title: scBSseq_LK_DNA_2_A3

data_processing:
BS-seq libraries were aligned to the bisulfite-converted hg38 human genome using Bismark (v.0.24.0) in a paired-end, non-directional mode. Then the unmapped reads were aligned again in a single-end, non-directional mode. We used the coverage2cytosine script from Bismark with the –nom-seq option to generate CpG report files containing only A–C–G and T–C–G positions and GpC report files containing only G–C–A, G–C–C, and G–C–T positions. The DNA methylation rate (CpG rate) at a given CpG site was determined by the ratio between the number of methylated CpG reads over unmethylated CpG reads. The accessibility rate or GpC rate was computed similarly.
Assembly: mm10
Supplementary files format and content: Methylation calling tsv.gz files which include the methylation level of covered cytosines, only including CpG contexts


title: Center1-036

status: Public on Nov 15 2024

type: genomic

city: Boston

first: Ze

last: Zhang

state: MA

address: 375 Longwood Ave

department: Medical Oncology & Population Sciences

country: USA

institute: Harvard Medical School

description: adult head and neck cancer peripheral blood before ICI treatment

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPICv1/v2 Beadchip using standard Illumina protocol

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

data_processing:
R studio
minfi Noob Processed Average Beta
Unmethylated and methylated signal intensities

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral Whole Blood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted and processed using the Zymo Quick DNA Miniprep Plus kit and quantified using a Qubit dsDNA Broad Range Assay kit (Thermo)

tag: Sex

value: Male

tag: age

tag: treatment

value: Immunotherapy only

tag: progression event

tag: days to progression

tag: death event

tag: days to death

tag: tmb

tag: pdl1 cps

tag: arraytypes


title: CONT_ATAC-Seq_Rep2

type: SRA

city: Philadelphia

first: Vikram

middle: R

last: Paralkar

state: PA

address: 421 Curie Boulevard

department: Division of Hematology and Oncology, Department of Medicine

institute: University of Pennsylvania Perelman School of Medicine

description: Selected for Cas9/GFP expression, clonally expanded and sequence verified

library_source: genomic

data_processing:
Sequence reads were trimmed for low quality/adapter sequence using Trimmomatic.
Trimmed reads were mapped to hg19 genome using Bowtie2.
Peaks were called using MACS2.
Differential peak analysis was performed using DiffBind.
Assembly: hg19
Supplementary files format and content: BigWig tracks of all samples

source_name: Hematopoietic

growth_protocol: Cells were transduced with lentiviral vector expressing GFP-Cas9 and PHF6 gRNAs. Resultant pools was sorted for GFP expression, and clones were verified for knockout or wildtype expression. Cells were grown in complete media (RPMI1640 + FBS).

extract_protocol:
5,000 cells were collected for each sample, lysed and their nuclei were isolated. Tagmentation was performed using Nextera Tn5 transposase (Illumina Nextera ATAC seq kit, 20034197).
Libraries were prepared using dual end indexing with NEBNext Ultra II DNA Library Prep Kit (E7645L) using the manufacturer's protocol. Concentrations and sizes of libraries were determined using Agilent 2200 Tapestation and KAPA library quantification kit (Roche KK4824). LIbraries from all samples were pooled in equimolar concentrations and denatured for single-end sequencing. Pooled library quantification was determined using KAPA library quantification kit (Roche KK4824).

tag: tissue

value: Hematopoietic

tag: cell line

tag: cell type

value: AML cell line

tag: genotype

value: Wildtype


title: Center1-035

value: Female


title: scBSseq_LK_DNA_2_A2

city: Hangzhou

first: Shou-Wen

last: Wang

address: No. 18 Shilongshan Road, Xihu District

country: China

institute: Westlake University

organism: Mus musculus

source_name: Blood cells

extract_protocol:
Individual cells were directly sorted into 96-well plates containing the mild lysis buffer and incubated for 5 minutes at 4°C. Dynabeads Myone Carboxylic Acid (Invitrogen, 65011) were used to capture nuclei. The Dynabeads containing genomic DNA were used to carry out DNA bisulfite conversion through EZ-96 DNA Methylation-Direct MagPrep Kit (ZYMO, D5045).
Bisulfite-converted DNA was amplified with random primer and klenow exo– polymerase (Qiagen, P7010-HC-L) for 5 rounds and excess primer was removed by AMPure XP beads (Beckman, A63881). After second strand synthesis, the library was amplified by KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602) for 14 cycles.

value: Blood cells


title: scBSseq_LK_DNA_2_A4


title: DoxPHF6-PHIPKO_0h_THP1_RNA-Seq_Rep1

description: Selected for Cas9/GFP and Tet/DsRed expression, clonally expanded and sequence verified

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for low quality/adapter sequence using Trimmomatic.
Trimmed reads were mapped to hg19 genome using STAR.
Read quantification and feature annotation were performed using featureCounts.
Differential expression analysis was performed using DESeq2.
Assembly: hg19
Supplementary files format and content: text file includes mapped reads to genomic features for all samples

molecule: polyA RNA

growth_protocol: THP1 cells were transduced with lentiviral vector expressing GFP-Cas9 and PHF6 gRNAs, and a PHF6 knockout clone was expanded and validated. The clone was transduced with DsRed expressing lentivirus containing PHF6 wildtype or PHF6R274Q mutant cassette under a TET promoter. Clones were picked for absence of leaky expression and for induction with Doxycycline treatment. For DoxPHF6-PHIPKO clones, DoxPHF6 clonal cells were electroporated with PHIP gRNA, and PHIP knockout clones were expanded and validated. Cells were grown in complete media (RPMI1640 +FBS) and used for RNA extraction.

extract_protocol:
1 million cells from each clone were used for total RNA extraction using RNeasy mini kit (Qiagen 74106) following the manufacturer recommended protocol. RNA concentration was determined by using Agilent 2200 TapeStation and a high sensitivity RNA Screentape (Agilent 5067-5579). Samples with RIN greater than 8 were used to construct RNA-Seq libraries.
RNA libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB E7530L) using the manufacturer recomended protoco. Concentration and the size of the libraries were detremined using Agilent 2200 Tapestation and KAPA library quantification kit (Roche KK4824). Libraries from all samples were pooled in equimolar concentrations and denatured for paired-end sequencing. Pooled libraries were quantified using KAPA library quantification kit (Roche KK4824).

treatment_protocol: Doxycycline treatment

value: PHF6 knockout/DoxPHF6/PHIP knockout


title: DoxPHF6-PHIPKO_0h_THP1_RNA-Seq_Rep2


title: DoxR274Q_48h_THP1_RNA-Seq_Rep1

value: PHF6 knockout/DoxPHF6R274Q

value: 250ng/ul Doxycyclin for 48 hours


title: DoxR274Q_0h_THP1_RNA-Seq_Rep2


title: Center1-033

value: Immunotherapy + EGFRi


title: scBSseq_LK_DNA_2_A12


title: Center1-032


title: DoxPHF6_48h_THP1_RNA-Seq_Rep3

value: PHF6 knockout/DoxPHF6


title: Center1-031


title: DoxPHF6_48h_THP1_RNA-Seq_Rep2


title: DoxPHF6-PHIPKO_48h_THP1_RNA-Seq_Rep2


title: Center1-034


title: scBSseq_LK_DNA_2_A11


title: Center1-029


title: Center1-030


title: DoxPHF6_24h_THP1_RNA-Seq_Rep1

value: 250ng/ul Doxycyclin for 24 hours


title: DoxPHF6_24h_THP1_RNA-Seq_Rep2


title: scBSseq_LK_DNA_2_A10


title: DoxPHF6_12h_THP1_RNA-Seq_Rep2

value: 250ng/ul Doxycyclin for 12 hours


title: scBSseq_LK_DNA_1_H9


title: DoxPHF6_12h_THP1_RNA-Seq_Rep3


title: DoxR274Q_48h_THP1_RNA-Seq_Rep2


title: scBSseq_LK_DNA_1_H8


title: DoxPHF6_12h_THP1_RNA-Seq_Rep1


title: scBSseq_LK_DNA_2_A6


title: Center1-028


title: scBSseq_LK_DNA_2_A1


title: Center1-027


title: DoxR274Q_0h_THP1_RNA-Seq_Rep1


title: DoxPHF6_0h_THP1_RNA-Seq_Rep2


title: DoxPHF6_0h_THP1_RNA-Seq_Rep1


title: scBSseq_LK_DNA_1_H7


title: Center1-026


title: scBSseq_LK_DNA_2_D11


title: Center1-025

value: Immunotherapy + Chemotherapy


title: DoxPHF6_48h_THP1_RNA-Seq_Rep1


title: scBSseq_LK_DNA_1_H6


title: scBSseq_LK_DNA_1_H5


title: Center1-024


title: Center1-023


title: PHIPKO_THP1_RNA-Seq_Rep2

description: clonally expanded and sequence verified

growth_protocol: Cells were electroporated with Cas9 protein and i) PHF6 gRNAs for exon 4 for PHF6 knockouts, ii) PHF6 gRNAs for exon 8 and ssODN for PHF6R274Q mutant for mutant clones, iii) PHIP gRNAs for exon 6 for PHIP knockouts, and iv) PHF6 gRNAs for exon 4 and PHIP gRNAs for exon 6 for DKO clones. Resultant pools were sorted and selected for individual clones, and validated using sanger sequencing and immunoblotting. Cells were grown in complete media (RPMI1640 +FBS) and used for RNA extraction.

extract_protocol:
1 million cells from each clone were used for total RNA extraction using RNeasy mini kit (Qiagen 74106) following the manufacturer recommended protocol. RNA concentration was determined by using Agilent 2200 TapeStation and a high sensitivity RNA Screentape (Agilent 5067-5579). Samples with RIN greater than 8 were used to construct RNA-Seq libraries.
RNA libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB E7530L) using the manufacturer recomended protocol. Concentration and size of libraries were determined using Agilent 2200 Tapestation and KAPA library quantification kit (Roche KK4824). Libraries from all samples were pooled in equimolar concentrations and denatured for paired-end sequencing. Pooled libraries were quantified using KAPA library quantification kit (Roche KK4824).

value: PHIP knockout


title: PHIPKO_THP1_RNA-Seq_Rep1

description: clonally expanded and sequence verified


title: DKO_THP1_RNA-Seq_Rep3

description: clonally expanded and sequence verified

value: PHF6/PHIP double knockout


title: scBSseq_LK_DNA_1_H4


title: PHIPKO_THP1_RNA-Seq_Rep3

description: clonally expanded and sequence verified


title: R274Q_THP1_RNA-Seq_Rep4

description: clonally expanded and sequence verified

value: PHF6R274Q mutant


title: scBSseq_LK_DNA_1_H3


title: R274Q_THP1_RNA-Seq_Rep2

description: clonally expanded and sequence verified


title: Center1-022

value: Male

value: Immunotherapy only


title: scBSseq_LK_DNA_1_H2


title: R274Q_THP1_RNA-Seq_Rep3

description: clonally expanded and sequence verified

value: Hematopoietic

value: AML cell line


title: Center1-021


title: PHF6KO_THP1_RNA-Seq_Rep5

description: clonally expanded and sequence verified

value: PHF6 knockout


title: R274Q_THP1_RNA-Seq_Rep1

description: clonally expanded and sequence verified


title: scBSseq_LK_DNA_1_H1

value: Blood cells


title: PHF6KO_THP1_RNA-Seq_Rep4

description: clonally expanded and sequence verified


title: Center1-020


title: DKO_THP1_RNA-Seq_Rep2

description: clonally expanded and sequence verified


title: DKO_THP1_RNA-Seq_Rep1

description: clonally expanded and sequence verified


title: PHF6KO_THP1_RNA-Seq_Rep2

description: clonally expanded and sequence verified


title: scBSseq_LK_DNA_1_H12


title: PHF6KO_THP1_RNA-Seq_Rep1

description: clonally expanded and sequence verified


title: scBSseq_LK_DNA_1_H11


title: Center1-019


title: DoxPHF6-PHIPKO_plus_Dox_THP1_PHF6-ChIP_Rep2

data_processing:
Sequence reads were trimmed for low quality/adapter sequence using Trimmomatic.
Trimmed reads were mapped to hg19 genome using Bowtie2.
Peaks were called using MACS2.
Assembly: hg19
Supplementary files format and content: BigWig tracks of all samples

growth_protocol: THP1 cells were transduced with lentiviral vector expressing GFP-Cas9 and PHF6 gRNAs, and a PHF6 knockout clone was expanded and validated. The clone was transduced with DsRed expressing lentivirus containing PHF6 wildtype or PHF6R274Q mutant cassette under a TET promoter. Clones were picked for absence of leaky expression and for induction with Doxycycline treatment. For DoxPHF6-PHIPKO clones, DoxPHF6 clonal cells were electroporated with PHIP gRNA, and PHIP knockout clones were expanded and validated. Cells were grown in complete media (RPMI1640 +FBS) and used for ChIP.

