title: lin28a-esc-wt-5

description: Naïve cells were grown in 1 mM PD0325901, 3 mM CHIR99021 and 1,000 U/ml LIF. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780

data_processing:
iCLIP 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,  grouped cross-link bed files and peaks bedgraphs

growth_protocol: mouse ESC lines 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.   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.

extract_protocol:
Cells were UV crosslinked on ice and then lysed in RIPA buffer. 0.4 Units of RNaseI and 4 Units Turbo DNase were added per 1 ml of cell lysate at 1mg/ml protein concentration for RNA fragmentation. Negative controls (no-UV) were prepared. 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.
iCLIP

treatment_protocol: We used iCLIP to identify a repertoir of RBP binding sites in mESCs.

tag: group

value: Endogenous


title: DF16835, Control, input

status: Public on Mar 01 2024

type: SRA

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

country: USA

institute: MD Anderson Cancer Center

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
bigWig files were generated using the bamCoverage. broadPeak files were generated using MACS v2 with default settings.
Assembly: GRCh38
Supplementary files format and content: broadPeak/narrowPeak

molecule: genomic DNA

organism: Homo sapiens

source_name: Patient-derived AML cells

growth_protocol: Human AML MOLM13  and patient derived AML cells were cultured in 20% FBS containing RPMI-1640 media.

extract_protocol:
Chromatin immunoprecipitation followed by Tn5 mediated tagmentation of de-crosslinked fragments.
Libraries were constructed following standard Illumina protocols for paired end indexing. DNA fragments were PCR amplified for 12 cycles. SPRI beads were used to double-size select fragments in the range of 250 bp.

treatment_protocol: 1 x 10^7 Human AML MOLM13 cells or 20 x 10^7 patient-derived AML cells were treated for 16 hours with DMSO or 100 nM of FHD-286. Cells were crosslinked with 1% formaldehyde for 10 minutes, then quenched with 2.5 M Glycine for 5 minutes. Cells were washed with 1X PBS, harvested by centrifugation at 2000 rpm for 5 minutes and snap frozen with liquid nitrogen. Ultra-sonication was used to shear the chromatin for chromatin immunoprecipitation analysis.

tag: tissue

value: Patient-derived AML cells

tag: cell line

tag: cell type

value: Acute myeloid leukemia

tag: genotype

tag: antibody

tag: treatment

value: Control


title: DF16835, 100 nM FHD-286, input


title: AB8580

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
20191214_D2_Ctrl_T9_3
MARSseq

library_source: transcriptomic single cell

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

molecule: polyA RNA

organism: Mus musculus

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: lin28a-esc-wt-4

city: London

first: Jernej

last: Ule

address: 10-12 Russell sq

department: Neuromuscular Diseases

country: United Kingdom

institute: UCL Institute of Neurology

library_source: transcriptomic

molecule: total RNA

source_name: ESC

tag: strain

value: mESC V6.5

tag: developmental stage

value: naive embryonic stem cells

tag: tag


title: AB8581

description:
20191214_D2_Ctrl_T10_1
MARSseq


title: ChIP-seq_MLL4_WT_Th2_24h_H3K27ac_rep2

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

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

value: Th2 CD4+ T cells

value: Cell culture

value: MLL4 WT(DAPI-)


title: lin28a-esc-wt-3


title: AB8579

description:
20191214_D2_Ctrl_T9_2
MARSseq


title: ChIP-seq_MLL4_WT_Th2_24h_H3K27ac_rep1


title: DF16835, Control, H3K27Ac

value: H3K27Ac Active Motif RRID:AB_2793305


title: DF16835, 100 nM FHD-286, H3K27Ac


title: AB8578

description:
20191214_D2_Ctrl_T9_1
MARSseq


title: ChIP-seq_MLL4_WT_Th1_72h_H3K4me3_rep2

value: Th1 CD4+ T cells


title: ChIP-seq_MLL4_WT_Th1_72h_H3K4me3_rep1


title: AB8577

description:
20191214_D2_Ctrl_T8_2
MARSseq


title: DF16835, 100 nM FHD-286, BRM

value: BRM Cell Signaling Cat # 11966S RRID:AB_2797783


title: lin28a-nls-gfp-esc-naive2

value: mESC J1

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


title: ChIP-seq_MLL4_WT_Th1_72h_H3K4me1_rep2


title: AB8576

description:
20191214_D2_Ctrl_T8_1
MARSseq


title: MOLM13, 100 nM FHD-286, input


title: ChIP-seq_MLL4_WT_Th1_72h_H3K4me1_rep1


title: lin28a-nls-gfp-esc-naive1


title: lin28a-gfp-esc-naive7

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


title: MOLM13 Control, input

value: Patient-derived AML cells


title: AB8574

description:
20191214_D2_Ctrl_T6_1
MARSseq


title: lin28a-gfp-esc-naive6


title: ChIP-seq_MLL4_WT_Th1_72h_H3K27ac_rep2


title: MOLM13, 100 nM FHD-286, BRG1

value: Acute myeloid leukemia

value: BRG1 Abcam Cat# Ab110641 RRID:AB_10861578


title: ChIP-seq_MLL4_WT_Th1_72h_H3K27ac_rep1


title: lin28a-gfp-esc-naive5


title: MOLM13, Control, BRG1

value: Control


title: AB8572

description:
20191214_D2_PD1_T5_1
MARSseq

value: tumor

value: OT1 CD8+_or_bystander CD8+


title: lin28a-nls-gfp-esc-naive3

value: naive embryonic stem cells


title: lin28a-gfp-esc-naive4


title: ChIP-seq_MLL4_WT_Th1_24h_H3K4me3_rep2

value: mixed C57BL/6 and 129


title: MOLM13, 100 nM FHD-286, H3K27Ac


title: AB8571

description:
20191214_D2_PD1_T4_3
MARSseq


title: DF16835, Control, BRM


title: AB8570

description:
20191214_D2_PD1_T4_2
MARSseq


title: ChIP-seq_MLL4_WT_Th1_24h_H3K4me3_rep1


title: ChIP-seq_MLL4_WT_Th1_24h_H3K4me1_rep2


title: MOLM13, Control, H3K27Ac


title: AB8575

description:
20191214_D2_Ctrl_T6_2
MARSseq


title: lin28a-gfp-esc-naive2


title: MOLM13 Bulk RNA 100 nM FHD-286 3

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data FASTQ files were generated by standard illumina base calling pipeline. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, Reads were aligned to hg38 reference genome using STAR with default parameters
STAR was used to generate the "raw count" from an aligned bam againt transcript file
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each annotated gene for each sample

growth_protocol: AML MOLM13 cells were cultured in 20% FBS containing RPMI media.

extract_protocol:
Total RNA was isolated with a kit from Ambion, Inc. The RNA was DNAse I treated to eliminate genomic DNA, then the purified RNA was utilized to make libraries for next generation sequencing.
Bulk RNA Libraries were constructed following standard Illumina protocols for RNA sequencing in a sequencing and microarray core facility. Indexed cDNA libraries were minimally PCR amplified, pooled and sequenced.
Stranded mRNA-Seq

treatment_protocol: AML cells were treated with FHD-286 (100 nM) for 16 hours at 37°C and harvested into RNA lysis buffer. Lysed cells were frozen at -80°C until they were processed for total RNA.

value: cell line

value: MOLM13 100 nM FHD-286


title: ChIP-seq_MLL4_WT_Th1_24h_H3K4me1_rep1

value: Cell culture

value: MLL4 WT(DAPI-)


title: AB8573

description:
20191214_D2_PD1_T5_2
MARSseq


title: lin28a-gfp-esc-naive1


title: AB8569

description:
20191214_D2_PD1_T4_1
MARSseq


title: AB8568

description:
20191214_D2_PD1_T2_4
MARSseq


title: lin28a-gfp-esc-highrnase


title: ChIP-seq_MLL4_WT_Th1_24h_H3K27ac_rep2

value: Th1 CD4+ T cells


title: AB8567

description:
20191214_D2_PD1_T2_3
MARSseq


title: ChIP-seq_MLL4_WT_Th1_24h_H3K27ac_rep1


title: lin28a-gfp-episc-primed6

description: Epiblast cells were grown for 12hours in grown , 20 ng ml–1 Activin A and 12 ng ml–1 bFGF. More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780

value: epiblast stem cells


title: ChIP-seq_MLL4_WT_Naive_H3K4me3_rep2

value: Naive CD4+ T cells

value: lymph nodes

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


title: MOLM13 Bulk RNA 100 nM FHD-286 1

value: Patient-derived AML cells


title: AB8566

description:
20191214_D2_PD1_T2_1
MARSseq


title: lin28a-gfp-esc-naive3

value: mESC J1

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


title: MOLM13 Bulk RNA Control 3

value: MOLM13 Control

value: Control


title: MOLM13 Bulk RNA Control 2


title: AB8565

description:
20191214_D2_PD1_T1_2
MARSseq

value: tumor

value: OT1 CD8+_or_bystander CD8+


title: lin28a-gfp-episc-primed5


title: lin28a-gfp-episc-primed4


title: ChIP-seq_MLL4_WT_Naive_H3K4me1_rep2

value: mixed C57BL/6 and 129


title: lin28a-gfp-episc-primed3


title: ChIP-seq_MLL4_WT_Naive_H3K4me1_rep1


title: MOLM13 Bulk RNA 100 nM FHD-286 2

value: cell line


title: ChIP-seq_MLL4_WT_Naive_H3K4me3_rep1


title: AB8564

description:
20191214_D2_PD1_T1_1
MARSseq


title: AB8305

description:
20191115_D8_Ctrl_T7
MARSseq

value: OT1 CD8+


title: MOLM13 100 nM FHD-286 2

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ATAC-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ATAC-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
bigWig files were generated using the bamCoverage. narrowPeak files were generated using MACS v2 with default settings.
Assembly: GRCh38
Supplementary files format and content: narrowPeak

growth_protocol: Cultured AML MOLM13 cells were cultured in 20% FBS containing RPMI media.

