_H3K27ac_rep1

value: GATA3 KO(CD4+CD8-CD62L+CD44-)


title: Hi-TrAC_HSS3_WT_Th2_72h_rep1


title: D7-Myb-screen


title: iLIN28AGFP_clone A3_a_dox_1hrs

description:
iLIN28AGFP inducible overexpression, More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A3_a_dox_1

value: mESC V6.5.

value: naive embryonic stem cells

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 1hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium

value: dooxycyclin treated


title: iLIN28AGFP_clone A1_b_dox_1hrs

description:
iLIN28AGFP inducible overexpression, More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A1_b_dox_1


title: Hi-TrAC_HSS3_WT_Naive_rep5

value: mixed C57BL/6 and 129

value: Naive CD4+ T cells

value: lymph nodes

value: HSS3 WT(CD4+CD8-CD62L+CD44-)


title: batch5_hs_Control-2

value: Human embryonic kidney cells

value: Retina


title: D7-NfKB-CMV-screen


title: iLIN28AGFP_clone A1_b_dox_6hrs

description:
iLIN28AGFP inducible overexpression, More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A1_b_dox_6

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 6hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: D7-Pu1-screen


title: batch5_hs_Cas13VEGF-3


title: D7-EWS-library-control


title: batch5_hs_Control-1


title: iLIN28AGFP_clone A1_a_dox_4hrs

description:
iLIN28AGFP inducible overexpression, More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A1_a_dox_4

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 4hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: iLIN28AGFP_clone A1_b_dox_3hrs

description:
iLIN28AGFP inducible overexpression, More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A1_b_dox_3

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 3hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: D14-NfKB-library-control


title: batch5_hs_Cas13VEGF-2


title: iLIN28AGFP_clone A1_a_dox_6hrs

description:
iLIN28AGFP inducible overexpression, More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A1_a_dox_6


title: Hi-TrAC_HSS3_WT_Naive_rep4


title: D7-GR-library-control


title: Hi-TrAC_HSS3_WT_Naive_rep3


title: iLIN28AGFP_clone A1_a_dox_3hrs

description:
iLIN28AGFP inducible overexpression, More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A1_a_dox_3


title: Hi-TrAC_HSS3_WT_Naive_rep2


title: iLIN28AGFP_clone A1_b_dox_0hrs

description:
iLIN28AGFP inducible overexpression, More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A1_b_dox_0

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.


title: iLIN28AGFP_clone A1_a_dox_2hrs

description:
iLIN28AGFP inducible overexpression, More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A1_a_dox_2

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 2hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: D6-Pu1-library-control


title: batch5_hs_Cas13NT-2


title: Hi-TrAC_HSS3_KO_Th2_72h_rep2

value: Th2 CD4+ T cells

value: Cell culture

value: HSS3 KO(DAPI-)


title: D6-Irf1-library-control


title: iLIN28AGFP_clone A1_a_dox_0hrs

description:
iLIN28AGFP inducible overexpression, More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A1_a_dox_0

value: mESC V6.5.

value: naive embryonic stem cells


title: Hi-TrAC_HSS3_WT_Naive_rep1


title: iLIN28AGFP_clone A1_a_dox_1hrs

description:
iLIN28AGFP inducible overexpression, More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A1_a_dox_1

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 1hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium

value: dooxycyclin treated


title: D6-EWS-library-control


title: Hi-TrAC_HSS3_KO_Th2_72h_rep1

value: mixed C57BL/6 and 129


title: Hi-TrAC_HSS3_KO_Naive_rep5

value: Naive CD4+ T cells

value: lymph nodes

value: HSS3 KO(CD4+CD8-CD62L+CD44-)


title: iLIN28AGFP_clone A3_b_untreated_6hrs

description:
iLIN28AGFP inducible overexpression, not induced. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A3_b_untreated_6

value: Untreated


title: batch5_hs_Cas13NT-1

value: Human embryonic kidney cells

value: Retina


title: iLIN28AGFP_clone A3_b_untreated_4hrs

description:
iLIN28AGFP inducible overexpression, not induced. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A3_b_untreated_4

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 4hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: batch5_hs_Cas13-2


title: Hi-TrAC_HSS3_KO_Naive_rep4


title: Hi-TrAC_HSS3_KO_Naive_rep3


title: D6-Myb-screen


title: D6-VP64-screen


title: D6-GR-library-control


title: D6-Notch-screen


title: iLIN28AGFP_clone A3_b_untreated_3hrs

description:
iLIN28AGFP inducible overexpression, not induced. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A3_b_untreated_3

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 3hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: batch2_hs_XVEGF-3

value: XVEGF


title: batch5_hs_Cas13NT-3


title: batch5_hs_Cas13-1


title: iLIN28AGFP_clone A3_b_untreated_2hrs

description:
iLIN28AGFP inducible overexpression, not induced. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A3_b_untreated_2

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 2hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: Hi-TrAC_HSS3_KO_Naive_rep2


title: iLIN28AGFP_clone A3_b_untreated_1hrs

description:
iLIN28AGFP inducible overexpression, not induced. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A3_b_untreated_1


title: batch2_hs_XVEGF-2


title: D6-GR-screen


title: Hi-TrAC_HSS3_KO_Naive_rep1


title: RNA-seq_HSS3_WT_Th2_72h_rep2

value: Th2 CD4+ T cells

value: Cell culture

value: HSS3 WT(DAPI-)


title: iLIN28AGFP_clone A3_b_untreated_0hrs

description:
iLIN28AGFP inducible overexpression, not induced. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A3_b_untreated_0

value: mESC V6.5.

value: naive embryonic stem cells

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.


title: batch2_hs_XVEGF-1


title: D6-p53-screen


title: RNA-seq_HSS3_WT_Th2_72h_rep1

value: mixed C57BL/6 and 129


title: D6-Pu1-screen


title: D6-EWS-screen


title: RNA-seq_HSS3_KO_Th2_72h_rep2

value: HSS3 KO(DAPI-)


title: batch2_hs_XNT-3

value: XNT


title: iLIN28AGFP_clone A3_a_untreated_4hrs

description:
iLIN28AGFP inducible overexpression, not induced. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A3_a_untreated_4


title: D6-p53-library-control


title: RNA-seq_HSS3_KO_Th2_72h_rep1


title: batch2_hs_XNT-2


title: iLIN28AGFP_clone A3_a_untreated_3hrs

description:
iLIN28AGFP inducible overexpression, not induced. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A3_a_untreated_3


title: D6-Irf1-screen


title: batch2_hs_SHRNA-3

value: SHRNA


title: D6-NfKB-CMV-screen


title: ChIP-seq_HSS3_WT_Th2_72h_H3K4me3_rep1


title: batch2_hs_XNT-1


title: ChIP-seq_HSS3_WT_Th2_72h_H3K4me3_rep2


title: iLIN28AGFP_clone A3_a_untreated_1hrs

description:
iLIN28AGFP inducible overexpression, not induced. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A3_a_untreated_1

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 1hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium

value: Untreated


title: iLIN28AGFP_clone A3_a_untreated_6hrs

description:
iLIN28AGFP inducible overexpression, not induced. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A3_a_untreated_6

