title: Induced human sensory neurons alone Replicate 2

value: induced human sensory neurons

value: iSNs alone


title: Induced human sensory neurons alone Replicate 3

status: Public on Jul 24 2024

type: SRA

city: Boston

first: Chelsey

last: LeBlang

state: Massachusetts

address: 360 Longwood Ave

department: Cancer Biology

country: USA

institute: Dana Farber Cancer Institute

library_source: transcriptomic

data_processing:
Fastq files were generated using bcl2fastq v2.20
Reads were aligned with STAR (v2.7.3a)
Assembly: UCSC Hg38 and UCSC Rn6
Supplementary files format and content: CSV file contains raw counts aligned to human genome
Supplementary files format and content: CSV file contains raw counts aligned to rat genome

molecule: total RNA

organism: Homo sapiens

source_name: iPSC NCRM5

growth_protocol: Primary e14.5 rat DRG glia were cultured for one week in base media. After one week, rDRG glia were either maintained in base media, treated with neuronal maturation media, or cocultured with terminally differentiating human induced neural crest precursors for one week. Human induced neural crest precursors were also plated alone and terminally differentiated one week.

extract_protocol:
RNA was collected using the RNeasy Plus Mini Kit from Qiagen acording to manufacturer's protocol.
Roche Kapa mRNA HyperPrep strand specific sample preparation kits  according to the manufacturer’s protocol on a Beckman Coulter Biomek i7.

tag: cell type

tag: cell line

value: iPSC NCRM5

tag: genotype

value: WT

tag: treatment


title: Wild Type cultivated in LB 2

city: Montpellier

first: Anne

last: Lanois

address: 75 rue du Truel CC54

country: France

institute: INRA

data_processing:
Alignment to the Xenorhabdus nematophila F1 (XENF1.2) genome was performed with BWA v0.7.17-r1188. The resulting file were sorted and filtered (with option -q 3) with Samtools v1.9
The counting by CDS was performed using featureCounts v2.0.0, with a gff file downloaded on 07-27-2020 from the MaGe platform (https://mage.genoscope.cns.fr)
Assembly: XENF1.2
Supplementary files format and content: tab-delimited text file include raw gene counts for every gene and every sample

organism: Xenorhabdus nematophila F1

growth_protocol: logarithmic culture phase in LB broth supplemented or not with paraquat (during 30 min) at 28°C

extract_protocol:
RNEasy miniprep QIAGEN kit
MICROBExpress™ Bacterial mRNA Enrichment Kit (Ambion) was used to remove ribosomal RNA
Illumina TruSeq Stranded mRNA Sample Preparation kit

treatment_protocol: RNA Protect Bacteria reagent 5 min

tag: strain

value: Wild type

value: no treatment


title: Induced human sensory neurons alone Replicate 1


title: Primary uveal melanoma tumor 39

type: genomic

city: Philadelphia

first: Arupa

last: Ganguly

state: PA

address: 560 Clinical Research Building 415 Curie Boulevard

institute: University of Pennsylvania

hyb_protocol: Standard protocol

scan_protocol: HiScan

data_processing: minfi

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Uveal melanoma tumor

label_protocol: Standard protocol

extract_protocol: See manuscript

tag: tissue

value: Uveal melanoma tumor


title: total RNA-seq from sample_284

city: Munich

first: Janine

last: Knauer-Arloth

address: Kraepelinstr. 2-10

country: Germany

institute: Max Planck Institute of Psychiatry

description:
raw_counts_replication.tsv
normalized_data_replication.tsv

data_processing:
Quality control with FastQC version 0.11.8
Unique Molecular Identifiers extraction with UMI-tools version 1.1.1
Adapter trimming with cutadapt version 2.10
Read aligning to the reference genome with STAR version 2.7.7a
Read deduplication with UMI-tools version 1.1.1
Quantification of gene expression with featureCounts version 1.6.4
Batch correction for the GC content and randomization_batch with ComBat_seq from the sva package version 3.38.0
Normalization with vst from DESeq2 version 1.30.1
Assembly: GRCh38.p12
Supplementary files format and content: raw_counts.tsv contains the output of featureCounts (unfiltered raw counts)
Supplementary files format and content: normalized_data.tsv contains the batch corrected and normalized data with low-count genes and genes that are heavily influenced by the GC content filtered out

source_name: PBMCs

extract_protocol:
Blood was collected in the morning under fasted conditions, peripheral blood mononuclear cells (PBMCs) were extracted and stored at in the gas phase of liquid nitrogen. The RNA was extracted automatically with the chemagic 360 instrument by using the chemagic RNA Kit according to the manufacturer’s instructions and 25µl eluate stored in a PCR plate at -80°C until further processing.
200ng RNA was used for rRNA depletion with the RiboCop rRNA Depletion Kit V1.3. 10µl of the depleted RNA was used for library preparation with the Lexogen CORALL total RNA-Seq Library Prep Kit with UDIs 12 nt Sets A1-A4. The library was sequenced on an NovaSeq 6000 using an S4 200 flow cell with paired-end 100bp reads.

value: PBMCs

tag: age

tag: Sex

value: female

tag: bmi

tag: status

value: affected; for replication analysis

tag: plate

tag: row

value: C

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: total RNA-seq from sample_283

value: male

value: H


title: Wild Type cultivated in LB 3


title: Primary uveal melanoma tumor 37


title: Induced human sensory neurons alone Replicate 4


title: Primary uveal melanoma tumor 38


title: Primary uveal melanoma tumor 36


title: Primary uveal melanoma tumor 41


title: Primary uveal melanoma tumor 35


title: total RNA-seq from sample_280

value: B


title: total RNA-seq from sample_281


title: total RNA-seq from sample_277

value: D


title: total RNA-seq from sample_279

value: G


title: total RNA-seq from sample_278


title: Wild Type cultivated in LB 1


title: total RNA-seq from sample_276

value: E


title: Primary uveal melanoma tumor 28


title: total RNA-seq from sample_274


title: total RNA-seq from sample_275


title: K562, TET2 KO, caRNA, m5C-IP, MeRIP, r2

city: Shanghai

first: Xiaoyang

last: Dou

address: 320 Yue Yang Road

country: China

institute: CAS Center for Excellence in Molecular Cell Science, CAS

description:
chromatin-associated RNA
hg38.Onecodetofindthemall.elem_featureCounts.sel.txt
K562_TET2KO_caRNA-IP-m5C-MeRIP_r2_c20_human_20240508

library_source: other

data_processing:
Raw reads were trimmed with Trimmomatic (version 0.39), then aligned to mouse (mm10) or human (hg38) genome and transcriptome, together with 5-methylcytosine (m5C) modified or unmodified mRNA spike-ins (see the “m5C methylated RNA immunoprecipitation with spike-in” section for details), using HISAT2 (version 2.1.0).
Mapped reads were deduplicated using a Picard tool ‘MarkDuplicates’ (version 2.26.2) (http://broadinstitute.github.io/picard/).
Assembly: mouse (mm10), human (hg38)
Supplementary files format and content: Counts

