title: normal upper urinary tract treated with tap water5


title: Control1

status: Public on Nov 16 2024

type: SRA

city: Houston

first: Kristin

last: Mahan

address: 1825 Pressler St

department: MDD

country: USA

institute: UTHealth science

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through Novogene in-house perl scripts. Inthis step, clean data (clean reads) were obtained by removing reads containing adapter, readscontaining ploy-N and low quality reads from raw data
Reference genome and gene model annotation files were downloaded fromgenome websitedirectly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-endclean 2 reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Andthen FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Differential expression analysis of twoconditions/groups (two biological replicates per condition) was performed using the DESeq2R package (1.20.0).
Assembly: GRCh38/hg38
Supplementary files format and content: Microsoft Excel 97-2003 Worksheet (.xls)

molecule: total RNA

organism: Homo sapiens

growth_protocol: HepG2 cells were cultured in Eagle's Minimal Essential Medium, supplemented with 10% fetal bovine serum, 100 units/ml of penicillin G sodium, and 100 μg/ml of streptomycin.

extract_protocol:
RNA was isolated using TRIzol reagent, followed by TRIzol cleanup column following manufacturer protocols.
RNA library was formed by polyA capture (or rRNA removal) and reverse transcription of cDNA using Novogene’s Transcriptome Sequencing services

treatment_protocol: Cells were treated with Vehicle control,5µM NOB or 2µM SOR, or a combination of both

tag: cell line

tag: cell type

value: human liver cancer cell

tag: treatment

value: VEH


title: Control2


title: Medulloblastoma frozen tumor, SHH, M008RB10

city: Paris

first: Mathilde

last: Filser

address: 26 rue d'Ulm

department: Genetics Department

country: France

institute: Institut Curie

library_source: genomic

data_processing:
Downstream analysis relied on a custom bioinformatic pipeline called NanoCliD, available on GitHub (https://github.com/InstituteCurieClinicalBioinformatics/NanoCliD). Methylation calling was performed using Nanopolish 0.14.0, and the Guppy 5.0.17 data processing toolkit facilitated the conversion of FAST5 files to FASTQ files. Sequences were aligned to the reference genome hg19 with Minimap 2.24-r1122. CNV Calling was performed, adapted from NanoDX7, using QDNASeq and DeepTools v3.5.1 (Fig 1b). The obtained copy number profiles were then manually analyzed, focusing on key alterations encountered in medulloblastoma which are chromosome 6 monosomy, GLI2, MYC, MYCN, MYCL, SNCAIP and OTX2 amplifications, loss of chromosome 9q and 10q and isochromosome 17.
For each sample, Nanopore sequencing methylation data werre compared to the 3,905 publicly available Illumina arrays (Accession series GSE109381 updated version; https://www.ncbi.nlm.nih.gov/gds), corresponding to the v11b4 Heidelberg classifier (https://www.molecularneuropathology.org/mnp/). The NanoDx pipeline7 was integrated into NanoCliD for tumor classification. The CpG called during Nanopore sequencing were cross-referenced with those from the 850,000 covered by the EPIC array to retain only common sites. Random forest algorithm was employed to obtain methylation profiling, enabling tumor assignment to a group based on the analyzed CpG overlapping those of Illumina arrays (as illustrated in Fig. 2). The score, representing the sample's passage through the algorithm's decision trees, was obtained by counting each class returned by each tree. As described by other teams before, Aa random forrest score above 0.15 was considered satisfactory for reliable classification7. Uniform Manifold Approximation and Projection (UMAP) (Fig. 2) and t-distributed Stochastic Neighbor Embedding (t-SNE) were also generated for each sample for visualization.
Assembly: hg19
Supplementary files format and content: MethylationTables.tar.gz : list of tsv files obtained after methylation calling
Library strategy: Nanopore whole genome long read sequencing

molecule: genomic DNA

source_name: Brain Tumor

extract_protocol:
DNA were extracted from frozen MB samples using the standard phenol-chloroform procedure. The quality and quantity of DNA were assessed using Nanodrop (Thermo Fisher Scientific) and Qubit (Thermo Fisher Scientific). Quantification of DNA was performed using the Qubit Fluorometer (Quant-iT dsDNA BR Assay Kit; Thermo Fisher Scientific) and quality assessment was carried out using TapeStation (Genomic DNA screenTape; Agilent) following the manufacturer’s instructions.
For whole-genome Nanopore sequencing, DNA libraries were prepared using the SQK-RBK004 rapid barcoding kit from Oxford Nanopore Technologies. Two types of flow cells were used: MinION R9.4.1 (FLO-MIN106D) and Flongle R9.4.1 (FLO-FLG001). For MinION flow cells, 400 ng of DNA were tagmented, barcoded, repaired, and pooled in batches of six samples before adaptor ligation. Sequencing involved multiplexing six libraries, with each batch taking 48 to 72 hours per MinION R9.4.1 flow cell. For Flongle flow cells, the same SQK-RBK004 kit (Oxford Nanopore Technologies) was used, but 200 ng of DNA per tumor sample was sequenced individually on a Flongle flow cell for 24 hours. All sequencing was performed on MinION Mk1B or Mk1C devices, and sequencing runs were initiated and monitored using MinKnow software from Oxford Nanopore Technologies.

tag: tissue

value: Brain Tumor

value: Medulloblastoma


title: Control3


title: H1299 cells, TTC28-KO-2

city: Beijing

first: Ge

last: Zhang

address: Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Aetiology, Peking University Cancer Hospital and Institute, Beijing 100142, China

country: China

institute: Beijing Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education)

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Lung

growth_protocol: H1299 cells were cultured in RPMI1640 medium with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin, maintained at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: We used the CRISPR/Cas9 editing system to generra TTC28 knockout cells.

value: Lung

value: NSCLC Cells

tag: genotype

value: TTC28 Knockout

value: untreated


title: Medulloblastoma frozen tumor, SHH, M008RB09


title: normal upper urinary tract treated with tap water4

city: Suita

first: Akinaru

last: Yamamoto

state: Outside U.S./Canada

address: Yamadaoka, 2-2

country: Japan

institute: Osaka University Graduate School of Medicine

data_processing:
The sequenced reads were mapped to mouse reference genome sequences (GRCm38/mm10) using TopHat2 v2.1.1
Raw counts were calculated using feature counts v2.0.0.
Fragments per kilobase of exons per million mapped fragments were calculated using Cuffdiff v2.2.1.
Assembly: mm38
Supplementary files format and content: text file includes raw counts for each Sample

organism: Mus musculus

source_name: left ureter

extract_protocol:
Total RNA was extracted from each sample stored in RNAlater (-20 °C) using the miRNeasy Mini Kit (QIAGEN).
The library preparation was performed using a combination of the SMARTerHT (TaKaRa) and NexteraXT (Illumina) kits, following the TAKARA protocol.

value: left ureter

tag: tissue region

value: normal upper urinary tract

value: WT

value: No


title: Medulloblastoma frozen tumor, WNT, M008RB08


title: H1299 cells, WT-2


title: H1299 cells, WT-1


title: normal upper urinary tract treated with tap water3

source_name: right ureter

value: right ureter


title: Medulloblastoma frozen tumor, WNT, M008RB07


title: normal bladder treated with tap water1

source_name: bladder

value: bladder

value: normal bladder


title: Medulloblastoma frozen tumor, SHH, M007RB06


title: normal bladder treated with tap water2


title: normal upper urinary tract treated with tap water1


title: normal upper urinary tract treated with tap water2


title: Medulloblastoma frozen tumor, SHH, M007RB05


title: Medulloblastoma frozen tumor, Group 4, M007RB04


title: H1299 cells, TTC28-KO-1


title: bladder treated with BBN7

value: BBN


title: WT-9Gy-rep4

type: RNA

city: Irvine

first: Munjal

middle: M

last: Acharya

state: CA

address: 811, Health Sciences Dr, ROOM B-149, Medical Sciences B

department: Anatomy & Neurobiology

institute: University of California Irvine

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 59

hyb_protocol: For each 12-lane cartridge, 70 µl of Master Mix were combined with 42 µl of the fluorescent labeled Reporter CodeSet, flicked to mix, and briefly spun down before 8 µl of combined solution were added to each lane. 5 µl of total RNA (20 ng/µl) per sample was then added to individual lanes. Next, 2 µl of the biotin Capture ProbeSet was added to each lane. Then, loaded cartridges were placed in a thermocycler at 65 degrees Celsius for approximately 20 hours. Following hybridization, cartridges are loaded onto nCounter Prep Station (NanoString™) to perform liquid transfers, magnetic bead separations, and immobilization of molecular labels on the sample cartridge surface. Protocol as described per the manufacture’s instructions: NanoString™ (Seattle, WA).

scan_protocol: Scanning of hybridized cartridges was performed on an nCounter Digital Analyzer (NanoString™) per the manufacturer’s instructions: NanoString™ (Seattle, WA).

data_processing: The raw value data were normalized utilizing a two-step normalization process: an initial Positive Control Normalization, followed by a CodeSet Content Normalization using 13 internalized housekeeping genes that accompanied the Neuroinflammation Panel. Both processes were performed by the nSolver Analysis Software 4.0 (NanoString™).

label: Color-Coded Reporter Probe

source_name: fresh-frozen brain tissue

label_protocol: 5 µl of total RNA (20 ng/µl) per sample were labeled with a fluorescent Reporter ProbeSet per the manufacturer’s instructions: NanoString™ (Seattle, WA).

extract_protocol: Total RNA was isolated from 100 mg of fresh-frozen brain tissue per sample. Brain samples were first homogenized in QIAzol Lysis Reagent (Qiagen) and then underwent RNA isolation with RNeasy Plus Universal Mini Kit (Qiagen) to obtain a minimum of 100 ng of unreplicated RNA, whose purity was verified with both NanoDrop (ThermoFisher) and Bioanalyzer 2100 (Agilent Technologies).

value: fresh-frozen brain tissue

tag: Sex

value: male

tag: strain

tag: tumor induction

tag: tumor cell line

tag: radiation dose

value: 9 Gy

tag: pmx205 drug tx


title: WT-9Gy-rep1

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 56


title: WT-9Gy-PMX-rep3

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 54

value: Yes


title: Medulloblastoma frozen tumor, SHH, M007RB02

value: Brain Tumor

value: Medulloblastoma


title: WT-9Gy-rep2

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 57.