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 6hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: iLIN28AGFP_clone A3_a_untreated_0hrs

description:
iLIN28AGFP inducible overexpression, not induced. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A3_a_untreated_0


title: D6-Myb-library-control


title: ChIP-seq_HSS3_WT_Th2_72h_H3K4me1_rep2


title: batch5_hs_Cas13-3

value: Human embryonic kidney cells

value: Retina


title: batch2_hs_SHRNA-1


title: ChIP-seq_HSS3_WT_Th2_72h_H3K4me1_rep1


title: iLIN28AGFP_clone A1_b_untreated_6hrs

description:
iLIN28AGFP inducible overexpression, not induced. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A1_b_untreated_6


title: batch2_hs_RXVEGF-3

value: RXVEGF


title: ChIP-seq_HSS3_WT_Th2_72h_H3K27ac_rep2


title: batch2_hs_SHRNA-2


title: iLIN28AGFP_clone A1_b_untreated_4hrs

description:
iLIN28AGFP inducible overexpression, not induced. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A1_b_untreated_4

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 4hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: batch2_hs_RXVEGF-2


title: D6-VP64-library-control


title: ChIP-seq_HSS3_WT_Th2_72h_H3K27ac_rep1

value: Th2 CD4+ T cells


title: iLIN28AGFP_clone A1_b_untreated_3hrs

description:
iLIN28AGFP inducible overexpression, not induced. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A1_b_untreated_3

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 3hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: D6-NfKB-CMV-library-control


title: ChIP-seq_HSS3_KO_Th2_72h_H3K4me3_rep2

value: Cell culture


title: batch2_hs_RXVEGF-1


title: iLIN28AGFP_clone A1_b_untreated_2hrs

description:
iLIN28AGFP inducible overexpression, not induced. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A1_b_untreated_2

value: mESC V6.5.

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 2hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: D5-VP64-screen


title: D5-p53-screen


title: batch2_hs_RXNT-2

value: RXNT


title: ChIP-seq_HSS3_KO_Th2_72h_H3K4me3_rep1

value: mixed C57BL/6 and 129


title: D5-Notch-screen


title: batch2_hs_RXNT-1


title: ChIP-seq_HSS3_KO_Th2_72h_H3K4me1_rep2

value: HSS3 KO(DAPI-)


title: iLIN28AGFP_clone A1_a_untreated_6hrs

description:
iLIN28AGFP inducible overexpression, not induced. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A1_a_untreated_6

value: naive embryonic stem cells


title: iLIN28AGFP_clone A1_b_untreated_0hrs

description:
iLIN28AGFP inducible overexpression, not induced. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A1_b_untreated_0

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.


title: D5-EWS-library-control


title: ChIP-seq_HSS3_KO_Th2_72h_H3K4me1_rep1


title: batch2_hs_Control-3

value: Control


title: D5-p53-library-control


title: ChIP-seq_HSS3_KO_Th2_72h_H3K27ac_rep2


title: D5-NfKB-CMV-screen


title: batch2_hs_Control-2


title: batch2_hs_RXNT-3


title: iLIN28AGFP_clone A1_b_untreated_1hrs

description:
iLIN28AGFP inducible overexpression, not induced. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A1_b_untreated_1

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 1hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium

value: Untreated


title: D5-Myb-screen


title: batch2_hs_Control-1

value: Human embryonic kidney cells


title: iLIN28AGFP_clone A1_a_untreated_2hrs

description:
iLIN28AGFP inducible overexpression, not induced. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A1_a_untreated_2


title: Hi-C_GATA3_WT_Th2_rep2

value: GATA3 WT(DAPI-)


title: D5-Irf1-library-control


title: Hi-C_GATA3_WT_Th2_rep1


title: D5-GR-screen


title: Hi-C_GATA3_KO_Th2_rep2

value: GATA3 KO(DAPI-)


title: iLIN28AGFP_clone A1_a_untreated_0hrs

description:
iLIN28AGFP inducible overexpression, not induced. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A1_a_untreated_0


title: batch1_hs_XVEGFARR-3

value: Retina

value: XVEGFARR


title: iLIN28AGFP_clone A1_a_untreated_1hrs

description:
iLIN28AGFP inducible overexpression, not induced. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A1_a_untreated_1


title: Hi-C_GATA3_KO_Th2_rep1

value: Th2 CD4+ T cells


title: batch1_hs_XVEGFARR-4


title: D5-Myb-library-control


title: iLIN28AGFP_clone A1_a_untreated_4hrs

description:
iLIN28AGFP inducible overexpression, not induced. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A1_a_untreated_4

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 4hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: batch1_hs_XVEGFARR-1


title: Hi-TrAC_MLL4_WT_Th2_72h_rep3

value: Cell culture

value: MLL4 WT(DAPI-)


title: Wt_naive_3hrs_3

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433820
naive_3hrs_3

value: mESC IDG3.2.

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 3hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: batch1_hs_XVEGFARR-2


title: batch1_hs_XVEGF-4

value: XVEGF


title: ChIP-seq_HSS3_KO_Th2_72h_H3K27ac_rep1

value: mixed C57BL/6 and 129

value: HSS3 KO(DAPI-)


title: D5-VP64-library-control


title: iLIN28AGFP_clone A1_a_untreated_3hrs

description:
iLIN28AGFP inducible overexpression, not induced. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A1_a_untreated_3

value: mESC V6.5.

value: naive embryonic stem cells


title: Hi-TrAC_MLL4_WT_Th2_72h_rep2


title: Wt_naive_3hrs_2

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433819
naive_3hrs_2

value: Untreated


title: Hi-TrAC_MLL4_WT_Th2_72h_rep1


title: batch1_hs_XVEGF-3

value: Human embryonic kidney cells


title: D5-EWS-screen


title: Wt_naive_2hrs_3

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433818
naive_2hrs_3

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 2hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: D5-NfKB-CMV-library-control


title: Wt_naive_3hrs_4

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433821
naive_3hrs_4


title: batch1_hs_XVEGF-2


title: D5-Pu1-screen


title: batch1_hs_XVEGF-1


title: Wt_naive_6hrs_3

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433817
naive_6hrs_3

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 6hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: D5-Irf1-screen


title: Hi-TrAC_MLL4_WT_Th2_24h_rep5


title: D5-Pu1-library-control


title: batch1_hs_XNT-4

value: Retina

value: XNT


title: Hi-TrAC_MLL4_WT_Th2_24h_rep4

value: Th2 CD4+ T cells


title: Wt_naive_6hrs_2

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433816
naive_6hrs_2


title: Hi-TrAC_MLL4_WT_Th2_24h_rep3


title: Wt_naive_6hrs_1

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433815
naive_6hrs_1


title: D5-GR-library-control


title: Wt_naive_4hrs_3

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433814
naive_4hrs_3

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 4hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: iLIN28AGFP_clone A3_a_untreated_2hrs

description:
iLIN28AGFP inducible overexpression, not induced. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A3_a_untreated_2


title: D5-Notch-library-control


title: Hi-TrAC_MLL4_WT_Th2_24h_rep2

value: Cell culture


title: batch1_hs_XNT-3


title: batch1_hs_XNT-2


title: batch1_hs_XNT-1


title: Hi-TrAC_MLL4_WT_Th2_24h_rep1

value: MLL4 WT(DAPI-)


title: Wt_naive_4hrs_2

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433813
naive_4hrs_2

value: mESC IDG3.2.