molecule: other

source_name: bone marrow

growth_protocol: K-562 cells were kept in RPMI-1640 medium plus 10% FBS. All mESCs were kept in DMEM (Gibco,11995065) supplemented with 15% Stem Cell Qualified Fetal Bovine Serum, Heat Inactivated (Gemini Bio Products, 100-525), 1 × L-glutamine (Gibco, 25030081), NEAA (Gibco, 25030081), LIF (MilliporeSigma, ESG1107), 1 × β-mercaptoethanol (Gibco, 21985023), 3 μM CHIR99021 (STEMCELL Technologies, 72052) and 1 μM PD0325901 (STEMCELL Technologies, 72182) at 37 °C and 5% CO2. The medium was replaced every 24 hours.m ESCls were passaged on gelatin coated plates twice to clear feeder cells before experiments. HSPCs (lineage-positive cells (Lin+ ) were depleted from total BM cells of 6–8 weeks old mice using the Direct Lineage Cell Depletion Kit (Miltenyi Biotec, 130-110-470), and then the lineage-negative cells (Lin- ) were sorted with c-Kit (CD117) MicroBeads (Miltenyi Biotec, 130-091-224). The purity of selected cells was analyzed by flow cytometry.

extract_protocol:
Fractionation of mESCs and K-562 cells was performed following the published protocol with the optimized concentration of NP-40 (MilliporeSigma, 492018) for each cell line. In brief, 5 × 106 to 1 × 107 724 cells were harvested and washed with 1 mL cold PBS/1 mM EDTA buffer, then centrifuged at 4 °C with 500 g to collect the cell pellet. 200 μL ice-cold lysis buffer (10 mM Tris726 HCl, pH = 7.4, 0.05% NP-40, 150 mM NaCl) were added to the cell pellet and incubated on ice for 5 minutes, then gently pipetted up the cell lysate over 2.5 volumes of chilled sucrose cushion (24% RNase-free sucrose in lysis buffer) and centrifuged at 4 °C with 15,000 g for 10 minutes. All the supernatant was collected as cytoplasmic fraction and the nuclei pellet was washed once by gently adding 200 μL ice-cold PBS/1 mM EDTA to the nuclei pellet without dislodging the pellet. The nuclei pellet was resuspended in 200 μL prechilled glycerol buffer (20 mM Tris-HCl, pH = 7.4, 75 mM NaCl, 0.5 mM EDTA, 0.85 mM DTT, 0.125 mM PMSF, 50% glycerol) with gentle flicking of the tube. Then an equal volume of cold nuclei lysis buffer (10 mM HEPES, pH = 7.6, 1 mM DTT, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3 M NaCl, 1 M urea, 1% NP-40) was added, followed by vigorous vertexing for 5 seconds twice. The nuclei pellet mixtures were incubated for 2 minutes on ice, then centrifuged at 4 °C with 15,000 g for 2 minutes. The supernatant was collected as the soluble nuclear fraction (nucleoplasm). The pellet was gently rinsed with cold PBS/1 mM  EDTA without dislodging and then collected as the chromosome-associated fraction. caRNA was extracted with standard TRIZol protocol. Fractionation of LK cells were performed similar to ES cells with minor modification. Briefly, LK cells were cultured in vitro for 2 hours followed sorting from autoMACS® Pro Separator, and then ice-cold lysis buffer (10 mM Tris-HCl, pH = 7.4, 0.15% IGEPAL 741 ® CA-630, 75 mM NaCl) was used to separate cytoplasmic fraction.
caRNAs were fragmented by soniation on a Bioruptor pico (Diagenode) device with 30 cycles, 30s on/30s off. Then in vitro transcribed spike-in RNA from firefly luciferase mRNA or renilla luciferase mRNA with different m5C levels were added to the immunoprecipitation reaction. Immunoprecipitated RNA was extracted by using Dynabeads™ MyOne™ Silane (Invitrogen, 37002D). Library construction was performed according to the standard protocol of SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (TaKaRa bio, 634417).
MeRIP-seq

treatment_protocol: siRNA transfections in leukemic cells were performed with SG Cell Line 4D-Nucleofector™ X Kit L (Lonza, V4XC-3024) or SF kit (V4XC-2012) using programs recommended by the manufacturer. siRNA transfections in mESCs were performed using Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen, 13778100) following the standard protocol.  Gene overexpression in mESCs were performed by using the piggyBac transposase system with a hygromycin selection marker. Stable expression clones were selected by applying hygromycin B to the culture system for two weeks.

value: bone marrow

value: lymphoblast cell

value: TET2 KO

value: m5C (Diagenode, #MAb-081-100)


title: K562, TET2 KO, caRNA, m5C-IP, MeRIP, r1

description:
chromatin-associated RNA
hg38.Onecodetofindthemall.elem_featureCounts.sel.txt
K562_TET2KO_caRNA-IP-m5C-MeRIP_r1_c8_human_20240508


title: K562, WT, caRNA, m5C-IP, MeRIP, r2

description:
chromatin-associated RNA
hg38.Onecodetofindthemall.elem_featureCounts.sel.txt
K562_TET2WT_caRNA-IP-m5C-MeRIP_r2_c19_human_20240508

value: WT


title: K562, TET2 KO, caRNA, m5C-IP, MeRIP, r3

description:
chromatin-associated RNA
hg38.Onecodetofindthemall.elem_featureCounts.sel.txt
K562_TET2KO_caRNA-IP-m5C-MeRIP_r3_c32_human_20240508


title: Primary uveal melanoma tumor 27


title: Primary uveal melanoma tumor 33


title: Primary uveal melanoma tumor 34


title: Primary uveal melanoma tumor 30


title: Primary uveal melanoma tumor 32


title: Primary uveal melanoma tumor 31


title: sisnar_scr_mRNA_3

city: Urbana

first: Sihang

last: Zhou

state: IL

address: 601 S Goodwin Ave

institute: University of Illinois Urbana-Champaign

data_processing:
poly(A)+ RNA reads were first trimmed using TrimGalore and then mapped to the transcriptome using quasi-mapper Salmon to generate read counts
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: polyA RNA

source_name: Kidney

growth_protocol: HEK293T cells were maintained in DMEM supplied with 10% fetal bovine serum (FBS) and 1% Pen-Strep in the cell incubator with 5% CO₂ at 37°C

extract_protocol:
Total RNA extraction was performed using E.Z.N.A.® Total RNA Kit I (Omega Bio-tek)according to the manufacturer’s instructions
Total RNA was rRNA depleted and poly(A)+ RNA enriched. The RNAseq libraries were prepared with the Kapa Hyper Stranded mRNA library kit (Roche) according to the instructions.