title: WT-9Gy-rep3

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 58


title: WT-9Gy-PMX-rep2

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 53


title: Medulloblastoma frozen tumor, Group 3, M007RB03


title: cancer side of upper urinary tract treated with BBN7

value: cancer side of upper urinary tract


title: non-cancer side of upper urinary tract treated with BBN7

value: non-cancer side of upper urinary tract


title: Medulloblastoma frozen tumor, WNT, M007RB01


title: WT-9Gy-PMX-rep1

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 52


title: WT-0Gy-rep1

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 48

value: 0 Gy


title: WT-0Gy-rep4

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 51


title: WT-0Gy-PMX-rep4

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 47


title: non-cancer side of upper urinary tract treated with BBN6

value: left ureter


title: WT-0Gy-PMX-rep2

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 45


title: bladder treated with BBN6


title: WT-9Gy-PMX-rep4

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 55


title: Medulloblastoma frozen tumor, SHH, M006RB10


title: Medulloblastoma frozen tumor, WNT, M006RB12


title: WT-0Gy-PMX-rep1

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 44


title: cancer side of upper urinary tract treated with BBN6


title: Medulloblastoma frozen tumor, Group 4, M005RB04


title: WT-CT2A-0Gy-PMX-rep3

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 42


title: WT-0Gy-rep3

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 50


title: WT-0Gy-rep2

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 49


title: cancer side of lt upper urinary tract treated with BBN5

value: cancer side of lt upper urinary tract


title: bladder treated with BBN5

value: WT


title: WT-CT2A-0Gy-PMX-rep4

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 43


title: Medulloblastoma frozen tumor, Group 3, M005RB03


title: WT-CT2A-0Gy-PMX-rep2

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 41


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M005RB02


title: C5aR KO-CT2A-9Gy-rep2

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 37


title: C5aR KO-CT2A-9Gy-rep3

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 38


title: WT-CT2A-0Gy-PMX-rep1

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 40


title: cancer side of rt upper urinary tract treated with BBN5

value: cancer side of rt upper urinary tract


title: C5aR KO-CT2A-9Gy-rep1

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 36


title: Medulloblastoma frozen tumor, SHH, M005RB01


title: WT-0Gy-PMX-rep3

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 46

value: No


title: bladder treated with BBN4

value: bladder


title: C5aR KO-CT2A-0Gy-rep4

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 35


title: Medulloblastoma frozen tumor, SHH, M001RB10


title: cancer side of upper urinary tract treated with BBN4


title: non-cancer side of upper urinary tract treated with BBN4

value: right ureter


title: FT3

city: Boston

first: Mark

middle: Aurel

last: Nagy

state: Massachusetts

address: 220 Longwood Ave

department: Department of Neurobiology

institute: Harvard Medical School

description: ATAC-seq from 50k nuclei with 10 amplification cycles

data_processing:
ATAC-seq: Previously published pipeline (Sharma et al., 2019) against Ensembl GRCm38 genome. ATAC-seq experiments were sequenced to a minimum depth of 20 million reads. All samples were aligned to the mm10 genome using default parameters for the Subread alignment software (subread-1.4.6-p3) after quality trimming with Trimmomatic v0.33 with the following command: java -jar trimmomatic-0.33.jar SE -threads 1 -phred33 [FASTQ_FILE] ILLUMINACLIP:[ADAPTER_FILE]:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:45. Nextera adapters were specified for ATAC-seq data. Regions of ATAC-seq enrichment were determined using MACS2 (v 2.1.0) parameters -p 1e-5–nolambda –keep-dup all –slocal 10000, as previously described. Peaks from individual sample replicates were intersected to find only reproducible regions of enrichment. Blacklist regions were removed as previously described. To identify sites with enriched ATAC-seq signal (peaks), we applied the IDR pipeline using the MACS2 peak calling algorithm with the following parameters: –nomodel –extsize 200 –keep-dup all. An IDR threshold of 0.01 was used for self-consistency, true replicate, and pooled-consistency analyses. The ‘optThresh’ cutoff was then used to obtain a final set of high-confidence, reproducible ATAC-seq peaks for each sample.  To produce a final list of reference coordinates containing 42,680 genomic regions that were accessible in at least one spinal ATAC-seq sample, the MACS2 peaks for each experimental replicate were unioned using the bedops --everything command. Bedtools merge was then used to combine any peaks that overlapped in this unioned bed file; in this way, any region that was significantly called a peak in at least one ATAC-seq dataset was incorporated in the final aggregated peak list. The featureCounts package was then used to obtain ATAC-seq read counts for each of these accessible putative CREs for downstream enrichment analyses.
RNA-seq: Previously published pipeline (Sharma et al., 2019) against custom transciptome built with same pipeline (Ensembl GRCm38 genome and GRCm38.84 annotation, filtering the annotation gtf file gencode.v17.annotation.gtf for feature_type=”gene”, gene_type="protein_coding" and gene_status="KNOWN") as appropriate. RNA-seq experiments were sequenced to a depth of at least 30 million reads. All samples were aligned to the mm10 genome using default parameters for the Subread alignment software (subread-1.4.6-p3) after quality trimming with Trimmomatic v0.33 with the following command: java -jar trimmomatic-0.33.jar SE -threads 1 -phred33 [FASTQ_FILE] ILLUMINACLIP:[ADAPTER_FILE]:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:45. Truseq adapters were trimmed out in RNA-seq experiments. To quantify gene expression, we applied the featureCounts package  after aligning RNA-seq libraries to the genome as described above, using a custom filtered annotation file: gencode.v17.annotation.gtf filtered for feature_type=“gene”, gene_type=“protein_coding” and gene_status=“KNOWN” to obtain gene counts for each sample. These counts tables were TMM-normalized using the EdgeR software analysis package. Any genes that were not expressed in at least 3 samples with TMM-normalized counts per million (CPM) >1 were dropped from further analysis. Differential expression (DE) analyses were conducted using the voom/limma analysis software packages (requiring FDR-corrected q<0.05).
Assembly: mm10 (GRCm38)
Supplementary files format and content: ATAC_ALL.csv.gz: MACS2 narrowPeak file listing consensus ATAC-seq peak list (union of IP and FT samples). ATAC_FT.csv.gz: MACS2 narrowPeak file listing FT ATAC-seq peak list. ATAC_IP.csv.gz: MACS2 narrowPeak file listing FT ATAC-seq peak list. ATAC_counts.csv.gz: Raw ATAC-seq read counts table across consensus ATAC-seq peak lists for all samples. RNA_counts.csv.gz: Raw RNA-seq read counts table for all RNA-seq samples

source_name: spinal cord

extract_protocol: ATAC-seq was performed using the OMNI-ATAC protocol (58), starting with the steps that immediately follow cell lysis. Nuclei (50,000) were pelleted at 500 g for 10 minutes at 4 C in a fixed angle centrifuge and resuspended in 50 μL transposition buffer (prepared from Illumina kit components TD buffer and 100 nM transposase [Illumina], as well as 0.01% digitonin, 0.1% Tween-20) via careful pipetting. Transposition occurred at 37 C in a thermomixer at 1000 rpm for 30 minutes before resuspension in 250 μL of DNA binding buffer (Zymo DNA Clean and Concentrator Kit) and reaction cleanup per manufacture instructions, with final elution volume of 21 μL in elution buffer. Samples were amplified following NEBNext High-Fidelity 2X PCR Master Mix manufacturer protocols (NEB) in a total reaction volume of 50 μL (1.25 μM each of i5 and i7 sequencing primers) at 72 C for 5 minutes, [98 C for 10 seconds, 63 C for 30 seconds, and 72 C for 1 minute] x10 cycles. PCR samples were re-purified following the Zymo manufacturer protocol and eluted into 21 μL of elution buffer. Size selection was performed via agarose gel (150-1000 bp) followed by Qiagen MinElute gel extraction according to the manufacturer’s instructions, with two serial 10 μL elution steps. Seventy-five bp paired-end sequencing was performed on an Illumina NextSeq500. For RNA-seq: Nuclei from INTACT immunopurification were immediately pelleted at 500 g for 10 minutes at 4 C in a fixed angle centrifuge and resuspended in 350 μL RLT buffer [Qiagen]. RNA purification was performed following the Qiagen RNEasy MinElute manufacturer’s protocol, with a final elution volume of 20 μL. Libraries were prepared following the SMART-seq manufacturer’s protocol [Takara Bio] with 15 amplification cycles and purified following the AMPure XP [Beckmann Coulter] manufacturer’s instructions.

treatment_protocol: Nuclear isolation: Animals were deeply anesthetized with isoflurane (1-3% in air) and sacrificed by decapitation (surgical scissors) before dissection and processing of thoracic and lumbar spinal cords. Spinal cords from two mice were combined per experimental replicate. Spinal cords were dounced 10 times in 5 mL of HB buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH pH 7.8, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, DTT 1 mM [Sigma], half of a Roche proteinase inhibitor tablet) in a 7 mL dounce-homogenizer, supplemented with IGEPAL CA-630 to final concentration of 0.3%, and dounced an additional ten times. Nuclei were filtered through a 40 μm strainer and combined 1:1 with 50% iodixanol. Nuclei were then underlaid with a gradient of 1 mL 40% iodixanol and 1 mL 30% iodixanol and centrifuged at 10,000g for 19 minutes using the “no brake” setting. Purified nuclei (0.8 mL) were then collected from the 30/40% interface. A 20 μL aliquot was taken for visual inspection and cell counting, with typical yield of ~1 million nuclei per two spinal cords. For RNA-seq experiments, all buffers were supplemented with 1.5 μL/mL RNAse inhibitor (Promega). Affinity purification: A modified version of the published INTACT protocol was applied, with the following changes. 1) Each experimental sample was split across two LoBind tubes to accommodate the larger volumes obtained. 2) Immunoprecipitation (IP) was completed over 30 minutes of end-to-end rotation at 4C. 3) Flowthrough during the IP step was also collected, filtered through a 20 μm CellTRICs filter, and centrifuged at 800g for 10 minutes at 4C before resuspension in 400 μL wash buffer (buffer HB supplemented with 0.4% IGEPAL CA-630) with careful pipetting. 4) The final immunoprecipitate was then resuspended 400 μL wash buffer. A 20 μL aliquot was taken from each sample for cell counting and verification of effective purification of GFP-positive (GFPPOS) nuclei. Typical yield was approximately 25,000 GFPPOS nuclei per spinal cord (>95% GFPPOS) in the immunoprecipitate and approximately 150,000 nuclei per spinal cord from flowthrough (<1% GFPPOS).

value: spinal cord

value: SUN1-CHAT depleted flow-through

value: CHAT-IRES-CRE x SUN1-GFP F1


title: C5aR KO-CT2A-0Gy-rep2

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 33

value: fresh-frozen brain tissue

value: male


title: FT2


title: bladder treated with BBN3

value: BBN


title: C5aR KO-9Gy-rep3

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 30

value: 9 Gy


title: C5aR KO-9Gy-rep4

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 31


title: cancer side of upper urinary tract treated with BBN3

value: cancer side of upper urinary tract


title: C5aR KO-9Gy-rep2

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 29


title: non-cancer side of upper urinary tract treated with BBN3

value: non-cancer side of upper urinary tract


title: C5aR KO-0Gy-rep1b

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 25b

value: 0 Gy


title: IP3

value: SUN1-CHAT enriched immunoprecipitate


title: C5aR KO-9Gy-rep1

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 28


title: IP2


title: C5aR KO-0Gy-rep2a

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 26a


title: C5aR KO-0Gy-rep2b

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 26b


title: C5aR KO-CT2A-0Gy-rep3

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 34

value: Yes


title: IP1


title: WT-CT2A-9Gy-PMX-rep4

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 24


title: C5aR KO-0Gy-rep1a

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 25a


title: non-cancer side of upper urinary tract treated with BBN2

value: left ureter

value: WT


title: WT-CT2A-9Gy-PMX-rep1

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 21


title: C5aR KO-CT2A-0Gy-rep1

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 32


title: IP_B

description: SMART-seq library prep with 15 amplification cycles

molecule: polyA RNA


title: FT1


title: WT-CT2A-9Gy-rep4

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 20

value: No


title: cancer side of upper urinary tract treated with BBN2


title: IP_A


title: WT-CT2A-9Gy-rep2

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 18


title: WT-CT2A-9Gy-rep3

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 19


title: bladder treated with BBN2

value: bladder


title: bladder treated with BBN1


title: FT_B


title: WT-CT2A-9Gy-PMX-rep3

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 23


title: WT-CT2A-9Gy-rep1

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 17


title: WT-CT2A-0Gy-rep4

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 16


title: FT_A


title: Center1-091

status: Public on Nov 15 2024

type: genomic

first: Ze

state: MA

address: 375 Longwood Ave

department: Medical Oncology & Population Sciences

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

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)