title: human-chromatin-BFP-plasmid


title: Hi-TrAC_MLL4_WT_Th1_72h_rep3

value: Th1 CD4+ T cells


title: Wt_naive_4hrs_1

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433812
naive_4hrs_1


title: S3_NTtreated

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
After checking the reads quality, the sequencing files were aligned to reference human genome (version GRCh38) using 10X Genomics CellRanger software (v7.1.0) count pipeline to remove non-cellular barcodes and keep the cellular barcodes and gene matrix.
Blastn 61 was used to compute the similarity between cellular reads and Cas13bt3 reference sequence.
Seurat  v4.3 was used for data pre-processing, data normalization, feature selection, data scaling, dimensional reduction and clustering.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Retina

extract_protocol:
RNA extraction from harvested retinal organoids were performed using Rneasy Mini kit (Qiagen)
Library was prepared using standard and optimised Genewiz's protocols

value: NTtreated


title: Hi-TrAC_MLL4_WT_Th1_72h_rep2

value: mixed C57BL/6 and 129


title: Wt_naive_3hrs_1

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433811
naive_3hrs_1

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 3hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: BV173 cells, sgPRDX1, 250nM imatinib, 24h, biol rep 2

city: Warsaw

first: Łukasz

middle: Wit

last: Komorowski

state: Mazovian

address: Jana Nielubowicza 5

department: Department of Immunology

country: Poland

institute: Medical University of Warsaw

data_processing:
FASTQ files were processed with StrandNGS 3.3 Software (Licence for Medical University of Lodz).
Paired-end reads were aligned to the human genome assembly (hg19) and transcriptome (USS transcript model), indexes and poor-quality bases at both ends were then trimmed from the reads.
According to filtering by reading metrics, reads with low base quality, low alignment score, failing vendor’s QC and shorter than 20bp  were removed.
The reads were quantified according to TMM (trimmed mean of m-values) algorithm, entities where at least 50% of samples in any 4 out of 8 conditions have values lower than 10, were filtered out. Finally the 15022 out of  40437 genes passed all criteria.
Statistical analysis was performed in StrandNGS 3.3 Software (Licence for Medical University of Lodz), differentially expressed genes between subgroups were assessed and P values were calculated using the moderated T-test with Benjamini-Hochberg correction.
Assembly: hg19
Supplementary files format and content: Excel format. Table 1 - Normalised expression level of all genes for all samples. Table 2 - List of differentially activated pathways identified through GSEA in BV173 sgPRDX1 treated with 250nM IMAT for 12h in comparison to sgNTC cells. Table 3 - List of differentially activated pathways identified through GSEA in BV173 sgPRDX1 treated with 250nM IMAT for 24h in comparison to sgNTC cells.

growth_protocol: BV173 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was alcohol extracted from the cells resuspended in Trizol (Invitrogen) following manufacturer's protocols.
RNA sequencing was performed using Illumina® Stranded mRNA Prep, Ligation (Illumina,  20040532) according to the manufacturers' protocol. The messenger RNA was captured form 1 μg of total RNA, fragmented and primed for cDNA synthesis followed by the second strand synthesis resulting in double-stranded cDNA. Secondly, pre-index anchors were ligated to the ends of the cDNA fragments, in the subsequent PCR amplification step the indexes (IDT® for Illumina® RNA UD Indexes Set A, Illumina, 20040553) and primer sequences for cluster generation were added. In order to optimize cluster densities across every lane of the flow cell, quantification of DNA libraries using DNA 1000 chip on an Agilent Technologies 2200 TapeStation System was performed. Indexed DNA libraries were normalized to 4 nM and then pooled in equal volumes. The library was sequenced on a Next Seq 550 system (Illumina) using NextSeq® Reagent Kit v3 (150 cycles) with a TG NextSeq 500/550 High Output Flow Cell. Images from the instrument were processed to generate FASTQ sequence files.

treatment_protocol: Cells were treated with 250nM imatinib added to cell media for either 12h or 24h prior to RNA extraction

value: B cell precursor leukemia

value: PRDX1 knockout

value: 250nM imatinib


title: Hi-TrAC_MLL4_WT_Th1_72h_rep1


title: Hi-TrAC_MLL4_WT_Th1_24h_rep3


title: BV173 cells, sgPRDX1, 250nM imatinib, 24h, biol rep 1


title: Wt_naive_2hrs_1

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433809
naive_2hrs_1

value: naive embryonic stem cells

value: Untreated


title: BV173 cells, sgPRDX1, 250nM imatinib, 12h, biol rep 2


title: Wt_naive_2hrs_2

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433810
naive_2hrs_2

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 2hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: Wt_naive_1hrs_3

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433808
naive_1hrs_3

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 1hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: Hi-TrAC_MLL4_WT_Th1_24h_rep1


title: NIM_28d_DNSCM_1

city: Beijing

first: sun

last: zheng

address: NO.1 West Beichen Road,Chaoyang District

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
Cells whose gene number was less than 200 or gene number ranked in the top 1%, or mitochondrial gene ratio was more than 25% were regarded as abnormal and filtered out. Dimensionality reduction was performed using PCA, and visualization was realized by TSNE and UMAP.
Assembly: 36
Supplementary files format and content: Tar archives include single-cell sequencing matrix data (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Spinal cord motor neuron organoid

extract_protocol:
To characterize the cell subtype population of spinal cord motor neuron organoid induced in DNSCM and DASCM, single-cell RNA sequencing was performed using 10x Genomics. To digest the spinal cord motor neuron organoids (day28) into single cells, the DNSCM encasing the organoids was first removed by incubating with 2mg/mL collagenase Ⅰ at 37℃ for 15min. Organoid spheroids were collected by centrifugation at 500g for 5min and incubated with Accutase at 37 ° C for 5min. After digestion, the cell suspension was formed by gently blowing up and down with 1mL tips. The dissociated cells were filtered using a 40um cell strainer and then centrifuged at 500g for 5min, resuspended in the neurobasal medium. After measuring the density and viability of scMN-Organ-dissociated cells, the final cell density was modified into 700-1000 cells/μL.
Dissociated cells were loaded onto the Chromium single cell controller (10x Genomics) to generate single cell gel beads in the emulsion according to the manufacture’s protocol. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 min, followed by 85°Cfor 5 min, and hold at 4°C. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200. Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1 The libraries were finally sequenced using an IlluminaNovaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150).

value: Spinal cord motor neuron organoid

value: Neural cells

tag: constructed in

value: Decellularized spinal cord ECM from neonatal rabbit


title: BV173 cells, sgPRDX1, untreated, 24h, biol rep 2

value: untreated


title: BV173 cells, sgPRDX1, untreated, 24h, biol rep 1


title: NIM_28d_DASCM_1

value: Decellularized spinal cord ECM from adult rabbit


title: Wt_naive_1hrs_2

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433807
naive_1hrs_2

value: mESC IDG3.2.


title: Hi-TrAC_MLL4_WT_Th1_24h_rep2

value: Th1 CD4+ T cells

value: Cell culture

value: MLL4 WT(DAPI-)


title: BV173 cells, sgPRDX1, 250nM imatinib, 12h, biol rep 1


title: Hi-TrAC_MLL4_KO_Th2_72h_rep2

value: mixed C57BL/6 and 129

value: Th2 CD4+ T cells

value: MLL4 KO(DAPI-)


title: Wt_naive_1hrs_1

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433806
naive_1hrs_1


title: EB73 Daclatasvir 2

city: Madison

first: Andrew

middle: Perry

last: South

state: Wisconsin

address: 1111 Highland Avenue

institute: University of Wisconsin-Madison

data_processing:
Sequence read data were processed and converted to FASTQ format for downstream analysis by Illumina BaseSpace analysis software (v2.0.13).
Using PartekFlow (Partek, St. Louis, MO, USA), data filtering steps started with pre-alignment QC. The raw reads corresponding to the Illumina RNA-Seq FASTQ files were mapped with Star aligner against the human genome hg38 using STAR 2.7.8a in Partek Flow software.
After alignment, we performed post-alignment QC. Aligned reads were then quantified using Partek E/M method (Annotation model: Ensembl Transcripts release 108).
We filtered the data by noise reduction, excluding features where the value ≤1 in at least 80% of samples. The data was normalized using the DESeq2 normalization method (median ratio).
We used differential statistics (gene list) by the normalized DESeq2 counts.
Assembly: hg-38
Supplementary files format and content: Excel file with normalized data (averaged by treatment group)
Supplementary files format and content: Excel file with normalized data (by individual sample)

source_name: skin

growth_protocol: Fibroblasts seeded at 100,000 cells/well in a 6 well plate with 10% FBS in DMEM media.