extract_protocol:
40 million cells from each clone were double-crosslinked using EGS and 1% paraformaldehyde, treated with MNase, and lysed using freeze-thaw cycles and sonication. Cell lysate from 40 million cells was used for PHF6 pulldown (Bethyl, A301-452A) and IgG control pulldown (Invitrogen, 02-6102).
DNA concentration and fragment length was determined by using Agilent 2200 TapeStation and a High Sensitivity DNA screentape (Agilent 5067-5584). RNA libraries were prepared using Nextera DNA Library Prep Kit (Illumina FC-121-1030) using the manufacturer recomended protocol. Concentrations and sizes of libraries were determined using Agilent 2200 TapeStation and KAPA library quantification kit (Roche KK4824). Libraries from all samples were pooled in equimolar concentrations and denatured for single-end sequencing. Pooled libraries were quantified using KAPA library quantification kit (Roche KK4824).

value: PHF6 knockout/DoxPHF6/PHIP knockout

value: 50ng/ul Doxycyclin for 24 hours


title: R274Q_THP1_RNA-Seq_Rep5

description: clonally expanded and sequence verified


title: Center1-018


title: WT_THP1_RNA-Seq_Rep5

description: clonally expanded and sequence verified

value: Wildtype


title: WT_THP1_RNA-Seq_Rep3

description: clonally expanded and sequence verified


title: scBSseq_LK_DNA_1_H10


title: Center1-016

value: Female


title: WT_THP1_RNA-Seq_Rep1

description: clonally expanded and sequence verified


title: scBSseq_LK_DNA_1_G9


title: scBSseq_LK_DNA_1_G8


title: RfxCas13d expressing HAP1 cells, pooled lncRNA library, before or 7 days after dox induction, rep1 or 2

city: New York

first: Wen-Wei

last: Liang

state: NY

address: 101 Avenue of the Americas

institute: New York Genome Center

description: HAP1_Day_00_R1, HAP1_Day00_R2, HAP1_Day07_R1

data_processing:
Quality of the raw fastq files was assessed using MultiQC .We processed reads from pooled Cas13d screens following established pipelines. In brief, reads were de-multiplexed based on Illumina i7 barcodes and custom i5 barcodes. We trimmed reads to the expected gRNA length by identifying known anchor sequences relative to the guide sequence. We did this using Cutadapt (v.1.13) with the following parameters: -g CTGGTCGGGGTTTGAAAC -e 0.2 -O 5 --discard-untrimmed and -a TTTTTGAATTCGCTAGCT -e 0.1 -O 5 --minimum-length 15 --discard-untrimmed. We aligned processed reads to the designed crRNA reference using bowtie (v.1.1.2) allowing for up to three mismatches (parameters: -v 1 -m 3 –best -q). The raw gRNA counts were normalized using median-of-ratios (geometric mean), similar to DESeq2, and batch correction was applied using combat from the SVA R package (v.3.34.0). We removed nonreproducible technical outliers by pair-wise linear regression for each sample, collecting residuals, and taking the median value for each gRNA across biological replicates.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include raw counts for each sample.

source_name: bone marrow

growth_protocol: HEK293FT and MDA-MB-231 cells were cultured in D10 medium:  Dulbecco’s Modified Eagle Medium with high glucose and stabilized L-glutamine (Cytiva SH30022.01) supplemented with 10% Serum Plus II (Sigma-Aldrich 14009C) and 5 µg/ml blasticidin. HAP1 and K562 cells were cultured in I10 medium: Iscove’s Modified Dulbecco’s Medium with L-glutamine (Cytiva SH30228.FS) supplemented with 10% Serum Plus II and 5 µg/ml blasticidin. THP-1 cells were cultured in R10 medium: HyClone RPMI 1640 Medium (Cytiva SH30255.FS) supplemented with 10% Serum Plus II and 5 µg/ml blasticidin. All cells were incubated at 37 °C with 5% carbon dioxide.

extract_protocol:
Genomic DNA was isolated from cell pellets via a modified salting out procedure. For that, 12 ml of NK Lysis Buffer (50 mM Tris, 50 mM EDTA, 1% SDS, pH 8) and 60 µl of 20 mg/ml Proteinase K (QIAGEN 19131) were added to 80 million cells and incubated at 55 °C overnight. The next day, 6 µl of 100 mg/ml RNase A (A.G. Scientific R-2000) was added to the lysed sample, which was then inverted 25 times and incubated at 37 °C for 30 min. Samples were cooled on ice before addition of 4 ml of pre-chilled 7.5M ammonium acetate (Sigma A1542) to precipitate proteins. After adding ammonium acetate, the samples were vortexed and centrifuged at 4,000 × g for 10 minutes. After the spin, 12 ml isopropanol was added to the collected supernatant, inverted 50 times and centrifuged at 4,000 × g for 10 minutes. The supernatant was discarded, 12 ml of freshly prepared 70% ethanol was added, the tube was inverted 10 times, and then centrifuged at 4,000 × g for 10 minutes. The supernatant was discarded, and remaining ethanol was removed. After air drying for 30 minutes, 500 µl of 0.2× TE buffer (Sigma 93283) was added, the tube was incubated at 65 °C for 1 hour and at room temperature overnight to fully resuspend the DNA. The next day, the gDNA samples were vortexed briefly. The gDNA concentration was measured using a Nanodrop (Thermo). We excluded one biological replicate (K562 day 0) due to low recovery after gDNA extraction.
We amplified gRNA cassettes and prepared them for sequencing using a two-step PCR. PCR1 was performed to amplify a region containing the crRNA cassette in the lentiviral genomic integrant using TaqB polymerase (Enzymatics P7250L). We performed 70 PCR1 reactions for each gDNA sample using 5 μg gDNA per 100 μl PCR1 reaction as follows: 94 °C for 3 min, 20× (94 °C for 10 s, 55 °C for 30 s, 68 °C for 45 s), 68 °C for 5 min. We then combined PCR1 products for the same sample together before PCR2, which was done to incorporate Illumina adaptors using Q5 High-Fidelity DNA Polymerase (NEB M0491). We performed 10 PCR2 reactions for each sample using 10 μl unpurified PCR1 product per 50 μl reaction as follows: 98 °C for 30 s, 6-10× (98 °C for 10 s, 63 °C for 30 s, 72 °C for 45 s), 72 °C for 5 min. The resulting amplicons from PCR2 (~270 bp) were pooled and then purified using double-sided SPRI beads clean up (Beckman B23317) or gel extracted using a QiaQuick Gel Extraction kit (Qiagen 28704). For double-sided SPRI clean up, the amplicon was first incubated with 0.6× SPRI to remove larger fragments (>350 bp bound to beads and removed), the supernatant was then transferred and further incubated with 0.8× SPRI beads (<200 bp in supernatant and removed).

treatment_protocol: Cas13d-expressing cells were transduced with the library lentivirus through separate infection replicates by spinfection at 1000 rpm for 1 hour at 37 °C, followed by overnight incubation. After 24 hours, new media with 1 μg/ml puromycin (Invivogen ant-pr-1) was added. Puromycin selection was completed within 48 hours for all cell lines, except for THP1. Because THP1 required an extended selection time, we maintained it in R10 but with 10% Tet-system approved serum (Gibco A4736201) substituted for Serum Plus II and with 1 μg/ml puromycin. THP1 cells took approximately two weeks for full selection. Following puromycin selection, RfxCas13d expression was induced by replenishing the growth medium containing 1 μg/ml puromycin, 5 μg/ml blasticidin and 1 μg/ml doxycycline. Cells were passaged every 2 to 4 days and split as needed, ensuring a guide representation of >1,000×. Samples with a guide abundance of 1,000-fold were harvested at 0, 7, and 14 days post-Cas13d induction.

value: bone marrow

value: cancer cells

value: lncRNAs knockdown

value: doxycycline induction


title: Center1-015


title: RfxCas13d expressing HAP1 cells, pooled lncRNA library, 7 or 14 days after dox induction, rep1 or 2

description: HAP1_Day07_R2, HAP1_Day14_R1, HAP1_Day14_R2


title: RfxCas13d expressing HEK293FT cells, pooled lncRNA library, 7 or 14 days after dox induction, rep1 or 2

description: HEK293FT_Day07_R2, HEK293FT_Day14_R1, HEK293FT_Day14_R2

source_name: kidney

value: kidney

value: embryonic kidney cells


title: RfxCas13d expressing HEK293FT cells, pooled lncRNA library, before or 7 days after dox induction, rep1 or 2

description: HEK293FT_Day00_R1, HEK293FT_Day00_R2, HEK293FT_Day07_R1


title: scBSseq_LK_DNA_1_G7


title: PHF6KO_THP1_RNA-Seq_Rep3

description: clonally expanded and sequence verified


title: Center1-013


title: Center1-014


title: RfxCas13d expressing K562 cells, pooled lncRNA library, before, 7 days after, or 14 days after dox induction, rep2

description: K562_Day07_R2, K562_Day14_R2


title: WT_THP1_RNA-Seq_Rep4

description: clonally expanded and sequence verified


title: Center1-012


title: RfxCas13d expressing MDA-MB-231 cells, pooled lncRNA library, 14 days after dox induction, reps 1 and 2

description: MDA-MB-231_Day14_R1, MDA-MB-231_Day14_R2

source_name: breast

value: breast


title: scBSseq_LK_DNA_1_G4


title: scBSseq_LK_DNA_1_G5


title: RfxCas13d expressing K562 cells, pooled lncRNA library, before, 7 days after, or 14 days after dox induction, rep1

description: K562_Day00_R1, K562_Day07_R1, K562_Day14_R1


title: RfxCas13d expressing MDA-MB-231 cells, pooled lncRNA library, before dox induction, reps 1 and 2

description: MDA-MB-231_Day00_R1, MDA-MB-231_Day00_R2


title: RfxCas13d expressing MDA-MB-231 cells, pooled lncRNA library, 7 days after dox induction, reps 1 and 2

description: MDA-MB-231_Day07_R1, MDA-MB-231_Day07_R2


title: Center1-017


title: Center1-011

value: Male


title: WT_THP1_RNA-Seq_Rep2

description: clonally expanded and sequence verified


title: scBSseq_LK_DNA_1_G3


title: Center1-009

value: Immunotherapy only


title: scBSseq_LK_DNA_1_G2


title: scBSseq_LK_DNA_1_G1


title: Center1-008

value: Immunotherapy + Chemotherapy


title: Center1-007


title: scBSseq_LK_DNA_1_G12


title: scBSseq_LK_DNA_1_G11


title: Center1-004


title: scBSseq_LK_DNA_1_G10


title: Center1-005


title: Center1-002


title: scBSseq_LK_DNA_1_F9


title: scBSseq_LK_DNA_1_F8


title: Center1-003


title: Center1-006


title: scBSseq_LK_DNA_1_F7


title: (G4C2)36; elavGS induced biol rep 3

city: London

first: Adrian

last: Isaacs

address: Cruciform Building, Gower Street

department: Neurodegenerative Diseases

country: United Kingdom

institute: University College London

data_processing:
Raw sequence reads were aligned to the Dm6 reference genome.
DESeq2 (default parameters) was used to perform differential expression analysis.
Assembly: Dm6
Supplementary files format and content: tab-delimited text file includes raw counts and DESeq2 results for each Sample

organism: Drosophila melanogaster

source_name: Heads

growth_protocol: Drosophila stocks were maintained on SYA food (15 g/L agar, 50 g/L sugar, 100 g/L autolysed yeast, 30 ml/L nipagin [10% in ethanol], and 3 ml/L propionic acid) at 25°C in a 12-hr light/dark cycle with 60% constant humidity.

extract_protocol:
Total RNA was isolated from 15 heads per replicate using Trizol, and the experiment was performed in quadruplicate.
RNA libraries for RNA-seq were prepared using the KAPA mRNA HyperPrep kit following manufacturer's instructions. RNA-seq was performed with an Illumina NextSeq2000, using 16 million paired-end reads/sample and 100 bp read length.

treatment_protocol: Food was supplemented with 200 μM RU486 (mifepristone) or ethanol.

value: Heads

value: (G4C2)36; elavGS

value: 5 days 200 µM RU486


title: scBSseq_LK_DNA_1_F3

value: Blood cells


title: scBSseq_LK_DNA_1_F2


title: (G4C2)36; elavGS induced biol rep 2


title: scBSseq_LK_DNA_1_F6


title: (G4C2)36; elavGS induced biol rep 4


title: scBSseq_LK_DNA_1_F4


title: scBSseq_LK_DNA_1_F1


title: Embryoid bodies, day16, experiment2, sample2

city: Planegg

first: Ines

last: Hellmann

address: Großhaderner Straße 2

department: Anthropology and Human Genomics, Faculty of Biology

country: Germany

institute: Ludwig-Maximilians-Universität München

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Reads were processed using the 10x CellRanger software (Version 7.0.0)
All samples were aligned to 4 reference genomes: GRCh38 (Homo sapiens), Susie_PABv2/ponAbe3 (Pongo abelii), macFas6 (Macaca fascicularis), rheMac10 (Macaca mulatta)
For non-human primate genomes, custom GTF files were created by transferring the hg38 annotation via the tool Liftoff
Assembly: GRCh38, ponAbe3, macFas6, rheMac10
Supplementary files format and content: Cellranger output: 4 filtered count matrices per sample (one per genome) in HDF5 matrix format

organism:
Macaca fascicularis
Macaca mulatta
Pongo abelii

source_name: Embryoid bodies

extract_protocol:
For dissociation, floating EBs (on day8) / attached EBs (on day16) were washed with DPBS and incubated with Accumax (Sigma-Aldrich, SCR006) for 10-20 min at 37°C. Next, EBs were pipetted up and down with a p1000 pipette until they were completely dissociated to single cells and DFK20 medium was added. Cells were pelleted at 300 xg for 5 min and then resuspended in 1 mL DPBS. If remaining cell clumps were observed, the cell suspension was filtered through a 40 µm cell strainer, then cells were counted using a Countess II automated cell counter (Thermo Fisher Scientific, C10228). Equal cell numbers from each cell line were pooled, washed with DPBS + 0.04% BSA and resuspended in an appropriate volume of DPBS + 0.04 % BSA leading to a final concentration of 800 - 1000 cells/µL. The pooled cells were kept on ice and loaded on a 10x Chromium Controller Chip within 15 min.
scRNA-seq libraries were generated using the 10x Genomics Chromium Next GEM Single Cell 3´Kit V3.1 workflow in three replicates. Each time, evenly pooled single cells from the different clones were loaded on 2 to 6 lanes of a 10x chip, with a targeted cell recovery of 16,000 cells per lane.