treatment_protocol: HEK293T cells were transfected with 12.5nM siRNA(sicontrol or sisnaR-A-1,-2,-3) using Lipofectamine® RNAi Max for 48 hours at 37 °C with 5% CO2 before collection

value: Kidney

value: epithelial

value: Control knockdown


title: Primary uveal melanoma tumor 29

value: Uveal melanoma tumor


title: sisnar_3_mRNA_3

value: snaR-A kockdown #3


title: sisnar_scr_mRNA_2


title: sisnar_2_mRNA_3

value: snaR-A kockdown #2


title: K562, WT, caRNA, m5C-IP, MeRIP, r1

description:
chromatin-associated RNA
hg38.Onecodetofindthemall.elem_featureCounts.sel.txt
K562_TET2WT_caRNA-IP-m5C-MeRIP_r1_c7_human_20240508


title: Primary uveal melanoma tumor 26


title: Primary uveal melanoma tumor 25


title: Primary uveal melanoma tumor 40


title: sisnar_1_mRNA_2

value: snaR-A kockdown #1


title: sisnar_scr_mRNA_1


title: sisnar_2_mRNA_2


title: sisnar_3_mRNA_1


title: sisnar_1_mRNA_1


title: sisnar_2_mRNA_1


title: Wild Type cultivated in LB supplemented with Paraquat 3

value: Wild type

value: Paraquat 30min


title: A375_TNF_24h_20220329

city: Toulouse

first: Marie

last: Tosolini

address: 2 avenue Hubert Curien

department: CRCT

institute: INSERM

data_processing:
FASTQ files were aligned using bowtie2 and Homo sapiens transcriptome reference GRCh38 (v97)
the raw count matrix was generated using  RSEM (v1.2.25)
Assembly: GRCh38 (v97)
Supplementary files format and content: Tab-delimited text file including raw count for each sample

growth_protocol: The A375 cells were grown in DMEM medium supplemented with 10% FBS

extract_protocol:
RNAs were extracted using a Qiagen RNA extraction kit (RNeasy Plus mini kit)
RNA Libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep Ligation kit following manufacturer's instructions (Illumina).

treatment_protocol: Cells were seeded at Day 0, and then treated at Day 1 with or without 50 ng/mL human recombinant TNF (Peprotech).

value: TNF

tag: time


title: A375_TNF_24h_20220422


title: sisnar_1_mRNA_3

tag: cell type


title: A375_TNF_24h_20220331

tag: cell line


title: total RNA-seq from sample_282

value: PBMCs

value: female

value: affected; for replication analysis

value: F


title: A375_NT_24h_20220329

value: NT


title: A375_NT_24h_20220422


title: A375_NT_24h_20220322


title: K562, TET2 KO; siNSUN2, H2AK119ub, CUT&Tag, r2

library_source: genomic

data_processing:
Raw reads were trimmed with Trimmomatic (version 0.39) and then mapped to mouse genome (mm10) or human genome (hg38), together with Drosophila melanogaster chromatin (Spike-in Chromatin), using bowtie2 (version 2.4.1) with default mode, where multiple alignments are searched and the best one is reported.
Mapped reads were deduplicated using a Picard tool ‘MarkDuplicates’ (version 2.26.2) (http://broadinstitute.github.io/picard/).
Peaks were called using MACS2 with the default mode, except for the parameters “--broad --broad-cutoff 0.01”. For both ATAC-seq and CUT&Tag-seq, peaks that appeared in at least two biological replicates were retained for subsequent downstream analyses.
Assembly: mm10 (mouse), hg38 (human)
Supplementary files format and content: Peaks
Library strategy: CUT&Tag

growth_protocol: K-562 cells were kept in RPMI-1640 medium plus 10% FBS. All mESCs were kept in DMEM (Gibco,11995065) supplemented with 15% Stem Cell Qualified Fetal Bovine Serum, Heat Inactivated (Gemini Bio Products, 100-525), 1 × L-glutamine (Gibco, 25030081), NEAA (Gibco, 25030081), LIF (MilliporeSigma, ESG1107), 1 × β-mercaptoethanol (Gibco, 21985023), 3 μM CHIR99021 (STEMCELL Technologies, 72052) and 1 μM PD0325901 (STEMCELL Technologies, 72182) at 37 °C and 5% CO2. The medium was replaced every 24 hours. mESCs were passaged on gelatin coated plates twice to clear feeder cells before experiments. HSPCs (lineage-positive cells (Lin+ ) were depleted from total BM cells of 6–8 weeks old mice using the Direct Lineage Cell Depletion Kit (Miltenyi Biotec, 130-110-470), and then the lineage-negative cells (Lin- ) were sorted with c-Kit (CD117) MicroBeads (Miltenyi Biotec, 130-091-224). The purity of selected cells was analyzed by flow cytometry. HSPCs were also incubated in suspension culture containing 30% FBS and 2% BSA in complete RPMI-1640 medium supplemented with 100 ng/mL mSCF, 10 ng/mL mIL-3, 50 ng/mL mTPO and 10 ng/ml mGM-CSF for 7 days before assaying.

extract_protocol:
Tagged DNA extraction was performed directly on cells following the instructions by the manufacturer (Active Motif, 53160) after adding equal amount of Drosophila spike-in (Active Motif, 53154).
Library construction was performed directly on cells following the instructions by the manufacturer (Active Motif, 53160) after adding equal amount of Drosophila spike-in (Active Motif, 53154).

treatment_protocol: siRNA transfections in leukemic cells were performed with SG Cell Line 4D-Nucleofector™ X Kit L (Lonza, V4XC-3024) or SF kit (V4XC-2012) using programs recommended by the manufacturer. siRNA transfections in mESCs were performed using Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen, 13778100) following the standard protocol. shRNA transfections in HSPCs were performed using electroporation. Gene overexpression in mESCs were performed by using the piggyBac transposase system with a hygromycin selection marker. Stable expression clones were selected by applying hygromycin B to the culture system for two weeks.

value: bone marrow

value: lymphoblast cell

tag: genotype

value: TET2 KO, siNSUN2

tag: cut&tag antibody


title: K562, TET2 KO; siNSUN2, H2AK119ub, CUT&Tag, r3


title: K562, TET2 KO; siNSUN2, H2AK119ub, CUT&Tag, r1


title: K562, TET2 KO; siMBD6, H2AK119ub, CUT&Tag, r2

value: TET2 KO, siMBD6


title: K562, TET2 KO; siNC, H2AK119ub, CUT&Tag, r1

value: TET2 KO, siNC


title: K562, TET2 KO; siMBD6, H2AK119ub, CUT&Tag, r1


title: K562, TET2 KO; siNC, H2AK119ub, CUT&Tag, r3


title: K562, TET2 KO; siNC, H2AK119ub, CUT&Tag, r2


title: K562, TET2 KO; siNSUN2; siNC, ATAC, r2

data_processing:
Raw reads were trimmed with Trimmomatic (version 0.39) and then mapped to mouse genome (mm10) or human genome (hg38), together with Drosophila melanogaster chromatin (Spike-in Chromatin), using bowtie2 (version 2.4.1) with default mode, where multiple alignments are searched and the best one is reported.
Mapped reads were deduplicated using a Picard tool ‘MarkDuplicates’ (version 2.26.2) (http://broadinstitute.github.io/picard/). Reads that mapped to the mitochondrial genome were discarded prior to deduplication.
Peaks were identified using MACS266 with the default mode, except for the parameters “--shift -75 --extsize 150 --nomodel --call-summits”.
Assembly: mm10 (mouse), hg38 (human)
Supplementary files format and content: Peaks