extract_protocol:
Cells were extracted 48 hours after treatment using the RNA STAT-60 protocol.
Sequencing libraries weregenerated with 100ng each sample using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus (Illumina, Inc) following manufactory instruction.

treatment_protocol: One day after seeding, cells received fresh media with ascorbic acid and either DMSO vehicle or 1µM daclatasvir treatment.

value: skin

value: primary patient

value: dermal fibroblast

value: COL7A1 c.2471dupG / c.2471dupG

value: daclatasvir


title: Hi-TrAC_MLL4_KO_Th2_72h_rep1


title: BV173 cells, sgPRDX1, untreated, 12h, biol rep 2

value: B cell precursor leukemia

value: PRDX1 knockout


title: BV173 cells, sgPRDX1, untreated, 12h, biol rep 1


title: EB73 Daclatasvir 1


title: Hi-TrAC_MLL4_KO_Th2_24h_rep4


title: batch5_hs_Cas13VEGF-1

value: Human embryonic kidney cells

value: Retina


title: Wt_naive_0hrs_2

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433804
naive_0hrs_2

value: naive embryonic stem cells

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.

value: Untreated


title: S2_VEGFAtreated

description: 10X Genomics

value: VEGFAtreated


title: EB73 Daclatasvir 3


title: BV173 cells, sgNTC, 250nM imatinib, 24h, biol rep 2

value: wild type

value: 250nM imatinib


title: S1_H9untreated

description: 10X Genomics


title: Wt_naive_0hrs_1

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433803
naive_0hrs_1

value: mESC IDG3.2.


title: EB73 Control 3

value: vehicle control


title: BV173 cells, sgNTC, 250nM imatinib, 24h, biol rep 1


title: KO_priming_6hr_U_3

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433802
KO_6hr_U_3

value: naive embryonic stem cells treated for 12hrs with Fgf2+ActivinA, plus the indicated time of chase labeling

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 6hours with 10mM Uridine-containing (Sigma, U3750-25G) growth medium

value: Lin28a KO, CRISPR excision exon 2


title: Hi-TrAC_MLL4_KO_Th2_24h_rep1

value: mixed C57BL/6 and 129

value: Th2 CD4+ T cells

value: Cell culture

value: MLL4 KO(DAPI-)


title: KO_priming_6hr_U_2

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433801
KO_6hr_U_2


title: AB1080 t(4;10) clone 6 myotubes rep3

city: Villejuif

first: Anna

last: Schwager

state: Please Select

address: 114 Rue Edouard Vaillant

country: France

institute: Institut Gustave Roussy

data_processing:
Raw sequencing data was processed by the nfcore RNA-seq pipeline (v3.10.1) with default parameters (Patel et al. 2024). Briefly, the reads were trimmed with trimgalore (0.6.7) and cutadapt (3.4) (Martin 2011) to remove the Illumina adapter sequences from the 3′-ends. The trimmed reads were mapped to the GRCh38 genome from the Illumina iGenomes using STAR (2.6.1d)  (Dobin et al. 2013) and quantified with Salmon (1.9.0) (Patro et al. 2017).
Assembly: GRCh38
Supplementary files format and content: Salmon counts

source_name: muscle

extract_protocol:
Zymo Quick-RNA Miniprep Kit (R1055)
Novogene NGS RNA Library Prep Set (PT042)

value: muscle

value: myotubes

value: no


title: D6-Notch-library-control


title: Hi-TrAC_MLL4_KO_Th2_24h_rep2


title: Hi-TrAC_MLL4_KO_Th2_24h_rep3


title: Wt_naive_0hrs_3

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433805
naive_0hrs_3

value: naive embryonic stem cells

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.


title: KO_priming_6hr_U_1

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433800
KO_6hr_U_1


title: Hi-TrAC_MLL4_KO_Th1_72h_rep2

value: Th1 CD4+ T cells


title: AB1080 t(4;10) clone 6 myotubes rep2


title: BV173 cells, sgNTC, untreated, 24h, biol rep 2

value: B cell precursor leukemia

value: wild type

value: untreated


title: BV173 cells, sgNTC, 250nM imatinib, 12h, biol rep 1

value: 250nM imatinib


title: Wt_priming_6hr_U_3

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433799
WT_6hr_U_3

value: mESC IDG3.2.

value: naive embryonic stem cells treated for 12hrs with Fgf2+ActivinA, plus the indicated time of chase labeling

value: WT


title: Wt_priming_6hr_U_2

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433798
WT_6hr_U_2

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 6hours with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: BV173 cells, sgNTC, untreated, 24h, biol rep 1


title: Hi-TrAC_MLL4_KO_Th1_24h_rep3

value: mixed C57BL/6 and 129


title: AB1080 t(4;10) clone 6 myotubes rep1


title: EB73 Control 2

value: skin

value: primary patient

value: dermal fibroblast

value: COL7A1 c.2471dupG / c.2471dupG

value: vehicle control


title: AB1080 t(4;10) clone 5 myotubes rep3

value: muscle

value: myotubes

value: no


title: BV173 cells, sgNTC, untreated, 12h, biol rep 2

value: B cell precursor leukemia


title: EB73 Control 1


title: BV173 cells, sgNTC, 250nM imatinib, 12h, biol rep 2

value: wild type


title: AB1080 t(4;10) clone 5 myotubes rep2


title: BV173 cells, sgNTC, untreated, 12h, biol rep 1

value: untreated


title: Hi-TrAC_MLL4_KO_Th1_24h_rep2

value: Th1 CD4+ T cells

value: Cell culture

value: MLL4 KO(DAPI-)


title: AB1080 t(4;10) clone 5 myotubes rep1


title: KO_priming_3hs_U_2

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433795
KO_3hs_U_2

value: mESC IDG3.2.

value: naive embryonic stem cells treated for 12hrs with Fgf2+ActivinA, plus the indicated time of chase labeling

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 3hours with 10mM Uridine-containing (Sigma, U3750-25G) growth medium

value: Lin28a KO, CRISPR excision exon 2


title: RNA-seq_MLL4_WT_Th2_72h_rep2

value: mixed C57BL/6 and 129

value: Th2 CD4+ T cells

value: MLL4 WT(DAPI-)


title: ATAC_4T1-sgTgfbr2, rep2

first: Jae Young

last: So

state: MD

address: 37 Convent Drive, Rm 3134

department: LCBG

institute: NCI/NIH

data_processing:
Deduplication by Picard,s MarkDuplicate, mapping by Bowtie2, Cyclic loess normalziation, peak calling by Macs (v 2.1.2)
Assembly: mm10
Supplementary files format and content: ATAC_Count_Matrix.CPM.txt

source_name: in vitro cell culture

extract_protocol:
Genomic DNA extraction from cells by using the Dneasy Blood & Tissue kit (QIAGEN, #69506)
DNA library prepartaion by using NEBNext-Ultra II DNA kit (NEB, #E7103)

tag: growth protocol

value: in vitro cell culture

value: mammary tumor cell

value: TGFBR2 knockout


title: AB1080 myotubes rep3

value: muscle

value: myotubes

value: FSHD

value: no


title: ATAC_4T1-sgTgfbr2, rep1


title: RNA-seq_MLL4_WT_Th2_72h_rep1


title: AB1080 myotubes rep2


title: Hi-TrAC_MLL4_KO_Th1_72h_rep1

value: Th1 CD4+ T cells


title: KO_priming_3hs_U_1

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433794
KO_3hs_U_1


title: ATAC_4T1-sgTsc1, rep2

value: TSC1 knockout


title: RNA-seq_MLL4_WT_Th2_24h_rep2

value: Cell culture


title: Wt_priming_3hs_U_3

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433793
WT_3hs_U_3

value: mESC IDG3.2.