value: Embryoid bodies


title: (G4C2)36; elavGS induced biol rep 1


title: scBSseq_LK_DNA_1_F5


title: scBSseq_LK_DNA_1_F12


title: scBSseq_LK_DNA_1_F11


title: scBSseq_LK_DNA_1_F10


title: (G4C2)36; elavGS uninduced biol rep 2

value: 5 days ethanol


title: (G4C2)36; elavGS uninduced biol rep 3

value: Female


title: scBSseq_LK_DNA_1_G6


title: scBSseq_LK_DNA_1_E9


title: Center1-001


title: (G4C2)36; elavGS uninduced biol rep 4


title: scBSseq_LK_DNA_1_E8


title: (G4C2)36; elavGS uninduced biol rep 1


title: scBSseq_LK_DNA_1_E7


title: scBSseq_LK_DNA_1_E5


title: scBSseq_LK_DNA_1_E6


title: Patient-016-Day-28-4, Itacitinib Treated, Day 28_VDJ

city: Saint Louis

first: Li

last: Ding

state: MO

address: 660 S. Euclid Avenue

institute: Washington University in St. Louis

description: 10x Genomics

data_processing:
For each sample, we obtained the unfiltered feature-barcode matrix per sample by passing the demultiplexed FASTQs to Cell Ranger v.6.1.0 ‘count’ command using default parameters and the prebuilt GRCh38 genome reference (refdata-gex-GRCh38-2020-A) for scRNA.
Seurat v. 4.4.0 and 5.0.0 {29608179; 31870423} were used for subsequent analyses. First, a series of quality filters are applied to the data to remove barcodes that fell into any one of these categories: too few total transcript counts (<300); possible debris with too few genes expressed (<200) and too few unique molecular identifiers (UMIs) (<1,000); possible more than one cell with too many genes expressed (>10,000) and too many unique molecular identifiers (>80,000); possible dead cell or a sign of cellular stress and apoptosis with too high proportion of mitochondrial gene expression over the total transcript counts (>=20%). We constructed a Seurat object using the unfiltered feature-barcode matrix for each sample. Each sample was scaled and normalized using Seurat’s ‘SCTransform’ function to correct for batch effects (with parameters: vars.to.regress = c("nCount_RNA","S.Score","G2M.Score","percent_mito","percent_hb","percent_ribo"), method = "glmGamPoi"). Any merged analysis or subsequent subsetting of cells/samples underwent the same scaling and normalization method. Cells were clustered using the original Louvain algorithm and top 20 PCA dimensions via ‘FindNeighbors’ (dims=1:20) and ‘FindClusters’ (with parameters: resolution = 0.6) functions. DoubletFinder {30954475} was used to identify potential doublets using default parameters for each sample (https://github.com/chris-mcginnis-ucsf/DoubletFinder). After performing aforementioned steps for each sample separately, all samples were integrated and any cells annotated as doublets were removed. Further batch correction was applied using Harmony to correct for any sequencing batch related artifacts. Samples were sequenced in two batches. Populations with high erythrocyte genes expressed ("HBB", "HBA1", "CA1", "AHSP", "HBA2", "BLVRB", "TFRC", "GYPA", "SLC25A37", "HBM", "HBD") and doublet annotation were removed from the object. The resulting merged and normalized matrix was used for the subsequent analysis. Donor cells were only used for cell type annotation and excluded from any differential expression analysis or other downstream comparisons.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files (RNA count matrices).
Library strategy: VDJ-Seq

molecule: total RNA

source_name: Blood

extract_protocol:
Peripheral blood and serum samples were collected from patients on study and banked at multiple time points. Control samples were collected from patients undergoing standard-of-care PB haplo-HCT during the same time period; these patients all received the same tac/MMF/PtCy GvHD prophylaxis except did not receive itacitinib.
cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps. Purified cDNA was amplified for 11-16 cycles before being cleaned up using SPRIselect beads. Samples were then run on a Bioanalyzer to determine the cDNA concentration. V(D)J target enrichment (Tcell/Bcell – TCR/BCR) was performed on the full length cDNA. Gene Expression and Enriched TCR/BCR libraries were prepared as recommended by the 10x Genomics Chromium Chromium Single Cell 5' Reagent Kits User Guide (v2 Chemistry Dual Index) user guide, with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell 5’ Kit v2, 16 rxns (PN-1000263), Chromium Next GEM Chip K Single Cell Kit, 48 rxns (PN-1000286), Chromium Single Cell Human TCR Amplification Kits (PN-1000252), Chromium Single Cell Human BCR Amplification Kits (PN-1000253), Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 151x10x10x151 sequencing recipe according to the manufacturer protocol. A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression library and 5000 reads/cell for each V(D)J library.

value: Blood

value: Peripheral Blood


title: Patient-022-Day-60-8, Itacitinib Treated, Day 60_VDJ

description: 10x Genomics


title: scBSseq_LK_DNA_1_E4


title: Patient-016-Day-60-5, Itacitinib Treated, Day 60_VDJ

description: 10x Genomics


title: Patient-009-Day-28-1, Itacitinib Treated, Day 28_VDJ

description: 10x Genomics


title: Patient-009-Day-60-2, Itacitinib Treated, Day 60_VDJ

description: 10x Genomics


title: scBSseq_LK_DNA_1_E1


title: scBSseq_LK_DNA_1_E2


title: Patient_38_Donor-32, Donor_VDJ

description: 10x Genomics


title: Patient_38_Day_28-30, Itacitinib Treated, Day 28_VDJ

description: 10x Genomics


title: scBSseq_LK_DNA_1_E12


title: scBSseq_LK_DNA_1_E11


title: Patient_38_Day_60-31, Itacitinib Treated, Day 60_VDJ

description: 10x Genomics


title: Patient-026-Day-28-10, Itacitinib Treated, Day 28_VDJ

description: 10x Genomics


title: Patient_33_Day_60-25, Itacitinib Treated, Day 60_VDJ

description: 10x Genomics


title: Patient_36_Donor-29, Donor_VDJ

description: 10x Genomics


title: Patient_36_Day_60-28, Itacitinib Treated, Day 60_VDJ

description: 10x Genomics


title: scBSseq_LK_DNA_1_E10


title: scBSseq_LK_DNA_1_D7


title: Patient_33_Day_28-24, Itacitinib Treated, Day 28_VDJ

description: 10x Genomics


title: scBSseq_LK_DNA_1_D9


title: Patient_31_Day_28-22, Itacitinib Treated, Day 28_VDJ

description: 10x Genomics


title: Patient_31_Day_60-23, Itacitinib Treated, Day 60_VDJ

description: 10x Genomics


title: scBSseq_LK_DNA_1_D3


title: scBSseq_LK_DNA_1_D2


title: scBSseq_LK_DNA_1_D1


title: Patient_29_Donor-21, Donor_VDJ

description: 10x Genomics


title: scBSseq_LK_DNA_1_D8


title: Patient_33_Donor-26, Donor_VDJ

description: 10x Genomics


title: scBSseq_LK_DNA_1_D4


title: Patient_29_Day_60-20, Itacitinib Treated, Day 60_VDJ

description: 10x Genomics


title: scBSseq_LK_DNA_1_D6


title: scBSseq_LK_DNA_1_D5


title: Patient_36_Day_28-27, Itacitinib Treated, Day 28_VDJ

description: 10x Genomics


title: Patient_27_Donor-18, Donor_VDJ

description: 10x Genomics


title: Patient_27_Day_60-17, Itacitinib Treated, Day 60_VDJ

description: 10x Genomics


title: scBSseq_LK_DNA_1_D12


title: Patient_27_Day_28-16, Itacitinib Treated, Day 28_VDJ

description: 10x Genomics


title: scBSseq_LK_DNA_1_D10


title: scBSseq_LK_DNA_1_D11


title: Patient_24_Donor-15, Donor_VDJ

description: 10x Genomics


title: scBSseq_LK_DNA_1_C8


title: scBSseq_LK_DNA_1_C9


title: scBSseq_LK_DNA_1_C7


title: Patient_24_Day_28-13, Itacitinib Treated, Day 28_VDJ

description: 10x Genomics


title: scBSseq_LK_DNA_1_C6


title: Patient_17_Donor-12, Donor_VDJ

description: 10x Genomics


title: Patient_17_Day_60-11, Itacitinib Treated, Day 60_VDJ

description: 10x Genomics


title: Patient_29_Day_28-19, Itacitinib Treated, Day 28_VDJ

description: 10x Genomics


title: Patient_17_Day_28-10, Itacitinib Treated, Day 28_VDJ

description: 10x Genomics


title: scBSseq_LK_DNA_1_C5


title: Patient_11_Day_60-8, Itacitinib Treated, Day 60_VDJ

description: 10x Genomics


title: scBSseq_LK_DNA_1_C4


title: scBSseq_LK_DNA_1_C2


title: Patient_11_Day_28-7, Itacitinib Treated, Day 28_VDJ

description: 10x Genomics


title: scBSseq_LK_DNA_1_C3


title: scBSseq_LK_DNA_1_C12


title: Patient_11_Donor-9, Donor_VDJ

description: 10x Genomics


title: Center1-010


title: scBSseq_LK_DNA_1_C1


title: scBSseq_LK_DNA_1_C11


title: Control-2-Day-28-15, Control, Day 28_VDJ

description: 10x Genomics


title: Control-2-Day-60-16, Control, Day 60_VDJ

description: 10x Genomics


title: Control-1-Day-60-14, Control, Day 60_VDJ

description: 10x Genomics


title: Patient_24_Day_60-14, Itacitinib Treated, Day 60_VDJ

description: 10x Genomics


title: scBSseq_LK_DNA_1_B9


title: Control-1-Day-28-13, Control, Day 28_VDJ

description: 10x Genomics


title: scBSseq_LK_DNA_1_B8


title: scBSseq_LK_DNA_1_C10


title: Control_7_Day_60-6, Control, Day 60_VDJ

description: 10x Genomics


title: scBSseq_LK_DNA_1_B7


title: Control_6_Day_60-4, Control, Day 60_VDJ

description: 10x Genomics


title: scBSseq_LK_DNA_1_B5


title: Control_6_Day_28-3, Control, Day 28_VDJ

description: 10x Genomics


title: scBSseq_LK_DNA_1_E3


title: Control_5_Day_60-2, Control, Day 60_VDJ

description: 10x Genomics


title: scBSseq_LK_DNA_1_B4


title: scBSseq_LK_DNA_1_B3


title: 1703980a_5-9_VDJ

description: 10x Genomics


title: Control_5_Day_28-1, Control, Day 28_VDJ

description: 10x Genomics


title: scBSseq_LK_DNA_1_B1


title: scBSseq_LK_DNA_1_B2


title: scBSseq_LK_DNA_1_B12


title: 1692941a_10-6_VDJ

description: 10x Genomics


title: PDX_06, H3K27ac

first: Christopher

last: Booth

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
Cut&Run reads were aligned using Bowtie2 and the following parameters: --very-sensitive-local --soft-clipped-unmapped-tlen --no-unal --no-mixed --no-discordant --dovetail --phred33 -I 10 -X 700
Coverage tracks were generated using Bedtools genomecov -bg on paired-end DNA fragments, then UCSC-tools bedGraphToBigWig
For MYB, peak files were generated using MACS2 and the following parameters: -q 0.01 --keep-dup all
For H3K27ac, peak files were generated using MACS2 and the following parameters: -q 0.01 --keep-dup all --broad
Assembly: hg38
Supplementary files format and content: Coverage tracks: bigWig
Supplementary files format and content: Peak files: narrowPeak or broadPeak
Library strategy: Cut&Run

growth_protocol: CAL1 cells were cultured in RPMI-1640 with 10% FBS and 1% Pen/Strep

extract_protocol:
Cut&Run performed as described: Skene et al. Nat Protoc 2018
NEBNext Ultra II DNA Library Prep

treatment_protocol:
Normal pDCs were purified from peripheral blood by Ficoll-Paque, magnetic beads (Miltenyi Biotec 130-097-415) and FACS: CD45+CD123+CD4+BDCA2+
PDX cells were purified from recipient mouse spleen samples by magnetic beads (Miltenyi Biotec 130-104-694)
Primary BPDCN cells were purified from bone marrow samples by FACS: CD45lowCD123+CD4+BDCA2+

value: Blastic plasmacytoid dendritic cell neoplasm patient derived xenograft cells

tag: antibody


title: PDX_06, MYB_2

value: MYB (Abcam, ab45150)