growth_protocol: K-562 cells were kept in RPMI-1640 medium plus 10% FBS. All mESCs were kept in DMEM (Gibco,11995065) supplemented with 15% Stem Cell Qualified Fetal Bovine Serum, Heat Inactivated (Gemini Bio Products, 100-525), 1 × L-glutamine (Gibco, 25030081), NEAA (Gibco, 25030081), LIF (MilliporeSigma, ESG1107), 1 × β-mercaptoethanol (Gibco, 21985023), 3 μM CHIR99021 (STEMCELL Technologies, 72052) and 1 μM PD0325901 (STEMCELL Technologies, 72182) at 37 °C and 5% CO2. The medium was replaced every 24 hours. mESCs  were passaged on gelatin coated plates twice to clear feeder cells before experiments. HSPCs (lineage-positive cells (Lin+ ) were depleted from total BM cells of 6–8 weeks old mice using the Direct Lineage Cell Depletion Kit (Miltenyi Biotec, 130-110-470), and then the lineage-negative cells (Lin- ) were sorted with c-Kit (CD117) MicroBeads (Miltenyi Biotec, 130-091-224). The purity of selected cells was analyzed by flow cytometry. HSPCs were also incubated in suspension culture containing 30% FBS and 2% BSA in complete RPMI-1640 medium supplemented with 100 ng/mL mSCF, 10 ng/mL mIL-3, 50 ng/mL mTPO and 10 ng/ml mGM-CSF for 7 days before assaying.

extract_protocol:
ATAC-seq was performed using a commercial kit (Active Motif, 53150) with ATAC-Seq Spike-In Control (Active Motif, 53154) following the standard protocol recommended by the manufacturer.
ATAC-seq was performed using a commercial kit (Active Motif, 53150) with ATAC-Seq Spike-In Control (Active Motif, 53154) following the standard protocol recommended by the manufacturer.


title: K562, TET2 KO; siNSUN2; siNC, ATAC, r1


title: K562, TET2 KO; siMBD6; siNC, ATAC, r3


title: K562, TET2 KO; siMBD6; siNC, ATAC, r1


title: K562, TET2 KO; siNSUN2; siNC, ATAC, r3


title: K562, TET2 KO; siMBD6; siNC, ATAC, r2


title: A375_NT_24h_20220331

tag: treatment


title: A375_TNF_24h_20220322


title: K562, TET2 KO; siNC, ATAC, r3

tag: tissue


title: K562, TET2 KO; siNC, ATAC, r2


title: K562, WT; siNC, ATAC, r3

value: WT, siNC


title: K562, TET2 KO; siNC, ATAC, r1


title: K562, TET2 KO; siMBD6, H2AK119ub, CUT&Tag, r3


title: K562, WT; siNC, ATAC, r2


title: K562, WT; siNC, H2AK119ub, CUT&Tag, r3


title: K562, WT; siNC, H2AK119ub, CUT&Tag, r2


title: HeLa, IMPDH2 knockout, TMZ_3

city: Beijing

first: Yundong

last: Xiong

address: 38 Xueyuan Road, Haidian District, Beijing

institute: Peking University

data_processing:
We used Fastp (version 0.19.7) to perform basic statistics on the quality of the raw reads. The steps of data processing were as follows: (1) Discard a paired reads if either one read contains adapter contamination; (2) Discard a paired reads if more than 10% of bases are uncertain in either one read; (3) Discard a paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one read.
Trimmed sequence reads were mapped to  GRCh38/hg38 using hisat2
Read count extraction and nomalization were performed using featureCounts of Subread
Assembly: hg38
Supplementary files format and content: tap-delimited text file includes raw counts for each Sample

source_name: cervical adenocarcinoma

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Trizol. 1 ug of total RNA was use for the construction of sequencing libraries
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Temozolomide: 200uM TMZ was added for 24h after the cells adhere to the wall

value: cervical adenocarcinoma

value: HeLa

value: cervical adenocarcinoma cell

value: IMPDH2 knockout

value: Temozolomide


title: K562, WT; siNC, H2AK119ub, CUT&Tag, r1


title: HeLa, IMPDH2 knockout, TMZ_1


title: HeLa, IMPDH2 knockout, TMZ_2


title: HeLa, IMPDH2 knockout, NT_1

value: non treatment


title: HeLa, IMPDH2 knockout, NT_3


title: HeLa, IMPDH2 knockout, NT_2


title: HeLa, IMPDH1 knockout, TMZ_1

value: IMPDH1 knockout


title: HeLa, IMPDH1 knockout, NT_3


title: HeLa, IMPDH1 knockout, TMZ_2


title: HeLa, IMPDH1 knockout, TMZ_3


title: HeLa, IMPDH1 knockout, NT_2


title: HeLa, IMPDH1 knockout, NT_1


title: HeLa, WT, TMZ_1

value: WT


title: K562, WT; siNC, ATAC, r1


title: HeLa, WT, TMZ_2


title: HeLa, WT, NT_3


title: HeLa, WT, NT_2


title: MO_MCC_124.2_T_RNA, bulk RNA

city: Chicago

first: Jaehyuk

last: Choi

state: Illinois

address: 303 E. Superior St. 5-220

department: Dermatology

institute: Northwestern University

data_processing: Sequence reads were trimmed and filtered using Trim Galore! (v0.6.7) to remove low-quality reads, adapter sequences, and bases with low Phred scores. Reads were then aligned to the reference human genome (GRCh38.p13 primary assembly ) augmented with the Merkel cell polyomavirus transcriptome, using the GENCODE v32 transcript annotation with STAR (v2.7.10b) on two-pass mode.  The dataset was quality-controlled to remove significant outliers. Differential gene expression analysis was performed using DESeq2 (v1.28.1) or other appropriate software. The limma package was used to fit differential expression to a generalized linear model. Pathway analysis was conducted with GSVA and GSEA. ClusterProfiler4.0 was used to visualize resulting enrichment plots.

source_name: skin

extract_protocol:
Formalin-fixed paraffin-embedded (FFPE) tissue blocks were sectioned at a thickness of 5 μm. RNA was extracted from the FFPE tissue sections using the RNeasy FFPE Kit (Qiagen) according to the manufacturer's instructions. The extracted RNA was treated with RNase-Free DNase Set (Qiagen) to remove any genomic DNA contamination. RNA quality and quantity were assessed using a Bioanalyzer (Agilent) and Qubit fluorometer (Thermo Fisher Scientific), respectively.
RNA sequencing libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) according to the manufacturer's instructions. Briefly, 500 ng of total RNA was used for poly(A) mRNA selection, fragmentation, and cDNA synthesis. The resulting cDNA was end-repaired, adenylated, and ligated with Illumina-specific adapters. PCR amplification was then performed to enrich the adapter-ligated fragments. The final library was purified and validated for size distribution using a Bioanalyzer (Agilent) and quantified by qPCR using a Kapa Library Quantification Kit (Kapa Biosystems). Libraries were pooled at equimolar concentrations and sequenced on an Illumina NovaSeq 6000.