extract_protocol:
Bulk ATAC-Seq analysis was performed following the protocol of Buenrostro et al 2015. Tn5 transposase-tagmented genomic DNA was utilized to make libraries for next generation sequencing.
Bulk ATAC Sequencing Libraries were constructed following standard Illumina protocols for paired-end sample indexing with I7 and I5 sequencing indices.

treatment_protocol: AML cells were treated with FHD-286 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: 100 nM FHD-286, 16 hours


title: AB8304

description:
20191115_D8_Ctrl_T6
MARSseq


title: ChIP-seq_MLL4_WT_Naive_H3K27ac_rep2


title: MOLM13 100 nM FHD-286 1


title: lin28a-gfp-episc-primed2


title: ChIP-seq_MLL4_WT_Naive_H3K27ac_rep1


title: TumCrePos#2

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

description:
Tumor_Prox1CrePos_rep2
MHCIIΔProx-1

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads
Genome_build: GRCm38.96
Supplementary_files_format_and_content: Raw counts measurements

source_name: Tumor

extract_protocol:
Tumor were excised, digested and regulatory T cells were FACS-sorted based on RFP fluorescence. They were collected in RNAprotect Cell Reagent (Qiagen). RNA was isolated using RNeasy Plus Micro kit (Qiagen)
cDNA libraries were constructed by the Genomic platform of the University of Geneva as followed: the SMARTer™ Ultra Low RNA kit from Clontech was used for the reverse transcription and cDNA amplification according to manufacturer’s specifications, starting with 1 ng of total RNA. 200 pg of cDNA were used for library preparation using the Nextera XT kit from Illumina.Pools of 10 libraries were loaded for clustering on a Single-read Illumina Flow cell. Reads of 50 bases were generated using the TruSeq SBS chemistry on an Illumina HiSeq 4000 sequencer.

value: Tumor

tag: age

value: 10 weeks


title: ChIP-seq_MLL4_KO_Th2_72h_GATA3_rep2

value: Th2 CD4+ T cells

value: Cell culture

value: MLL4 KO(DAPI-)


title: MOLM13 Control 1


title: AB8301

description:
20191115_D8_PD1_T3
MARSseq


title: ChIP-seq_MLL4_KO_Th2_72h_GATA3_rep1


title: MOLM13 Bulk RNA Control 1


title: wild-type, rep 3

city: Kuala Lumpur

first: Eng Wee

last: Chua

address: Jalan Raja Muda Abdul Aziz

country: Malaysia

institute: The National University of Malaysia

data_processing:
To eliminate technical sequences, such as adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and bases with a quality score less than 20, the pass-filter data in the fastq format were processed using Cutadapt (RRID:SCR_011841) (version 1.9.1). The data were filtered with a Phred cutoff of 20, an error rate of 0.1, an adapter overlap of 1 bp, a minimum length of 75, and a proportion of N of 0.1 to obtain high-quality and clean data. The reference genome sequences and gene model annotation files for the relevant species were obtained from various genome databases, including UCSC, NCBI, and ENSEMBL. The reference genome sequence was indexed using Hisat2 (version 2.0.1) (Kim et al. 2015). Lastly, the clean data were aligned to the GRCh38 using the Hisat2 software (RRID:SCR_015530) (version 2.0.1). To begin estimating gene and isoform expression levels from the pair-end clean data, the transcripts in the fasta format were converted from a known gff annotation file and indexed properly. With the file as a reference gene file, HTSeq (RRID:SCR_005514) (version 0.6.1) (Anders et al. 2015) estimated gene and isoform expression levels from the paired-end clean data.
Assembly: GRCh38
Supplementary files format and content: txt file contains raw counts and FPKM for each sample

growth_protocol: HEK293 cells (RRID: CVCL_0045) were maintained in DMEM (Gibco, USA) containing 10% FBS (Capricorn Scientific GmbH, Ebsdorfergrund, Germany) and 1% penicillin–streptomycin (Nacalai tesque, Japan) in an incubator containing 5% CO2 at 37 °C.

extract_protocol:
The total RNA of each sample was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions, and the residual DNA was removed using the RapidOut DNA Removal Kit (Thermo Fisher Scientific, USA).
To prepare the library, 1 μg of total RNA was used. Poly(A) mRNA isolation was performed using Oligo(dT) beads, and mRNA fragmentation was carried out using divalent cations and high temperature. Random primers were used for priming, and first and second-strand cDNA synthesis was performed. The double-stranded cDNA was then purified, and both ends were repaired and dA-tailed in a single reaction, followed by T-A ligation to add adaptors to both ends. Size selection of adaptor-ligated DNA was performed using DNA Clean Beads. Each sample was amplified by PCR using P5 and P7 primers, and the PCR products were validated. The libraries with different indexes were then multiplexed, and the Illumina NovaSeq 6000 instrument was used for sequencing in a 2 ×150 paired-end configuration following the manufacturer's instructions.

treatment_protocol: rs16851030 was introduced into HEK293 cells through CRISPR homology-directed repair.

value: Human Embryonic Kidney

value: WT


title: TumCreNeg#3

description:
Tumor_Prox1CreNeg_rep3
MHCIIfl/fl

value: MHCIIfl/fl


title: wild-type, rep 2


title: ChIP-seq_MLL4_KO_Th2_72h_H3K4me3_rep2


title: AB8300

description:
20191115_D8_PD1_T2
MARSseq


title: TumCreNeg#2

description:
Tumor_Prox1CreNeg_rep2
MHCIIfl/fl


title: wild-type, rep 1


title: AB8299

description:
20191109_D2_Ctrl_T8_2
MARSseq


title: ChIP-seq_MLL4_KO_Th2_72h_H3K4me3_rep1


title: lin28a-gfp-episc-primed1

value: mESC J1

value: epiblast stem cells

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


title: MOLM13 Control 2

value: Patient-derived AML cells

value: Control


title: rs16851030-mutant, rep 3


title: TumCreNeg#1

description:
Tumor_Prox1CreNeg_rep1
MHCIIfl/fl


title: AB8303

description:
20191115_D8_Ctrl_T5
MARSseq

value: tumor


title: ChIP-seq_MLL4_KO_Th2_72h_H3K4me1_rep2

value: mixed C57BL/6 and 129


title: AB8298

description:
20191109_D2_Ctrl_T8_1
MARSseq

value: OT1 CD8+_or_bystander CD8+


title: LNCrePos#2

description:
LN_Prox1CrePos_rep2
MHCIIΔProx-1

source_name: LN

value: LN


title: rs16851030-mutant, rep 2


title: AB8302

description:
20191115_D8_PD1_T4
MARSseq

value: OT1 CD8+


title: TumCrePos#1

description:
Tumor_Prox1CrePos_rep1
MHCIIΔProx-1

value: Tumor

value: 10 weeks


title: rs16851030-mutant, rep 1


title: AB8296

description:
20191109_D2_Ctrl_T6_1
MARSseq


title: LNCrePos#1

description:
LN_Prox1CrePos_rep1
MHCIIΔProx-1


title: ChIP-seq_MLL4_KO_Th2_72h_H3K4me1_rep1

value: Th2 CD4+ T cells

value: Cell culture


title: AB8297

description:
20191109_D2_Ctrl_T7_1
MARSseq


title: AB8295

description:
20191109_D2_Ctrl_T5_1
MARSseq


title: Omentum_melanoma

city: Aurora

first: Richard

last: Tobin

state: Colorado

institute: University of Colorado Anschutz Medical Campus

data_processing:
Cell ranger  v6.1.2 to map and extract counts
seurat v4.4.0, filtered, plotted clusters on umap and determined differential gene expression all in seurat
Assembly: GRCH38
Supplementary files format and content: Tumor_2_Fin.RDS is a final analyzed R seurat object
Supplementary files format and content: tumor_2_filtered_feature_bc_matrix.h5 is the output of cell ranger cell and counts matrix

source_name: Metastatic melanoma

extract_protocol:
Samples were prepared by manual and enzymatic (Liberase DL) digestion to generate a singel cell suspension and then myeloid cells purified by FACS as Live/CD3-/CD19-/CD56-/CD11b+ cells.
We used the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 to generate single cell libraries

value: Metastatic melanoma


title: ChIP-seq_MLL4_KO_Th2_72h_H3K27ac_rep1

value: MLL4 KO(DAPI-)