title: scBSseq_LK_DNA_1_B11


title: PDX_05, IgG


title: 1713398a_7-12_VDJ

description: 10x Genomics


title: PDX_06, IgG


title: Primary, H3K27ac

value: Primary blastic plasmacytoid dendritic cell neoplasm cells


title: PDX_05, H3K27ac


title: 1683278a_14-3_VDJ

description: 10x Genomics


title: PDX_05, MYB


title: PDX_06, MYB_1


title: scBSseq_LK_DNA_1_B6


title: scBSseq_LK_DNA_1_B10


title: PDX_04, IgG


title: Patient-026-Day-28-10, Itacitinib Treated, Day 28_GEX

description: 10x Genomics

data_processing:
For each sample, we obtained the unfiltered feature-barcode matrix per sample by passing the demultiplexed FASTQs to Cell Ranger v.6.1.0 ‘count’ command using default parameters and the prebuilt GRCh38 genome reference (refdata-gex-GRCh38-2020-A) for scRNA.
Seurat v. 4.4.0 and 5.0.0 {29608179; 31870423} were used for subsequent analyses. First, a series of quality filters are applied to the data to remove barcodes that fell into any one of these categories: too few total transcript counts (<300); possible debris with too few genes expressed (<200) and too few unique molecular identifiers (UMIs) (<1,000); possible more than one cell with too many genes expressed (>10,000) and too many unique molecular identifiers (>80,000); possible dead cell or a sign of cellular stress and apoptosis with too high proportion of mitochondrial gene expression over the total transcript counts (>=20%). We constructed a Seurat object using the unfiltered feature-barcode matrix for each sample. Each sample was scaled and normalized using Seurat’s ‘SCTransform’ function to correct for batch effects (with parameters: vars.to.regress = c("nCount_RNA","S.Score","G2M.Score","percent_mito","percent_hb","percent_ribo"), method = "glmGamPoi"). Any merged analysis or subsequent subsetting of cells/samples underwent the same scaling and normalization method. Cells were clustered using the original Louvain algorithm and top 20 PCA dimensions via ‘FindNeighbors’ (dims=1:20) and ‘FindClusters’ (with parameters: resolution = 0.6) functions. DoubletFinder {30954475} was used to identify potential doublets using default parameters for each sample (https://github.com/chris-mcginnis-ucsf/DoubletFinder). After performing aforementioned steps for each sample separately, all samples were integrated and any cells annotated as doublets were removed. Further batch correction was applied using Harmony to correct for any sequencing batch related artifacts. Samples were sequenced in two batches. Populations with high erythrocyte genes expressed ("HBB", "HBA1", "CA1", "AHSP", "HBA2", "BLVRB", "TFRC", "GYPA", "SLC25A37", "HBM", "HBD") and doublet annotation were removed from the object. The resulting merged and normalized matrix was used for the subsequent analysis. Donor cells were only used for cell type annotation and excluded from any differential expression analysis or other downstream comparisons.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files (RNA count matrices).


title: Patient-022-Day-60-8, Itacitinib Treated, Day 60_GEX

description: 10x Genomics


title: PDX_04, MYB_1


title: PDX_03, IgG


title: Control_7_Day_28-5, Control, Day 28_VDJ

description: 10x Genomics


title: scBSseq_LK_DNA_1_A8


title: PDX_04, H3K27ac


title: Primary, IgG


title: PDX_03, H3K27ac


title: PDX_02, IgG


title: scBSseq_LK_DNA_1_A7


title: PDX_01, IgG


title: Patient-016-Day-28-4, Itacitinib Treated, Day 28_GEX

description: 10x Genomics


title: scBSseq_LK_DNA_1_A6


title: Patient-009-Day-60-2, Itacitinib Treated, Day 60_GEX

description: 10x Genomics


title: PDX_02, H3K27ac


title: PDX_04, MYB_2


title: scBSseq_LK_DNA_1_A5


title: pDC_03, MYB

value: Normal plasmacytoid dendritic cells


title: PDX_01, H3K27ac


title: pDC_03, IgG


title: Patient-009-Day-28-1, Itacitinib Treated, Day 28_GEX

description: 10x Genomics


title: scBSseq_LK_DNA_1_A9


title: scBSseq_LK_DNA_1_A4


title: pDC_03, H3K27ac


title: Patient_38_Donor-32, Donor_GEX

description: 10x Genomics


title: pDC_02, MYB


title: pDC_02, H3K27ac


title: pDC_01, MYB


title: Patient-016-Day-60-5, Itacitinib Treated, Day 60_GEX

description: 10x Genomics


title: pDC_01, H3K27ac


title: scBSseq_LK_DNA_1_A2


title: pDC_02, IgG


title: Patient_36_Donor-29, Donor_GEX

description: 10x Genomics


title: Patient_38_Day_28-30, Itacitinib Treated, Day 28_GEX

description: 10x Genomics


title: scBSseq_LK_DNA_1_A1


title: pDC_01, IgG


title: CAL1, MYB

value: Human leukemia cell line


title: scBSseq_LK_DNA_1_A12


title: Patient_36_Day_60-28, Itacitinib Treated, Day 60_GEX

description: 10x Genomics


title: CAL1, IgG


title: scBSseq_LK_DNA_1_A11


title: Patient_36_Day_28-27, Itacitinib Treated, Day 28_GEX

description: 10x Genomics


title: NTC, IgG

data_processing:
Cut&Run reads were aligned using Bowtie2 and the following parameters: --very-sensitive-local --soft-clipped-unmapped-tlen --no-unal --no-mixed --no-discordant --dovetail --phred33 -I 10 -X 700
Coverage tracks were generated using Bedtools genomecov -bg on paired-end DNA fragments, then UCSC-tools bedGraphToBigWig
For MYB and V5, peak files were generated using MACS2 and the following parameters: -q 0.01 --keep-dup all
For H3K27ac, peak files were generated using MACS2 and the following parameters: -q 0.01 --keep-dup all --broad
Assembly: hg38
Supplementary files format and content: Coverage tracks: bigWig
Supplementary files format and content: Peak files: narrowPeak or broadPeak
Library strategy: Cut&Run

growth_protocol: K562 cells were cultured in RPMI-1640 with 10% FBS and 1% Pen/Strep

tag: genetic modification

value: Cas9 expression

value: NTC


title: NTC, V5Ab2


title: NTC, V5Ab1

value: V5 (ThermoFisher, R960-25)


title: Patient_33_Day_60-25, Itacitinib Treated, Day 60_GEX

description: 10x Genomics


title: scBSseq_LK_DNA_1_A3


title: scBSseq_LK_DNA_1_A10


title: Patient_38_Day_60-31, Itacitinib Treated, Day 60_GEX

description: 10x Genomics


title: Hoxb8 MS5, Cdkn2a-WT MYB-WT, Rep2

data_processing:
Raw reads were trimmed using Trimmomatic with settings ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:1:true MINLEN:20.
Trimmed reads were aligned to the mm10 genome using STAR and default settings.
Duplicate reads were removed with Picard and reads were assigned to gene exons using Subread featureCounts.
Only genes with at least 6 counts in at least 3 samples were used to prepare TPM values.
Assembly: mm10
Supplementary files format and content: CSV file containing raw counts
Supplementary files format and content: CSV file containing TPM values

growth_protocol: Hoxb8 in vitro undifferentiated cells were cultured in RPMI-1640 + 10% FBS + 1% Pen/Strep + 50 ng/ml mFLT3L + 1 μM estradiol. Hoxb8 in vitro pDCs were derived from undifferentiated cells by withdrawing estradiol for 7 days. Hoxb8 MS5 cells were co-cultured with MS5 stroma in the same media without estradiol.

extract_protocol:
RNA was extracted using RNeasy Mini kit (Qiagen 74104).
Libraries were constructed using KAPA mRNA HyperPrep Kit (Roche KK8580)

treatment_protocol: Hoxb8 leukemia cells were obtained from recipient mouse spleens by FACS

value: Hematopoietic

value: Hoxb8-FL co-cultured with MS5

value: Cdkn2a-WT MYB-WT

value: Male


title: MYB-PLEKHO1, IgG

value: Cas9 expression, MYB-V5 knock-in


title: NTC, MYB


title: Hoxb8 MS5, Cdkn2a-WT MYB-WT, Rep3


title: MYB-PLEKHO1, V5Ab2


title: Patient_33_Day_28-24, Itacitinib Treated, Day 28_GEX

description: 10x Genomics


title: MYB-PLEKHO1, V5Ab1


title: MYB-PLEKHO1, H3K27ac


title: Patient_31_Day_60-23, Itacitinib Treated, Day 60_GEX

description: 10x Genomics


title: Hoxb8 MS5, Cdkn2a-WT MYB-WT, Rep1


title: MYB-PLEKHO1, MYB


title: Hoxb8 MS5, Cdkn2a-WT MYB-TR, Rep3

value: Cdkn2a-WT MYB-TR


title: Patient_31_Day_28-22, Itacitinib Treated, Day 28_GEX

description: 10x Genomics


title: MYB-TR, IgG

value: MYB-TR


title: CAL1, H3K27ac


title: MYB-TR, V5Ab2


title: Patient_33_Donor-26, Donor_GEX

description: 10x Genomics

value: Blood


title: NTC, H3K27ac


title: MYB-TR, H3K27ac


title: MYB-WT, IgG

value: MYB-WT


title: Hoxb8 MS5, Cdkn2a-WT MYB-TR, Rep1


title: MYB-TR, V5Ab1


title: Hoxb8 MS5, Cdkn2a-WT MYB-PLEKHO1, Rep3

value: Cdkn2a-WT MYB-PLEKHO1


title: MYB-TR, MYB

value: MYB (Abcam, ab45150)


title: MYB-WT, V5Ab2


title: Patient_29_Day_28-19, Itacitinib Treated, Day 28_GEX

description: 10x Genomics

value: Peripheral Blood


title: Patient_29_Day_60-20, Itacitinib Treated, Day 60_GEX

description: 10x Genomics


title: Hoxb8 MS5, Cdkn2a-WT MYB-PLEKHO1, Rep2


title: MYB-WT, V5Ab1


title: MYB-WT, MYB


title: Hoxb8 MS5, Cdkn2a-WT MYB-PLEKHO1, Rep1


title: MYB-WT, H3K27ac


title: Thoracic-E72-BR2_S3

city: Stanford

first: Daniel

last: Richard

state: CA

address: 290 Jane Stanford Way

department: Genetics

institute: Stanford University

description: Human products of conception were collected from late first-trimester and early second-trimester terminations through the Laboratory of Developmental Biology in full compliance with the ethical guidelines of the National Institutes of Health and with the approval of the University of Washington Institutional Review Boards for the collection and distribution of human tissues for research, and Harvard University for the receipt and use of such materials. The Laboratory of Developmental Biology obtained written consent from all tissue donors.

data_processing:
alignment to hg19; Bowtie2 version 2.3.2; default parameters for hg19 alignment;
filter for duplicates; picard; default parameters;
peak calling; MACS2 version 2.1.1.2; macs2 bampe -f BAMPE --nolambda;
peak filtering ; IDR https://github.com/nboley/idr; idr --samples rep1file rep2file --peak-list pooled_peaks --input-file-type narrowPeak --output-file IDR_output --rank p.value --soft-idr-threshold 0.05 ?plot;
Assembly: hg19
Supplementary files format and content: ATAC_peaks.xlsx; bed format; contains the coordinates of the peaks called and filtered following IDR consolidation - one sheet per tissue/time-point;

extract_protocol:
ATAC-seq: Samples were subjected to PCR amplification and barcoding following Buenrostro et al., 2015. 10 ul of transposed DNA was then placed in a reaction containing NEBNext High-Fidelity PCR Master Mix, ddH20, and primers. After amplification, samples were transferred to micro-centrifuge tubes and subjected to the OMEGA Bead Purification Protocol following manufacturers protocol. The samples were eluted in 30 ul of TE, run on a nanodrop, diluted to 5 ng/ul and run on a bioanalyzer. Prior to sequencing sample concentrations were determined using the KAPA Library Quantification Complete Kit (KK4824). Samples were then sent out to the Harvard University Bauer Core Facility for sequencing on one lane of the Illumina NextSeq 500, for three rounds, after which raw reads for each sample were pooled.
PCR Amplification and Barcoding following Buenrostro et al., 2015

value: chondrocytes


title: Hoxb8 MS5, Cdkn2a-WT MYB-TR, Rep2


title: Patient_29_Donor-21, Donor_GEX

description: 10x Genomics


title: Patient_27_Day_60-17, Itacitinib Treated, Day 60_GEX

description: 10x Genomics


title: Thoracic-E74-BR3_S5

treatment_protocol: Samples were subjected to PCR amplification and barcoding following Buenrostro et al., 2015. 10 ul of transposed DNA was then placed in a reaction containing NEBNext High-Fidelity PCR Master Mix, ddH20, and primers. After amplification, samples were transferred to micro-centrifuge tubes and subjected to the OMEGA Bead Purification Protocol following manufacturers protocol. The samples were eluted in 30 ul of TE, run on a nanodrop, diluted to 5 ng/ul and run on a bioanalyzer. Prior to sequencing sample concentrations were determined using the KAPA Library Quantification Complete Kit (KK4824). Samples were then sent out to the Harvard University Bauer Core Facility for sequencing on one lane of the Illumina NextSeq 500, for three rounds, after which raw reads for each sample were pooled.