value: WT


title: AB1080 myotubes rep1


title: ATAC_4T1-sgTsc1, rep1


title: Wt_priming_3hs_U_1

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433792
WT_3hs_U_1

value: naive embryonic stem cells treated for 12hrs with Fgf2+ActivinA, plus the indicated time of chase labeling

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 3hours with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: RNA-seq_MLL4_WT_Th2_24h_rep1

value: mixed C57BL/6 and 129


title: ATAC_4T1-sgNf1, rep2

value: NF1 knockout


title: Wt_priming_6hr_U_1

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433797
WT_6hr_U_1

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 6hours with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: RNA-seq_MLL4_WT_Th1_72h_rep2

value: MLL4 WT(DAPI-)


title: AB1190 myotubes rep2

value: healthy


title: KO_priming_1hr_U_3

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433791
KO_1hr_U_3

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 1hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium

value: Lin28a KO, CRISPR excision exon 2


title: Hi-TrAC_MLL4_KO_Th1_24h_rep1

value: MLL4 KO(DAPI-)


title: RNA-seq_MLL4_WT_Th1_72h_rep1


title: ATAC_4T1-sgNf1, rep1

value: in vitro cell culture

value: mammary tumor cell


title: KO_priming_3hs_U_3

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433796
KO_3hs_U_3


title: AB1190 myotubes rep1

value: muscle

value: myotubes

value: no


title: ATAC_4T1-C1, rep2

value: control


title: RNA-seq_MLL4_WT_Th1_24h_rep1

value: Th1 CD4+ T cells

value: Cell culture


title: RNA-seq_MLL4_WT_Th1_24h_rep2


title: ATAC_4T1-C1, rep1


title: AB1080 t(4;10) clone 6 myoblasts rep3

value: myoblasts


title: KO_priming_1hr_U_1

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433789
KO_1hr_U_1

value: mESC IDG3.2.

value: naive embryonic stem cells treated for 12hrs with Fgf2+ActivinA, plus the indicated time of chase labeling


title: Wt_priming_1hr_U_2

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433787
WT_1hr_U_2

value: WT


title: AB1080 t(4;10) clone 6 myoblasts rep2


title: AB8604

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
20191217_D5_Ctrl_T10_2
MARSseq

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: metadata_q.txt

source_name: tumor

growth_protocol: 8 to 10 weeks-old mice housed at the Weizmann Institute animal facility.

extract_protocol:
Mice were sacrificed at various time points by cervical dislocation. Tumor, spleen, and tdLN were collected and put through a process of mechanical and enzymatic digestion. For single-cell suspensions, tumors were chopped into small pieces and suspended in RPMI supplemented with DNase (2mg/ml, Sigma-Aldrich) and collagenase IV (100mg/ml, Worthington). Tumors were homogenized by GentleMacs tissue homogenizer (Miltenyi Biotec) and incubated at 37oC for 30min, with frequent agitation. Following dissociation procedures, cells were washed with cold PBS, filtered through a 70-μm cell strainer, and centrifuged at 300g for 5 min at 4 °C. Spleen and tdLN were mashed through a 100uM cell strainer and washed with ice-cold MACS buffer (PBS supplemented with 0.2mM EDTA, pH 8, and 0.5% BSA). Cells were centrifuged at 300g, 5 min, and 4°C. Spleen was suspended in red blood lysis buffer (Sigma-Aldrich) and DNase (0.33U/ml, Sigma-Aldrich), incubated for 5min at room temperature, washed with cold PBS, passed through a 70μm mesh strainer, centrifuged at 300g, 5 min, 4°C and then resuspended in ice-cold MACS buffer.
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol:
Mice were anesthetized and the indicated inactivated pathogens were administered by intradermal injection into the ear pinna. PBS was injected into the ear pinna of control animals.
mice were treated with 250ug of aPD1 or/and 200ug of a41BB.

value: tumor

value: OT1 CD8+_or_bystander CD8+

tag: experiment id

tag: days post_adoptive_transfer

tag: mouse number


title: RNA-seq_MLL4_WT_Naive_rep2

value: mixed C57BL/6 and 129

value: Naive CD4+ T cells

value: lymph nodes

value: MLL4 WT(CD4+CD8-CD62L+CD44-)


title: Wt_priming_1hr_U_1

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433786
WT_1hr_U_1

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 1hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: AB1080 t(4;10) clone 6 myoblasts rep1

value: muscle


title: AB8603

description:
20191217_D5_Ctrl_T10_1
MARSseq


title: AB1080 t(4;10) clone 5 myoblasts rep3


title: AB8602

description:
20191217_D5_Ctrl_T9_2
MARSseq


title: AB1190 myotubes rep3

value: myotubes

value: healthy


title: RNA-seq_MLL4_KO_Th2_72h_rep2

value: Th2 CD4+ T cells

value: MLL4 KO(DAPI-)


title: KO_priming_4sU_only_3

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433785
KO_4sU_only_3

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.

value: Lin28a KO, CRISPR excision exon 2


title: AB8601

description:
20191217_D5_Ctrl_T9_1
MARSseq


title: KO_priming_4sU_only_2

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433784
KO_4sU_only_2

value: mESC IDG3.2.


title: AB1080 t(4;10) clone 5 myoblasts rep1

value: myoblasts

value: no


title: AB1080 t(4;10) clone 5 myoblasts rep2


title: RNA-seq_MLL4_KO_Th2_72h_rep1

value: Cell culture


title: RNA-seq_MLL4_WT_Naive_rep1


title: AB8600

description:
20191217_D5_Ctrl_T8_bys_1
MARSseq

value: tumor

value: bystander CD8+


title: KO_priming_4sU_only_1

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433783
KO_4sU_only_1

value: naive embryonic stem cells treated for 12hrs with Fgf2+ActivinA, plus the indicated time of chase labeling


title: Wt_priming_1hr_U_3

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433788
WT_1hr_U_3

value: WT


title: AB1080 myoblasts rep3

value: FSHD


title: KO_priming_1hr_U_2

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433790
KO_1hr_U_2

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 1hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium


title: AB8599

description:
20191217_D5_Ctrl_T8_2
MARSseq

value: OT1 CD8+_or_bystander CD8+


title: RNA-seq_MLL4_KO_Th2_24h_rep2

value: mixed C57BL/6 and 129


title: RNA-seq_MLL4_KO_Th2_24h_rep1


title: Wt_priming_4sU_only_3

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433782
WT_4sU_only_3


title: AB8598

description:
20191217_D5_Ctrl_T8_1
MARSseq


title: RNA-seq_MLL4_KO_Th1_72h_rep2

value: Th1 CD4+ T cells


title: AB1080 myoblasts rep2

value: muscle


title: Wt_priming_4sU_only_2

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433781
WT_4sU_only_2


title: AB8597

description:
20191217_D5_Ctrl_T7_3
MARSseq


title: RNA-seq_MLL4_KO_Th1_72h_rep1

value: MLL4 KO(DAPI-)


title: Wt_priming_4sU_only_1

description:
WT mESC used to calculate half-lives comparing naïve versus priming ESCs. Culturing conditions explained in more detail in doi: https://doi.org/10.1101/2021.03.15.433780
WT_4sU_only_1