title: LNCreNeg#3

description:
LN_Prox1CreNeg_rep3
MHCIIfl/fl

value: MHCIIfl/fl


title: LNCreNeg#2

description:
LN_Prox1CreNeg_rep2
MHCIIfl/fl


title: ChIP-seq_MLL4_KO_Th2_72h_H3K27ac_rep2


title: AB8294

description:
20191109_D2_PD1_T4_1
MARSseq


title: Mixed lymphocyte reactions, G22, scTCR-seq

city: Rotterdam

first: Hector

last: Tejeda Mora

address: Doctor Molewaterplein 40

department: Developmental Biology

country: Netherlands

institute: Erasmus MC

data_processing:
The raw data were processed into FASTQ files.
Raw sequences were inspected for quality using FastQC
Reads containing sequence information were mapped to the GRCh38 human genome.
The generation of BAM files and filtered gene-barcode matrices was accomplished using Cell Ranger Software
Assembly: GRCh38 human genome
Supplementary files format and content: Comma separated values file containing the normalized data from the generated Seurat-Object, containing all integrated samples. Briefly, all cells from all samples were QC checked, normalized, integrated (to remove batch effects), scaled and clustered using Seurat.
Supplementary files format and content: Comma separated values file containing the high-level annotations of each high-confidence contigs from cell-associated barcodes, per sample.  These were generated via the CellRanger vdj pipeline.
Library strategy: scTCR-seq

source_name: blood

growth_protocol: Mixed lymphocyte reactions (MLRs) were performed to identify alloreactive T cells. In brief, frozen donor splenocytes and recipient PBMCs were thawed on the day of the experiment. Donor splenocytes were labeled with CellTrace™ Violet Cell Proliferation dye (VPD; Thermo Fisher Scientific, Waltham, MA, USA) and subsequently exposed to gamma irradiation (40 Gy). Recipient PBMCs were labeled with carboxyfluorescein succinimidyl ester (CFSE; Thermo Fisher Scientific). Subsequently, irradiated VPD-labeled donor cells and CFSE-labeled recipient cells were cocultured for 6 days.

extract_protocol:
After 6 days of coculture, cells were harvested and stained with 7-AAD (BD Biosciences, Franklin Lakes, NJ, USA) and CD3 (Biolegend, San Diego, CA, USA). Viable CD3+Violet-lowCFSE-low cells (=proliferated recipient T cells) were then sorted using a FACS Aria II cell sorter (BD Biosciences).
The Chromium Next GEM Single Cell 5’ Reagent Kit V2 and the Chromium Single Cell Human TCR amplification Kit (10X Genomics, Pleasanton, CA, USA) were used for preparation of single-cell RNA and V(D)J libraries.

value: blood

value: Lymphocytes


title: ChIP-seq_MLL4_KO_Th2_24h_H3K4me3_rep2


title: Mixed lymphocyte reactions, G10, scTCR-seq


title: AB8293

description:
20191109_D2_PD1_T3_2
MARSseq


title: LNCreNeg#1

description:
LN_Prox1CreNeg_rep1
MHCIIfl/fl


title: ChIP-seq_MLL4_KO_Th2_24h_H3K4me3_rep1


title: Thirty-hour old TgBAC(neurod1:EGFP)nl1 zebrafish embryos, scRNAseq

city: Portland

first: Alex

last: Nechiporuk

state: OR

address: 3181 SW Sam Jackson Park Road

institute: Oregon Health and Science Univ

description: 10x Genomics

data_processing:
using Cell Ranger (version 3.1.0; 10X Genomics, Pleasanton, CA. USA)
Assembly: ZebraFishGRCz11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: zebrafish embryo

extract_protocol:
Thirty-hour old TgBAC(neurod1:EGFP)nl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium-free Ringer’s solution (116 mM NaCl, 2.6 mM KCl, 5 mM HEPES pH 7.0), by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre-warmed protease solutions (0.25% trypsin, 1 mM EDTA, pH 8.0, PBS) and collagenase P/HBSS (100 mg/mL) was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution (6X, 30% calf serum, 6 mM CaCl2, PBS) was added and samples were centrifuged (350xg, 4° C for 5 minutes). Supernatant was removed and 1 mL of chilled suspension solution was added (1% FBS, 0.8 mM CaCl2, 50 U/mL penicillin, 0.05 mg/mL streptomycin, DMEM). Samples were centrifuged again (350g, 4° C for 5 minutes) and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer (50 μl PBS/ 2% BSA) in a siliconized 1.5mL tube.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: neuron

value: zebrafish embryo

value: mixed

value: 30 hours post-fertilization


title: Gene expression in KMS34 cells cultured with RK-552

type: RNA

city: Shimotsuke

first: Sae

last: Matsuoka

state: Tochigi

department: Center for Molecular Medicine

country: Japan

institute: Jichi  Medical  University

hyb_protocol: Labeled cRNAs were hybridized with SurePrint G3 Human Gene Expression 8x60K version 3.0 Microarray (Agilent-072363) in Agilent In Situ Hybridization buffer Kit Plus enclosed in Agilent SureHyb-enabled hybridization chambers.

scan_protocol: Arrays were scanned on an Agilent G2505C scanner.  Images were quantified using the Agilent Feature Extraction Software (version 12.0.3.1).

data_processing:
Agilent Feature Extraction Software (version 12.0.3.1) was used for background subtraction and LOWESS normalization.
LOWESS-normalized data of Cy3- and Cy5-signals.

source_name: KMS34 cells

label_protocol: RNA samples (50 ng) were primed with T7 primer at 65°C for 10 min and reversed transcribed at 40°C for 2 h in the presence of AffinityScript, followed by T7 transcription in the presence of  Cy3- or Cy5-CTP at 40°C for 2 h.

growth_protocol: We cultured KMS 34 cells in RPMI1640 medium supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was extracted after 24 hours using Trizol according to manufacturer's instructions.

treatment_protocol: KMS 34 cells were cultured with  5μM RK-552 or 0.1% dimethylsulfoxide (DMSO) for 24 hours.

tag: agent

value: Cultured with RK-552

tag: time

value: 24 hours in culture


title: AB8292

description:
20191109_D2_PD1_T3_1
MARSseq

value: tumor

value: OT1 CD8+_or_bystander CD8+


title: Mixed lymphocyte reactions, G9, scTCR-seq


title: Gene expression in KMS34 cells cultured with vehicle (DMSO) alone

value: Cultured with DMSO


title: AB8291

description:
20191109_D2_PD1_T2_2
MARSseq


title: ChIP-seq_MLL4_KO_Th2_24h_H3K4me1_rep1

value: mixed C57BL/6 and 129


title: Mixed lymphocyte reactions, G1, scTCR-seq


title: Mixed lymphocyte reactions, G22, scRNA-seq

data_processing:
The raw data were processed into FASTQ files.
Raw sequences were inspected for quality using FastQC
Reads containing sequence information were mapped to the GRCh38 human genome.
The generation of BAM files and filtered gene-barcode matrices was accomplished using Cell Ranger Software
Assembly: GRCh38 human genome
Supplementary files format and content: Comma separated values file containing the normalized data from the generated Seurat-Object, containing all integrated samples. Briefly, all cells from all samples were QC checked, normalized, integrated (to remove batch effects), scaled and clustered using Seurat.
Supplementary files format and content: Comma separated values file containing the high-level annotations of each high-confidence contigs from cell-associated barcodes, per sample.  These were generated via the CellRanger vdj pipeline.


title: AB8290

description:
20191109_D2_PD1_T2_1
MARSseq


title: ChIP-seq_MLL4_KO_Th2_24h_H3K27ac_rep2

value: Th2 CD4+ T cells


title: ChIP-seq_MLL4_KO_Th2_24h_H3K27ac_rep1

value: Cell culture


title: AB8289

description:
20191109_D2_PD1_T1_2
MARSseq


title: UACa11 grown in RPMI-1640, 3

city: Aberdeen

first: Centre for Genome-Enabled Biology and Medicine

last: on behalf of listed contributors

state: Aberdeenshire

address: 23 St Machar Drive

department: CGEBM

institute: University of Aberdeen

description:
Phenotype Displayed: Non-aggregating
12_S12

data_processing:
Quality of sequencing data and read was analysesd by FastQC (version 0.11.8), TrimGalore! (version 0.6.4) was used to remove low quality reads and adaptor content, with phred quality score threshold of 30.
Genome (Cand_auris_B11221_V1) and annotation file were prepeard for use with HISAT2. Reads were aligned to this reference by HISAT2 using stranded library preparation.
SAMtools was used to process the alignments and reads at gene locations counted by featureCounts (part of the sub read version 1.6.2 package) utilising the parameter to split multi-mapped reads as a fraction across all genes that they align to, with the parameter for stranded analysis.
edgeR (version 3.30.3) was used to detect which genes had a significant differential change in expression. All genes that had a CPM (count per million) value of more than one in three or more samples were kept for analysis, and all other genes were removed as low count genes
Assembly: Cand_auris_B11221_V1

organism: Candidozyma auris

extract_protocol:
Cells were homogenised in TRIazole (Invitrogen) by bead beating. RNA was isolated by addition of chloroform and isopropanol precipitation. Remaining DNA was removed by RNase-Free DNase kit (Qiagen) following  manufacturer's protocols. RNA was cleaned further by using the RNeasy Mini Kit (Qiagen) following  manufacturer's protocols.
External RNA Controls Consortium spike-in controls were added to samples before library preperation with Illumina TruSeq Stranded mRNA kit (Illumina Inc.) following the manufacturer's protocols.