value: skin

value: Merkel Cell Carcinoma (MCC) cell


title: NU_MCC_006.2_T_RNA, bulk RNA


title: HeLa, WT, NT_1


title: NU_MCC_006.1_T_RNA, bulk RNA


title: MO_MCC_122.2_T_RNA, bulk RNA


title: MO_MCC_130.2_T_RNA, bulk RNA


title: MO_MCC_122.1_T_RNA, bulk RNA


title: MO_MCC_121.3_T_RNA, bulk RNA


title: MO_MCC_120.1_T_RNA, bulk RNA


title: MO_MCC_130.1_T_RNA, bulk RNA


title: MO_MCC_121.1_T_RNA, bulk RNA


title: MO_MCC_113.2_T_RNA, bulk RNA


title: MO_MCC_059.1_T_RNA, bulk RNA


title: MO_MCC_124.1_T_RNA, bulk RNA


title: MO_MCC_138Post_abVDJ, skin

library_source: transcriptomic single cell

data_processing:
scRNA-seq Pre-processing: The GRCh38.p13 primary assembly from Ensembl Release 98 and the GENCODE v32 primary assembly were modified as follows. The sequence headers in the Ensembl FASTA were modified to match the primary assembly from GENCODE, by replacing metadata with original contig names, appending "chr" to names of autosomes and sex chromosomes, and handle the mitochondrial chromosome. The GTF file was modified to remove the version suffixes from transcript, gene, and exon IDs to match Previous CellRanger references. The GTF file was further filtered to include genes passing one or more of allowable gene_type, allowable transcript_type, no "PAR" tag, or no "readthrough_transcript" tag. Cellranger 6.1.0 was used to create a reference for scRNA-seq alignment. The MCPyV sequence was added to the primary assembly and to the final GTF file. FASTQ files containing gene exPression and feature barcodes were aligned to the human hg38 genome and MCPyV genome using CellRanger 6.1.0. Ambient RNA was removed using the CellBender pipeline. Processed read counts for each sample were imported as a Seruat object after which TCR-seq data was added. We then filtered the data based on mitochondrial reads (25% cutoff) and minimum RNA genes (200 genes). Doublets were removed using DoubletFinder, and cells were annotated with ProjectTILS and SingleR, using Monaco and HPCA reference datasets. The data were merged into a single Seurat object. We performed standard Seurat (4.0) clustering, Harmony batch correction, and manual cell cluster annotation based on marker genes, including transcription factors, effector molecules, and Previously annotated cell types. The data were subset by major cell types and subclustered. Contaminating cells were filtered out based on marker gene exPression. Differential gene exPression, gene enrichment, and GSVA were performed, followed by comparison of cell type proportions, analysis of TCR clonotype exPression, and TCR linkage analysis.
Assembly: FASTQ files containing gene exPression and feature barcodes were aligned to the human hg38 genome and MCPyV genome using CellRanger 6.1.0. Ambient RNA was removed using the CellBender pipeline.
Supplementary files format and content: tsv and csv file formats are used for processed files. Processed read counts for each sample were imported as a Seruat object after which TCR-seq data was added.

extract_protocol: CryoPreserved digested MCC tumor samples were thawed and processed following a modified version of the 10x Demonstrated Protocol ""Thawing Dissociated Tumor Cells for Single Cell RNA Sequencing"" and BioLegend TotalSeq C protocol. The protocol aimed to maintain high cell viability, decrease background, and reduce costs. Samples were thawed, labeled with TotalSeq C antibodies, and stained with 7-AAD viability staining solution. Cells were then subjected to FACS to sort CD45+ and CD45- cell populations for target enrichment of 2/3 CD45+ cells. After sorting, the final cell Preparation was resuspended in RPMI + 10% FBS + RNase Inhibitor, filtered, and counted to ensure the optimal concentration of 1e6 cells/mL. Finally, the cell suspension was processed for encapsulation and reverse transcription using the 10x 5’ v2 Chromium platform according to manufacture instructions."

treatment_protocol: Tissue dissociation: Human skin tumor biopsies (4mm punch) were dissociated into single-cell suspensions using the Miltenyi Biotec human tumor dissociation kit. Tissue punches were received on ice in biopsy transport media (PBS + FBS + antibiotics). Enzymes H, R, and A were reconstituted following the manufacturer's instructions and mixed with Pre-warmed RPMI 1640 medium. Biopsies were minced into 1-2mm pieces, transferred to enzyme mix, and incubated at 37°C for 30 minutes at 800 rpm in a thermomixer. Following incubation, samples were pipetted to break up clumps and filtered through a 70µm cell strainer into a 50ml conical tube. Tubes were centrifuged at 1500 rpm for 10 minutes at 4°C, and cells were resuspended in cold PBS. Cell viability and concentration were assessed using trypan blue and a cell counting slide. Cells were pelleted again and resuspended in a 1:1 mixture of FBS and FBS + 20% DMSO for cryoPreservation. Cryovials were stored at -80°C overnight before transferring to liquid nitrogen storage.

tag: library type

value: ab VDJ


title: MO_MCC_120.2_T_RNA, bulk RNA


title: MO_MCC_113_T_RNA, bulk RNA


title: HeLa, WT, TMZ_3


title: MO_MCC_124Post_gdVDJ, skin

value: gd VDJ


title: MO_MCC_138Post_ADT, skin

value: ADT


title: MO_MCC_138Post_gdVDJ, skin


title: MO_MCC_138Post_RNA, skin

value: RNA


title: MO_MCC_124Post_ADT, skin


title: MO_MCC_122Post_gdVDJ, skin


title: MO_MCC_124Post_abVDJ, skin


title: MO_MCC_121Post_abVDJ, skin


title: MO_MCC_122Post_ADT, skin


title: MO_MCC_124Post_RNA, skin


title: MO_MCC_122Post_RNA, skin


title: MO_MCC_120Post_abVDJ, skin


title: MO_MCC_122Post_abVDJ, skin


title: MO_MCC_121Post_gdVDJ, skin


title: sisnar_3_mRNA_2

value: Kidney

value: epithelial

value: snaR-A kockdown #3


title: MO_MCC_121Post_ADT, skin


title: MO_MCC_120Post_gdVDJ, skin


title: MO_MCC_059.2_T_RNA, bulk RNA


title: MO_MCC_121Post_RNA, skin


title: Diploid_NT_1

city: Los Angeles

first: Joshua

last: Park

state: California

address: 1050 Childs Way Room 108

department: Molecular and Computational Biology

institute: University of Southern California

data_processing:
Reads were aligned to S. pombe reference genome using STAR 2.7.0e.
Mapped reads were assigned to genomic features and read counts were summarized using featureCounts.
Assembly: GCF_000002945.2
Supplementary files format and content: tab-delimited file contains raw counts for each sample

organism: Schizosaccharomyces pombe

source_name: yeast cell

growth_protocol: S. pombe cells were cultured in yeast extract plus supplements (YES) liquid media at 32C until mid-log phase

extract_protocol:
Total RNA was extracted using Qiagen RNeasy kit. On-column DNase digestion was performed during the extraction and an additional DNase treatment using Turbo DNase (Invitrogen) was performed. RNA clean up was performed using Qiagen RNeasy kit.
Total RNA was sent to Novogene where library was constructed.