title: Patient_24_Donor-15, Donor_GEX

description: 10x Genomics


title: Hoxb8 MS5, Cdkn2a-KO MYB-WT, Rep1

value: Cdkn2a-KO MYB-WT


title: ProxTibia__67DayBR3_S10

source_name: ProxTibia

value: ProxTibia


title: Thoracic-E72-BR1_S1


title: ProxTibia_LANNISTER_54_S10


title: ProxTibia_STARK_53_S10


title: Patient_24_Day_28-13, Itacitinib Treated, Day 28_GEX

description: 10x Genomics


title: ProxTibia_TARGARYEN_57_S10


title: Patient_17_Donor-12, Donor_GEX

description: 10x Genomics


title: Hoxb8 MS5, Cdkn2a-KO MYB-TR, Rep2

value: Cdkn2a-KO MYB-TR


title: ProxTibia_67Day_S8


title: ProxTibia_67Day_S5


title: Hoxb8 MS5, Cdkn2a-KO MYB-WT, Rep3


title: Lumbar-E74-BR3_S6


title: Hoxb8 MS5, Cdkn2a-KO MYB-TR, Rep1


title: Patient_17_Day_60-11, Itacitinib Treated, Day 60_GEX

description: 10x Genomics


title: Lumbar-E72-BR2_S4


title: Hoxb8 MS5, Cdkn2a-KO MYB-PLEKHO1, Rep3

value: Cdkn2a-KO MYB-PLEKHO1


title: Patient_24_Day_60-14, Itacitinib Treated, Day 60_GEX

description: 10x Genomics


title: Hoxb8 MS5, Cdkn2a-KO MYB-TR, Rep3

value: Hematopoietic


title: Hoxb8 MS5, Cdkn2a-KO MYB-WT, Rep2

value: Hoxb8-FL co-cultured with MS5


title: ProxTibia_54Day_S10


title: ProxRadius_TARGARYEN_57_S14

source_name: ProxRadius

value: ProxRadius


title: Patient_27_Day_28-16, Itacitinib Treated, Day 28_GEX

description: 10x Genomics


title: Patient_17_Day_28-10, Itacitinib Treated, Day 28_GEX

description: 10x Genomics


title: Lumbar-E72-BR1_S2


title: Patient_27_Donor-18, Donor_GEX

description: 10x Genomics


title: Patient_11_Donor-9, Donor_GEX

description: 10x Genomics


title: ProxRadius__67DayBR3_S14


title: ProxTibia_67Day_S10


title: Hoxb8 MS5, Cdkn2a-KO MYB-PLEKHO1, Rep1

value: Male


title: Patient_11_Day_60-8, Itacitinib Treated, Day 60_GEX

description: 10x Genomics


title: ProxRadius_67Day_S14


title: Hoxb8 leukemia, Cdkn2a-WT MYB-PLEKHO1, Rep4

value: Hoxb8-FL derived leukemia


title: ProxTibia_54Day_S8


title: Patient_11_Day_28-7, Itacitinib Treated, Day 28_GEX

description: 10x Genomics


title: ProxRadius_54Day_S12


title: ProxRadius_54Day_S14


title: ProxRadius_STARK_53_S14


title: Control-2-Day-60-16, Control, Day 60_GEX

description: 10x Genomics


title: Hoxb8 leukemia, Cdkn2a-WT MYB-PLEKHO1, Rep3


title: Hoxb8 MS5, Cdkn2a-KO MYB-PLEKHO1, Rep2


title: Control-2-Day-28-15, Control, Day 28_GEX

description: 10x Genomics


title: ProxHumerus_TARGARYEN_57_S12

source_name: ProxHumerus

value: ProxHumerus


title: Hoxb8 leukemia, Cdkn2a-WT MYB-PLEKHO1, Rep1


title: Hoxb8 leukemia, Cdkn2a-WT MYB-PLEKHO1, Rep2


title: ProxHumerus_STARK_53_S12


title: ProxHumerus_LANNISTER_54_S12


title: ProxHumerus__67DayBR3_S12


title: Control-1-Day-60-14, Control, Day 60_GEX

description: 10x Genomics


title: ProxHumerus_67Day_S7


title: ProxRadius_LANNISTER_54_S14


title: ProxHumerus_54Day_S12


title: Hoxb8 leukemia, Cdkn2a-KO MYB-TR, Rep3


title: ProxHumerus_67Day_S12


title: ProxHumerus_54Day_S10


title: ProxRadius_67Day_S12


title: Control-1-Day-28-13, Control, Day 28_GEX

description: 10x Genomics


title: Control_7_Day_60-6, Control, Day 60_GEX

description: 10x Genomics


title: Hoxb8 leukemia, Cdkn2a-KO MYB-TR, Rep4


title: Hoxb8 leukemia, Cdkn2a-KO MYB-TR, Rep2


title: Hoxb8 leukemia, Cdkn2a-KO MYB-TR, Rep1


title: ProxHumerus_67Day_S10


title: ProxFemur_LANNISTER_54_S8

source_name: ProxFemur

value: ProxFemur


title: Hoxb8 leukemia, Cdkn2a-KO MYB-PLEKHO1, Rep4


title: ProxFemur_TARGARYEN_57_S8


title: ProxFemur_STARK_53_S8


title: Control_5_Day_28-1, Control, Day 28_GEX

description: 10x Genomics

value: Blood


title: Hoxb8 leukemia, Cdkn2a-KO MYB-PLEKHO1, Rep2


title: ProxFemur_67Day_S3


title: ProxFemur_54Day_S8


title: Control_6_Day_28-3, Control, Day 28_GEX

description: 10x Genomics


title: Hoxb8 leukemia, Cdkn2a-KO MYB-PLEKHO1, Rep3


title: ProxFemur_67Day_S8


title: ProxFemur_67Day_S6


title: Control_5_Day_60-2, Control, Day 60_GEX

description: 10x Genomics


title: Hoxb8 leukemia, Cdkn2a-KO MYB-PLEKHO1, Rep1


title: 1713398a_7-12_GEX

description: 10x Genomics


title: HeadNeck_TARGARYEN_57_S7

source_name: HeadNeck

value: HeadNeck


title: HeadNeck_STARK_53_S7


title: HeadNeck__67DayBR3_S7


title: HeadNeck_LANNISTER_54_S7


title: Control_6_Day_60-4, Control, Day 60_GEX

description: 10x Genomics


title: HeadNeck__67Day_S2


title: HeadNeck_54Day_S7


title: Hoxb8 in vitro, Undifferentiated, Rep6

value: Hoxb8-FL Undifferentiated

value: Wild-type


title: 1692941a_10-6_GEX

description: 10x Genomics

value: Peripheral Blood


title: Hoxb8 in vitro, Undifferentiated, Rep8


title: ProxFemur__67DayBR3_S8

value: chondrocytes


title: Hoxb8 in vitro, Undifferentiated, Rep7


title: 1703980a_5-9_GEX

description: 10x Genomics


title: HeadNeck_67Day_S7


title: DistTibia_TARGARYEN_57_S11

source_name: DistTibia

value: DistTibia


title: Hoxb8 in vitro, Undifferentiated, Rep5


title: RfxCas13d expressing THP1 cells, pooled lncRNA library, 7 days after dox induction, reps 1 and 2

description: THP1_Day07_R1, THP1_Day07_R2

source_name: peripheral blood

value: peripheral blood

value: cancer cells

value: lncRNAs knockdown

value: doxycycline induction


title: HeadNeck_67Day_S5


title: DistTibia_LANNISTER_54_S11


title: Hoxb8 in vitro, Undifferentiated, Rep4

value: Hematopoietic

value: Female


title: DistTibia_67Day_S11


title: DistTibia_54Day_S9


title: Control_7_Day_28-5, Control, Day 28_GEX

description: 10x Genomics


title: DistTibia_STARK_53_S11


title: DistTibia_67Day_S9


title: DistRadius__67DayBR3_S15

source_name: DistRadius

value: DistRadius


title: DistTibia__67DayBR3_S11


title: 1683278a_14-3_GEX

description: 10x Genomics


title: Hoxb8 in vitro, Undifferentiated, Rep3


title: DistTibia_54Day_S11


title: Hoxb8 in vitro, Undifferentiated, Rep1


title: RfxCas13d expressing THP1 cells, pooled lncRNA library, 14 days after dox induction, reps 1 and 2

description: THP1_Day14_R1, THP1_Day14_R2


title: Donor 4_CoX5_DPCA

city: Singapore

first: Shijun

last: Ma

address: 60 Biopolis St, Singapore 138672

country: Singapore

institute: Genome Institute of Singapore, A*STAR

data_processing:
Raw fastq files were examined for quality using FastQC (v0.11.9) and MultiQC (v1.10).
Paired fastq files were aligned to human genome hg38 using HISAT2 (v2.2.1).
Count were quantified from BAM files using featureCounts (v2.0.2).
Assembly: hg38
Supplementary files format and content: Processed data is saved in csv format with raw counts for different samples.

source_name: CD8 T cell

extract_protocol:
Human CD8 T cells were collected and lysed directly with Trizol (Invitrogen). Total RNA was isolated and purified with the RNeasy Mini Kit (Qiagen, USA). The RNA samples were sent to Novogene AIT (Singapore) for sequencing and mRNA library generation.
Directional mRNA library preparation.

value: CD8 T cell

value: DPCA


title: Hoxb8 in vitro, pDC, Rep8

source_name: Hematopoietic

value: Hoxb8-FL pDC

value: Male


title: RfxCas13d expressing THP1 cells, pooled lncRNA library, before dox induction, reps 1 and 2

description: THP1_Day00_R1, THP1_Day00_R2


title: DistRadius_67Day_S15


title: Hoxb8 in vitro, pDC, Rep6


title: Hoxb8 in vitro, Undifferentiated, Rep2


title: DistRadius_TARGARYEN_57_S15


title: DistRadius_LANNISTER_54_S15


title: DistRadius_STARK_53_S15


title: Donor 4_CoX5_DMSO

value: DMSO


title: Donor 3_CoX5_DPCA


title: Hoxb8 in vitro, pDC, Rep5


title: Hoxb8 in vitro, pDC, Rep7


title: DistRadius_67Day_S9


title: Donor 4_Exp D10_DMSO


title: DistHumerus_TARGARYEN_57_S13

source_name: DistHumerus

value: DistHumerus


title: Hoxb8 in vitro, pDC, Rep3

value: Wild-type


title: Donor 3_Exp D10_DMSO


title: DistTibia_67Day_S6


title: DistRadius_67Day_S13


title: DistRadius_54Day_S15


title: Donor 3_CoX5_DMSO


title: DistRadius_54Day_S13


title: Hoxb8 in vitro, pDC, Rep1


title: Donor 4_Exp D10_DPCA


title: DistHumerus_54Day_S11


title: Donor 1_Hyp_CoX3_PX


title: DistFemur__67DayBR3_S9

source_name: DistFemur

value: DistFemur


title: DistHumerus__67DayBR3_S13

value: chondrocytes


title: DRG, RIP 2

city: Shenzhen

first: Jun

last: Yu

state: Guangdong

address: Xue Yuan, Nanshan

department: Department of Neuroscience

institute: SUSTech

data_processing:
Pair-end sequencing was performed on Illumina platform (Illumina, CA, USA). Clean reads were mapped to the mouse reference genome (GRCm39) using BWA mem (v 0.7.12).
After peak calling using MACS2 (version 2.1.0) software, the distribution of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed. Fold enrichment greater than 2 was considered to be enriched.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: DRG

extract_protocol:
Using EZ-MagnaTM RIP RNA-Binding Protein Immunoprecipitation Kit (Millipore), RNA from E13.5 wildtype mouse DRGs was pulled down by rabbit polyclonal anti-Ybx1 (abcam). RNA was extracted following the protocol of kit.
The library was constructed by Novogene Corporation. Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: DRG

value: Wildtype

tag: rip antibody

value: anti-Ybx1 (abcam)


title: Hoxb8 in vitro, pDC, Rep4

tag: Sex


title: DistHumerus_STARK_53_S13

tag: age


title: DistFemur_LANNISTER_54_S9


title: DistHumerus_67Day_S8


title: Donor 3_Exp D10_DPCA

tag: treatment


title: Hoxb8 in vitro, pDC, Rep2


title: DistHumerus_67Day_S13


title: Donor 1_Hyp_CoX3


title: DistFemur_67Day_S7


title: Donor 2_Hyp_CoX3_PX


title: DistFemur_67Day_S4


title: DistHumerus_67Day_S11


title: DRG, RIP 1


title: Donor 2_Hyp_CoX3


title: DistFemur_TARGARYEN_57_S9


title: DistHumerus_LANNISTER_54_S13


title: DistFemur_STARK_53_S9


title: Acetabulum_TARGARYEN_57_S1

source_name: Acetabulum

value: Acetabulum


title: DRG, Input 2


title: WT, scRNA-seq, rep2

city: Münster

first: Frank

last: Rosenbauer

address: Robert-Koch-Str. 43

department: Institut of Molecular Tumor Biology

institute: University Hospital Münster

data_processing:
Quantification of reads with salmon-alevin against a genome-decoyed (GRCm38) transcriptome (GENCODE vM25) following code in this tutorial from the salmon developers: https://combine-lab.github.io/alevin-tutorial/2020/alevin-velocity/
"Spliced" reads were used for all downstream analysis. See the manuscript, containing a methods section and a link to our GitHub repository that contains full code documentation for preprocessing and downstream analysis in R.
Assembly: GRCm38
Supplementary files format and content: Raw- and normalized counts with column and row annotations for both the "unfiltered" data that went into downstream analysis in R as well as for the "filtered" which is the data after all processing and filtering in downstream analysis was applied.