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.


title: AB1190 myoblasts rep3

value: healthy


title: AB8596

description:
20191217_D5_Ctrl_T7_2
MARSseq


title: RNA-seq_MLL4_KO_Th1_24h_rep2


title: AB1190 myoblasts rep2


title: embryo_LIN28AGFPNLS_2

description:
tetraploid complemented E7.5 embryo were FACS sorted for 500 GFP expressing cells.
MOD246A5

data_processing:
Reads were quantified using STAR, with a transcriptome built from ENSEMBL 92 ERCC SIRV transcripts, using default settings, excluding rRNA and globin reads.
featureCounts was used to summarize mapped reads for genomic features and  count both RNA-seq reads
Cuffnorm was used to generate tables of expression values that are normalized for library size.
Differential expression analysis was performed using DESeq2, with effect size shrinkage using the apeglm package.
Genome_build: ENSEMBL 92

source_name: FACS sorted embryonic tissue

growth_protocol: Tetraploid chimeras were generated according to standard protocols (Engert et al., 2013; Modic et al., 2019) . Embryos were collected from the mT/mG expressing mouse line (Muzumdar et al., 2007) , maintained on C57/Bl6J background.

extract_protocol:
Total RNA was prepared from cell pellets using PicoPure™ RNA Isolation Kit (Thermo, KIT0204)  according to the manufacturer’s instructions
For total RNA sequencing Ovation RNA Amplification System V2 was used according to manufacturer’s instruction (Nugen, 3100-A01).

treatment_protocol: Embryos were dissociated into single cell suspension using Accutaseusing Accutase (A6964, Sigma-Aldrich) for 5 min in 37 °C for 30 min at 37 °C and washed with 5% FBS (EmbryoMax® ES Cell Qualified FBS, ES-009-B, Merck) in PBS

value: mESC J1

tag: tag

value: CRISPR fusion of GFPNLS to C-terminus of Lin28a gene


title: RNA-seq_MLL4_KO_Th1_24h_rep1


title: AB8595

description:
20191217_D5_Ctrl_T7_1
MARSseq


title: embryo_LIN28AGFPNLS_1

description:
tetraploid complemented E7.5 embryo were FACS sorted for 500 GFP expressing cells.
MOD246A4


title: embryo_LIN28AGFP_2

description:
tetraploid complemented E7.5 embryo were FACS sorted for 500 GFP expressing cells.
MOD246A3

value: CRISPR fusion of GFP to C-terminus of Lin28a gene


title: RNA-seq_MLL4_KO_Naive_rep2

value: Naive CD4+ T cells

value: lymph nodes

value: MLL4 KO(CD4+CD8-CD62L+CD44-)


title: AB8594

description:
20191217_D5_PD1_T5_bys_1
MARSseq

value: tumor

value: bystander CD8+


title: AB8593

description:
20191217_D5_PD1_T5_2
MARSseq


title: RNA-seq_MLL4_KO_Naive_rep1


title: AB1190 myoblasts rep1

value: myoblasts

value: no


title: embryo_LIN28AGFP_1

description:
tetraploid complemented E7.5 embryo were FACS sorted for 500 GFP expressing cells.
MOD246A1


title: AML340 100 nM FHD-286 scRNA Seq

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

description: AML340_FHD scRNA Seq

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Patient-derived AML cells

growth_protocol: Patient-derived AML cells were cultured in 20% FBS-containing RPMI media.

extract_protocol:
Frozen patient derived AML BM cells stored in liquid nitrogen were retrieved right before sample processing. To maximize the cellular viability recovery, samples were processed in batches according to thawing protocol. Briefly, cells were gently thawed in water bath at 37 °C for 2 minutes until partially thawed and immediately transferred to a 50 mL conical tube with 1ml of prewarmed media (RPMI1640 supplemented with 10% FBS) and centrifuged (300 g for 5 min). Cells were sequentially diluted 1:1 3 times with prewarmed RPMI containing 10% FBS. Cells were centrifuged at 300 x g for 5 minutes in a swinging bucket centrifuge. After finishing centrifugation, supernatant was disposed, the cell pellet was carefully re-suspended in 1 mL of 2% FBS/PBS, centrifuged at 300 x g for 5 minutes and resuspended in 900 uL of 2% FBS/PBS. To removed dead cells and debris, cells were passed through a 40 micron Flow-mi strainer and the cell concentration of the concentrated cell stock was determined with a Countess counting device.  The desired number of targeted cells (5000-10,000) from the concentrated cell stock were separated on the 10X Chromium Controller.
scRNA Seq libraries were constructed following the 10X Genomics protocol for single cell RNA Seq analysis.

treatment_protocol: PD AML cells were treated with FHD-286 for 16 hours at 37°C and cryopreserved in 90% FBS, 10% DMSO until nuclei isolation for multiomics (sc-ATAC + sc-RNA) analysis

value: Patient-derived AML cells

value: Bone marrow


title: AB1080 myoblasts rep1

value: FSHD


title: Quantseq_naïve_iLIN28AGFP_dox_4

description:
inducible LIN28A-GFP cell line has been used to compare untreated versus inducible LIN28A-GFP overexpression in naïve ESCs. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433787
6hrs_dox_4 MOD970A13_S29_L004_R1_001.fastq.gz

data_processing:
Reads were quantified using Salmon, with a transcriptome built from GENCODE M22 transcripts, using default settings.
To monitor the expression level of the Lin28a-GFP transgene, the sequence was included with decoy sequences derived from the whole genome sequence.
Differential expression analysis was performed using DESeq2, with effect size shrinkage using the apeglm package.
Genome_build: GENCODE M22