treatment_protocol: When cultures reached mid-log phase, cultures were divided in half and grown for an additional 4 hours with and without the addition of 0.0075% methyl methanesulfonate (MMS)

value: yeast cell

tag: ploidy

value: Diploid

value: No Treatment


title: Diploid_MMS_1


title: Diploid_NT_3


title: Diploid_MMS_2


title: MO_MCC_120Post_ADT, skin


title: Haploid_MMS_2

value: Haploid


title: P15_iliaccrest_periosteum

city: Créteil

first: Céline

last: Colnot

address: 8 rue du Général Sarrail

institute: INSERM U955

description: 10x Genomics

data_processing:
Fastq files were processed with the CellRanger pipeline with the default’s parameters
Reads were align against the HG38 2020-A reference genome
Filtered features barcodes matrices were used to perform data analysis
Assembly: HG38 2020-A
Supplementary files format and content: Cell Ranger output Files

source_name: Periosteum

extract_protocol:
Nuclei extraction was performed on snap-frozen human periosteum samples from PA site and IC of patient P13 and from PA site of patient P5. RNA integrity was checked beforehand on identical tissue samples (RIN > 6.5). Periosteum samples were briefly defrosted in nuclei extraction buffer before mincing and nuclei extraction. Collected tissues were minced and placed 5 min in ice-cold Nuclei Buffer (NUC101, Merck) before mechanical nuclei extraction using a glass douncer. Extraction was performed by 20 strokes of pestle A followed by 10-20 of pestle B. Nuclei suspension was filtered, centrifuged and resuspensed in RNAse-free PBS with 2% Bovine Serum Albumin and 0.2 U/µL RNAse inhibitor. A second step of centrifugation was performed to reduce contamination by cytoplasmic RNAs. Sytox™ AADvanced™ was added (1/200) to label nuclei and Sytox-AAD+ nuclei were sorted using Sony SH800.
The snRNA-seq libraries were generated using Chromium Single Cell Next GEM 3′ Library & Gel Bead Kit v.3.1 (10x Genomics) according to the manufacturer’s protocol. Briefly, 10 000 to 20 000 nuclei were loaded in the 10x Chromium Controller to generate single-nuclei gel- beads in emulsion. After reverse transcription, gel-beads in emulsion were disrupted. Barcoded complementary DNA was isolated and amplified by PCR. Following fragmentation, end repair and A-tailing, sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq (Illumina) with 28 cycles of read 1, 8 cycles of i7 index and 91 cycles of read 2. Sequencing data were processed using the Cell Ranger Count pipeline and reads were mapped on the HG38 2020-A reference human genome, with intronic and exonic sequences.
Library prepared following the manufacturer's recommendation.

value: Periosteum

value: Control periosteum


title: MDSL-Cas9, BRUNELLO, T19, AZA, Rp2

city: Randwick

first: Julie

last: Thoms

state: NSW

address: Level 2, C25 Lowy Cancer Research Centre, UNSW Sydney, High St

department: Adult Cancer Program

country: Australia

institute: UNSW Sydney

data_processing:
CRISPR screen data was pre-processed using MAgeCK’s count function with standard parameters to generate sgRNA count tables.
Hit identification was performed using MAGeCK MLE using standard parameters using a 3-condition design (day 0, drug treatment, and DMSO treatment).
Functional analysis and visualization of the MAGeCK MLE results were performed using MAGeCkFlute with standard parameters and normalized with the cell cycle parameter.
Assembly: Reads were mapped against Brunello sgRNA library to generate read count matrices
Supplementary files format and content: Xls file including raw sgRNA counts for each sample

source_name: MDS-L cell line

growth_protocol: MDSL cells were maintained in RPMI, supplemented with 10% Feta Bovine Serum, antibiotics, 25ng/mL hIL-3, and 50nM β-mercaptoethanol

extract_protocol:
Large scale DNA Extractions were performed using the Qiagen Blood & Cell Culture DNA Maxi Kit (Qiagen, #13362).
sgRNA cassettes were amplified by PCR through multiple 50uL reactions, each containing 5ug gDNA, using staggered P7 primers and indexed P5 primers, and 2X NEBNext Q5 high fidelity master mix (NEB, #M0541L)as previously described. PCR products were pooled, purified using AMPure XP beads. 1.0pM of the pooled CRISPR libraries were sequenced on the NextSeq 500 platform using the NextSeq 550 high-output kit with a read length of 1 x 75bp and a 20% PhiX spike-in.
CRISPR-Cas9 dropout screen

treatment_protocol: MDSL cells were treated daily with 0.3uM AZA or DMSO, until the AZA-treated cells reached 12 cellular divisions.

value: MDS-L cell line

value: MDS-L

value: Myeloblast

value: 0.3uM AZA


title: Diploid_NT_2


title: MO_MCC_120Post_RNA, skin

value: skin

value: Merkel Cell Carcinoma (MCC) cell


title: Haploid_MMS_3


title: Haploid_MMS_1


title: Diploid_MMS_3


title: MDSL-Cas9, BRUNELLO, T19, DMSO, Rp2

value: DMSO


title: Haploid_NT_2


title: MDSL-Cas9, BRUNELLO, T19, DMSO, Rp1


title: MDSL-Cas9-sgTOPORS, D4, AZA, Rp3

data_processing:
Paired-end reads were mapped to the hg38 reference genome (ENSEMBL) using STAR (Version 2.7.0) (342) and quantified using featureCounts (Version 2.0.0) (343). The parameters “--outFilterMismatchNoverLmax” and “--alignEndsType” of STAR (Version 2.7.0) aligner was set to “0.05” and “EndToEnd” to filter out reads harbouring artifact mismatches from the mapping process.
Read counts were quantified and read count matrices were generated with FeatureCounts using default arguments with “requireBothEndsMapped” and “countChimericFragments” options.
DESeq2 R package (Version 1.34.0) was used to identify differentially expressed genes (DEG).
rMATS (Version 4.1.2) was used for detecting splicing events as well as identifying differentially spliced events.
Assembly: hg38
Supplementary files format and content: Table of differentially expressed genes
Supplementary files format and content: Table of differential splicing

extract_protocol:
Total RNA extracted with Bioline Isolate II RNA extraction Kit (Bioline, BIO-52072). Residual DNA was eliminated using the RNase-free DNase Qiagen Kit (Qiagen, #79254),
Libraries were prepared using the Illumina Stranded mRNA prep Ligation kit as per manufacturer’s instructions

treatment_protocol: MDSL cells were treated daily with 0.3uM AZA or DMSO for 4 days.