value: Female

tag: age

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: Center2-511

value: Male

tag: treatment

value: Immunotherapy + Chemotherapy


title: Center1-087


title: WT-CT2A-9Gy-PMX-rep2

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 22

tag: tissue

value: fresh-frozen brain tissue


title: Center2-512


title: Center2-513


title: non-cancer side of upper urinary tract treated with BBN1

tag: tissue region

tag: genotype


title: WT-CT2A-0Gy-rep2

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 14

tag: Sex

value: male

tag: strain


title: Center1-080


title: WT-CT2A-0Gy-rep3

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 15

tag: tumor induction

tag: tumor cell line


title: Center1-083


title: WT-CT2A-0Gy-rep1

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 13

tag: radiation dose

tag: pmx205 drug tx


title: Center1-079

tag: age

tag: progression event


title: Center1-090

tag: days to progression

tag: death event


title: C5aR KO-CT2A-9Gy-rep4

description:
Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material
PMX 39


title: Center2-510

tag: days to death

tag: tmb


title: Center1-082

tag: pdl1 cps

tag: arraytypes


title: Center3-702

tag: treatment


title: Center1-085


title: Center1-081


title: Center1-088


title: Center1-070


title: Center1-068


title: Center1-077


title: cancer side of upper urinary tract treated with BBN1

tag: tissue

value: right ureter

tag: tissue region

value: BBN


title: Center1-066

tag: Sex


title: Center3-701


title: Center1-073


title: Center1-078


title: Center2-508


title: Center1-075


title: Center1-072


title: Center1-065


title: Center1-069


title: Retina, C57Normoxia4

first: Charandeep

last: Singh

address: 150 Harrison Avenue

institute: Tufts Medical Center

data_processing:
Fastq formatted files were processed to remove reads containing adapters, lower quality reads and poly-N reads. Reference genome index was prepared using Hisat2 v2.0.5. Mus Musculus reference genome GRCm38/mm10 was used as reference. Quantification of gene expression was performed with the help of featureCounts v1.5.0-p3
Assembly: Mus Musculus reference genome GRCm38/mm10
Supplementary files format and content: Excel sheet containing matrix

source_name: Retina

growth_protocol: Mice were maintained in room air from P0-P7, on P7 mice were exposed to hyperoxia (75% oxygen) until P12 which caused vaso-obliteration Phase I

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) as per instructions provided with the reagent
The library was prepared with the help of a NEBNext Ultra II library prep kit for Illumina.

treatment_protocol: Hyperoxia 75% or Normoxia room air

value: Retina

value: Normoxia


title: Center1-076


title: Center1-074


title: Center1-067


title: Retina, C57Hyperoxia3

value: Hyperoxia


title: Center1-071


title: Retina, BALBcNormoxia4


title: Retina, BALBcHyperoxia4


title: Retina, C57Hyperoxia2


title: Retina, BALBcNormoxia3


title: Retina, C57Normoxia1


title: Retina, C57Hyperoxia4


title: Retina, C57Normoxia2


title: Retina, C57Hyperoxia1


title: Retina, C57Normoxia3


title: Retina, BALBcHyperoxia3


title: Retina, BALBcNormoxia1


title: Retina, BALBcNormoxia2


title: Retina, BALBcHyperoxia2


title: Retina, BALBcHyperoxia1


title: C57Normoxia4

source_name: Liver

value: Liver


title: C57Hyperoxia4


title: C57Hyperoxia2


title: C57Hyperoxia1


title: BALBcNormoxia2


title: BALBcNormoxia3


title: C57Normoxia3


title: C57Normoxia1


title: BALBcHyperoxia4


title: C57Normoxia2


title: C57Hyperoxia3


title: BALBcNormoxia1


title: BALBcHyperoxia1


title: BALBcHyperoxia2


title: BALBcHyperoxia3


title: whole kidney snRNA seq of mouse #4443

city: Ann Arbor

first: Jeffrey

middle: A

last: Beamish

state: MI

address: 1500 E. Medical Center Drive, SPC 5364

department: Department of Internal Medicine, Division of Nephrology

institute: University of Michigan

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using CellRanger (10X Genomics, version cellranger-6.1.2).
Assembly: mm10 with EGFP, Cre, and tdTomato
Supplementary files format and content: Processed data files include archived (.tar) versions of the filtered_feature_bc_matrix and raw_feature_bc_matrix folders generated by CellRanger (each of which contains the files: barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz)

molecule: nuclear RNA

source_name: kidney

extract_protocol:
Nuclei were extracted from flash frozen whole kidney samples. The specimens were thawed and minced thoroughly for one minute in NP40 lysis buffer (0.1% NP40, 10 mM Tris pH 7.5, 146 mM NaCl, 1 mM CaCl2, 21 mM MgCl2, and 40 U/mL RNAse inhibitor). Next, the suspension was further homogenized in 1 mL lysis buffer using a Dounce homogenizer (Kimble) with 20 strokes each using pestle A and pestle B. Subsequently, 4 mL of wash buffer (10 mM Tris, 146 mM NaCl, 1 mM CaCl2, 21 mM MgCl2, 1% BSA [7.5% Fraction V], and 40 U/mL RNAse inhibitor) was added, filtered through a 30 µm strainer (Milteni), and centrifuged for 10 min at 200×g at 4 °C. The supernatant with debris was carefully removed using a glass Pasteur pipette and house vacuum, and the pellet was then resuspended in 5 mL wash buffer, filtered through a 5 µm strainer (Pluriselect), and centrifuged again.  Nuclei were submitted to the Advanced Genomics Core at the University of Michigan for single-nucleus RNA sequencing using the 10X Genomics Chromium platform, following manufacturer instructions.
cDNA libraries were prepared using the Chromium platform following manufacturer instructions (10X Genomics).

value: kidney


title: liver，HFrD induced NAFLD model，rep4

city: Shanghai

first: Zheng

last: Hui

address: 170 Xinsong Road, Minhang District

institute: Minhang Hospital, Fudan University

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.2).
Then, trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs. The trimmed reads were aligned to the merged pre-miRNA databases (known pre-miRNA from miRBase v22 plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch.
The numbers of mature miRNA mapped tags were defined as the raw expression levels of that miRNA.
Assembly: mm10
Supplementary files format and content: The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach.

source_name: liver

growth_protocol: HFrD containing 10% kcal from fat, 70% kcal from carbohydrate, and 20% kcal from protein were purchased from Research Diets (D08040107, Research Diets, USA). Male C57BL/6J mice aged 10-11 weeks were fed either a normal diet (ND) or HFrD for two weeks.

extract_protocol:
According to the manufacturer's instructions, liver total RNA in HFrD mice and control mice was extracted from TRIzol (Invitrogen, CA, USA). Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). 10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina NovaSeq 6000 Sequencer according to the manufacturer's instructions.

value: liver

tag: diet

value: HFrD


title: Fgf9_WT2

city: St. Louis

first: Spencer

middle: G.

last: Willet

state: MO

address: 660 S. Euclid Avenue, Campus Box 8103

department: Department of Developmental Biology

institute: Washington University in St. Louis

data_processing:
Quality control of reads was performed using FastQC v.0.10.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.33.
Trimmed sequence reads were mapped to GrCM38/mm10 using Salmon v.1.8.0 with default parameters.
Read count extraction and normalization were performed using EdgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw gene counts for each Sample

source_name: stomach

extract_protocol:
RNA was harvested using Rneasy midi kit (Qiagen). 0.5 to 1ug of total RNA was used for the construction of sequencing libraries.
Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt-ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired-end reads extending 150 bases.

value: stomach

tag: genotype

value: control


title: Fgf9_Mut2


title: Fgf9_Mut3


title: Fgf9_WT3


title: liver，HFrD induced NAFLD model，rep1


title: liver，HFrD induced NAFLD model，rep3


title: whole kidney snRNA seq of mouse #4441

description: Processed data files include archived (.tar) versions of the filtered_feature_bc_matrix and raw_feature_bc_matrix folders generated by CellRanger (each of which contains the files: barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz)


title: liver，chow diet model，rep3

value: normal


title: whole kidney snRNA seq of mouse #4442


title: Camellia_LK_LARRY_6

city: Hangzhou

first: Shou-Wen

last: Wang

address: No. 18 Shilongshan Road, Xihu District

institute: Westlake University

data_processing: not provided

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) was used to remove nuclei. Assisted with magnetic stand, the binding buffer containing cytoplasmic mRNA was transferred to a separate 96-well plate.
The cytoplasmic mRNA was processed with RNA-seq with designed primers to profile the LARRY fragments

tag: cell type

value: Blood cells

value: Lin-cKit+Sca1- blood progenitors


title: liver，chow diet model，rep2


title: Camellia_LK_LARRY_5


title: Camellia_LK_LARRY_3


title: Camellia_LK_LARRY_1


title: Camellia_LK_LARRY_4


title: Camellia_LK_RNA_3

data_processing:
We first extract cell barcode (8bp) and UMI (8bp) with UMI_tools
Then, we use customized script to trim TSO and polyA, and discard low-quality reads
Next, we use featureCounts to add gene annotation, use samtools to sort and index bam files, and finally run umi_tools to generate the count matrix
Assembly: mm10
Supplementary files format and content: tsv files, cell-by-gene matrix from UMI_counts software

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) was used to remove nuclei. Assisted with magnetic stand, the binding buffer containing cytoplasmic mRNA was transferred to a separate 96-well plate.
The cytoplasmic mRNA was processed with scSTRT-seq with minor modifications to profile the whole transcriptome


title: Camellia_LK_RNA_5


title: Camellia_LK_RNA_4


title: Camellia_LK_RNA_6


title: Camellia_LK_RNA_2


title: liver，HFrD induced NAFLD model，rep2


title: liver，chow diet model，rep4


title: Camellia_LK_RNA_1


title: scBSseq_LK_DNA_6_H8

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

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.