treatment_protocol: Cells grown for 16 hours in specified medium to form aggregates or single cells

value: Yeast

value: WT


title: Mixed lymphocyte reactions, G10, scRNA-seq


title: UACa11 grown in RPMI-1640, 2

description:
Phenotype Displayed: Non-aggregating
11_S11


title: Mixed lymphocyte reactions, G9, scRNA-seq


title: Mixed lymphocyte reactions, G1, scRNA-seq


title: AB8288

description:
20191109_D2_PD1_T1_1
MARSseq


title: AB7780

description:
20190826_D14_Ctrl_T8_2
MARSseq

value: OT1 CD8+


title: ChIP-seq_MLL4_KO_Th1_72h_H3K4me3_rep2

value: Th1 CD4+ T cells

value: MLL4 KO(DAPI-)


title: UACa11 grown in RPMI-1640, 1

description:
Phenotype Displayed: Non-aggregating
10_S10


title: UACa11 grown in Sabouraud's Dextrose, 3

description:
Phenotype Displayed: Non-aggregating
9_S9

value: Sabouraud's Dextrose


title: ChIP-seq_MLL4_KO_Th1_72h_H3K4me3_rep1


title: HUVECs, siEPCR transfection, rep4

city: 上海/上海市/杨浦区

first: 青

last: 李

address: 长海路168号

country: China

institute: 中国人民解放军海军军医大学第一附属医院

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter and trimming low qulity base with Trimmomatic
paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
Htseq-count was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCm39
Supplementary files format and content: count, FPKM

source_name: HUVEC

growth_protocol: HUVECs were maintained DMEM media supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C˚

extract_protocol:
Total RNA was extracted by TRIzol and subjected to RNA-seq analysis. 1ug of total RNA was used for the construction of sequencing libraries.
Poly-A tailed mRNA molecules were captured using attached oligo-dT and subjected to library construction according to the manufacturer’s recommendations.

treatment_protocol: siRNA transfection  was made by using RNAiMAX reagent

value: HUVEC

value: endothelial cell

value: siEPCR

value: siRNA transfection


title: ChIP-seq_MLL4_KO_Th1_72h_H3K4me1_rep2


title: UACa11 grown in Sabouraud's Dextrose, 2

description:
Phenotype Displayed: Non-aggregating
8_S8


title: ChIP-seq_MLL4_KO_Th2_24h_H3K4me1_rep2


title: AB7779

description:
20190826_D14_Ctrl_T8_1
MARSseq


title: HUVECs, siEPCR transfection, rep3

institute: 中国人民解放军海军军医大学第一附属医院


title: AB7778

description:
20190826_D14_Ctrl_T7_2
MARSseq


title: ChIP-seq_MLL4_KO_Th1_72h_H3K27ac_rep2


title: HUVECs, siEPCR transfection, rep2

institute: 中国人民解放军海军军医大学第一附属医院


title: UACa20 grown in RPMI-1640, 3

description:
Phenotype Displayed: Non-aggregating
6_S6


title: HUVECs, siEPCR transfection, rep1

institute: 中国人民解放军海军军医大学第一附属医院


title: ChIP-seq_MLL4_KO_Th1_72h_H3K4me1_rep1


title: AB7777

description:
20190826_D14_Ctrl_T7_1
MARSseq


title: UACa11 grown in Sabouraud's Dextrose, 1

description:
Phenotype Displayed: Non-aggregating
7_S7


title: AB7776

description:
20190826_D14_Ctrl_T5_2
MARSseq


title: UACa20 grown in RPMI-1640, 2

description:
Phenotype Displayed: Non-aggregating
5_S5


title: HUVECs, siCtr transfection, rep4

institute: 中国人民解放军海军军医大学第一附属医院

value: siCtr


title: ChIP-seq_MLL4_KO_Th1_72h_H3K27ac_rep1


title: ChIP-seq_MLL4_KO_Th1_24h_H3K4me3_rep2


title: HUVECs, siCtr transfection, rep3

institute: 中国人民解放军海军军医大学第一附属医院


title: AB7774

description:
20190826_D14_PD1_T4_1
MARSseq

value: tumor


title: HUVECs, siCtr transfection, rep2

institute: 中国人民解放军海军军医大学第一附属医院


title: UACa20 grown in Sabouraud's Dextrose, 3

description:
Phenotype Displayed: Aggregation
3_S3


title: ChIP-seq_MLL4_KO_Th1_24h_H3K4me3_rep1


title: AB7773

description:
20190826_D14_PD1_T3_1
MARSseq


title: HUVECs, siCtr transfection, rep1

institute: 中国人民解放军海军军医大学第一附属医院


title: AB7771

description:
20190826_D14_PD1_T2_1
MARSseq


title: AB7772

description:
20190826_D14_PD1_T2_2
MARSseq


title: UACa20 grown in Sabouraud's Dextrose, 1

description:
Phenotype Displayed: Aggregation
1_S1


title: Treat-3

city: Shanghai

first: Jian

last: Wang

address: Pujian Load 160th, Pudong New Aera

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Trimmomatic software
Sequence reads were trimmed for adapter and low-quality reads.
Assembly: rn6
Supplementary files format and content: tabe-delimited text file includes raw counts for each sample

organism: Rattus norvegicus

source_name: Heart

extract_protocol:
RNA was harvested using Trjzol (Thermo Fisher). 5ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA=seq were prepared by NEBNext UltraTM RNA Library Prep Kit following the manufacturers' protocols.

value: Heart

value: Cardiac fibroblasts

value: Primary cell

value: FTO overexpression

value: Noway


title: MM1144, p52KD, RNAseq, biorep2

city: Singapore

first: Yinghui

last: Li

state: Singapore

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

data_processing:
counts across GENCODE v35 features by featureCounts
Assembly: hg38
Supplementary files format and content: tsv, counts generated by featureCounts

source_name: Haematopoietic and Lymphoid

growth_protocol: Cells were cultured in RPMI 1640 media with 2.05 mM L-Glutamine (SH30027.01; Hyclone).

extract_protocol:
phenol-chloroform extraction followed by DNAse treatment and rRNA depletion
NEBNext® UltraTM II Directional RNA Library Prep Kit

treatment_protocol: Cells were transduced with TLCV2-containing virus and selected with 0.5 µg/ml puromycin for 72H. Transduced cells were subjected to 1 µg/ml Doxycycline to induce Cas9 expression before GFP sorting.

value: Haematopoietic and Lymphoid

value: Plasma Cell Myeloma

tag: Sex

value: Female


title: AB7692

description:
20190823_D11_Ctrl_T8_1
MARSseq

value: OT1 CD8+


title: Treat-1


title: MM1144, control, RNAseq, biorep2

value: WT

value: control


title: ChIP-seq_MLL4_KO_Th1_24h_H3K27ac_rep1

value: mixed C57BL/6 and 129

value: Th1 CD4+ T cells

value: Cell culture

value: MLL4 KO(DAPI-)


title: ChIP-seq_MLL4_KO_Th1_24h_H3K27ac_rep2


title: AB7775

description:
20190826_D14_Ctrl_T5_1
MARSseq


title: AB7691

description:
20190823_D11_Ctrl_T7_1
MARSseq


title: ChIP-seq_MLL4_KO_Naive_H3K4me3_rep2

value: Naive CD4+ T cells

value: lymph nodes

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


title: UACa20 grown in RPMI-1640, 1

description:
Phenotype Displayed: Non-aggregating
4_S4

value: Yeast


title: MM1144, control, RNAseq, biorep1


title: Treat-2

value: Heart

value: Cardiac fibroblasts

value: Primary cell


title: C-3

value: Noway


title: ChIP-seq_MLL4_KO_Naive_H3K4me3_rep1


title: ChIP-seq_MLL4_KO_Th1_24h_H3K4me1_rep2


title: MM1144, p52KD, H3K27ac ChIP, biorep2

data_processing:
Reads aligned to hg38 using bwa mem and filtered for duplicates, poor quality and blacklisted regions
Coverage across 20 bp windows quantified by BAMscale
Peaks called by MACS2
Assembly: hg38
Supplementary files format and content: bigWig, fragment coverage across 20 bp windows
Supplementary files format and content: narrowPeak, MACS2 peak calls

extract_protocol:
Cells were fixed in 1% formaldehyde for 12 minutes, swelled in 0.5% SDS buffer then lysed in 0.5% SDS + 5% Triton buffer (2:1). Genomic DNA was sheared to 100-500bp by sonication.
ChIP libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).