value: TOPORS-ko

value: AZA


title: Haploid_NT_1


title: MDSL-Cas9, BRUNELLO, T0, Untreated, Rp1

value: Untreated


title: K562, WT, caRNA, m5C-IP, MeRIP, r3

description:
chromatin-associated RNA
hg38.Onecodetofindthemall.elem_featureCounts.sel.txt
K562_TET2WT_caRNA-IP-m5C-MeRIP_r3_c31_human_20240508

value: bone marrow

value: lymphoblast cell

value: WT

value: m5C (Diagenode, #MAb-081-100)


title: MDSL-Cas9-sgTOPORS, D4, AZA, Rp2


title: MDSL-Cas9, BRUNELLO, T0, Untreated, Rp2


title: Proliferating MEF 3

first: Nissim

last: Hay

address: 900 South Ashland Ave

department: BMG

institute: University of Illinois Chicago

data_processing:
Paired end 150 bp raw reads were trimmed to remove Truseq adapters and bases from the 3’ end with quality scores less than 20 using cutadap
Trimmed reads shorter than 40bp were discarded
Trimmed reads were aligned to the mm39 genome in a splice-aware manner using the STAR aligner
Raw read counts were generated using FeatureCounts
Assembly: mm39
Supplementary files format and content: tab-delimited file includes raw counts for each sample

organism: Mus musculus

source_name: mouse embryonic fibroblasts

growth_protocol: A total of 3.0 × 105 cells were plated onto 6-well plates. The cells were analyzed while actively proliferating (2 days after plating) and when they were quiescent (contact-inhibited for 6 days, 11 days after plating). Cell culture medium was changed every other day for both proliferating and quiescent states.

extract_protocol:
The cells were rapidly washed two times in ice-cold PBS, and total RNA was isolated following the Direct-zol RNA Microprep Kit (ZYMO RESEARCH) manufacturer’s manual.
The library kit was the CORALL RNA-Seq V2 Library Prep Kit with UDI 12 nt. rRNA depletion was done with RiboCop rRNA Depletion Kit for Human/Mouse/Rat (HMR) V2

value: mouse embryonic fibroblasts


title: Quiescent MEF 3


title: Quiescent MEF 2


title: Quiescent MEF 1


title: MDSL-Cas9-sgTOPORS, D4, AZA, Rp1


title: Haploid_NT_3

value: yeast cell

value: Haploid

value: No Treatment


title: Proliferating MEF 2


title: MDSL-Cas9-sgROSA, D4, AZA , Rp1

value: MDS-L cell line

value: MDS-L

value: Control


title: MDSL-Cas9-sgTOPORS, D4, DMSO, Rp3

value: Myeloblast


title: MDSL-Cas9, BRUNELLO, T19, AZA, Rp1

value: 0.3uM AZA


title: MDSL-Cas9-sgROSA, D4, AZA , Rp3


title: mESC, WT, caRNA, UBS Amplicon, r3

description:
chromatin-associated RNA
mESC_Tet2KOvsWT_caRNA-BS-UBS-Amplicon_sites.bed

data_processing:
Adapter sequences and low-quality reads were trimmed using the cutadapt (version 4.0) tool. Only properly paired reads with a length less than 20 bp were retained. The 7 nucleotides (nt) of the UMI at the 5′-end of the insert fragments (R2) were extracted. Clean reads were then mapped to the mouse genome sequence (mm10) using the HISAT-3n tool76 with the ‘--base-change C,T’ argument. To leverage the strand-specific property of the library, the ‘--directional-mapping’ parameter was applied. To increase the accuracy of site identification, only properly paired reads without soft clipping were retained. To eliminate unconverted clusters, reads containing more than three unconverted C sites, or where more than one-third of the total C sites were unconverted, were discarded. A binomial model was used to calculate a P-value for each site, and sites with a P-value less than 0.01 were classified as m5C sites.
Assembly: mm10 (mouse)
Supplementary files format and content: Sites

source_name: embryos

growth_protocol: All mESCs were kept in DMEM (Gibco,11995065) supplemented with 15% Stem Cell Qualified Fetal Bovine Serum, Heat Inactivated (Gemini Bio Products, 100-525), 1 × L-glutamine (Gibco, 25030081), NEAA (Gibco, 25030081), LIF (MilliporeSigma, ESG1107), 1 × β-mercaptoethanol (Gibco, 21985023), 3 μM CHIR99021 (STEMCELL Technologies, 72052) and 1 μM PD0325901 (STEMCELL Technologies, 72182) at 37 °C and 5% CO2. The medium was replaced every 24 hours. ES cells were passaged on gelatin coated plates twice to clear feeder cells before experiments.

extract_protocol:
Fractionation of mESCs was performed following the published protocol with the optimized concentration of NP-40 (MilliporeSigma, 492018) for each cell line. In brief, 5 × 106 to 1 × 107 724 cells were harvested and washed with 1 mL cold PBS/1 mM EDTA buffer, then centrifuged at 4 °C with 500 g to collect the cell pellet. 200 μL ice-cold lysis buffer (10 mM Tris726 HCl, pH = 7.4, 0.05% NP-40, 150 mM NaCl) were added to the cell pellet and incubated on ice for 5 minutes, then gently pipetted up the cell lysate over 2.5 volumes of chilled sucrose cushion (24% RNase-free sucrose in lysis buffer) and centrifuged at 4 °C with 15,000 g for 10 minutes. All the supernatant was collected as cytoplasmic fraction and the nuclei pellet was washed once by gently adding 200 μL ice-cold PBS/1 mM EDTA to the nuclei pellet without dislodging the pellet. The nuclei pellet was resuspended in 200 μL prechilled glycerol buffer (20 mM Tris-HCl, pH = 7.4, 75 mM NaCl, 0.5 mM EDTA, 0.85 mM DTT, 0.125 mM PMSF, 50% glycerol) with gentle flicking of the tube. Then an equal volume of cold nuclei lysis buffer (10 mM HEPES, pH = 7.6, 1 mM DTT, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3 M NaCl, 1 M urea, 1% NP-40) was added, followed by vigorous vertexing for 5 seconds twice. The nuclei pellet mixtures were incubated for 2 minutes on ice, then centrifuged at 4 °C with 15,000 g for 2 minutes. The supernatant was collected as the soluble nuclear fraction (nucleoplasm). The pellet was gently rinsed with cold PBS/1 mM  EDTA without dislodging and then collected as the chromosome-associated fraction. caRNA was extracted with standard TRIZol protocol.
uBS conversion was performed according to the published procedure (PMID: 38168991). Then RNAs were amplified by PCR using amplicon-specific primers and then pooled together before final amplification using PCR primers that contain sequence for Illumina I5 and I7 sequences.