growth_protocol: All mouse ESC lines e.g., J1 IDG3.2 and V6.5, were maintained in 1:1 Neurobasal (21103049) DMEM (11320033) medium containing N2 (17502048) and B27 (17504044) supplements, 1% Glutamax (35050), 1% nonessential amino acids (1140050), 0.1 mM 2-mercaptoethanol (31350-010) (all Thermo Fisher Scientific), 1 mM MEK inhibitor PD0325901 (1408, Axon Medchem), 3 mM GSK3 inhibitor CHIR99021 (4953/50 Tocris), and 1,000 U/ml LIF (ESGRO ESG1107, Merck), a condition named 2iLIF. Cells were passaged using Stempro-Accutase (A1110501, Thermo Fisher Scientific). Cells were grown on gelatin coated plates which were prepared by first incubating the wells 0.1% gelatin (EmbryoMax® ES-006-B, Merck) with 1% FBS (EmbryoMax® ES Cell Qualified FBS, ES-009-B, Merck) for 1 h at 37 °C followed by a rinse with PBS. To transit from naive ESC to priming ESC cells, accutased naive ESCs were seeded onto gelatine and FBS-coated plates in N2B27 medium supplemented with recombinant 20 ng ml–1activin A (338-AC-050, R&D Systems) and 12 ng ml–1 bFGF (100-18B, Peprotech) for 12 hours or as indicated in the Figure legends (12, 24, 36 or 48 hours). To determine developmental genes that are downregulated during naive-to-primed transition, the publicly available data were used (Yang et al., 2019a) and analyzed as described in the RNAseq analysis section. Primed epiblast stem cells (EpiSCs) were cultured on gelatine and FCS-coated plates in N2B27 medium supplemented with recombinant 20 ng ml–1activin A (338-AC-050, R&D Systems) and  2 μM IWP2 (3533, Tocris) to suppress spontaneous differentiation. EpiSCs were passaged 1:4–1:10 every 3 days by triturating the colonies into small clumps using 0.5 mg ml–1 collagenase IV (Sigma). MEK/WNT-inhibited RSCs were cultivated with 1,000 U ml–1 LIF, 2 μM IWP2, 1 μM PD (manufacturers as mentioned above) and were passaged as ESCs. To induce primitive streak differentiation we utilized a double reporter mESC line modified to express distinct fluorescent proteins regulated by the promoters of T (Brachyury) and Foxa2 genes, where the expression of T and Foxa2 alone is indicative of mesodermal and endodermal commitment, respectively (Burtscher and Lickert, 2009). First, EpiSCs from these cells were derived by transiting ESCs to primed cells with 1,000 U ml–1 LIF, 2 μM IWP2, 20 ng ml–1 Activin A and 12 ng ml–1 bFGF (manufacturers as mentioned above). After 3 days, LIF has been omitted and derived EpiSCs can be passaged 1:4–1:10 every by triturating the colonies into small clumps using 0.5 mg ml–1 collagenase IV (Sigma). To derive mesodermal progenitors utilizing the T-eGFP FoxA2-tagRFP double knock-in reporter cell lines, the IWP2 that is in EpiSCs used to suppress differentiation was replaced by 250ng/mL of WNT3A (in house produced as described previously (Neagu et al., 2020)) and fresh medium was applied daily. Expression of T-eGFP and FoxA2-tagRFP, indicative of mesodermal and endodermal progenitors, was monitored by Flow cytometry.  All cell lines in culture were tested for mycoplasma contamination every 2–3 months.

extract_protocol:
Total RNA was prepared from cell pellets using miRNeasy Micro Kit (Qiagen, 217084) according to the manufacturer’s instructions
For 3’mRNA-seq, 0.5 μg of totalRNA was used per library prepared using Lexogen QuantSeq-FWD kit (Lexogen GmbH, 0.15).

treatment_protocol: mESCs were co-transfected with 4 μg of transposable vector and 1 μg of the piggyBac transposase using Lipofectamine 3000 (Thermo Fisher Scientific) according to the manufacturer’s instructions. Selection in 5μg/ml blasticidin was initiated 3 days after transfection and maintained until resistant colonies became visible. The LIN28A-GFP overexpression was induced by adding 1μg/ml doxycycline (dox) (ThermoFisher Scientific) in 2iLIF medium.

value: mESC V6.5

value: naive embryonic stem cells

tag: transgene

value: inducible LIN28A-GFP transgene stably integrated using enhanced Piggybac system

value: doxycylin treatment_iLIN28AGFP inducible overexpression grown in 1 mM PD0325901, 3 mM CHIR99021 and 1,000 U/ml LIF


title: AML336 100 nM FHD-286 scRNA Seq

description: AML336_FHD scRNA Seq

tag: cell line


title: Quantseq_naïve_iLIN28AGFP_dox_3

description:
inducible LIN28A-GFP cell line has been used to compare untreated versus inducible LIN28A-GFP overexpression in naïve ESCs. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433786
6hrs_dox_3 MOD970A12_S28_L004_R1_001.fastq.gz

tag: strain


title: AB8591

description:
20191217_D5_PD1_T4_bys_1
MARSseq


title: AB8592

description:
20191217_D5_PD1_T5_1
MARSseq

value: OT1 CD8+_or_bystander CD8+


title: ChIP-seq_MLL4_WT_Th2_72h_GATA3_rep2

value: mixed C57BL/6 and 129

value: Th2 CD4+ T cells

value: Cell culture

value: MLL4 WT(DAPI-)


title: AB8590

description:
20191217_D5_PD1_T4_2
MARSseq


title: AML336 Control scRNA Seq

description: AML336_Ctrl scRNA Seq

value: Control


title: Quantseq_naïve_iLIN28AGFP_dox_2

description:
inducible LIN28A-GFP cell line has been used to compare untreated versus inducible LIN28A-GFP overexpression in naïve ESCs. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433785
6hrs_dox_2 MOD970A11_S27_L004_R1_001.fastq.gz

tag: developmental stage


title: ChIP-seq_MLL4_WT_Th2_72h_H3K4me3_rep2


title: AML323 100 nM FHD-286 scRNA Seq

description: AML323_FHD scRNA Seq

tag: treatment


title: AB8589

description:
20191217_D5_PD1_T4_1
MARSseq

value: tumor


title: ChIP-seq_MLL4_WT_Th2_72h_H3K4me3_rep1


title: AML323 Control scRNA Seq

description: AML323_Ctrl scRNA Seq


title: AB8588

description:
20191217_D5_PD1_T2_3
MARSseq


title: ChIP-seq_MLL4_WT_Th2_72h_H3K4me1_rep2


title: Quantseq_naïve_iLIN28AGFP_untreated_4

description:
inducible LIN28A-GFP cell line has been used to compare untreated versus inducible LIN28A-GFP overexpression in naïve ESCs. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433783
6hrs_untreated_4 MOD970A9_S53_L004_R1_001.fastq.gz

value: untreated_iLIN28AGFP inducible overexpression grown in 1 mM PD0325901, 3 mM CHIR99021 and 1,000 U/ml LIF


title: AML340 100 nM FHD-286 scATAC Seq

description: AML340_FHD scATAC Seq

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, detection of accessible chromatin peaks were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Patient-derived xenograft AML cells

growth_protocol: Patient-derived AML cells were cultured in 20% FBS containing RPMI media.

extract_protocol:
Frozen patient derived AML BM cells stored in liquid nitrogen were retrieved right before sample processing. To maximize the cellular viability recovery, samples were processed in batches according to thawing protocol. Briefly, cells were gently thawed in water bath at 37 °C for 2 minutes until partially thawed and immediately transferred to a 50 mL conical tube with 1ml of prewarmed media (RPMI1640 supplemented with 10% FBS) and centrifuged (300 g for 5 min). Cells were sequentially diluted 1:1 3 times with prewarmed RPMI containing 10% FBS. Cells were centrifuged at 300 x g for 5 minutes in a swinging bucket centrifuge. After finishing centrifugation, supernatant was disposed, the cell pellet was carefully re-suspended in 1 mL of 2% FBS/PBS, centrifuged at 300 x g for 5 minutes and resuspended in 900 uL of 2% FBS/PBS. To removed dead cells and debris, cells were passed through a 40 micron Flow-mi strainer and the cell concentration was determined with a Countess counting device. Nuclei were isolated following the demonstrated protocol for Nuclei isolation for single cell ATAC from 10X Genomics. Briefly, cells were lysed in chilled lysis buffer for 3 minutes, washed 3 times in chilled nuclei Wash Buffer, centrifuged for 5 minutes to remove the wash buffer and resuspened in Diluted Nuclei buffer (10X Genomics). The desired number of targeted nuclei (5000-10,000) in diluted Nuclei buffer were separated on the 10X Chromium Controller.
Single cell ATAC-Seq libraries were generated following the manufacturer's protocol provided by 10X Genomics for sc-ATAC seq analysis.

treatment_protocol: AML cells were treated with FHD-286 (100 nM) for 16 hours at 37°C and cryopreserved in freezing buffer composed of 90% FBS+ 10% DMSO until the time of nuclei isolation and Tn5 tagmentation.