title: liver，chow diet model，rep1


title: scBSseq_LK_DNA_6_H9


title: scBSseq_LK_DNA_6_G9


title: scBSseq_LK_DNA_6_H5


title: scBSseq_LK_DNA_6_H4


title: scBSseq_LK_DNA_6_G8


title: scBSseq_LK_DNA_6_H11


title: scBSseq_LK_DNA_6_H3


title: scBSseq_LK_DNA_6_H7


title: scBSseq_LK_DNA_6_H2


title: scBSseq_LK_DNA_6_H6


title: scBSseq_LK_DNA_6_H10


title: scBSseq_LK_DNA_6_H1


title: scBSseq_LK_DNA_6_G7


title: scBSseq_LK_DNA_6_G6


title: scBSseq_LK_DNA_6_G5


title: Camellia_LK_LARRY_2


title: scBSseq_LK_DNA_6_G4


title: scBSseq_LK_DNA_6_G3


title: scBSseq_LK_DNA_6_G2


title: scBSseq_LK_DNA_6_G1


title: scBSseq_LK_DNA_6_G11


title: scBSseq_LK_DNA_6_G12


title: scBSseq_LK_DNA_6_F8


title: scBSseq_LK_DNA_6_H12


title: scBSseq_LK_DNA_6_F9


title: scBSseq_LK_DNA_6_F7


title: scBSseq_LK_DNA_6_F6


title: scBSseq_LK_DNA_6_F4


title: scBSseq_LK_DNA_6_F5


title: scBSseq_LK_DNA_6_F2


title: scBSseq_LK_DNA_6_F3


title: scBSseq_LK_DNA_6_F10


title: scBSseq_LK_DNA_6_E9


title: scBSseq_LK_DNA_6_E4


title: scBSseq_LK_DNA_6_E5


title: scBSseq_LK_DNA_6_E7


title: scBSseq_LK_DNA_6_F12


title: scBSseq_LK_DNA_6_E6


title: scBSseq_LK_DNA_6_E8


title: scBSseq_LK_DNA_6_G10


title: scBSseq_LK_DNA_6_E3


title: scBSseq_LK_DNA_6_E10


title: scBSseq_LK_DNA_6_E1


title: scBSseq_LK_DNA_6_E11


title: scBSseq_LK_DNA_6_E2


title: scBSseq_LK_DNA_6_E12


title: scBSseq_LK_DNA_6_D8


title: scBSseq_LK_DNA_6_D6


title: scBSseq_LK_DNA_6_D7


title: scBSseq_LK_DNA_6_D9


title: scBSseq_LK_DNA_6_D5


title: scBSseq_LK_DNA_6_D4


title: scBSseq_LK_DNA_6_D3


title: scBSseq_LK_DNA_6_D1


title: scBSseq_LK_DNA_6_D2


title: scBSseq_LK_DNA_6_F1


title: scBSseq_LK_DNA_6_D12


title: scBSseq_LK_DNA_6_F11


title: scBSseq_LK_DNA_6_D11


title: scBSseq_LK_DNA_6_C9


title: scBSseq_LK_DNA_6_D10


title: scBSseq_LK_DNA_6_C7


title: scBSseq_LK_DNA_6_C8


title: scBSseq_LK_DNA_6_C5


title: scBSseq_LK_DNA_6_C3


title: scBSseq_LK_DNA_6_C6


title: scBSseq_LK_DNA_6_C1


title: scBSseq_LK_DNA_6_B8


title: scBSseq_LK_DNA_6_C10


title: scBSseq_LK_DNA_6_B7


title: scBSseq_LK_DNA_6_B6


title: scBSseq_LK_DNA_6_B3


title: scBSseq_LK_DNA_6_C11


title: scBSseq_LK_DNA_6_B5


title: scBSseq_LK_DNA_6_C12


title: scBSseq_LK_DNA_6_B9


title: scBSseq_LK_DNA_6_B4


title: scBSseq_LK_DNA_6_B12


title: scBSseq_LK_DNA_6_B11


title: scBSseq_LK_DNA_6_B1


title: scBSseq_LK_DNA_6_B2


title: scBSseq_LK_DNA_6_A9


title: scBSseq_LK_DNA_6_B10


title: scBSseq_LK_DNA_6_C2


title: scBSseq_LK_DNA_6_A7


title: scBSseq_LK_DNA_6_A5


title: scBSseq_LK_DNA_6_A6


title: scBSseq_LK_DNA_6_A8


title: scBSseq_LK_DNA_6_C4


title: scBSseq_LK_DNA_6_A2


title: scBSseq_LK_DNA_6_A3


title: scBSseq_LK_DNA_6_A12


title: scBSseq_LK_DNA_6_A1


title: scBSseq_LK_DNA_5_H8


title: scBSseq_LK_DNA_5_H5


title: scBSseq_LK_DNA_5_H1


title: scBSseq_LK_DNA_5_H4


title: scBSseq_LK_DNA_5_H7


title: scBSseq_LK_DNA_5_H3


title: scBSseq_LK_DNA_5_H6


title: scBSseq_LK_DNA_5_H2


title: scBSseq_LK_DNA_5_H11


title: scBSseq_LK_DNA_5_H10


title: scBSseq_LK_DNA_5_G9


title: scBSseq_LK_DNA_5_G6


title: scBSseq_LK_DNA_5_G7


title: scBSseq_LK_DNA_5_G8


title: scBSseq_LK_DNA_6_A4


title: scBSseq_LK_DNA_5_G4


title: scBSseq_LK_DNA_5_G5


title: scBSseq_LK_DNA_5_G1


title: scBSseq_LK_DNA_5_G12


title: scBSseq_LK_DNA_6_A11


title: scBSseq_LK_DNA_5_G2


title: scBSseq_LK_DNA_5_G11


title: scBSseq_LK_DNA_5_G3


title: scBSseq_LK_DNA_6_A10


title: scBSseq_LK_DNA_5_H9


title: scBSseq_LK_DNA_5_F9


title: scBSseq_LK_DNA_5_F8


title: scBSseq_LK_DNA_5_G10


title: scBSseq_LK_DNA_5_H12


title: scBSseq_LK_DNA_5_F6


title: scBSseq_LK_DNA_5_F4


title: scBSseq_LK_DNA_5_F2


title: scBSseq_LK_DNA_5_F1


title: scBSseq_LK_DNA_5_F5


title: scBSseq_LK_DNA_5_F12


title: scBSseq_LK_DNA_5_F11


title: scBSseq_LK_DNA_5_E9


title: scBSseq_LK_DNA_5_F10


title: scBSseq_LK_DNA_5_E6


title: scBSseq_LK_DNA_5_E5


title: scBSseq_LK_DNA_5_E2


title: scBSseq_LK_DNA_5_E4


title: scBSseq_LK_DNA_5_E8


title: scBSseq_LK_DNA_5_E7


title: scBSseq_LK_DNA_5_E1


title: scBSseq_LK_DNA_5_E3


title: scBSseq_LK_DNA_5_E12


title: scBSseq_LK_DNA_5_E11


title: scBSseq_LK_DNA_5_F7


title: scBSseq_LK_DNA_5_D7


title: scBSseq_LK_DNA_5_D9


title: scBSseq_LK_DNA_5_D6


title: scBSseq_LK_DNA_5_D5


title: scBSseq_LK_DNA_5_D2


title: scBSseq_LK_DNA_5_E10


title: scBSseq_LK_DNA_5_D4


title: scBSseq_LK_DNA_5_D1


title: scBSseq_LK_DNA_5_D12


title: scBSseq_LK_DNA_5_C9


title: scBSseq_LK_DNA_5_D10


title: scBSseq_LK_DNA_5_C8


title: scBSseq_LK_DNA_5_F3


title: scBSseq_LK_DNA_5_D8


title: scBSseq_LK_DNA_5_C7


title: scBSseq_LK_DNA_5_C4


title: scBSseq_LK_DNA_5_C6


title: scBSseq_LK_DNA_5_C3


title: scBSseq_LK_DNA_5_B8


title: scBSseq_LK_DNA_5_C10


title: scBSseq_LK_DNA_5_B9


title: scBSseq_LK_DNA_5_D3


title: scBSseq_LK_DNA_5_C11


title: scBSseq_LK_DNA_5_C12


title: scBSseq_LK_DNA_5_C1


title: scBSseq_LK_DNA_5_B7


title: scBSseq_LK_DNA_5_B4


title: scBSseq_LK_DNA_5_B5


title: scBSseq_LK_DNA_5_B6


title: scBSseq_LK_DNA_5_B1


title: scBSseq_LK_DNA_5_D11


title: scBSseq_LK_DNA_5_B11


title: scBSseq_LK_DNA_5_B10


title: scBSseq_LK_DNA_5_B3


title: scBSseq_LK_DNA_5_A9


title: scBSseq_LK_DNA_5_A8


title: scBSseq_LK_DNA_5_B2


title: scBSseq_LK_DNA_5_A7


title: scBSseq_LK_DNA_5_A6


title: scBSseq_LK_DNA_5_C5


title: scBSseq_LK_DNA_5_C2


title: scBSseq_LK_DNA_5_A5


title: scBSseq_LK_DNA_5_A4


title: scBSseq_LK_DNA_5_A3


title: scBSseq_LK_DNA_5_A2


title: scBSseq_LK_DNA_5_A12


title: scBSseq_LK_DNA_5_A1


title: scBSseq_LK_DNA_4_H9


title: scBSseq_LK_DNA_4_H8


title: scBSseq_LK_DNA_4_H7


title: scBSseq_LK_DNA_5_A10


title: scBSseq_LK_DNA_4_H5


title: scBSseq_LK_DNA_5_A11


title: scBSseq_LK_DNA_5_B12


title: scBSseq_LK_DNA_4_H4


title: scBSseq_LK_DNA_4_H1


title: scBSseq_LK_DNA_4_H2


title: scBSseq_LK_DNA_4_H12


title: scBSseq_LK_DNA_4_H3


title: scBSseq_LK_DNA_4_H11


title: scBSseq_LK_DNA_4_G8


title: scBSseq_LK_DNA_4_G7


title: scBSseq_LK_DNA_4_G6


title: scBSseq_LK_DNA_4_G9


title: scBSseq_LK_DNA_4_G4


title: scBSseq_LK_DNA_4_G2


title: scBSseq_LK_DNA_4_G12


title: scBSseq_LK_DNA_4_G1


title: scBSseq_LK_DNA_4_G11


title: scBSseq_LK_DNA_4_H6


title: scBSseq_LK_DNA_4_F7


title: scBSseq_LK_DNA_4_F8


title: scBSseq_LK_DNA_4_F6


title: scBSseq_LK_DNA_4_F4


title: scBSseq_LK_DNA_4_F3


title: scBSseq_LK_DNA_4_F5


title: scBSseq_LK_DNA_4_H10


title: scBSseq_LK_DNA_4_F2


title: scBSseq_LK_DNA_4_F1


title: scBSseq_LK_DNA_4_F12


title: scBSseq_LK_DNA_4_E8


title: scBSseq_LK_DNA_4_F10


title: scBSseq_LK_DNA_4_F11


title: scBSseq_LK_DNA_4_G5


title: scBSseq_LK_DNA_4_E7


title: scBSseq_LK_DNA_4_G3


title: scBSseq_LK_DNA_4_E4


title: scBSseq_LK_DNA_4_E5


title: scBSseq_LK_DNA_4_E9


title: scBSseq_LK_DNA_4_E6


title: scBSseq_LK_DNA_4_E12


title: scBSseq_LK_DNA_4_E3


title: scBSseq_LK_DNA_4_G10


title: scBSseq_LK_DNA_4_E11


title: scBSseq_LK_DNA_4_D9


title: scBSseq_LK_DNA_4_F9


title: scBSseq_LK_DNA_4_D8


title: scBSseq_LK_DNA_4_E10


title: scBSseq_LK_DNA_4_D7


title: scBSseq_LK_DNA_4_D6


title: scBSseq_LK_DNA_4_D5


title: scBSseq_LK_DNA_4_D4


title: scBSseq_LK_DNA_4_D10


title: scBSseq_LK_DNA_4_D1


title: scBSseq_LK_DNA_4_D2


title: scBSseq_LK_DNA_4_D12


title: scBSseq_LK_DNA_4_D11


title: scBSseq_LK_DNA_4_E2


title: scBSseq_LK_DNA_4_C6


title: scBSseq_LK_DNA_4_E1


title: scBSseq_LK_DNA_4_C9


title: scBSseq_LK_DNA_4_C7


title: scBSseq_LK_DNA_4_C5


title: scBSseq_LK_DNA_4_C8


title: scBSseq_LK_DNA_4_C12


title: scBSseq_LK_DNA_4_C4


title: scBSseq_LK_DNA_4_C3


title: scBSseq_LK_DNA_4_C2


title: scBSseq_LK_DNA_4_C1


title: scBSseq_LK_DNA_4_C11


title: scBSseq_LK_DNA_4_C10


title: scBSseq_LK_DNA_4_B7


title: scBSseq_LK_DNA_4_B6


title: scBSseq_LK_DNA_4_B5


title: scBSseq_LK_DNA_4_B8


title: scBSseq_LK_DNA_4_B4


title: scBSseq_LK_DNA_4_B3


title: scBSseq_LK_DNA_4_B2


title: scBSseq_LK_DNA_4_B1


title: scBSseq_LK_DNA_4_B12


title: scBSseq_LK_DNA_4_A8


title: scBSseq_LK_DNA_4_B10


title: scBSseq_LK_DNA_4_B11


title: scBSseq_LK_DNA_4_A7


title: scBSseq_LK_DNA_4_A9


title: scBSseq_LK_DNA_4_A6


title: scBSseq_LK_DNA_4_A3


title: scBSseq_LK_DNA_4_A2