source_name: bone marrow

extract_protocol:
Mice were sacrified using CO2 inhalation, then one femur was removed. Cells were flused and lysed with ACK to remove erythrocytes. Cells were stained with a lineage cocktail (Cd45r, Cd3, Cd4, Cd8, Cd19, Ter119, Gr1) and c-Kit and then selected as Lin-minus and cKit-plus.
10x Chromium scRNA-seq v3 following the manual.

value: bone marrow

value: WT


title: DistFemur_67Day_S9


title: Donor 2_Norm_CoX3


title: Acetabulum_STARK_53_S1


title: DRG, Input 1


title: Donor 2_Hyp_CoX1


title: WT, scRNA-seq, rep1


title: DistHumerus_54Day_S13


title: URE, scRNA-seq, rep2

value: UREd/d


title: DistFemur_54Day_S9


title: Donor 1_Norm_CoX3


title: Acetabulum_LANNISTER_54_S1


title: Donor 1_Norm_CoX1


title: H06_ProxRadius_54A_S48

data_processing:
RNA-seq read mapping; Salmon version 0.14.0; salmon -l A --numBootstraps 100 --gcBias ?validateMappings
Read abundance normalization ; DESeq2 version 1.26.0;
Assembly: hg19
Supplementary files format and content: Raw and normalized abundance counts

extract_protocol:
RNA was extracted with Tryzol and submitted for Kapa (Roche) cDNA library preparation
Kapa Library Preparation for RNA-seq

treatment_protocol: Samples were prepared using Kappa (Roche) library preparation

value: ProxRadius


title: Donor 1_Hyp_CoX1

value: CD8 T cell


title: Acetabulum_67Day_S1


title: Donor 2_Exp_D12


title: Acetabulum_67DayBR3_S1


title: Acetabulum_54Day_S1


title: H04_Acetabulum_57B_S32


title: Donor 2_Norm_CoX1


title: H11_ProxRadius_53A_S88


title: WT LSK, ATAC-seq, rep1

data_processing:
Reads were trimmed from the Nextera adapter sequence (CTGTCTCTTATACACATCT) with cutadapt and mapped to GRCm38 with bowtie2 (--very-sensitive).
Duplicates were marked with SAMblaster. Only non-duplicate alignment to primary chromosomes (excl. chrM and random/unplaced contigs) were kept.
Peaks were called on alignments with insert size < 100bp using Genrich on each group separately with a FDR of 0.001 and filtered against a combined blacklist of ENCODE artifact regions and mitochondrial homologs in the mouse genome.
Peaks per group were combined with bedtools merge and a matrix of raw counts was created using featureCounts (--read2pos 5) using the filtered BAM files including all (that is non size-selected) alignments after applying filtering as described above. This count matrix is provided in the supplement of this submission as "raw_counts.txt.gz".
Assembly: GRCm38
Supplementary files format and content: Matrix of raw counts with 1-based peak coordinates created by featureCounts

extract_protocol:
ATAC-seq with the OmniATAC protocol (Corces et al. 2017 -- https://doi.org/10.1038/nmeth.4396) with the exception that KAPA HiFi HotStart Ready Mix was used as a polymerase.
See OmniATAC protocol.

value: LSK


title: H12_DistTibia_53A_S96

value: DistTibia


title: H05_DistFemur_53A_S40


title: WT GMP, ATAC-seq, rep3

value: GMP


title: WT LSK, ATAC-seq, rep3


title: WT LSK, ATAC-seq, rep2


title: Donor 1_Sti_D5


title: F12_DistHumerus_53A_S94


title: G12_Acetabulum_57C_S95


title: Donor 1_Exp_D12


title: G06_DistTibia_57C_S47


title: F07_ProxTibia_54B_S54

value: ProxTibia


title: H07_DistRadius_57A_S56

value: DistRadius


title: Donor 2_Sti_D5


title: G05_ProxHumerus_57B_S39

value: ProxHumerus


title: F11_DistRadius_53A_S86


title: URE, scRNA-seq, rep1


title: WT GMP, ATAC-seq, rep2


title: MDA-MB-231 cells, VIM-/-, rep3

city: Taipei

first: Ke-Wei

last: PAN

address: No. 155, Sec. 2, Linong St. Beitou Dist., Taipei City 112304, Taiwan

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
The original data obtained by high-throughput sequencing were transformed into raw sequenced reads by CASAVA base calling and stored in FASTQ format.
The obtained raw paired-end reads were filtered by Trimmomatic to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30.
The obtained high-quality data (clean reads) was used for subsequent analysis. Read pairs from each sample were aligned to the reference genome (e.g., H. sapiens, GRCh38) by the HISAT2 software.
For gene expression, the “Trimmed Mean of M-values” normalization (TMM) was performed DEGseq without biological duplicate and the “Relative Log Expression” normalization (RLE) was performed using DESeq2 with biological duplicate.
Differentially expressed genes (DEGs) analysis of two conditions was performed in R using DEGseq (without biological replicate) and DESeq2 (with biological replicate), which based on negative binomial distribution and Poisson distribution model, respectively.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes read counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: Breast

growth_protocol: MDA-MB-231 cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was isolated using the Quick-RNA™ Miniprep Kit.RNA Purity and quantification were checked using SimpliNanoTM - Biochrom Spectrophotometers (Biochrom, MA, USA). RNA degradation and integrity were monitored by Qsep 100 DNA/RNA Analyzer (BiOptic Inc., Taiwan). A total amount of 1 μg total RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Roche, Basel, Switzerland) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Breast

value: triple-negative breast cancer (TNBC) cell

value: VIM-/-


title: WT GMP, ATAC-seq, rep1


title: F06_ProxRadius_57B_S46

value: chondrocytes


title: Donor 2_Unsti_D0


title: E12_ProxHumerus_53A_S93


title: URE LSK, ATAC-seq, rep2


title: F03_Acetabulum_59_S22


title: E06_DistTibia_54B_S45


title: E11_ProxTibia_54A-redo_S85


title: URE GMP, ATAC-seq, rep3


title: E07_DistHumerus_54B_S53

value: DistHumerus


title: URE LSK, ATAC-seq, rep3


title: E04_Acetabulum_53A_S29

value: Acetabulum


title: URE LSK, ATAC-seq, rep1

value: bone marrow


title: E08_Acetabulum_54B_S61


title: F02_DistRadius_59_S14


title: MDA-MB-231 cells, VIM-/-, rep1


title: MDA-MB-231 cells, VIM-/-, rep2


title: URE GMP, ATAC-seq, rep2


title: E05_ProxFemur_54A_S37

value: ProxFemur


title: MDA-MB-231 cells, VIM+/+, rep3

value: VIM+/+


title: F05_DistTibia_57B_S38


title: E03_ProxHumerus_59_S21


title: MDA-MB-231 cells, VIM+/+, rep2


title: E02_Acetabulum_57A_S13


title: URE GMP, ATAC-seq, rep1

value: UREd/d


title: Donor 1_Unsti_D0

value: CD8 T cell


title: MDA-MB-231 cells, VIM+/+, rep1


title: D08_DistTibia_59_S60


title: D04_DistHumerus_54A_S28


title: D03_DistHumerus_57A_S20


title: CVST-7d-5

city: Wuhan

first: Ding

last: rui

address: 99 Zhang Zhidong Street

institute: Renmin Hospital of Wuhan University

data_processing:
Basecalling is performed by Illumina RTA software in sequencer.
Raw data (raw reads) of FASTQ format were firstly processed through fastp to generate clean reads.
Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Differential expression analysis of two conditions/groups (five biological replicates per condition) was performed using the DESeq2 R package (1.16.1).Genes with an  P-value <0.05 found by DESeq2 were assigned as differentially expressed.
GO and KEGG enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package.
Assembly: mm39
Supplementary files format and content: Fragments Per Kilo bases per Million mapped Reads (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene
Supplementary files format and content: Excel spreadsheet of differentially expressed genes

source_name: cerebral cortex

growth_protocol: Animals were housed in a specific pathogen-free laboratory with fixed 12-h light/dark cycles under controlled temperature and humidity conditions (22 ± 1°C; 45–55%)

extract_protocol:
At the set time points, fresh tissue samples from the bilateral cerebral cortex of mice were collected and rapidly frozen in liquid nitrogen, and then stored in a -80 ℃ refrigerator. After the tissues were homogenized, total RNA was extracted employing Trizol reagent (Invitrogen, CA, USA). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
Total RNA samples were converted into cDNA libraries using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (Catalog E7530L, NEB, USA) following the manufacturer's recommendations

value: cerebral cortex


title: shEGFR-WT-3 rep3

city: Tucson

first: Angelica

last: Escoto

state: AZ

address: 1007 E Lowell St

department: Molecular & Cellular Biology

institute: University of Arizona

data_processing:
Bam files were aligned using reference genome hg38
Counts were extracted from .bam files
Features were combined into one matrix, and those features with less than 10 counts across all rows were dropped
Counts were run through DESeq2 with results chosen based on alpha of 0.05 for the following comparisons: SNX1.3 vs. EGF, ERL vs. EGF, shEGFR-NLS vs. shEGFR-WT
Assembly: hg38
Supplementary files format and content: Bam files: aligned bam files using reference genome hg38 used for further processing
Supplementary files format and content: Tab-delimited text files includes raw counts for each sample

extract_protocol:
RNA was harvested and extracted by Azenta Life Sciences
RNA libraries for RNA-Seq were prepared by Azenta Life Sciences


title: D02_DistHumerus_59-redo_S12


title: CVST-7d-4


title: shEGFR-WT-2 rep2


title: CVST-7d-3


title: C05_ProxHumerus_54A_S35


title: shEGFR-WT-1 rep1


title: C03_ProxRadius_57A_S19

value: ProxRadius


title: CVST-7d-2


title: B09_ProxTibia_53A_S66

source_name: ProxTibia


title: CVST-7d-1


title: B12_DistFemur_54B_S90

value: DistFemur


title: B10_HeadNeck_54B_S74

value: HeadNeck


title: shEGFR-NLS-3 rep3


title: shEGFR-NLS-2 rep2


title: B07_ProxTibia_57B_S50

value: ProxTibia


title: CVST-2d-5


title: B06_ProxRadius_57C_S42

source_name: ProxRadius


title: B05_DistRadius_57B_S34

value: DistRadius


title: shEGFR-NLS-1 rep1


title: ERL-3 rep3


title: B02_ProxHumerus_54B_S10

source_name: ProxHumerus

value: ProxHumerus


title: CVST-2d-3


title: B01_ProxHumerus_57A_S98


title: C09_ProxRadius_54B_S67


title: ERL-2 rep2


title: A12_DistTibia_54A-redo_S89

value: DistTibia


title: CVST-2d-2


title: A10_ProxFemur_54B_S73

source_name: ProxFemur


title: C02_ProxTibia_59_S11


title: A08_DistRadius_54A_S57


title: A07_HeadNeck_53A_S49

source_name: HeadNeck


title: CVST-2d-1


title: B08_ProxFemur_57B_S58


title: EGF-3 rep3


title: 8_H01_Acetabulum_54A_S8


title: sham-4

value: sham


title: EGF-2 rep2


title: 7_G01_DistRadius_54B_S7

value: chondrocytes


title: sham-2


title: CVST-2d-4


title: sham-3


title: 6_F01_HeadNeck_59_S6


title: 2_B01_ProxTibia_57C_S2


title: sham-1


title: cSNX-2 rep2


title: 1_A01_HeadNeck_57B_S1


title: ERL-1 rep1


title: 124_A07_HeadNeck_53A-redo_S124


title: 5_E01_DistHumerus_57C_S5

value: DistHumerus


title: Organoid_AKPS_3

first: Ramesh

middle: A.

last: Shivdasani

address: 450 Brookline Ave. SM1060

department: Medical Oncology

data_processing:
The libraries were aligned using bowtie (version 2.3.4.3).
Peak calling was performed using MACS2 (version 2.1.2).
Analysis of enrichment in called peaks was performed using DEseq2 (version 1.22.2).
Assembly: mm10
Supplementary files format and content: The processed files are in the bigWig format.

source_name: Small intestine

extract_protocol:
For the primary cells, epithelium was isolated using a 5mM EDTA chelation at 4°C for 30 minutes followed by disaggregation in 3mg/mL Type 2 Collagenase in HBSS at 37°C for 30 minutes. ISCs were then isolated via flow cytometry. The organoids were disaggregated using 5mM EDTA and mechanical dissociation followed by flow cytometry for ISC isolation.
The ATAC-seq libraries were constructed using the Omni-ATAC-seq protocol using the Nextera kit (Illumina).