value: Haematopoietic and Lymphoid

value: Plasma Cell Myeloma

tag: chip antibody

value: H3K27ac antibody (07-360; Merck)


title: AB7690

description:
20190823_D11_Ctrl_T6_3
MARSseq

tag: tissue

value: tumor

value: OT1 CD8+


title: UACa20 grown in Sabouraud's Dextrose, 2

description:
Phenotype Displayed: Aggregation
2_S2

tag: cell line

value: WT

value: Sabouraud's Dextrose


title: C-2

tag: cell type


title: MM1144, p52KD, H3K27ac ChIP, biorep1

tag: genotype

value: Female


title: AB7689

description:
20190823_D11_Ctrl_T6_2
MARSseq


title: ChIP-seq_MLL4_KO_Th1_24h_H3K4me1_rep1

value: mixed C57BL/6 and 129

value: Th1 CD4+ T cells

value: Cell culture

value: MLL4 KO(DAPI-)


title: AB7688

description:
20190823_D11_Ctrl_T6_1
MARSseq


title: ChIP-seq_MLL4_KO_Naive_H3K4me1_rep1

value: Naive CD4+ T cells

value: lymph nodes

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


title: MM1144, p52KD, RNAseq, biorep1


title: MM1144, control, H3K27ac ChIP, biorep2

value: control


title: ChIP-seq_MLL4_KO_Naive_H3K27ac_rep2


title: MM1144, control, H3K27ac ChIP, biorep1


title: DASCM/scNPC day14 biol rep3

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

description: scNPC_14day_gene counts.txt

data_processing:
Raw data of fastq format were firstly processed through fastq software.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built  using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Feature counts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based  on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 R package (1.20.0). The resulting P-values were adjusted using  the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <=0.05 found by  DESeq2 were assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the cluster Profiler R package,  in which gene length bias was corrected. GO terms with corrected P value less than 0.05 were considered significantly enriched by  differential expressed genes. GO analysis was performed on differentially expressed genes using cluster Profiler v4.2.2. Heat maps  of differentially expressed genes were generated using TBtools software.

source_name: spinal cord

extract_protocol:
Total RNA was extracted with the use of the Ultrapure RNA kit (#CW0567S, CWBIO) according to the manufacturer's instructions.
Total RNA was used as input material for the RNA sample preparations. The clustering of the index-coded samples was performed  on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.  After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: spinal cord

value: spinal cord neural precursor cells

value: neuronal differentiation


title: AB7686

description:
20190823_D11_PD1_T3_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


title: ChIP-seq_MLL4_KO_Naive_H3K27ac_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: AB7685

description:
20190823_D11_PD1_T3_1
MARSseq


title: DASCM/scNPC day14 biol rep2

description: scNPC_14day_gene counts.txt


title: DASCM/scNPC day14 biol rep1

description: scNPC_14day_gene counts.txt


title: MM1144, p52KD, ATAC-seq, biorep2

data_processing:
Coverage across 20 bp windows quantified by BAMscale
Peaks called by MACS2
Assembly: hg38
Supplementary files format and content: bigWig, fragment coverage across 20 bp windows
Supplementary files format and content: narrowPeak, MACS2 peak calls

extract_protocol:
The cells were resuspended cold ATAC-Resuspension Buffer containing 0.1% NP40, 0.1% Tween20, and 0.01% Digitonin and incubated on ice for 3 min. The cells were then washed in RBS containing 0.1% Tween-20 at 500 g at 4 °C before subjecting the nuclei to the transposase reaction for 30 min at 37 °C. Termination of the reaction and DNA purification was performed using Zymo DNA clean and Concentrator kit.
The purified DNA was amplified with NEBNext High-Fidelity 2x PCR Master Mix then purified and size selected twice with AMPure beads. Nextera Tn5 Transposase is employed for tagmentation.

value: Haematopoietic and Lymphoid

value: Plasma Cell Myeloma


title: MM1144, p52KD, ATAC-seq, biorep1


title: XEN cells, Flag-Esrrb-KR (lysine to arginine substitution), ChIP-seq

city: New York

first: XIANLE

last: SHI

state: NY

address: 168 street

institute: CUMC

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality.
Alignment was done by using Bowtie2
Reads that mapped to multiple locations in the genome were discarded
Annotation was done by using the script annotatePeaks.pl of HOMER.
Assembly: mm9
Supplementary files format and content: bigWig

source_name: Cell line

growth_protocol: mESCs were plated at a 10 cm dishes in XEN media. The XEN medium was prepared as follows: RPMI 1640 media (Gibco), 15% fetal bovine serum (HyClone), 2 mM L-glutamine (Invitrogen), 100 units/mL penicillin and 100 µg/mL streptomycin (Invitrogen), 0.1 mM β-mercaptoethanol (Sigma), 10 ng/ml Activin A (PeproTech) and 0.1 μM Retinoic acid (MCE).

extract_protocol:
Chromatin fragmentation by Mnase and immunoprecipitation were carried out following the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology) according to the manufacturer’s protocols.
Purified ChIP DNA was used for library construction following the Illumina ChIP–seq library generation protocol (NEB)

treatment_protocol: Under normal culture

value: Extraembryonic endoderm stem (XEN) cells from mouse embryonic stem cells

value: XEN

value: wildtype

tag: expressing

value: Flag-Esrrb-KR mutant

value: Flag (Sigma, F1804-50UG)

value: In vitro differentiation


title: AB7684

description:
20190823_D11_PD1_T2_2
MARSseq

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)

value: tumor

value: OT1 CD8+

tag: treatment


title: ChIP-seq_MLL4_KO_Naive_H3K4me1_rep2

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

value: Naive CD4+ T cells


title: XEN cells, Flag-Esrrb-KQ (lysine to glutamine substitution), ChIP-seq

value: Flag-Esrrb-KQ mutant


title: MM1144, control, ATAC-seq, biorep2

value: WT

value: Female

value: control


title: XEN cells, Flag-Esrrb-WT (wildtype), ChIP-seq

value: Flag-Esrrb-wildtype


title: AB7683

description:
20190823_D11_PD1_T2_1
MARSseq

tag: experiment id


title: DNSCM/scNPC,day14 biol rep3

description: scNPC_14day_gene counts.txt

value: spinal cord

value: spinal cord neural precursor cells

value: neuronal differentiation


title: DNSCM/scNPC,day14 biol rep1

description: scNPC_14day_gene counts.txt


title: MM1144, control, ATAC-seq, biorep1

value: Haematopoietic and Lymphoid

value: Plasma Cell Myeloma


title: DNSCM/scNPC,day14 biol rep2

description: scNPC_14day_gene counts.txt


title: Human Nasal Epithelial Cells from a 0.3835616 year old; with 24hr PIC treatment [NL-216_S214]

city: Washington,DC

first: Nino

last: Gustavo

state: Washington,DC,

address: Sheikh Zayed Campus,111 Michigan Avenue,

department: Center for Precision Medicine and Genomics Research

institute: Childrens National Hospital

data_processing:
BCL files generated from sequencer were converted using bcl2fastq (Illumina) to fastq files, quality-checked using fastqc
Adapter and quality trimming was performed using trimgalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Summary QC files for before and after quality trimming was performed using MultiQC.
Alignment to was performed using STAR, followed by count estimation using RSEM (version1.3.1).
For differential expression analysis, read counts were estimated using tximport, followed by normalization and differential expression analysis performed using  DESeq2 (version 1.38.3). Genes with adjusted p-value < 0.05 and log fold change >= |1|, is considered significant.
Assembly: hg38 reference
Supplementary files format and content: TPMCounts_TSLP

source_name: Human Nasal Epithelial

growth_protocol: We obtained AECs using 2.7 mm cytology brushes rotated in each nostril for nasal AECs or at the carina for bronchial AECs. Immediately after collection, AECs were detached from the brushes by scrapping and agitation within the transport medium and subsequent centrifugation at 500g for 5 min at 4 °C. Conditionally reprogrammed cell (CRC) methods were used to optimize initial proliferation and survival of neonatal/infant AEC cultures.

extract_protocol:
AECs were collected for RNA studies using TRIzol (Thermo Fisher), and RNA was subsequently extracted using phase separation.
RNA sequencing libraries were prepared using IIIumina Standard mRNA prep from Illumina using the manufacturer’s instructions.

treatment_protocol: AECs were plated on collagen coated 6 well dishes (pureCol) for approximately 24 hours before placement in airway epithelial growth media (Promocell supplement pack)and then exposed to a viral mimic (Poly I:C. 10 ng/μl) at different time points (1hr, 3hr, 5hr, 8hr and 24hr).

value: Human Nasal Epithelial

value: High TSLP

value: PIC


title: AB7682

description:
20190823_D11_PD1_T1_2
MARSseq

value: tumor

tag: days post_adoptive_transfer


title: C-1

value: Heart

value: Cardiac fibroblasts

value: Primary cell

value: Noway


title: AB7681

description:
20190823_D11_PD1_T1_1
MARSseq

value: OT1 CD8+

tag: mouse number


title: M1-BMDM-KD [D5_counts]

city: Boston

first: Jingshu

last: Chen

address: 77 Avenue Louis PasteurBoston

department: Medicine

institute: Harvard Medical School

data_processing:
All samples were processed using an RNA-seq pipeline implemented by Genewiz (South Plainfield, NJ).
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
BAM files were generated as a result
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: GRCm38
Supplementary files format and content: rawcounts_new.csv
Supplementary files format and content: normlaized_counts.csv

extract_protocol:
RNA was harvested using Trizol reagent.
RNAseq: RNA libraries were prepared for sequencing using standard Illumina protocols;

value: Bone Marrow

value: BMDM


title: DASCM/scNPC day7 biol rep3

description: scNPC_7day_gene counts.txt

value: WT


title: AB7687

city: Rehovot

first: Ido

last: Amit

description:
20190823_D11_Ctrl_T5_1
MARSseq


title: Human Nasal Epithelial Cells from a 0.3835616 year old; with 3hr PIC treatment [NL-213_S211]


title: AB7680

description:
20190820_D8_Ctrl_T8_2
MARSseq


title: M0-BMDM-KD [C4_counts]