title: scBSseq_LK_DNA_4_A4


title: scBSseq_LK_DNA_4_A12


title: scBSseq_LK_DNA_3_H8


title: scBSseq_LK_DNA_4_A5


title: scBSseq_LK_DNA_4_A11


title: scBSseq_LK_DNA_4_A10


title: scBSseq_LK_DNA_3_H6


title: scBSseq_LK_DNA_4_A1


title: scBSseq_LK_DNA_3_H7


title: scBSseq_LK_DNA_3_H9


title: scBSseq_LK_DNA_3_H1


title: scBSseq_LK_DNA_4_D3


title: scBSseq_LK_DNA_3_H5


title: scBSseq_LK_DNA_3_H4


title: scBSseq_LK_DNA_3_H2


title: scBSseq_LK_DNA_3_H12


title: scBSseq_LK_DNA_3_H3


title: scBSseq_LK_DNA_3_H11


title: scBSseq_LK_DNA_3_G3


title: scBSseq_LK_DNA_3_G7


title: scBSseq_LK_DNA_3_G6


title: scBSseq_LK_DNA_3_G9


title: scBSseq_LK_DNA_3_G4


title: scBSseq_LK_DNA_3_G5


title: scBSseq_LK_DNA_3_G2


title: scBSseq_LK_DNA_3_G12


title: scBSseq_LK_DNA_3_G1


title: scBSseq_LK_DNA_3_G11


title: scBSseq_LK_DNA_3_G10


title: scBSseq_LK_DNA_3_F9


title: scBSseq_LK_DNA_3_F6


title: scBSseq_LK_DNA_3_F7


title: scBSseq_LK_DNA_3_F4


title: scBSseq_LK_DNA_3_F3


title: scBSseq_LK_DNA_3_F5


title: scBSseq_LK_DNA_3_F2


title: scBSseq_LK_DNA_3_F8


title: scBSseq_LK_DNA_3_H10


title: scBSseq_LK_DNA_3_F12


title: scBSseq_LK_DNA_3_E9


title: scBSseq_LK_DNA_3_E7


title: scBSseq_LK_DNA_3_G8


title: scBSseq_LK_DNA_3_E8


title: scBSseq_LK_DNA_3_F1


title: scBSseq_LK_DNA_3_E5


title: scBSseq_LK_DNA_3_E12


title: scBSseq_LK_DNA_3_E4


title: scBSseq_LK_DNA_3_E11


title: scBSseq_LK_DNA_3_E10


title: scBSseq_LK_DNA_3_D9


title: scBSseq_LK_DNA_3_E1


title: scBSseq_LK_DNA_3_E2


title: scBSseq_LK_DNA_3_E3


title: scBSseq_LK_DNA_3_F11


title: scBSseq_LK_DNA_3_D5


title: scBSseq_LK_DNA_3_D6


title: scBSseq_LK_DNA_3_D8


title: scBSseq_LK_DNA_3_D2


title: scBSseq_LK_DNA_3_F10


title: scBSseq_LK_DNA_3_D4


title: scBSseq_LK_DNA_3_D7


title: scBSseq_LK_DNA_4_B9


title: scBSseq_LK_DNA_3_D3


title: scBSseq_LK_DNA_3_C8


title: scBSseq_LK_DNA_3_D11


title: scBSseq_LK_DNA_3_E6


title: scBSseq_LK_DNA_3_D1


title: scBSseq_LK_DNA_3_D10


title: scBSseq_LK_DNA_3_C9


title: JE03-294 rep3

city: New Haven

first: Jason

last: Sheltzer

state: CT

address: 300 George Street

department: Surgery

institute: Yale University

data_processing:
Custom Novogene QC scripts
Novogene: Remove reads containing adapters; Remove reads containing N > 10% (N represents base that could not be determined); Remove low quality reads: The Qscore (Quality value) of over 50% bases of the read is <= 5.
Reads were then mapped to hg38 with HISAT2 (version 2.0.5)
featureCounts v1.5.0-p3 was used to count the numbers of reads mapped to each gene.
Assembly: hg38
Supplementary files format and content: xls file including gene counts for each sample
Supplementary files format and content: xls file including FPKM values for each sample

growth_protocol: iPS cells were maintained in mTeSR+ in humidified atmosphere with 5% CO2 and 5% O2 at 37C. Media was replenished every day. If cells were plated as single cells, media was supplemented with 10 uM Y-27632

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen).
RNA libraries were prepared by Novogene following Novogene's standard protocols.

treatment_protocol: To generate Revertant cells, JE03 294 cells were treated with 1.5 uM AZ3146 for 48 hours to generate cell line with trisomy for chromosome 8.  This trisomic intermediate was then transiently transfected with KaryoCreate plasmids to induce missegregation events at Chromsoome 8

tag: cell line

value: Induced pluripotent stem cell


title: scBSseq_LK_DNA_3_C7


title: JE03-294 rep2


title: scBSseq_LK_DNA_3_C6


title: JE03-294 rep1


title: JE02-255 rep3

value: diploid


title: scBSseq_LK_DNA_3_C4


title: scBSseq_LK_DNA_3_C5


title: JE02-255 rep2


title: scBSseq_LK_DNA_3_C2


title: scBSseq_LK_DNA_3_C3


title: JE01-214 rep3


title: scBSseq_LK_DNA_3_D12


title: scBSseq_LK_DNA_3_C12


title: scBSseq_LK_DNA_3_C1


title: JE01-214 rep2


title: 31.3 rep2

value: Was derived from JE03 294 after treatment with AZ3146, and transfection of KaryoCreate plasmids


title: 31.3 rep3


title: scBSseq_LK_DNA_3_C10


title: scBSseq_LK_DNA_3_B9


title: scBSseq_LK_DNA_3_C11


title: 31.3 rep1


title: JE01-214 rep1


title: WSA1

city: Qinzhou City

first: Xin

last: Lu

address: 12 Binhai Avenue, Qinnan District, Qinzhou City, Guangxi, China

institute: Beibu Gulf University

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text fles include FPKM values for each Sample

organism: Tilapia

source_name: intestine

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen).1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA Ilbraries for RNA-seq were prepared using SMAR TER mRNA-Seq library Prep Kit following manufacturer's protocols.

value: intestine

tag: group


title: scBSseq_LK_DNA_3_B8


title: LRRSA3

value: Streptococcus agalactis challenge

value: experiemental


title: LRRSA1


title: scBSseq_LK_DNA_3_B7


title: WSA3


title: scBSseq_LK_DNA_3_B5


title: scBSseq_LK_DNA_3_B6


title: scBSseq_LK_DNA_3_B4


title: WSA2


title: JE02-255 rep1


title: scBSseq_LK_DNA_3_B3


title: LRRSA2

description: On-LRR-SA


title: scBSseq_LK_DNA_3_B2


title: scBSseq_LK_DNA_3_B12


title: scBSseq_LK_DNA_3_B1


title: scBSseq_LK_DNA_3_B10


title: scBSseq_LK_DNA_3_A9


title: scBSseq_LK_DNA_3_B11


title: scBSseq_LK_DNA_3_A7


title: scBSseq_LK_DNA_3_A8


title: scBSseq_LK_DNA_3_A3


title: scBSseq_LK_DNA_3_A5


title: scBSseq_LK_DNA_3_A6


title: Cd+ WT cells biological rep3

city: Yoshida-gun

first: Kazuyasu

last: Chihara

state: Fukui

address: 23-3 Matsuoka-Shimoaizuki, Eiheiji

department: Genome Science and Microbiology

institute: University of Fukui

description: Gene expression data from bone marrow-derived dendritic cells stimulated with curdlan

hyb_protocol: Following fragmentation, 1.85 ug of cDNA were hybridized for 16 h at 45 degrees on Clariom S array (mouse). GeneChips were washed and stained in the Affymetrix fluidics station 450.

scan_protocol: GeneChips were scanned by GeneChip Scanner 3000 7G using Affymetrix GeneChip Command Console Software.

data_processing: The data were analyzed with SST-RMA algorithm using Expression Console.

label: biotin

source_name: Bone marrow-derived dendritic cells obtained from wild-type mice treated with curdlan for 4 h

label_protocol: Biotinylated cDNA were prepared from 5.5 ug of synthesized cDNA by using GeneChip WT Terminal labeling kit according to the manufacturer instructions.

growth_protocol: To obtain bone marrow-derived dendritic cells, bone marrow cells of mice were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, penicillin, streptomycin, and 40 ng/ml of recombinant granulocyte-macrophage colony-stimulating factor. On day 6, bulk cultures were harvested and used in the experiments.

extract_protocol: Total RNA was extracted and purified by acid guanidium thiocyanate-phenol-chloroform extraction and treated with DNase I.

treatment_protocol: To stimulate bone marrow-derived dendritic cells, cells were plated and cultured on 6 well plate coated with or without curdlan for 4 h. After cells were washed with PBS, total RNA was extracted.

value: wild-type

value: BMDM

value: curdlan


title: Hmga1 OE 3, sortChIC with H3K27me3 antibody

city: Utrecht

first: Mara

last: Bouwman

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Data preprocessing has been performed using the SingleCellMultiOmics package (https://github.com/BuysDB/SingleCellMultiOmics) and the sequences were mapped to the mus musculus GRC38m38.p6 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: mouse (GRCm38/mm10)
Supplementary files format and content: bigwigs, CPM normalized, >50 mapping quality, samflag exlude 1536

source_name: adult heart 14dpi

extract_protocol:
Unfixed ventricles were dissociated to obtain single nuclei solutions. sortChIC protocol was followed as in (Zeller, 2023 nature genetics)
As in (Zeller, 2023 nature genetics).

treatment_protocol: mouse were treated with control (AAV9Myo4a-hTNNT2p-mcherry-p2A-H2BGFP) or Hmga1 OE (AAV9Myo4a-hTNNT2p-HA-mHmga1-p2A-H2BGFP) virus retro orbitally at day -1. at day 0, mice received an MI through permanent LAD ligation. At day 14, hearts were collected and sortchic was performed on GFP+ nuclei from the border zone.