value: Small intestine

value: Intestinal stem cells (organoids)

value: Apc mutant/mutant, KrasG12D, Tp53 mutant/mutant, Smad4 mutant/mutant


title: Organoid_AKPS_2


title: 4_D01_ProxTibia_57A_S4


title: cSNX-3 rep3


title: control patient, male, sampling age 67, ID=C859

city: Kuopio

first: Kai

last: Kaarniranta

address: Yliopistonrinne 3

department: Department of Ophthalmology

country: Finland

institute: University of Eastern Finland

data_processing:
FIMM-RNAseq 2.0.7 workflow
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing raw counts for each Sample

source_name: Blood

extract_protocol:
RNA was extracted using Maxwell® RSC 48 Instrument and Maxwell RSC miRNA Plasma and Serum Kit, including a DNase treatment.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA with Ribo-Zero Plus.

tag: patient group

value: control

value: Blood

value: male

tag: bmi

tag: smoking habit

value: random

tag: age at_sampling


title: A06_DistFemur_54A_S41


title: cSNX-1 rep1


title: 123_B03_DistHumerus_57B-redo_S123


title: 122_H02_ProxRadius_59-redo_S122

value: ProxRadius


title: 120_H03_ProxFemur_59_S120

value: ProxFemur


title: Organoid_AKPS_1


title: control patient, male, sampling age 69, ID=C857

value: active


title: 126_F09_ProxFemur_53A-redo_S126


title: 114_B03_DistTibia_57A_S114

source_name: DistTibia


title: control patient, male, sampling age 57, ID=C856


title: 112_H02_DistFemur_59_S112

value: DistFemur


title: EGF-1 rep1


title: 117_E03_HeadNeck_57C_S117

value: HeadNeck


title: Organoid_AK_L2

treatment_protocol: ISCs sorted from Apc null and KrasG12D organoids.

value: Apc mutant/mutant, KrasG12D


title: Organoid_M36_AKP

treatment_protocol: ISCs sorted from Apc/Tp53 null and KrasG12D organoids.

value: Apc mutant/mutant, KrasG12D, Tp53 mutant/mutant


title: Organoid_AKP_L2


title: control patient, female, sampling age 81, ID=C855

value: female


title: 109_E02_HeadNeck_57A_S109

value: chondrocytes


title: 110_F02_ProxHumerus_57C_S110

value: ProxHumerus


title: 103_G01_ProxFemur_57C_S103


title: 104_H01_DistRadius_57C_S104

source_name: DistRadius

value: DistRadius


title: control patient, male, sampling age 69, ID=C854


title: Organoid_M16_AK_2

value: Small intestine

value: Intestinal stem cells (organoids)


title: control patient, female, sampling age 83, ID=C858

value: control

value: no


title: H,H-GFP,embryonic,Exp1,ChIP2

city: Seattle

first: Louis

last: Gevirtzman

state: WA

address: 3720 15th Ave NE

department: Genome Science

institute: University of Washington

description: TF co-regulator

data_processing:
alignment with BWA Version: 0.7.17-r1188
peak calling with SPP Version 1.15.5
Irreproducible Discovery Rate (IDR) Version 2.0.4.2
Signal tracks using macs2 version 2.2.4 for read pileup
Assembly: dm6
Supplementary files format and content: bigWig, narrowPeak, html

source_name: H-GFP

extract_protocol:
Fly growth was performed as described previously for the modENCODE and modERN projects Kudron et al., 2018(PMID: 29284660). Transgenic flies were expanded in vials and bottles containing standard Drosophila media at ~22℃ and larvae, white pre-pupae(WPP) and adults were collected from these expansion vials. Pupae were obtained by collecting WPP and incubating for 1-2 days at ~22℃. For embryonic collections, 0-8 day old adult flies were moved to embryo cages capped with apple juice plates. After a 24 hour hours, apple juice plates were replaced at appropriate intervals, restricting the collected embryos to their desired developmental stages. For late embryonic stages, collection plates were removed and embryos were grown at room temperature until the desired stage was reached prior to chromatin collection.    Chromatin was collected and ChIP was performed using the goat anti-GFP as described previously Kudron et al., 2018 (PMID: 29284660).  However, later experiments were performed using Ab290 (Abcam) and denoted as such in Kudron et al., 2024;
Library preparation during the modENCODE and early stages of the modERN project were performed as previously described in Zhong et al. 2010 (PMID: 20174564); Niu et al. 2011 (PMID: 21177963); Kasper et al. 2014(PMID: 25373775); and Kudron et al., 2018(PMID: 29284660). More recently, chromatin has been prepared for sequencing using the following methods at the Yale Center for Genome Analysis (Kudron et al., 2024 Supplemental_File_S1). ChIP and input control samples (genomic DNA from the same sample) for two technical replicates for worm and three for fly were used for library construction using approximately 5-10ng of DNA after the samples were end-repaired, A-tailed, adapter ligated and PCR enriched (8 -10 cycles) (KAPA Biosystems, Part#KK8504).  Indexed libraries were quantified by qPCR (KAPA Biosystems, Part#KK4854) and inserts were distributed by size using the Caliper LabChip GX system.  Samples that had a concentration of ≥0.5 ng/ul were used for sequencing.  Samples were normalized to 10 nM and sequenced using 100bp paired-end sequencing on an Illumina HiSeq NovaSeq Sequencer achieving > 5 million reads passing filter clusters.  A positive control provided by Illumina is spiked into every lane at a concentration of 0.3% to monitor quality in real time. Sequencing data that passed internal quality controls at YCGA were transferred to the Waterston Lab for downstream processing.

tag: strain

value: H-GFP

value: y[1] w[*]; PBac{y[+mDint2] w[+mC]=H-GFP.FPTB}VK00037

value: site-specific recombination

tag: developmental stage

value: embryonic

tag: chip antibody


title: H,H-GFP,embryonic,Exp1,Input1

description: TF co-regulator


title: control patient, male, sampling age 79, ID=C853

tag: tissue

value: Blood

value: male


title: H,H-GFP,embryonic,Exp1,ChIP1

description: TF co-regulator


title: H,H-GFP,embryonic,Exp1,ChIP3

description: TF co-regulator


title: 119_G03_DistFemur_57B_S119

value: DistFemur


title: control patient, male, sampling age 76, ID=C852

value: random


title: Organoid_M16_AK_1

value: Apc mutant/mutant, KrasG12D


title: 116_D03_HeadNeck_54A_S116

value: HeadNeck


title: Organoid_ApcKO_C_HS

treatment_protocol: ISCs sorted from Apc null organoids generated with CRISPR.

value: Apc mutant/mutant


title: elB,elB-GFP,embryonic,Exp1,Input1

description: basal TF

source_name: elB-GFP

value: elB-GFP

value: y[1] w[*]; PBac{y[+mDint2] w[+mC]=elB-GFP.FPTB}VK00031


title: control patient, female, sampling age 81, ID=C851

value: female


title: elB,elB-GFP,embryonic,Exp1,ChIP4

description: basal TF


title: control patient, female, sampling age 72, ID=C850


title: Organoid_ApcKO_C_G

value: Small intestine

value: Intestinal stem cells (organoids)


title: Organoid_ApcKO_Flox

treatment_protocol: ISCs sorted from Apc null organoids generated using Cre-LoxP.


title: elB,elB-GFP,embryonic,Exp1,ChIP1

description: basal TF


title: 100_D01_DistFemur_57C_S100

source_name: DistFemur

value: chondrocytes


title: control patient, male, sampling age 78, ID=C849

value: control


title: Dsp1,Dsp1-GFP,embryonic,Exp1,Input1

description: chromatin factor


title: Dsp1,Dsp1-GFP,embryonic,Exp1,ChIP2

description: chromatin factor


title: Organoid_M36_WT_Rep2

value: Intestinal stem cells

value: WT


title: Organoid_M36_AK


title: Dsp1,Dsp1-GFP,embryonic,Exp1,ChIP3

description: chromatin factor

value: site-specific recombination

value: embryonic


title: Dsp1,Dsp1-GFP,embryonic,Exp1,ChIP1

description: chromatin factor


title: Organoid_M36_WT_Rep1


title: control patient, female, sampling age 73, ID=C847

value: Blood

value: no


title: control patient, female, sampling age 76, ID=C846


title: hmga1a mutant plate 3

city: Utrecht

first: Mara

last: Bouwman

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
HUB-DB-007_HNWVVBGX9_S6
scRNAseq_Hmga1a_mutant_modules

data_processing:
Based on the distribution of the log10 total reads plotted against the frequency, we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells (653 wildtype and 657 hmga1a-/- cells). Next, single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes, dimensions = 8, resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two-dimensional UMAP.
Monocle2 was used to identify genes that were differentially expressed over pseudo-time and organized in a self-organizing map with of 8 modules. Pseudo-temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules.
Assembly: danrer9
Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module
Supplementary files format and content: count tables transcriptcounts

organism: Danio rerio

source_name: adult heart

extract_protocol:
Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates, each well containing 1 cell, containing Vapor-Lock oil with CEL-Seq2 barcoded primers, spike-in mRNA and dNTPs (Single Cell Discoveries). Plates were spun down and frozen at -80oC until ready for library prep.
Single-cell sequencing libraries were prepared by Single Cell Discoveries (Utrecht, The Netherlands) using the SORT-seq protocol . The CEL-Seq2 protocol was used for library prep (Hashimshony et al., 2016)). Illumina sequencing libraries were prepared with the TruSeq small RNA primers (Illumina) and paired-end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384-well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.

treatment_protocol: cryoinjury was performed 7 days before hearts were extracted

value: adult heart

value: hmga1a mutant

value: (border zone) cardiomyocytes

value: 7 days post cryoinjury


title: control patient, female, sampling age 83, ID=C848


title: wildtype plate 3

description:
HUB-DB-006_HNWVVBGX9_S5
scRNAseq_Hmga1a_mutant_modules

value: wildtype


title: Organoid_M16_WT

city: Boston


title: wildtype plate 2

description:
HUB-DB-005_HNWVVBGX9_S4
scRNAseq_Hmga1a_mutant_modules


title: hmga1a mutant plate 4

description:
HUB-DB-008_HNWVVBGX9_S7
scRNAseq_Hmga1a_mutant_modules


title: control patient, female, sampling age 82, ID=C845

value: random


title: hmga1a mutant plate 2

description:
HUB-DB-004_AHVKTGBGX7_S7
scRNAseq_Hmga1a_mutant_modules


title: elB,elB-GFP,embryonic,Exp1,ChIP2

description: basal TF

value: elB-GFP

value: y[1] w[*]; PBac{y[+mDint2] w[+mC]=elB-GFP.FPTB}VK00031


title: elB,elB-GFP,embryonic,Exp1,ChIP3

description: basal TF


title: Organoid_M21_WT

value: Small intestine


title: control patient, male, sampling age 80, ID=C844

value: male


title: ISC-Cre_ApcNull_KrasG12D_P53Null_Rep1

treatment_protocol: Treated with 2x 1mg tamoxifen and primary ISCs from the proximal third of the small intestine were isolated 10 dpi.

value: Intestinal stem cells (proximal third of small Intestine)

value: 2x 1mg tamoxifen

tag: time point

value: 10 dpi


title: Hmga1a overexpression sample 4

description: Fastqs have been demultiplexed, hence no R1 and R2 separate files

data_processing:
FASTQ files were mapped with the STARandGO pipeline (https://github.com/anna-alemany/VASAseq/blob/main/mapping/map_star.sh) against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation.
Normalization and downstream analysis were performed in R. Due to low read-count, samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR, differentially expressed genes were obtained (FC <-1 or >1 and Pval<0.05).
Gene lists were subjected to GO analysis using the online tool DAVID.
Assembly: danrer11
Supplementary files format and content: excel file containing edgeR results and GO analysis results
Supplementary files format and content: count table spliced transcriptcounts

extract_protocol: Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.

treatment_protocol: zebrafish were treated with tamoxifen to induce Hmga1a overexpression

tag: genotype 1

tag: genotype 2

value: Hmga1a overexpression

tag: cell type

value: cardiomyocytes

value: 14 days post tamoxifen


title: ISC-Cre_ApcNull_KrasG12D_P53Null_Rep2

tag: genotype


title: control patient, female, sampling age 76, ID=C843

value: control

value: Blood

value: female

value: no


title: Hmga1a overexpression sample 3

value: adult heart


title: ISC-Cre_ApcNull_KrasG12D_Rep4


title: control patient, female, sampling age 80, ID=C842


title: Hmga1a overexpression sample 1


title: ISC-Cre_ApcNull_KrasG12D_Rep3


title: control sample 4


title: control sample 3


title: ISC-Cre_ApcNull_KrasG12D_Rep2


title: control sample 2


title: control patient, female, sampling age 75, ID=C840


title: control sample 1


title: ISC-Cre_ApcNull_KrasG12D_Rep1


title: zebrafish 14dpi heart3

description: 14dpi zebrafish heart 3 tomoseq

data_processing:
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2) with default parameters.
The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike-ins in sense direction. Reads mapping equally to multiple loci were discarded.
Mapped reads were assigned to sections based on barcodes according to the CEL-seq protocol (Hashimshony et al., Cell Reports, 2012)
processed data files contain transcript read counts normalized against spike-in read count and total read count per section
Assembly: GRCm38 for mouse, danrer9 for zebrafish
Supplementary files format and content: csv file containing transcript counts per gene (rows) and section (columns)
Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish

extract_protocol:
Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL-seq protocol (Hashimshony et al., Cell Reports, 2012) see also: Junker et al., 2014, Cell
CEL-seq protocol (Hashimshony et al., Cell Reports, 2012); also  see: Junker et al., 2014, Cell

treatment_protocol: Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned, and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. (2014) Cell.