title: DASCM/scNPC day7 biol rep2

description: scNPC_7day_gene counts.txt

value: spinal cord


title: M0-BMDM-KD [C2_counts]


title: AB7679

description:
20190820_D8_Ctrl_T8_1
MARSseq


title: Human Nasal Epithelial Cells from a 0.28493 year old; with 3hr PIC treatment [NL-183_S181]


title: DASCM/scNPC day7 biol rep1

description: scNPC_7day_gene counts.txt

value: spinal cord neural precursor cells


title: M1-BMDM-KD [D6_counts]


title: M0-BMDM-KD [C1_counts]


title: AB7677

description:
20190820_D8_Ctrl_T7_1
MARSseq


title: DNSCM/scNPC,day7 biol rep3

description: scNPC_7day_gene counts.txt

value: neuronal differentiation


title: Human Nasal Epithelial Cells from a 0.28493 year old; with no PIC treatment [NL-181_S179]

value: NT


title: M1-BMDM-NS [B4_counts]


title: DNSCM/scNPC,day7 biol rep1

description: scNPC_7day_gene counts.txt


title: M1-BMDM-NS [B2_counts]


title: DNSCM/scNPC,day7 biol rep2

description: scNPC_7day_gene counts.txt


title: Human Nasal Epithelial Cells from a 0.12055 year old; with 3hr PIC treatment [NL-153_S151]


title: AB7675

description:
20190820_D8_Ctrl_T5_1
MARSseq


title: AB7674

description:
20190820_D8_PD1_T4_2
MARSseq


title: Human Nasal Epithelial Cells from a 0.12055 year old; with no PIC treatment [NL-151_S149]


title: M0-BMDM-NS [A4_counts]


title: Human Nasal Epithelial Cells from a 0.12055 year old; with 24hr PIC treatment [NL-156_S154]


title: AB7676

description:
20190820_D8_Ctrl_T5_2
MARSseq


title: Stems 4

city: Turku

first: Laura

last: Laihonen

address: Tykistökatu 6 A 6th floor

country: Finland

institute: University of Turku

data_processing:
Data analysis were done with the CSC's Chipster v.4 platform (Kallio et al., 2011).
Reads were mapped to Arabidopsis genome TAIR10.42 with Bowtie2 (Langmead and Salzberg 2012).
The number of alignments mapped to each gene was counted using HTseq2 (Putri et al. 2022).
DESeq2 (Love et al., 2014) was used to identify differentially expressed (DE) genes
Assembly: Arabidopsis_thaliana.TAIR10.42

organism: Arabidopsis thaliana

source_name: Stem

extract_protocol:
RNA was extracted from 100 mg of each plant material using innuPREP Plant RNA kit (Analytik Jena, Germany) according to manufacturer’s protocol. Lysis Solution RL was used for young and mature rosettes, flowers and roots, while for stems and green siliques, lysis solution PL. DNase treatment was done with TURBO DNA-free Kit (Thermo Fisher Scientific, USA) and concentration was measured using DeNovix DS-11 series spectrophotometer (DeNovix Inc., United States).
RNA (500 ng) from each plant material was provided to the Finnish Functional Genomics Center (FFGC, University of Turku and Åbo Akademi and Biocenter Finland) for PolyA+ transcriptome sequencing (RUO). The RNA integrity was checked with Agilent Bioanalyzer 2100 and the library preparation was done with Illumina Stranded mRNA Preparation kit (Illumina, USA). The paired-end libraries were sequenced using the Illumina NovaSeq 6000 S1 v1.5 (Illumina, USA).

value: Stem

value: wild type

tag: cultivar


title: M1-BMDM-NS [B1_counts]


title: Human Nasal Epithelial Cells from a 0.28493 year old; with 24hr PIC treatment [NL-186_S184]

value: Human Nasal Epithelial

value: High TSLP


title: AB7673

institute: Weizmann Institute of Science

description:
20190820_D8_PD1_T4_1
MARSseq

value: tumor


title: Human Nasal Epithelial Cells from a 0.33973 year old; with 24hr PIC treatment [NL-210_S208]

value: PIC


title: Stems 3


title: M0-BMDM-NS [A2_counts]


title: AB7678

description:
20190820_D8_Ctrl_T7_2
MARSseq


title: Stems 2


title: AB7672

description:
20190820_D8_PD1_T3_2
MARSseq


title: Human Nasal Epithelial Cells from a 0.33973 year old; with no PIC treatment [NL-205_S203]


title: AB7671

description:
20190820_D8_PD1_T3_1
MARSseq


title: M0-BMDM-NS [A1_counts]


title: Human Nasal Epithelial Cells from a 0.33973 year old; with 3hr PIC treatment [NL-207_S205]


title: Flowers 4

source_name: Flower

value: Flower


title: Stems 1


title: 236 G0 Apcmin H3K27me3 CUT&RUN

city: Houston

first: Jiexi

state: TX

address: 1881 East Road

institute: The University of Texas MD Anderson Cancer Center

data_processing:
NextSeq RTA (version 2.4.11.0) was used for base calling
bcl2fastq (version 2.20.0) was used to convert the .bcl files into .fastq files
Fastq files were aligned to the mouse reference genome (mm9) using Bowtie (version 1.2.2)
SAMtools (version 1.9) was used to convert .sam file to .bam file
Deeptools (version 2.7.15) was used to generate .bigwig files
Peaks were called using MACS (version 1.4.2)
Assembly: mm9
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

extract_protocol:
200,000 nuclei were extracted from colonoids for each sample following CUTANA CUT&RUN Kit Version 3 protocol. CUT&RUN was performed following the directions in the provided protocol without any modifications.
CUT&RUN library preparation was performed using CUT&RUN library Prep Kit Version 1 following the directions in the provided protocol without any modifications.

value: mouse Apcmin colonoid

value: Histone H3 (tri methyl K27) antibody ab6002 (Abcam)


title: 236 G0 Apcmin EZH2 CUT&RUN

value: Ezh2 (D2C9) Rabbit mAb #5246 (Cell Signaling Technology)


title: AB7670

address: 234 Herzl st.

description:
20190820_D8_PD1_T2_2
MARSseq

source_name: tumor

value: OT1 CD8+


title: Flowers 3


title: Flowers 2


title: 75 G0 Apcmin EZH2 CUT&RUN


title: AB7669

description:
20190820_D8_PD1_T2_1
MARSseq


title: AB7656

description:
20190817_D5_Ctrl_T8_2
MARSseq


title: Human Nasal Epithelial Cells from a 0.14795 year old; with no PIC treatment [NL-193_S191]


title: Human Nasal Epithelial Cells from a 0.14795 year old; with 3hr PIC treatment [NL-195_S193]


title: Flowers 1


title: 75 G0 Apcmin H3K27me3 CUT&RUN


title: Roots 3

source_name: Root

value: Root


title: Human Nasal Epithelial Cells from a 1.8 year old; with 24hr PIC treatment [NL-84_S82]


title: AB7654

description:
20190817_D5_Ctrl_T7_2
MARSseq


title: brain, wild type, ICH+PTE3

city: Shijiazhuang

first: gen

middle: shen

last: zhang

state: Hebei

address: Hepingxi Road

institute: HEBEIMEDICAL UNIVERSITY

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the Solanum lycopersicum（https://solgenomics.net/ftp/genomes/Solanum_lycopersicum/assembly/build_3.00/S_lycopersicum_chromosomes.3.00.fa） reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: build_3.00
Supplementary files format and content: Excel file includes FPKM values for each Sample

source_name: Brain

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

tag: strain

value: Brain

value: 72 hours after ICH+PTE treatment


title: Roots 2


title: Human Nasal Epithelial Cells from a 1.8 year old; with no PIC treatment [NL-79_S77]


title: AB7653

description:
20190817_D5_Ctrl_T7_1
MARSseq


title: brain, wild type, ICH+PTE2


title: brain, wild type, ICH+PTE1


title: Human Nasal Epithelial Cells from a 0.14795 year old; with 24hr PIC treatment [NL-198_S196]


title: AB7652

description:
20190817_D5_Ctrl_T6_2
MARSseq


title: Roots 1


title: brain, wild type, ICH3

value: 72 hours after ICH


title: Mature rosette 4

source_name: Mature rosette

value: Mature rosette


title: Human Nasal Epithelial Cells from a 0.9 year old; with 24hr PIC treatment [NL-6_S6]


title: Human Nasal Epithelial Cells from a 0.9 year old; with 3hr PIC treatment [NL-3_S3]


title: brain, wild type, ICH2


title: AB7651

description:
20190817_D5_Ctrl_T6_1
MARSseq


title: Mature rosette 3


title: AB7655

description:
20190817_D5_Ctrl_T8_1
MARSseq


title: brain, wild type, ICH1


title: Human Nasal Epithelial Cells from a 0.9 year old; with no PIC treatment [NL-1_S1]

value: NT


title: Mature rosette 2


title: Human Nasal Epithelial Cells from a 1.8 year old; with 3hr PIC treatment [NL-81_S79]


title: AB7649

description:
20190817_D5_PD1_T3_2
MARSseq


title: Human Nasal Epithelial Cells from a 1.1 year old; with 24hr PIC treatment [NL-78_S76]


title: Mature rosette 1


title: Human Nasal Epithelial Cells from a 1.1 year old; with 3hr PIC treatment [NL-75_S73]