value: adult heart 14dpi

tag: chic antibody

value: cardiomyocytes

value: Hmga1a overexpression

value: 14 days post MI and 15 days post AAV transduction


title: scBSseq_LK_DNA_3_A2


title: Hmga1 OE 1, sortChIC with H3K27me3 antibody


title: Hmga1 OE 2, sortChIC with H3K27me3 antibody


title: scBSseq_LK_DNA_3_A1


title: control 4, sortChIC with H3K27me3 antibody

value: control


title: scBSseq_LK_DNA_3_A12


title: scBSseq_LK_DNA_3_A11


title: Cd+ WT cells biological rep1


title: Cd- WT cells biological rep2

description: Gene expression data from bone marrow-derived dendritic cells, non-stimulated

source_name: Bone marrow-derived dendritic cells obtained from wild-type mice treated without curdlan for 4 h


title: Cd+ DL cells biological rep2

source_name: Bone marrow-derived dendritic cells obtained from 3BP2 DL/DL mice treated with curdlan for 4 h

value: 3BP2 DL/DL


title: scBSseq_LK_DNA_3_A4

value: Blood cells


title: scBSseq_LK_DNA_2_H9


title: control 1, sortChIC with H3K27me3 antibody


title: Cd+ DL cells biological rep1


title: Cd+ WT cells biological rep2


title: Cd- DL cells biological rep1

source_name: Bone marrow-derived dendritic cells obtained from 3BP2 DL/DL mice treated without curdlan for 4 h


title: HoxWT, Input Library, rep3

city: Münster

first: Frank

last: Rosenbauer

address: Robert-Koch-Str. 43

department: Institut of Molecular Tumor Biology

country: Germany

institute: University Hospital Münster

data_processing:
Reads were quantified against the barcode library with bowtie2 (--end-to-end --very-sensitive --rdg 10000,10000 --rfg 10000,10000 --mp 10000,10000) to force that only perfect, ungapped end-to-end-matches were aligned.
A count matrix was created using featureCounts with option "-Q 42", thereby only counting the aforementioned perfect, ungapped end-to-end matches.
Assembly: custom barcode library
Supplementary files format and content: Matrix of raw counts for all samples per shRNA-attached barcode sequence.
Supplementary files format and content: Fasta file with barcode sequences.

source_name: HoxWT

growth_protocol: Cell lines grown at 37°C in IMDM with 20% FCS and 10ng/ml IL-3, IL-6, SCF and 1µM ß-estradiol.

extract_protocol:
Genomic DNA was harvested 24h after shRNA library transduction via lentivirus (input control) or after 10 cell divisions had happened (final library).
shRNA-attached barcodes were amplified from gDNA in a 2-step nested PCR to 1) enrich against gDNA and 2) amplify with Illumina adapters and sequencing index sequences.
targeted shRNA screen followed by NGS

value: HoxWT

value: hematopoietic progenitor

value: WT

tag: transfection

value: Input Library


title: Cd+ DL cells biological rep3


title: Cd- WT cells biological rep1


title: HoxWT, Input Library, rep2


title: scBSseq_LK_DNA_2_H7


title: HoxWT, Input Library, rep1


title: Cd- DL cells biological rep2


title: scBSseq_LK_DNA_2_H6


title: scBSseq_LK_DNA_2_H5


title: control 3, sortChIC with H3K27me3 antibody


title: scBSseq_LK_DNA_2_H4


title: HoxWT, Final Library, rep3

value: Final Library


title: HoxURE, Input Library, rep3

source_name: HoxURE

value: HoxURE

value: UREd/d


title: HoxWT, Final Library, rep2


title: HoxWT, Final Library, rep1


title: scBSseq_LK_DNA_2_H3


title: HoxURE, Input Library, rep2


title: control 2, sortChIC with H3K27me3 antibody


title: scBSseq_LK_DNA_2_H2


title: scBSseq_LK_DNA_2_H1


title: HoxURE, Input Library, rep1


title: scBSseq_LK_DNA_3_A10


title: HoxURE, Final Library, rep3


title: scBSseq_LK_DNA_2_H12


title: scBSseq_LK_DNA_2_H8


title: HoxURE, Final Library, rep2


title: scBSseq_LK_DNA_2_H10


title: HoxURE, Final Library, rep1


title: B22, Input Library, rep3

value: AML blast


title: scBSseq_LK_DNA_2_G9


title: B22, Input Library, rep2


title: scBSseq_LK_DNA_2_G7


title: B22, Input Library, rep1


title: scBSseq_LK_DNA_2_G5


title: B22, Final Library, rep3


title: B22, Final Library, rep2


title: scBSseq_LK_DNA_2_G2


title: scBSseq_LK_DNA_2_G6


title: HoxWT, RNA-seq, rep3

data_processing:
Reads were quantified with salmon (options --validateMappings --gcBias --seqBias -l A) against a genome-decoyed (GRCm38) transcriptome (GENCODE vM25). Transcript abundance estimates were then summarized to gene level with tximport and its lengthScaledTPM option. This matrix of gene-level counts corrected for average transcript length bias is provided in the supplement of this submission as "raw_counts.txt.gz".
Assembly: GRCm38
Supplementary files format and content: Matrix of raw counts created by tximport with lengthScaledTPM option based on transcript abundance estimates from salmon

growth_protocol: cell lines grown at 37°C in IMDM with 20% FCS and 10ng/ml IL-3, IL-6, SCF and 1µM ß-estradiol.

extract_protocol:
Total RNA extracted with Macherey Nagel RNA Plus Mini kit.
1 microgram of total RNA was for poly-A enrichment followed by construction of stranded libraries for Illumina using the NEBNext Ultra II Directional kit.


title: B22, Final Library, rep1


title: scBSseq_LK_DNA_2_G4


title: scBSseq_LK_DNA_2_G3


title: scBSseq_LK_DNA_2_G12


title: HoxURE, RNA-seq, rep2


title: HoxWT, RNA-seq, rep2


title: scBSseq_LK_DNA_2_G11


title: scBSseq_LK_DNA_2_H11


title: HoxURE, RNA-seq, rep1


title: scBSseq_LK_DNA_2_G10


title: scBSseq_LK_DNA_2_G8


title: B22, RNA-seq, rep1

value: AML blast-like


title: HoxWT, RNA-seq, rep1


title: B22, RNA-seq, rep2


title: B22, RNA-seq, rep3


title: scBSseq_LK_DNA_2_F7


title: scBSseq_LK_DNA_2_F8


title: scBSseq_LK_DNA_2_F6


title: Guide NT Induction 2, i3Neurons, DIV5 [i2_GNT]

city: London

first: Adrian

last: Isaacs

address: Cruciform Building, Gower Street

department: Neurodegenerative Diseases

country: United Kingdom

institute: University College London

data_processing:
Sequence reads were trimmed for adapter sequence and low quality using fastp
Trimmed sequence reads were pseudoaligned to the reference human transcriptome (Ensembl GRCh38 v96) using kallisto (v.0.46.0)
Read count extraction and normalization were performed using tximport and DESeq2 (v.1.36.0)
Assembly: Ensembl GRCh38 v96
Supplementary files format and content: comma-delimited text file includes raw counts for each Sample

source_name: C9 Line 1

growth_protocol: iPSCs were differentiated to cortical-like neurons via dox-inducible NGN2 expression as previously described (Fernandopulle et al.). Briefly, the cells were cultured to ~80% confluency prior to differentiation. On DIV0 of neuronal differentiation, NGN2 iPSCs were dissociated and lifted with Accutase (Gibco). Cells were replated at desired ratio (3.75 x 105 cells per well/of a 6-well plate) on Geltrex-coated wells in neuronal induction media: DMEM-F12 (Gibco) containing 1x N2 (Thermo Fisher Scientific), 1x Glutamine (Gibco), 1x HEPES (Gibco), 1x NEAA (Gibco), doxycycline (2µg/mL) and 10 µM Rock inhibitor Y-27632 (DIV0 only; Tocris). Cells were washed with PBS the following day to remove cell debris and fresh induction media was added without Rock inhibitor. On DIV3, induction media was removed and replaced with neuronal maintenance media: Neurobasal (Gibco), supplemented with 1x B27 (Gibco), 10 ng/mL BDNF (PeproTech), 10 ng/mL NT-3 (PreproTech) and 1 µg/mL laminin. Cells were given a half-media change on DIV4 with fresh maintenance media and then used for downstream processing on DIV5 as indicated.

extract_protocol:
Total RNA was extracted from FACS purified iPSC-neurons and frozen mouse brain tissue using the ReliaPrep RNA cell kit and ReliaPrep RNA tissue extraction kit (Promega) respectively.
RNA library was prepared for sequencing with KAPA RNA HyperPrep with RiboErase. RNA-sequencing (NextSeq 2000) was carried out at a depth of 20 million reads per sample.

treatment_protocol: NGN2 iPSCs were treated with lentiviruses on DIV0 of the differentiation protocol, 2 hours post dissociation with Accutase. 24 hours later, media was replaced with fresh induction media and the differentiation protocol followed. At DIV5, cells were lifted and dissociated with Accutase for downstream analyses. For FACS, cells were pelleted via centrifugation prior to resuspension in FACS buffer (PBS + 1% BSA + 2mM EDTA). Cell clumps were removed via a 100 µm cell strainer and cells were resuspended in FACS buffer at 3 x 106 cells/mL. Cells were sorted at the UCL Flow Cytometry Core Facility using the BD FACSAriaTM III Cell Sorter. Sorted cells were collected and pelleted via centrifugation and snap frozen for use in downstream analyses.

value: C9 Line 1

value: C9orf72 mutant

value: Guide NT


title: HoxURE, RNA-seq, rep3


title: scBSseq_LK_DNA_2_F5


title: scBSseq_LK_DNA_2_G1


title: Guide 17 Induction 3, i3Neurons, DIV5 [i3_G17]

value: Guide 17


title: Guide 11 Induction 3, i3Neurons, DIV5 [i3_G11]

value: Guide 11


title: Guide 17 Induction 2, i3Neurons, DIV5 [i2_G17]


title: Guide 17 Induction 1, i3Neurons, DIV5 [i1_G17]


title: scBSseq_LK_DNA_2_F4


title: scBSseq_LK_DNA_2_F3


title: Guide 11 Induction 1, i3Neurons, DIV5 [i1_G11]


title: Guide 10 Induction 2, i3Neurons, DIV5 [i2_G10]

value: Guide 10


title: Guide 10 Induction 3, i3Neurons, DIV5 [i3_G10]


title: scBSseq_LK_DNA_2_F2


title: Guide 10 Induction 1, i3Neurons, DIV5 [i1_G10]


title: Guide 8 Induction 3, i3Neurons, DIV5 [i3_G8]

value: Guide 8


title: scBSseq_LK_DNA_2_F12

value: Blood cells


title: scBSseq_LK_DNA_2_F1


title: Guide 8 Induction 2, i3Neurons, DIV5 [i2_G8]


title: knockdown, IgG, rep4, batch2

data_processing:
Data were aligned to GRCm38 with bowtie2 (--very-sensitive).
Duplicates were marked and removed with samblaster, then samtools was used to only keep alignments to primary chromosomes-
Peaks were called (macs2 -p 0.05 -g hs --seed 2020 --min-length 100) per group and batch as ChIP vs IgG, then sorted by pvalue and IDR was used to obtain reproducible peaks per group across the two batches.
Groupwise peaks (knockdown, control) were merged with bedtools merge and featureCounts was used to create a matrix of raw counts.
Assembly: GRCh38
Supplementary files format and content: Matrix of raw counts with 1-based peak coordinates.

growth_protocol: THP-1 cells were grown in RPMI with 10% FCS at 37°C.

extract_protocol:
Cells were lysed and chromatin was fixed in formaldehyde. Fixed chromatin was sonicated using a Diagenode BioRuptor. Anti-RUNX1 or IgG control antibody was used for IP.
The NEBNext Ultra II DNA Library Prep kit was used to create Illumina sequencing libraries.

treatment_protocol: Induction of knockdown or control shRNA cassette by addition of doxocycline to the medium.