tag: transgenic background

value: wildtype

tag: section thickness

value: Took every section

tag: section direction

value: from injured area into the remote myocardium

value: cryoinjury

tag: timepoint


title: ISC-Cre_LowDoseTam_ApcNull_Rep2

treatment_protocol: Treated with 2x 0.1mg tamoxifen and primary ISCs from the distal third of the small intestine were isolated 14 dpi.

value: Small intestine

value: Intestinal stem cells (distal third of small Intestine)

tag: treatment

value: 2x 0.1mg tamoxifen

value: 14 dpi


title: hmga1a mutant plate 1

description:
HUB-DB-003_AHVKTGBGX7_S6
scRNAseq_Hmga1a_mutant_modules

value: hmga1a mutant

value: (border zone) cardiomyocytes

value: 7 days post cryoinjury


title: control patient, male, sampling age 84, ID=C839

tag: patient group

tag: Sex

value: male

tag: bmi


title: zebrafish 14dpi heart2

description: 14dpi zebrafish heart 2 tomoseq


title: control patient, female, sampling age 73, ID=C838

value: control

tag: smoking habit

tag: age at_sampling


title: zebrafish 7dpi heart3

description: 7dpi zebrafish heart 3 tomoseq


title: ISC-Cre_LowDoseTam_ApcNull_Rep1


title: wildtype plate 1

description:
HUB-DB-001_AHVKTGBGX7_S5
scRNAseq_Hmga1a_mutant_modules


title: zebrafish 7dpi heart2

description: 7dpi zebrafish heart 2 tomoseq


title: control patient, female, sampling age 70, ID=C837

value: Blood

value: active


title: Hmga1a overexpression sample 2

value: Hmga1a overexpression

value: cardiomyocytes

value: 14 days post tamoxifen


title: zebrafish 7dpi heart1

description: 7dpi zebrafish heart 1 tomoseq

value: adult heart

value: wildtype

value: Took every section


title: control patient, female, sampling age 74, ID=C836

value: female

value: random


title: zebrafish 3dpi heart3

description: 3dpi zebrafish heart 3 tomoseq

value: from injured area into the remote myocardium

value: cryoinjury


title: zebrafish 3dpi heart1

description: 3dpi zebrafish heart 1 tomoseq


title: zebrafish 3dpi heart2

description: 3dpi zebrafish heart 2 tomoseq


title: WT_Ileal_ISC_Rep1

treatment_protocol: Treated with 2x 1mg tamoxifen and primary ISCs from the distal third of the small intestine were isolated 14 dpi.

value: Small intestine

value: Intestinal stem cells (distal third of small Intestine)

value: 2x 1mg tamoxifen

value: 14 dpi


title: control patient, female, sampling age 76, ID=C841

value: control

value: no


title: control patient, male, sampling age 72, ID=C835

value: Blood

value: male


title: Sec-Cre_ApcNull_Ileum_ISC_Rep4

treatment_protocol: Treated with 2x 1mg tamoxifen and primary ISCs from the distal third of the small intestine were isolated 21 dpi.

value: 21 dpi


title: zebrafish 14dpi heart1

description: 14dpi zebrafish heart 1 tomoseq


title: control patient, female, sampling age 83, ID=C834


title: Sec-Cre_ApcNull_Ileum_ISC_Rep3


title: control patient, female, sampling age 72, ID=C833


title: Sec-Cre_ApcNull_Ileum_ISC_Rep2


title: control patient, female, sampling age 77, ID=C832


title: control patient, female, sampling age 82, ID=C831


title: 26wk_Cancellous_Contralateral Control Limb_5d2_Animal5dAD

city: Ithaca

first: Carolyn

last: Chlebek

address: 110 Hoy Road

department: Biomedical Engineering

institute: Cornell University

data_processing:
Sequence reads were trimmed for adaptor sequence. 12bp were trimmed from the 5' end for quality assurance.
Trimmed sequence reads were mapped to mm10 using STAR (parameters- outFilterMismatchNmax: 2 - outFilterMultimapNmax: 1)
Fastqc was run for all files and only samples with high quality from both fastqc & RQN were included for analysis
Each sample contained over 1 million reads. Genes with less than 3 counts per million were not included for analysis.
Normalized gene counts were calculated in DESeq2 with Trimmed Mean of M-values correction
Assembly: mm10
Supplementary files format and content: .xlsx file with normalized gene counts and experimental conditions for each samle

source_name: Cancellous

extract_protocol:
Cancellous bone was separated from the cortical shell. The cortical bone was segmented into three sections: metaphyseal cortex, proximal diaphysis, and mid-diaphysis,and the metaphyseal cortex and mid-diaphysis were then analyzed. All tissues were flash frozen in liquid nitrogen. Samples were pulverized and RNA  isolated using a phenol-chloroform extraction followed by the RNeasy kit (Qiagen).
RNA libraries were prepared for 3' mRNA-seq

treatment_protocol: 10- and 26-week-old female C57Bl/6J were subjected to in vivo mechanical loading of the left tibia (9N peak load at 4 Hz for 1200 cycles per day). Mice were euthanized by cervical dislocation at 1-hour, 3-hours, or 24-hours following the completion of one bout of loading. To evaluate long term time points, a final group received 5 consecutive days of loading with euthanasia on the eighth day following the first loading session

tag: sample number

value: Cancellous

tag: loaded

value: R

tag: animal number

tag: age

value: Adult

value: Contralateral Control Limb_5d2


title: 26wk_Mid-Diaphysis_Contralateral Control Limb_5d2_Animal5dAF

source_name: Mid-Diaphysis

tag: tissue

value: Mid-Diaphysis


title: 26wk_Metaphyseal Shell_Contralateral Control Limb_5d2_Animal5dAD

source_name: Metaphyseal Shell

value: Metaphyseal Shell


title: 26wk_Metaphyseal Shell_Loaded Limb_5d2_Animal5dAE

value: L


title: 26wk_Cancellous_Loaded Limb_5d2_Animal5dAE


title: WT_Ileal_ISC_Rep2

tag: cell type

tag: time point


title: 26wk_Mid-Diaphysis_Contralateral Control Limb_5d2_Animal5dAE

tag: genotype


title: 26wk_Mid-Diaphysis_Loaded Limb_5d2_Animal5dAE


title: Sec-Cre_ApcNull_Ileum_ISC_Rep1


title: ISC-Cre_ApcNull_Duod_ISC_Rep1

treatment_protocol: Treated with 2x 1mg tamoxifen and primary ISCs from the proximal third of the small intestine were isolated 14 dpi.

value: Intestinal stem cells (proximal third of small Intestine)


title: 26wk_Metaphyseal Shell_Loaded Limb_5d2_Animal5dAD


title: 26wk_Cancellous_Loaded Limb_5d2_Animal5dAD


title: control patient, male, sampling age 73, ID=C829


title: 26wk_Mid-Diaphysis_Contralateral Control Limb_5d2_Animal5dAC


title: 26wk_Metaphyseal Shell_Contralateral Control Limb_5d2_Animal5dAC


title: Lgr5DTR-GFP_WT_Ileal_InVivo_ISC_Rep2

data_processing:
Processed with the Viper Pipeline using the default parameters using STAR.
Additional analysis was performed on the STAR counts using DEseq2 (version 1.22.2).
Assembly: mm10
Supplementary files format and content: *.tab: Tab-delimited text files with STAR counts.

extract_protocol:
Epithelium was isolated from the duodenum of adult mice using a 5mM EDTA chelation for 30 minutes at 4°C followed by disaggregation with 4x TrypLE Select for 30 minutes at 37°C for the Lgr5_ApcKO samples while the others were incubated in Type 2 collagenase at 3mg/mL in HBSS for 30 minutes at 37°C. For the primary cells, ISCs were isolated using flow cytometry while the whole organoids were collected for RNA. The RNA was isolated using Trizol extraction followed by column purification using RNeasy Plus micro kit (Qiagen).
Libraries were prepared using the NEBnext Ultra II non-directional library kit (New England Biolabs E7770S).

treatment_protocol: Treated with 2x 1mg tamoxifen and primary ISCs were isolated 21 dpi.

value: Small intestine

value: Ileal intestinal stem cell


title: control patient, male, sampling age 75, ID=C828

value: random


title: 26wk_Cancellous_Contralateral Control Limb_5d2_Animal5dAC


title: 26wk_Metaphyseal Shell_Contralateral Control Limb_5d2_Animal5dAE


title: 26wk_Cancellous_Contralateral Control Limb_5d2_Animal5dAE


title: 26wk_Mid-Diaphysis_Loaded Limb_5d2_Animal5dAF


title: control patient, female, sampling age 78, ID=C827

value: female


title: 26wk_Mid-Diaphysis_Loaded Limb_5d2_Animal5dAC


title: control patient, female, sampling age 79, ID=C830

value: control


title: 26wk_Metaphyseal Shell_Loaded Limb_5d2_Animal5dAC


title: ISC-Cre_ApcNull_Duod_ISC_Rep2

value: 2x 1mg tamoxifen

value: 14 dpi


title: control patient, female, sampling age 77, ID=C826

value: Blood


title: 26wk_Metaphyseal Shell_Contralateral Control Limb_5d2_Animal5dAB


title: 26wk_Cancellous_Contralateral Control Limb_5d2_Animal5dAB


title: Sec-Cre_ApcNull_InVivo_ISC_Rep1

value: 21 dpi


title: 26wk_Cancellous_Loaded Limb_5d2_Animal5dAB

value: Cancellous


title: WT_Organoid_Rep2

treatment_protocol: Treated with 2x 1mg tamoxifen followed by plating ileal crypts 10dpi in organoid culture.

value: Whole organoid

value: WT

value: 10 dpi


title: control patient, female, sampling age 81, ID=C822

value: no


title: 26wk_Metaphyseal Shell_Loaded Limb_5d2_Animal5dAB

value: Metaphyseal Shell

value: Adult


title: control patient, female, sampling age 74, ID=C824


title: 26wk_Mid-Diaphysis_Contralateral Control Limb _3h _Animal3h06

value: Mid-Diaphysis

value: R

value: Contralateral Control Limb _3h


title: 26wk_Cancellous_Loaded Limb_5d2_Animal5dAC

value: L


title: ISC-Cre_ApcNull_Organoid_Rep2

value: Small intestine


title: 26wk_Cancellous_Contralateral Control Limb _3h _Animal3h06


title: 26wk_Mid-Diaphysis_Loaded Limb _3h _Animal3h06

value: Loaded _3h


title: control patient, female, sampling age 63, ID=C818

value: control

value: female


title: 26wk_Metaphyseal Shell_Contralateral Control Limb _3h _Animal3h06


title: 26wk_Metaphyseal Shell_Loaded Limb _3h _Animal3h06


title: ISC-Cre_ApcNull_Organoid_Rep1

value: 2x 1mg tamoxifen


title: 26wk_Cancellous_Loaded Limb _3h _Animal3h06


title: control patient, female, sampling age 72, ID=C817

value: Blood


title: WT_Organoid_Rep1


title: 26wk_Mid-Diaphysis_Contralateral Control Limb _24h _Animal24hONext

value: Contralateral Control Limb _24h


title: 26wk_Metaphyseal Shell_Contralateral Control Limb _24h _Animal24hONext


title: Sec-Cre_ApcNull_InVivo_ISC_Rep2

value: Ileal intestinal stem cell

value: 21 dpi


title: control patient, female, sampling age 84, ID=C816


title: Sec-Cre_ApcNull_Organoid_Rep1

value: Whole organoid

value: 10 dpi


title: 26wk_Cancellous_Contralateral Control Limb _24h _Animal24hONext

value: Cancellous


title: 26wk_Mid-Diaphysis_Loaded Limb _24h _Animal24hONext

value: Adult

value: Loaded _24h


title: control patient, female, sampling age 77, ID=C815

value: random


title: control patient, male, sampling age 82, ID=C821

value: male

value: no


title: control patient, female, sampling age 77, ID=C814


title: 26wk_Metaphyseal Shell_Loaded Limb _24h _Animal24hONext

value: Metaphyseal Shell

value: L


title: Hmga1a OE, sortChIC with H3K27me3 antibody

data_processing:
Data preprocessing has been performed using the SingleCellMultiOmics package (https://github.com/BuysDB/SingleCellMultiOmics) and the sequences were mapped to the Zebrafish danRer11 ENSEMBL genome using Burrows-Wheeler Aligner (BWA).
bigwig files were generated in Galaxy.org using mapping quality treshold of 50 and samflag exclude code 1536
reads were normalised to counts per millinon (CPM)
Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation
Supplementary files format and content: bigwigs, CPM normalized, >50 mapping quality, samflag exlude 1536

extract_protocol:
Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. sortChIC protocol was followed as in (Zeller, 2023 nature genetics)
As in (Zeller, 2023 nature genetics).

value: adult heart

tag: chic antibody

value: cardiomyocytes

value: Hmga1a overexpression

value: 14 days post tamoxifen


title: 26wk_Cancellous_Loaded Limb _24h _Animal24hONext


title: 26wk_Metaphyseal Shell_Contralateral Control Limb _24h _Animal24hO4

value: R

value: Contralateral Control Limb _24h


title: 26wk_Mid-Diaphysis_Contralateral Control Limb _24h _Animal24hO4

value: Mid-Diaphysis


title: 26wk_Cancellous_Contralateral Control Limb _24h _Animal24hO4