value: Patient-derived xenograft AML cells

value: 100 nM FHD-286, 16 hours


title: AB8586

description:
20191217_D5_PD1_T2_1
MARSseq


title: AML340 Control scATAC Seq

description: AML340_Ctrl scATAC Seq


title: AML340 Control scRNA Seq

description: AML340_Ctrl scRNA Seq

value: Patient-derived AML cells


title: ChIP-seq_MLL4_WT_Th2_72h_GATA3_rep1


title: Quantseq_naïve_iLIN28AGFP_untreated_2

description:
inducible LIN28A-GFP cell line has been used to compare untreated versus inducible LIN28A-GFP overexpression in naïve ESCs. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433781
6hrs_untreated_2 MOD970A7_S51_L004_R1_001.fastq.gz


title: ChIP-seq_MLL4_WT_Th2_72h_H3K4me1_rep1


title: Quantseq_naïve_iLIN28AGFP_untreated_3

description:
inducible LIN28A-GFP cell line has been used to compare untreated versus inducible LIN28A-GFP overexpression in naïve ESCs. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433782
6hrs_untreated_3 MOD970A8_S52_L004_R1_001.fastq.gz


title: AB8587

description:
20191217_D5_PD1_T2_2
MARSseq


title: AML336 100 nM FHD-286 scATAC Seq

description: AML336_FHD scATAC Seq

value: Bone marrow


title: Quantseq_naïve_iLIN28AGFP_untreated_1

description:
inducible LIN28A-GFP cell line has been used to compare untreated versus inducible LIN28A-GFP overexpression in naïve ESCs. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
6hrs_untreated_1 MOD970A6_S50_L004_R1_001.fastq.gz


title: ChIP-seq_MLL4_WT_Th2_72h_H3K27ac_rep1


title: AB8584

description:
20191217_D5_PD1_T1_2
MARSseq


title: m6a-esc-mouse-2i-lif-wt-1

data_processing:
miCLIP reads were analysed on the iMaps server using the iCount software (https://github.com/tomazc/iCount).
Briefly, experimental barcodes were removed (Martin, 2011) and sequencing reads aligned with STAR (Dobin et al., 2013) to mouse genome build (GRCm38.p5 GENCODE version 15 annotation) allowing two mismatches. Unique Molecular Identifiers (UMIs), were used to distinguish and remove the PCR duplicates. To determine protein-RNA contact sites, the sequencing read preceding nucleotide was assigned as the cross-link event.
Significant contact sites were then identified, using the iCount function, based on false discovery rate (FDR) <0.05 comparing specific sites within a window of three nucleotides with randomised data (100 permutations) within co-transcribed regions. The significant cross-links signal was normalised by sequencing deep and million of tags (CPM).
Then replicates were merged and summary of cDNA counts within genes and genic regions were generated with iCount segments function, normalising the counts by the length of the corresponding region.
Genome_build: GRCm38.p5 GENCODE version 15 annotation
Supplementary_files_format_and_content: Individual cross-link bed files and grouped cross-link bedgraphs and peaks bedgraphs

growth_protocol: mouse ESCs were maintained in 1:1 Neurobasal (21103049) DMEM (11320033) medium containing N2 (17502048) and B27 (17504044) supplements, 1% Glutamax (35050), 1% nonessential amino acids (1140050), 0.1 mM 2-mercaptoethanol (31350-010) (all Thermo Fisher Scientific), 1 mM MEK inhibitor PD0325901 (1408, Axon Medchem), 3 mM GSK3 inhibitor CHIR99021 (4953/50 Tocris), and 1,000 U/ml LIF (ESGRO ESG1107, Merck), a condition named 2iLIF. Cells were passaged using Stempro-Accutase (A1110501, Thermo Fisher Scientific). Cells were grown on gelatin coated plates which were prepared by first incubating the wells 0.1% gelatin (EmbryoMax® ES-006-B, Merck) with 1% FBS (EmbryoMax® ES Cell Qualified FBS, ES-009-B, Merck) for 1 h at 37 °C followed by a rinse with PBS.

extract_protocol:
Antibodies were coupled to magnetic Protein G beads used to isolate Protein-RNA complexes, and RNA was ligated to a pre-adenylated infra-red labelled IRL3 adaptor (Zarnegar et al., 2016) with the following sequence:  /5rApp/AG ATC GGA AGA GCG GTT CAG AAA AAA AAA AAA /iAzideN/AA AAA AAA AAA A/3Bio/  The complexes were then size-separated by SDS-PAGE, blotted onto nitrocellulose and visualised by Odyssey scanning. For the multiplexed sample 1 replicated was run in parallel with the IRL3 to allow quality control of the RNP complex on the membrane and to help with cutting of the bands. RNA was released from membrane by proteinase K digestion and recovered by precipitation. cDNA was synthesized with Superscript IV Reverse Transcriptase (Life Technologies) and AMPure XP beads purification (Beckman- Coulter, USA), then circularised using Circligase II (Epicentre) followed by AMPure XP beads purification.
After PCR amplification, libraries were size-selected with Ampure beads (if necessary by gel-purification) and quality controlled for sequencing. Libraries were sequenced as single end 100bp reads on Illumina HiSeq 4000.
miCLIP

treatment_protocol: We used iCLIP to identify m6A methylation sites in mESCs.

value: mESC v6.5


title: AB8585

description:
20191217_D5_PD1_T1_3
MARSseq


title: ChIP-seq_MLL4_WT_Th2_24h_H3K4me3_rep1

data_processing:
Raw reads of RNA-seq data were mapped by STAR (v2.7.3a) (Dobin et al., 2013).   Raw reads of  ChIP-seq data were mapped by Bowtie2 (Langmead and Salzberg, 2012). Mapped unique paired-end reads with MAPQ 10 were used for the following analysis.  Raw reads of Hi-TrAC data were process by tracPre2.py in cLoops2 package (Cao et al., 2022).
Assembly: mm10
Supplementary files format and content: BigWig files for ChIP-seq were provided for visualization in genome browser.  TEXT files for RNA-seq gene expressions were provided. DIFF files for RNA-seq differential gene expression were provided. BEDPE files for Hi-TrAC or Hi-C data with high quality uniquely mapped paired-end tags (PETs) were provided.


title: Quantseq_naïve_iLIN28AGFP_dox_1

description:
inducible LIN28A-GFP cell line has been used to compare untreated versus inducible LIN28A-GFP overexpression in naïve ESCs. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433784
6hrs_dox_1 MOD970A10_S26_L004_R1_001.fastq.gz

value: mESC V6.5


title: AML336 Control scATAC Seq

description: AML336_Ctrl scATAC Seq


title: ChIP-seq_MLL4_WT_Th2_24h_H3K4me3_rep2


title: ChIP-seq_MLL4_WT_Th2_24h_H3K4me1_rep2


title: AB8583

description:
20191217_D5_PD1_T1_1
MARSseq


title: AB8582

description:
20191214_D2_Ctrl_T10_2
MARSseq


title: AML323 Control scATAC Seq

description: AML323_Ctrl scATAC Seq


title: m6a-esc-mouse-2i-lif-wt-2

value: naive embryonic stem cells


title: AML323 100 nM FHD-286 scATAC Seq

description: AML323_FHD scATAC Seq


title: ChIP-seq_MLL4_WT_Th2_72h_H3K27ac_rep2


title: m6a-esc-mouse-2i-lif-wt-3


title: ChIP-seq_MLL4_WT_Th2_24h_H3K4me1_rep1