value: knockdown

tag: chip antibody

value: IgG


title: scBSseq_LK_DNA_2_F11


title: Young3-scRNAseq

city: Kyoto

first: Satoshi

last: NAKAMIZO

state: Kyoto

address: 54 Shogoin-Kawahara, Sakyo

institute: Kyoto University

description: 10X Genomics

data_processing:
The CellRanger pipeline (v3.1.0) (10x genomics) was used to generate count matrices from FASTQ files using default parameters.
Assembly: GRCh38-3.0.0
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Epidermis

extract_protocol:
the epidermis was separated using dispase, and epidermal suspension was prepared using 0.25% trypsin/EDTA. The cells were used to prepare a library using the 10X Chromium Next GEM Single Cell 3' Kit, and scRNA-seq was performed.
Isolated cells were loaded onto a Chromium instrument (10X Genomics) according to the Chromium Single Cell 3’ Reagent Kit v3 user guide (https://support.10xgenomics.com/single-cell-gene-expression/library-prep/doc/user-guide-chromium-single-cell-3-reagent-kits-user-guide-v3-chemistry).

value: Epidermis

tag: age

value: F

tag: body site

value: Eyelid

value: Healthy


title: Guide NT Induction 1, i3Neurons, DIV5 [i1_GNT]


title: Old3-scRNAseq

description: 10X Genomics

value: M


title: Old2-scRNAseq

description: 10X Genomics


title: Old1-scRNAseq

description: 10X Genomics


title: Guide 8 Induction 1, i3Neurons, DIV5 [i1_G8]


title: Young2-scRNAseq

description: 10X Genomics


title: scBSseq_LK_DNA_2_F9


title: scBSseq_LK_DNA_2_F10


title: knockdown, RUNX1, rep6, batch2

description: chipseq_runx1_rawCounts.tsv (includes only the RUNX samples)


title: control, IgG, rep4, batch2

value: control


title: Guide 11 Induction 2, i3Neurons, DIV5 [i2_G11]


title: Young1-scRNAseq

description: 10X Genomics


title: scBSseq_LK_DNA_2_E9


title: knockdown, RUNX1, rep3, batch2


title: scBSseq_LK_DNA_2_E8


title: knockdown, RUNX1, rep4, batch2


title: scBSseq_LK_DNA_2_E7


title: control, RUNX1, rep6, batch2


title: zip-7,RW12339,lateembryonic,Exp1,Input1

city: Seattle

first: Louis

last: Gevirtzman

state: WA

address: 3720 15th Ave NE

department: Genome Science

institute: University of Washington

description: TF

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: ce11
Supplementary files format and content: bigWig, narrowPeak, html

organism: Caenorhabditis elegans

extract_protocol:
For the modENCODE and modERN project, worm growth and ChIP were conducted 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) with the following modifications. Embryonic stages were collected after bleaching and arresting in M9 at 20°C with shaking until the desired embryonic stage was visualized by DIC microscopy. Larval and the young adult stages were synchronized by bleaching and L1 starvation and then arrested L1s were plated on peptone-enriched plates seeded with OP50 bacteria and grown for 6 hrs at 20°C for L1 collection, or grown to the desired stage based on visual examination of their development (Brenner 1974 (PMID: 4366476). GFP fluorescent and DIC images were collected immediately before collection. Worm samples were then cross-linked with 2% formaldehyde for 28 min at room temperature and quenched with 1M Tris pH 7.5. The pelleted worms were rinsed with M9 buffer twice and then with 150 mM NaCl FA buffer (50mM HEPES/KOH pH7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150mM NaCl) with one Roche Complete tablet (Catalog number 11697498001) before the pellet was flash frozen in liquid nitrogen and stored at -80°C. Worm pellets resuspended in 150 mM FA Buffer containing one Roche Complete tablet, 25 ul 1M DTT and 125 ul of 100 mM PMSF per 25 mL chilled FA were sonicated using a microtip to achieve mostly 200–800 bp DNA fragments. For a subset of factors (OP662, OP565, OP579, OP638, OP553, OP550, OP658, OP696, OP552, OP563, OP688, OP685, OP707, OR3349, and XIL99), an additional dounce step was added prior to sonication as described in Kudron MM et al., 2018 (PMID: 29284660).    Worm lysate was measured by Bradford assay and extract corresponding to 2.2 or 4.4 mg was resuspended in 150 mM FA Buffer with Complete protease inhibitors along with 20µl 20% N-lauroylsarcosine sodium salt and spun for 5 minutes at 13,000 g at 4℃ in a non-stick Eppendorf tube. Samples were transferred to a fresh tube and 10% of the lysate was removed as input. Input samples were stored at -20℃ until the following day. ChIP samples were immunoprecipitated using 7.5 μg anti-GFP antibodies (gifts of Tony Hyman and Kevin White) overnight at 4℃ with rotation.    The following day, input samples were thawed and 2μl of 10 mg/mL RNase A was added and samples were digested at room temperature for 2 hours. Then input samples were brought up to 300 μl using Elution Buffer (1% SDS in TE pH 8.0 with 250 mM NaCl), and 4 μl of 10 mg/mL Proteinase K (Roche 03115887001) was added and they were incubated at 55℃ for 4 hours.   In the meantime, the ChIP samples were incubated with protein G sepharose beads for 2 hours at 4℃ with rocking (GE Healthcare Cat. # 17-0618-01). Beads were first washed 4 times in 150 mM FA buffer. All subsequent spins were at 2500 x g for 2 minutes each. The beads were then washed 2 times with room temperature 150 mM FA buffer for 5 minutes and then 1 time with 1M NaCl FA (50mM HEPES/KOH pH7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1M NaCl) for 5 minutes. Samples were then transferred to new tubes and washed one time with 500 mM NaCl FA (50mM HEPES/KOH pH7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 500mM NaCl) for 10 minutes, 1 time with TEL buffer (0.25M LiCl, 1% NP40, 1% sodium deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH8.0) for 10 minutes and then 2 times with TE pH 8.0 for 5 minutes. To elute the immunocomplexes, the beads were incubated two times for 15 minutes each with 150 μl Elution Buffer with gentle vortexing every 5 minutes. The two elutions were pooled after spinning down and 1 ul of 20 mg/mL Proteinase K was added to each ChIP sample. Both the eluted ChIP samples and the input samples were incubated overnight at 65℃ to reverse crosslinks. All samples were purified using either a minElute PCR Purification Kit from Qiagen (Catalog number 28006) or in later stages of the modERN project a ChIP DNA Clean and concentrator kit from Zymo (ZD5205).
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: st12339[TY1::EGFP::3xFLAG::zip-7] IV

tag: genetic modification

value: CRISPR

tag: developmental stage

value: lateembryonic


title: knockdown, IgG, rep3, batch2


title: control, RUNX1, rep4, batch2


title: knockdown, IgG, rep2, batch1


title: scBSseq_LK_DNA_2_E6


title: zip-7,RW12339,lateembryonic,Exp1,ChIP2

description: TF


title: zip-7,RW12339,lateembryonic,Exp1,ChIP1

description: TF


title: control, IgG, rep2, batch1


title: scBSseq_LK_DNA_2_E4


title: control, IgG, rep1, batch1


title: sptf-3,RW12349,youngadult,Exp1,ChIP2

description: TF

value: st12349[TY1::EGFP::3xFLAG::sptf-3] I

value: youngadult


title: control, IgG, rep3, batch1


title: sptf-3,RW12349,youngadult,Exp1,Input1

description: TF


title: knockdown, IgG, rep1, batch1


title: scBSseq_LK_DNA_2_E5


title: knockdown, RUNX1, rep2, batch1


title: knockdown, RUNX1, rep1, batch1


title: sptf-3,RW12349,youngadult,Exp1,ChIP1

description: TF


title: scBSseq_LK_DNA_2_E3


title: control, RUNX1, rep2, batch1


title: control, RUNX1, rep1, batch1


title: scBSseq_LK_DNA_2_E2


title: knockdown, RUNX1, rep5, batch2


title: control, RUNX1, rep3, batch1


title: scBSseq_LK_DNA_2_E1


title: pqn-47,PHX2564,L2larva,Exp1,Input1

description: TF

value: GFP::myrf-1::(syb2564) II


title: control, RUNX1, rep5, batch2


title: M01_Blood_Nod2KO_MDP_NCM_5

city: Chicago

first: Yuanqing

last: Yan

state: IL

address: 303 E Superior Street

institute: Northwestern University

data_processing:
Libraries were then prepared using the Nextera XT DNA Library Preparation Kit (Illumina), indexed using the Nextera Index Kit v2 (Illumina), and sequenced on a NextSeq500 (Illumina). FASTQ files were generated, then single-end reads mapped to the mouse reference genome mm10 using TopHat2 aligner software with the HTSeq package. Raw counts were used for a differential gene expression analysis using edgeR with an adjusted p.
Assembly: mm10
Supplementary files format and content: htseq.all.counts.txt for raw counts and fastq.gz for each sample

source_name: Blood

extract_protocol:
For I-NCM and N-NCM: PBS or MDP was administered to mice by I.V. injection at a dose of 10-20 mg/kg mouse body weight. At 36h post treatment, the blood samples were collected from submandibular (facial) vein or cardiac puncture.  For PD-L1+ and PD-L1- NCMs:  the blood samples were collected from wtB6 mice and the NCMs were isolated by Fluorescence-activated Cell Sorting (FACS). Total RNA was extracted from mouse blood monocytes using an Arcturus PicoPure RNA Isolation Kit (Cat#: KIT0204, Thermo Fisher Scientific) or RNeasy Plus Micro Kit (Cat#: 74034, Qiagen).
Qualified total RNA samples were preamplified, and cDNA synthesis was performed using the SMART-Seq v4 Ultra Low Input RNA Kit for sequencing (Clontech/Takara Bio, USA).

treatment_protocol: To purely collect N-NCM and I-NCM, we sorted the blood NCMs from muramyl dipeptide (MDP)-treated Nod2KO mice and Nr4a1KO mice, respectively.  The flow-sorted NCMs were used for bulk RNA sequencing.