title: brain, wild type, sham2

value: 72 hours after control treament


title: AB7648

description:
20190817_D5_PD1_T3_1
MARSseq


title: Young rosette 4

source_name: Young rosette

value: Young rosette

value: wild type


title: Young rosette 3


title: AB7647

description:
20190817_D5_PD1_T2_2
MARSseq


title: brain, wild type, sham1


title: Human Nasal Epithelial Cells from a 0.12877 year old; with 24hr PIC treatment [NL-192_S190]

value: Human Nasal Epithelial

value: Low TSLP


title: AB7646

description:
20190817_D5_PD1_T2_1
MARSseq

value: tumor


title: Human Nasal Epithelial Cells from a 1.1 year old; with no PIC treatment [NL-73_S71]

value: High TSLP


title: Young rosette 2


title: Young rosette 1


title: Hippocampus, Trap1Q641*, female, sample3

city: Warsaw

first: Anna

middle: Maria

last: Hojka-Osińska

address: 4 Ks. Trojdena Street

country: Poland

institute: International Institute of Molecular and Cell Biology

data_processing:
The Illumina sequencing reads were quality filtered using Cutadapt v1.18 to remove Illumina adapter sequences, trim low-quality fragments (minimum Q score = 20), and remove reads that were shorter than 30 nt after trimming
Reads were mapped to mouse genome (GRCm38) using STAR v2.7.5c. For downstream analysis, only uniquely mapped reads were used.
The feature assignemets of reads was performed with HTSeq v0.12.4, choosig genes as representative features.
Read normalizatios and analysis was performed with DESeq2
Assembly: mm10
Supplementary files format and content: comma separated file contain htseq generated gene counts
Supplementary files format and content: comma separated file contain normalized with DESeq2 gene counts

source_name: hippocampus

extract_protocol:
RNA was extracted from the mouse hipocampii using TRIzol (Thermo Fisher Scientific), DNA contamination was removed by 2 U of TURBO DNase (AM2238, Ambion) in the supplied buffer in 37°C for 30 min. Next, RNA was re-isolated with phenol/chloroform, precipitated with ethanol, and resuspended in 50 μl of RNase free water.
Total RNA libraries were prepared using TruSeq Stranded Total RNA Library Prep (Illumina, nr kat. 20020596) and adapters from Illumina TruSeq RNA UD Indexes (96 Indexes, 96 Samples) (Illumina, nr kat. 20022371), following manufacturer's protocols.

value: hippocampus

value: female


title: Hippocampus, Trap1Q641*, female, sample4


title: Human Nasal Epithelial Cells from a 0.12877 year old; with 3hr PIC treatment [NL-189_S187]

value: PIC


title: AB7645

description:
20190817_D5_PD1_T1_2
MARSseq

value: OT1 CD8+


title: AB7644

description:
20190817_D5_PD1_T1_1
MARSseq


title: Hippocampus, Trap1Q641*, female, sample2


title: P40.L109.day23

city: Stanford

first: Hong

last: Zheng

state: California

address: 240 Pasteur Dr

institute: Stanford university

description: patient40, day23

data_processing:
CellRanger v.3.1.0 (10xGenomics) was used to demultiplex raw sequencing data and quantify transcript levels against the 10x Genomics GRCh38 reference v.3.0.0.
Assembly: GRCh38
Supplementary files format and content: 1) matrix.mtx.gz: matrix containg read count; 2) barcodes.tsv.gz: cell names; 3) features.tsv.gz: gene/features names

source_name: blood

extract_protocol:
Live frozen PBMCs were thawed and washed twice with RPMI supplemented with 10% FBS and 20 μg ml−1 DNase I (Sigma Aldrich). Total PBMCs (1 million cells) were stained with a cocktail of TotalSeq-A antibodies (BioLegend) in PBS supplemented with 5% FBS, 2 mM EDTA and 5 mg ml−1 human IgG, washed twice with PBS supplemented with 5% FBS, and 2 mM EDTA, and resuspended in PBS supplemented with 1% BSA (Miltenyi Biotec), and 0.5 U μl−1 RNase Inhibitor (Sigma Aldrich). Approximately 9,000 cells were targeted for each experiment. Cells were mixed with the reverse transcription mix and subjected to partitioning along with the Chromium gel-beads using the 10X Chromium system to generate the gel-bead in emulsions (GEMs) using the 3′V3 chemistry (10X Genomics). The reverse transcription reaction was conducted in the C1000 touch PCR instrument (BioRad).
Barcoded cDNA was extracted from the GEMs by post-GEM reverse transcription cleanup and amplified for 12 cycles. Before amplification, the cDNA amplification mix was spiked in with ADT additive primer (0.2 μM stock) to amplify the antibody barcodes. Amplified cDNA was subjected to 0.6× SPRI beads cleanup (Beckman, B23318). Amplified antibody barcodes were recovered from the supernatant and were processed to generate TotalSeq-A libraries as instructed by the manufacturer (BioLegend, TotalSeq-A antibodies with 10x Single Cell 3′ Reagent Kit v.3 3.1 protocol). The rest of the amplified cDNA was subjected to enzymatic fragmentation, end repair, A tailing, adaptor ligation and 10X-specific sample indexing as per manufacturer’s protocol. Libraries were quantified using Bioanalyzer (Agilent) analysis. 10x Genomics scRNA-seq and TotalSeq-A libraries were pooled and sequenced on an Illumina HiSeq 4000 using the recommended sequencing read lengths of 28 bp (read 1), 8 bp (i7IndexRead) and 91 bp (read 2).

value: blood

tag: patient

value: F

tag: condition

value: SLE

tag: responder

value: NR

tag: time point


title: Human Nasal Epithelial Cells from a 0.12877 year old; with no PIC treatment [NL-187_S185]


title: brain, wild type, sham3

value: Brain


title: AB7650

description:
20190817_D5_PD1_T4_1
MARSseq


title: Hippocampus, Trap1Q641*, female, sample1

tag: Sex


title: Human Nasal Epithelial Cells from a 0.09041 year old; with 3hr PIC treatment [NL-177_S175]


title: Hippocampus, Trap1Q641*, male, sample3

value: male


title: AB7642

description:
20190814_D2_Ctrl_T7_2
MARSseq


title: AB7643

description:
20190814_D2_Ctrl_T8_1
MARSseq


title: Human Nasal Epithelial Cells from a 0.09041 year old; with 24hr PIC treatment [NL-180_S178]


title: P40.L108.day1-2

description: patient40, day1or2


title: AB7641

description:
20190814_D2_Ctrl_T7_1
MARSseq


title: Hippocampus, Trap1Q641*, male, sample2


title: P40.L107.day0

description: patient40, day0


title: Human Nasal Epithelial Cells from a 0.0520548 year old; with 24hr PIC treatment [NL-168_S166]


title: P38.L106.day23

description: patient38, day23


title: P38.L105.day1-2

description: patient38, day1or2


title: Human Nasal Epithelial Cells from a 0.0520548 year old; with 3hr PIC treatment [NL-165_S163]


title: Hippocampus, Trap1Q641*, male, sample1


title: AB7639

description:
20190814_D2_Ctrl_T5_1
MARSseq


title: Hippocampus, Trap1WT/Q641*, male, sample3


title: P38.L104.day0

description: patient38, day0


title: AB7638

description:
20190814_D2_PD1_T4_2
MARSseq


title: Human Nasal Epithelial Cells from a 0.0520548 year old; with no PIC treatment [NL-163_S161]

value: NT


title: P17.L103.day23

description: patient17, day23


title: Human Nasal Epithelial Cells from a 0.1260274 year old; with 24hr PIC treatment [NL-162_S160]


title: AB7637

description:
20190814_D2_PD1_T4_1
MARSseq


title: Human Nasal Epithelial Cells from a 0.09041 year old; with no PIC treatment [NL-175_S173]


title: Hippocampus, Trap1WT/Q641*, male, sample1


title: Human Nasal Epithelial Cells from a 0.1260274 year old; with 3hr PIC treatment [NL-159_S157]


title: P17.L102.day1-2

description: patient17, day1or2


title: Human Nasal Epithelial Cells from a 0.1260274 year old; with no PIC treatment [NL-157_S155]


title: AB7636

description:
20190814_D2_PD1_T3_2
MARSseq


title: P17.L101.day0

description: patient17, day0


title: Hippocampus, Trap1WT/Q641*, female, sample2


title: Normal human adult 46, XY primary dermal fibroblast (HDFa), with 8TF [5-c]

description:
Normal human adult 46, XY primary dermal fibroblast (HDFa), with 8TF
5-c

data_processing:
BCL files generated from sequencer were converted using bcl2fastq (Illumina) to fastq files, quality-checked using fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Adapter and quality trimming was performed using trimgalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Summary QC files for before and after quality trimming was performed using MultiQC.
Alignment to was performed using STAR, followed by count estimation using RSEM.
For differential expression analysis, read counts were estimated using tximport, followed by normalization and differential expression analysis performed using Deseq2.
Assembly: hg38 reference
Supplementary files format and content: rawCounts_Sertoli.csv
Supplementary files format and content: TPMCounts_Sertoli.csv