value: Blood

value: NCM

tag: treatment

value: MDP

tag: time


title: pqn-47,PHX2564,L2larva,Exp1,ChIP1

description: TF


title: M01_Blood_Nod2KO_MDP_NCM_3

tag: tissue


title: pqn-47,PHX2564,L2larva,Exp1,ChIP2

description: TF


title: nsy-7,RW12353,youngadult,Exp1,Input1

description: TF

value: st12353[nsy-7::TY1::EGFP::3xFLAG] IV


title: scBSseq_LK_DNA_2_E12

value: Blood cells


title: M01_Blood_Nod2KO_MDP_NCM_1


title: M01_Blood_Nod2KO_MDP_CM_3

value: CM


title: scBSseq_LK_DNA_2_E11


title: nsy-7,RW12353,youngadult,Exp1,ChIP2

description: TF


title: M01_Blood_wtB6_MDP_NCM_5


title: M01_Blood_Nod2KO_MDP_CM_1


title: nsy-7,RW12353,youngadult,Exp1,ChIP1

description: TF


title: scBSseq_LK_DNA_2_E10


title: scBSseq_LK_DNA_2_D9


title: M01_Blood_wtB6_MDP_NCM_4


title: end-1,RW12352,lateembryonic,Exp1,Input1

description: TF

value: st12352[end-1::TY1::EGFP::3xFLAG] V


title: M01_Blood_wtB6_MDP_NCM_1


title: M01_Blood_wtB6_MDP_CM_5


title: end-1,RW12352,lateembryonic,Exp1,ChIP1

description: TF


title: scBSseq_LK_DNA_2_D6


title: scBSseq_LK_DNA_2_D7


title: end-1,RW12352,lateembryonic,Exp1,ChIP2

description: TF


title: scBSseq_LK_DNA_2_D8


title: M01_Blood_wtB6_MDP_NCM_3


title: M01_Blood_Nod2KO_MDP_NCM_4


title: M01_Blood_Nod2KO_MDP_NCM_2


title: M01_Blood_wtB6_MDP_CM_2


title: ceh-89,OH16505,L4larva,Exp1,Input1

description: TF


title: scBSseq_LK_DNA_2_D4


title: M01_Blood_Nod2KO_MDP_CM_2


title: scBSseq_LK_DNA_2_D5


title: M01_Blood_wtB6_MDP_CM_3


title: ceh-89,OH16505,L4larva,Exp1,ChIP2

description: TF


title: scBSseq_LK_DNA_2_D3


title: M01_Blood_CD274ngeNCM_wtB6_1

value: Control


title: M01_Blood_CD274negNCM_wtB6_2


title: ceh-89,OH16505,L4larva,Exp1,ChIP1

description: TF


title: M01_Blood_CD274posNCM_wtB6_5


title: M01_Blood_CD274negNCM_wtB6_3


title: M01_Blood_wtB6_MDP_CM_1


title: scBSseq_LK_DNA_2_D2


title: M01_Blood_CD274negNCM_wtB6_4


title: M01_Blood_wtB6_MDP_NCM_2


title: scBSseq_LK_DNA_2_D1


title: Center2-505

last: Zhang

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

source_name: Peripheral Whole Blood

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

value: Immunotherapy + Chemotherapy

tag: progression event

tag: days to progression

tag: death event

tag: days to death

tag: tmb

tag: pdl1 cps

tag: arraytypes


title: M01_Blood_IntM_Nr4a1KO_MDP_3

tag: cell line

value: IntM

tag: genotype


title: M01_Blood_CD274posNCM_wtB6_2


title: M01_Blood_CD274posNCM_wtB6_1


title: M01_Blood_CD274posNCM_wtB6_3


title: scBSseq_LK_DNA_2_D12

tag: cell type


title: Center2-504

tag: age

value: Immunotherapy only


title: M01_Blood_IntM_Nr4a1KO_MDP_2


title: Center2-503


title: Center2-506


title: Center2-502


title: M01_Blood_CM_Nr4a1KO_MDP_3


title: M01_Blood_wtB6_MDP_CM_4


title: M01_Blood_CM_Nr4a1KO_MDP_2


title: Center1-064


title: M01_Blood_IntM_Nr4a1KO_MDP_1


title: scBSseq_LK_DNA_2_C9


title: M01_Blood_CM_Nr4a1KO_MDP_1


title: M01_Blood_NCM_Nr4a1KO_MDP_2


title: M01_Blood_NCM_Nr4a1KO_MDP_1


title: M01_Blood_NCM_Nr4a1KO_MDP_3


title: M01_Blood_NCM_Nod2KO_3


title: Center1-063


title: scBSseq_LK_DNA_2_D10


title: scBSseq_LK_DNA_2_C7


title: M01_Blood_CD274posNCM_wtB6_4


title: Center1-062

value: Female


title: M01_Blood_NCM_wtB6_3


title: Center1-060


title: M01_Blood_NCM_Nod2KO_2


title: scBSseq_LK_DNA_2_C6


title: M01_Blood_NCM_Nod2KO_1


title: Center1-061


title: M01_Blood_NCM_wtB6_1


title: M01_Blood_NCM_wtB6_2


title: scBSseq_LK_DNA_2_C5


title: scBSseq_LK_DNA_2_C4


title: scBSseq_LK_DNA_2_C3


title: Center1-059


title: Mosaic_beta-catCA_GFP_min_lot1

first: Yuki

last: Akieda

state: Osaka

address: 3-1, Yamadaoka

department: Research Institute for Microbial Diseases

institute: Osaka University

data_processing:
Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 (ver. 2.3.1).
UMI counts were extracted per HTSeq (ver. 0.6.1) from the CEL-Seq2 pipeline.
Assembly: GRCz10
Supplementary files format and content: Tab-delimited text file for expression data normalized by regularized logarithm.

organism: Danio rerio

source_name: early embryonic cell

extract_protocol:
Cells were dissolved in TRIzol reagent (Invitrogen) and extracted.
Samples were prepared according to the CEL-Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL-Seq2 protocol.

tag: strain

value: AB

value: early embryonic cell

value: 9 hpf (hour post fertilization)


title: Mosaic_GFP_control_GFP_min_lot1

tag: developmental stage


title: Center1-058

tag: treatment


title: Center1-057


title: scBSseq_LK_DNA_2_C1


title: Center1-056


title: Center1-055


title: WT_THP1_PHIP, ChIP_Rep2

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: clonally expanded

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

source_name: Hematopoietic

growth_protocol: THP1 clones wildtype for PHF6 and PHIP were grown in complete media (RPMI1640 + FBS)

extract_protocol:
20 million cells from each clone were crosslinked using 1% paraformaldehyde, treated with MNase, and lysed using freeze-thaw cycles and sonication. Cell lysate from 10 million cells was used for PHIP pulldown (ProteinTech, 20933-1-AP) and IgG control pulldown (Invitrogen, 02-6102).
DNA concentration and fragment length were 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: Hematopoietic

value: AML cell line

value: Wildtype


title: WT_THP1_IgG, ChIP

description: clonally expanded


title: WT_THP1_ChIP, Input

description: clonally expanded


title: scBSseq_LK_DNA_2_C12


title: DoxPHF6-PHIPKO_plus_Dox_THP1_PHF6-ChIP_Rep3

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

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).

treatment_protocol: Doxycycline treatment

value: PHF6 knockout/DoxPHF6/PHIP knockout

value: 50ng/ul Doxycyclin for 24 hours


title: WT_THP1_PHIP, ChIP_Rep1

description: clonally expanded


title: Mosaic_GFP_control_GFP_min_lot2

city: Suita


title: DoxR274Q_plus_Dox_THP1_PHF6-ChIP_Rep3

value: PHF6 knockout/DoxPHF6R274Q

value: 100ng/ul Doxycyclin for 24 hours


title: scBSseq_LK_DNA_2_C11

value: Blood cells


title: DoxPHF6-PHIPKO_plus_Dox_THP1_PHF6-ChIP_Rep1


title: scBSseq_LK_DNA_2_B9


title: Center1-054

first: Ze

address: 375 Longwood Ave

institute: Harvard Medical School


title: Center1-053


title: Center1-052


title: DoxR274Q_plus_Dox_THP1_PHF6-ChIP_Rep2


title: DoxPHF6_plus_Dox_THP1_PHF6-ChIP_Rep1

value: PHF6 knockout/DoxPHF6


title: scBSseq_LK_DNA_2_C2


title: Mosaic_beta-catCA_GFP_min_lot2


title: DoxR274Q_plus_Dox_THP1_PHF6-ChIP_Rep1


title: DoxPHF6_plus_Dox_THP1_PHF6-ChIP_Rep3


title: Center1-051


title: scBSseq_LK_DNA_2_B7


title: DoxPHF6_plus_Dox_THP1_PHF6-ChIP_Rep2


title: DoxPHF6_minus_Dox_THP1_PHF6-ChIP


title: scBSseq_LK_DNA_2_B8


title: scBSseq_LK_DNA_2_C8


title: scBSseq_LK_DNA_2_B6


title: DKO_THP1_H3K27ac-ChIP_Rep1

description: clonally expanded and sequence verified

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

growth_protocol: Cells were electroporated with Cas9 Ribonucleoprotein and gRNAs for i) exon 4 of PHF6 for PHF6 knockouts, ii) exon 8 of PHF6 and ssODN for PHF6R274Q mutant for R274Q clones, iii) exon 6 of PHIP for PHIP knockouts, and iv) exon4 of PHF6 and exon 6 of PHIP for DKO clones. Resultant pools was 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:
20 million cells from each clone were crosslinked using 1% paraformaldehyde, treated with MNase, and lysed using freeze-thaw cycles and sonication. Cell lysate from 10 million cells was used for H3K27ac pulldown (Active Motif, 39135) 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/PHIP double knockout


title: DoxPHF6_plus_Dox_THP1_IgG-ChIP

value: 250ng/ul Doxycyclin for 24 hours


title: scBSseq_LK_DNA_2_C10

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.


title: scBSseq_LK_DNA_2_B4


title: DoxPHF6_plus_Dox_THP1_ChIP-Input


title: DKO_THP1_H3K27ac-ChIP_Rep3

description: clonally expanded and sequence verified


title: Center1-049

value: Male

value: Immunotherapy + Chemotherapy


title: Center1-046

value: Immunotherapy only


title: scBSseq_LK_DNA_2_B3


title: R274Q_THP1_H3K27ac-ChIP_Rep2

description: clonally expanded and sequence verified

value: PHF6R274Q mutant


title: Center1-048


title: R274Q_THP1_H3K27ac-ChIP_Rep3

description: clonally expanded and sequence verified


title: scBSseq_LK_DNA_2_B5


title: PHIPKO_THP1_H3K27ac-ChIP_Rep3

description: clonally expanded and sequence verified

value: PHIP knockout


title: Center1-045


title: Center1-050

value: Female


title: PHIPKO_THP1_H3K27ac-ChIP_Rep1

description: clonally expanded and sequence verified

value: Hematopoietic


title: PHF6KO_THP1_H3K27ac-ChIP_Rep3

description: clonally expanded and sequence verified

value: AML cell line

value: PHF6 knockout


title: scBSseq_LK_DNA_2_B2


title: R274Q_THP1_H3K27ac-ChIP_Rep1

description: clonally expanded and sequence verified


title: PHIPKO_THP1_H3K27ac-ChIP_Rep2

description: clonally expanded and sequence verified


title: scBSseq_LK_DNA_2_B1


title: PHF6KO_THP1_H3K27ac-ChIP_Rep4

description: clonally expanded and sequence verified


title: DKO_THP1_H3K27ac-ChIP_Rep2

description: clonally expanded and sequence verified


title: PHF6KO_THP1_H3K27ac-ChIP_Rep1

description: clonally expanded and sequence verified


title: scBSseq_LK_DNA_2_B12


title: Center1-044


title: Center1-043


title: WT_THP1_H3K27ac-ChIP_Rep2

description: clonally expanded and sequence verified

value: Wildtype


title: scBSseq_LK_DNA_2_B10


title: WT_THP1_H3K27ac-ChIP_Rep3

description: clonally expanded and sequence verified


title: Center1-041


title: WT_THP1_ChIP-Input

description: clonally expanded and sequence verified


title: Center1-040


title: scBSseq_LK_DNA_2_B11


title: PHF6KO_THP1_H3K27ac-ChIP_Rep2

description: clonally expanded and sequence verified


title: Center1-047


title: Center1-042


title: WT_THP1_H3K27ac-ChIP_Rep1

description: clonally expanded and sequence verified


title: WT_THP1_IgG-ChIP

description: clonally expanded and sequence verified


title: scBSseq_LK_DNA_2_A9


title: KO_ATAC-Seq_Rep3

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

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).


title: scBSseq_LK_DNA_2_A8


title: Center1-038


title: KO_ATAC-Seq_Rep4


title: scBSseq_LK_DNA_2_A7


title: KO_ATAC-Seq_Rep2


title: KO_ATAC-Seq_Rep1


title: CONT_ATAC-Seq_Rep1


title: CONT_ATAC-Seq_Rep5


title: CONT_ATAC-Seq_Rep4


title: scBSseq_LK_DNA_2_A5


title: Center1-037


title: Center1-039


title: DoxPHF6-PHIPKO_48h_THP1_RNA-Seq_Rep1

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

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).

value: PHF6 knockout/DoxPHF6/PHIP knockout

value: 250ng/ul Doxycyclin for 48 hours


title: CONT_ATAC-Seq_Rep3


title: DoxPHF6-PHIPKO_48h_THP1_RNA-Seq_Rep3