source_name: Fibroblasts

growth_protocol: Normal human adult 46, XY primary dermal fibroblast (HDFa) (Cat. ATCC PCS-201-012) was purchased from American Type Culture Collection repository (ATCC). The following cell lines were purchased from Coriell cell repository:  GM03651: Skin fibroblasts derived from a 25-year-old 46, XX healthy female; GM00083: Gonadal fibroblasts derived from a 1-year-old 46, XY female; SRXY1; GM06938: fibroblasts derived from a 3-week-old male with a WT1 deletion; GM21894: skin fibroblasts derived from a 46,XY patient with campomelic dysplasia; and GM03368: gonadal fibroblasts derived from a 17-year-old 46, XY woman). HDFa was cultured in Medium 106 (Thermo Cat.M106-500), completed with low serum growth supplement (LSGS) (Thermo Cat. S00310), and 1X penicillin-streptomycin antibiotic (P/S) (Thermo Cat. 15140122). GM03651, GM00083, GM06938 and GM12896 were cultured in Eagle’s minimum essential medium (Thermo Cat. M0325) completed with 15% non-inactivated FBS (Thermo Cat. 16000044) and 1X P/S (Thermo Cat. 15140122).  GM21894 was cultured in DMEM (Genesee Cat. 25-500) completed with 10% non-inactivated FBS and 1X P/S. All these cells were grown as adherent monolayer cultures in tissue culture-treated T25 flasks (Genesee Cat. 25-207), harvested by trypsinization upon 80-90% confluence, quenched by trypsin neutralization solution (Thermo Cat. R002100), spun down at 150g for 4 min at RT and sub-cultured in 5ml of suitable complete media. The media was replaced every alternate day in all these cultures until they reached confluency.

extract_protocol:
Cells were lysed and total RNA was isolated using RNeasy micro kit (Qiagen Cat. 74004) following the manufacturer’s instructions.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit from Illumina using the manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: For the trans-differentiation culture, fibroblasts were seeded at 2.25x104 into each well of 6 well dishes (Millipore Sigma Cat. CLS3516) in 2ml complete M106 on Day 0 and grown overnight. On Day 1, cells were counted from an extra well to determine the number of lentiviral particles required to transduce the cells at a multiplicity of infection (MOI) of five. Three transduction sets were designed: A. GFP; B. 8 TFs:  FGF2, GATA6, GATA4, MXI1, JUNB, NFYB, NR5A1 and EBF1; C. 6TFs: FGF2, GATA6, GATA4, MXI1, JUNB, and NFYB. The old media in wells was replaced with transduction media consisting of 2 mL complete M106 mixed with an appropriate amount of respective lentivirus cocktail and 2 μL of 100 mg/mL Polybrene (Millipore Sigma Cat. TR-1003-G). The cells were left to transduce for 12 hours/overnight. On Day 2, transduction media was replaced with fresh complete M106 and cultured in it for 4 days with alternate days media change. On day 5, M106 was replaced with 2 mL of trans-differentiation media consisting of basal Sertoli Cell Media (SerCM) completed with 5% FBS, 1X Sertoli cell growth supplement (SerCGS) and 1X P/S  (ScienCell Cat. 4521). The culture was maintained in this media for another 24 days until day 30 with alternate days media change.

value: Fibroblasts

value: HDFa


title: AB7635

description:
20190814_D2_PD1_T3_1
MARSseq


title: AB7640

description:
20190814_D2_Ctrl_T6_1
MARSseq


title: Human Nasal Epithelial Cells from a 0.06301 year old; with 24hr PIC treatment [NL-150_S148]

value: Human Nasal Epithelial


title: AB7634

description:
20190814_D2_PD1_T2_1
MARSseq


title: Hippocampus, Trap1WT, female, sample3


title: Hippocampus, Trap1WT/Q641*, male, sample2


title: Normal human adult 46, XY primary dermal fibroblast (HDFa), with 8TF [5-a]

description:
Normal human adult 46, XY primary dermal fibroblast (HDFa), with 8TF
5-a


title: Human Nasal Epithelial Cells from a 0.06301 year old; with 3hr PIC treatment [NL-147_S145]

value: Low TSLP


title: Hippocampus, Trap1WT/Q641*, female, sample1


title: AB7633

description:
20190814_D2_PD1_T1_1
MARSseq

value: tumor


title: Human Nasal Epithelial Cells from a 0.06301 year old; with no PIC treatment [NL-145_S143]


title: Human Nasal Epithelial Cells from a 1.1 year old; with 24hr PIC treatment [NL-90_S88]


title: AB7412

description:
20190727_M4_spleen_ID3_WT_CD8_1nm_2
MARSseq

source_name: spleen

value: spleen

value: endogenous CD8+


title: AB7411

description:
20190727_M4_spleen_ID3_WT_CD8_1nm_1
MARSseq


title: Hippocampus, Trap1WT, female, sample1

value: hippocampus

value: female


title: Normal human adult 46, XY primary dermal fibroblast (HDFa), with 6TF [AP08]

description:
Normal human adult 46, XY primary dermal fibroblast (HDFa), with 6TF
AP08


title: Human Nasal Epithelial Cells from a 1.1 year old; with 3hr PIC treatment [NL-87_S85]

value: PIC


title: Normal human adult 46, XY primary dermal fibroblast (HDFa), with 6TF [AP09]

description:
Normal human adult 46, XY primary dermal fibroblast (HDFa), with 6TF
AP09


title: Hippocampus, Trap1WT/Q641*, female, sample3


title: Normal human adult 46, XY primary dermal fibroblast (HDFa), with 6TF [AP07]

description:
Normal human adult 46, XY primary dermal fibroblast (HDFa), with 6TF
AP07


title: AB7410

description:
20190727_M5_spleen_ID3_KO_CD8_1
MARSseq


title: Hippocampus, Trap1WT, male, sample3


title: AB7409

description:
20190727_M5_tumor_ID3_KO_CD8_3
MARSseq


title: Normal human adult 46, XY primary dermal fibroblast (HDFa), with 8TF [5-b]

description:
Normal human adult 46, XY primary dermal fibroblast (HDFa), with 8TF
5-b


title: Human Nasal Epithelial Cells from a 1.1 year old; with no PIC treatment [NL-85_S83]


title: Normal human adult 46, XY primary dermal fibroblast (HDFa), with GFPC [AP03]

description:
Normal human adult 46, XY primary dermal fibroblast (HDFa), with GFPC
AP03

value: GFPC


title: Hippocampus, Trap1WT, male, sample2


title: AB7408

description:
20190727_M5_tumor_ID3_KO_CD8_2
MARSseq


title: Human Nasal Epithelial Cells from a 0.9 year old; with 24hr PIC treatment [NL-30_S30]


title: Normal human adult 46, XY primary dermal fibroblast (HDFa), with GFPC [AP02]

description:
Normal human adult 46, XY primary dermal fibroblast (HDFa), with GFPC
AP02


title: Hippocampus, Trap1WT, female, sample2


title: Human Nasal Epithelial Cells from a 0.9 year old; with 3hr PIC treatment [NL-27_S27]


title: AB7407

description:
20190727_M5_tumor_ID3_KO_CD8_1
MARSseq


title: cKO_2

city: Hangzhou

first: Jun-Kai

last: Ma

address: Yuhangtang road No.866

institute: Zhejiang University

data_processing:
Demultiplexing and adapter trimming were performed with bcl2fastq v2.19. No quality trimming was performed for deposited fastq files.
Sequenced reads were quality trimmed using Cutadapt v1.16.5.
Reads were mapped to mm10 whole genome using HISAT2 v2.1 with default settings for paired-end reverse strand specific libraries.
featureCounts v1.6.4 and DESeq2 v2.11.40.6 were applied for differentially expression analysis.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample.

source_name: Bone marrow

extract_protocol:
Central macrophages were sorted from TFPIf/f mice or TFPIf/f;EpoR mice.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Bone marrow

value: Central macrophages

value: TFPI cKO


title: Human Nasal Epithelial Cells from a 0.9 year old; with no PIC treatment [NL-25_S25]


title: Normal human adult 46, XY primary dermal fibroblast (HDFa), with GFPC [AP01]

description:
Normal human adult 46, XY primary dermal fibroblast (HDFa), with GFPC
AP01


title: cKO_3


title: skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with GFPC [AP57]

description:
skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with GFPC
AP57


title: Human Nasal Epithelial Cells from a 1 year old; with 24hr PIC treatment [NL-18_S18]


title: AB7405

description:
20190727_M4_tumor_ID3_WT_CD8_2
MARSseq


title: cKO_1


title: skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with GFPC [AP56]

description:
skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with GFPC
AP56


title: Human Nasal Epithelial Cells from a 1 year old; with 3hr PIC treatment [NL-15_S15]


title: AB7404

description:
20190727_M4_tumor_ID3_WT_CD8_1
MARSseq


title: Human Nasal Epithelial Cells from a 1 year old; with no PIC treatment [NL-13_S13]

value: NT (No Treatment)


title: skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with GFPC [AP55]

description:
skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with GFPC
AP55


title: WT_2

value: WT


title: AB7034

description:
20190620_D10_Tumor4_endoPD1+_3
MARSseq


title: AB7033

description:
20190620_D10_Tumor4_endoPD1+_2
MARSseq


title: Hippocampus, Trap1WT, male, sample1

value: male


title: skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with 8TF [AP59]

description:
skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with 8TF
AP59

value: Fibroblasts