value: embryos

value: mESC

value: mouse embronic stem cell

value: Bisulfite


title: mESC, Tet2 KO, caRNA, UBS Amplicon, r2

value: Tet2 KO


title: MDSL-Cas9-sgROSA, D4, AZA , Rp2

value: AZA


title: MDSL-Cas9-sgTOPORS, D4, DMSO, Rp2

value: TOPORS-ko

value: DMSO


title: Proliferating MEF 1

value: mouse embryonic fibroblasts


title: MDSL-Cas9-sgROSA, D4, DMSO, Rp3


title: mESC, WT, caRNA, UBS Amplicon, r2

value: WT


title: mESC, Tet2 KO, caRNA, UBS Amplicon, r1


title: mESC, WT, caRNA, UBS Amplicon, r1


title: MDSL-Cas9-sgROSA, D4, DMSO, Rp2


title: MDSL-Cas9-sgROSA, D4, DMSO, Rp1


title: MDSL-Cas9-sgTOPORS, D4, DMSO, Rp1


title: mESC, Tet2 KO, caRNA, UBS Amplicon, r3


title: AS_IL33_3_S33

city: Detroit

first: Nikhlesh

last: Singh

state: MI

address: 6135  Woodward Avenue

institute: Wayne State University School of Medicine

data_processing:
STAR 2.7.5a alignment
htseq-count 0.6.1 tabulation
edgeR
Assembly: hg38
Supplementary files format and content: count data

source_name: IL-33, HMC3

growth_protocol: Effect of IL-33 in human microglia cell line (HMC3)

extract_protocol:
RNA was extracted using TRIZOL
Lexogen QuantSeq 3'mRNAseq Library Prep FWD

treatment_protocol: HMC3 were treated with IL-33 for 24 hours and gene expression profiling was performed using 3 prime RNA sequencing.

value: Microglia


title: AS_IL33_2_S32


title: mESC, Tet2 KO, caRNA, m5C-IP, MeRIP, r3

description:
chromatin-associated RNA
mm10.Onecodetofindthemall.elem_featureCounts.sel.txt
mESC_Tet2KO_caRNA-IP-m5C-MeRIP_r3_c26_mouse_20240508

value: m5C (Diagenode, #MAb-081-100)


title: mESC, Tet2 KO, caRNA, m5C-IP, MeRIP, r2

description:
chromatin-associated RNA
mm10.Onecodetofindthemall.elem_featureCounts.sel.txt
mESC_Tet2KO_caRNA-IP-m5C-MeRIP_r2_c14_mouse_20240508


title: mESC, Tet2 KO, caRNA, m5C-IP, MeRIP, r1

description:
chromatin-associated RNA
mm10.Onecodetofindthemall.elem_featureCounts.sel.txt
mESC_Tet2KO_caRNA-IP-m5C-MeRIP_r1_c2_mouse_20240508


title: mESC, WT, caRNA, m5C-IP, MeRIP, r3

description:
chromatin-associated RNA
mm10.Onecodetofindthemall.elem_featureCounts.sel.txt
mESC_Tet2WT_caRNA-IP-m5C-MeRIP_r3_c25_mouse_20240508


title: AS_C_3_S30

source_name: Control, HMC3


title: mESC, WT, caRNA, m5C-IP, MeRIP, r2

description:
chromatin-associated RNA
mm10.Onecodetofindthemall.elem_featureCounts.sel.txt
mESC_Tet2WT_caRNA-IP-m5C-MeRIP_r2_c13_mouse_20240508


title: mESC, WT, caRNA, m5C-IP, MeRIP, r1

description:
chromatin-associated RNA
mm10.Onecodetofindthemall.elem_featureCounts.sel.txt
mESC_Tet2WT_caRNA-IP-m5C-MeRIP_r1_c1_mouse_20240508


title: S4-3_S87

source_name: IL-33112-270, HRMVECs, 24 hours

growth_protocol: Human Retinal microvascular endothelial cells (HRMVECs) were exposed to IL-3395-270, IL-3399-270, IL-33109-270, and IL-33112-270 for 24 hours.

treatment_protocol: HRMVECS were exposed to recombinant IL-33s for 24 Hours

value: HRMVECs

value: Endothelial Cells


title: mESC, Tet2 KO; HxD OE, caRNA, RNA, r2

description:
chromatin-associated RNA
mm10.Onecodetofindthemall.elem_featureCounts_res2.txt

data_processing:
Raw reads were trimmed with Trimmomatic (version 0.39), then aligned to mouse (mm10) genome and their corresponding transcriptome, together with external RNA Control Consortium (ERCC) RNA spike-in control (Thermo Fisher Scientific) when applicable, using HISAT2 (version 2.2.1).
Reads were counted for each GENCODE annotated gene using HTSeq (version 0.12.4) and for carRNAs using featureCounts
Assembly: mm10 (mouse)
Supplementary files format and content: Counts

extract_protocol:
Fractionation of mESCs was performed following the published protocol with the optimized concentration of NP-40 (MilliporeSigma, 492018) for each cell line. In brief, 5 × 106 to 1 × 107 724 cells were harvested and washed with 1 mL cold PBS/1 mM EDTA buffer, then centrifuged at 4 °C with 500 g to collect the cell pellet. 200 μL ice-cold lysis buffer (10 mM Tris726 HCl, pH = 7.4, 0.05% NP-40, 150 mM NaCl) were added to the cell pellet and incubated on ice for 5 minutes, then gently pipetted up the cell lysate over 2.5 volumes of chilled sucrose cushion (24% RNase-free sucrose in lysis buffer) and centrifuged at 4 °C with 15,000 g for 10 minutes. All the supernatant was collected as cytoplasmic fraction and the nuclei pellet was washed once by gently adding 200 μL ice-cold PBS/1 mM EDTA to the nuclei pellet without dislodging the pellet. The nuclei pellet was resuspended in 200 μL prechilled glycerol buffer (20 mM Tris-HCl, pH = 7.4, 75 mM NaCl, 0.5 mM EDTA, 0.85 mM DTT, 0.125 mM PMSF, 50% glycerol) with gentle flicking of the tube. Then an equal volume of cold nuclei lysis buffer (10 mM HEPES, pH = 7.6, 1 mM DTT, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3 M NaCl, 1 M urea, 1% NP-40) was added, followed by vigorous vertexing for 5 seconds twice. The nuclei pellet mixtures were incubated for 2 minutes on ice, then centrifuged at 4 °C with 15,000 g for 2 minutes. The supernatant was collected as the soluble nuclear fraction (nucleoplasm). The pellet was gently rinsed with cold PBS/1 mM  EDTA without dislodging and then collected as the chromosome-associated fraction. caRNA was extracted with standard TRIZol protocol.
RNA-seq libraries were prepared according to the standard protocol of SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (TaKaRa bio, 634417) while ERCC spike-in (Invitrogen, 4456740) added to the same amount to individual samples.

treatment_protocol: siRNA transfections in mESCs were performed using Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen, 13778100) following the standard protocol. Gene overexpression in mESCs were performed by using the piggyBac transposase system with a hygromycin selection marker. Stable expression clones were selected by applying hygromycin B to the culture system for two weeks.

value: Tet2 KO, HxD OE


title: S4-2_S86


title: AS_C_1_S28

value: Control


title: mESC, Tet2 KO; HxD OE, caRNA, RNA, r3


title: AS_C_2_S29


title: mESC, Tet2 KO; WT OE, caRNA, RNA, r1

value: Tet2 KO, WT OE


title: S3-1_S82

source_name: IL-33109-270, HRMVECs, 24 hours


title: S3-3_S84


title: mESC, Tet2 KO; FH OE, caRNA, RNA, r3

value: embryos

value: Tet2 KO, FH OE


title: mESC, Tet2 KO; WT OE, caRNA, RNA, r2

value: mESC

value: mouse embronic stem cell


title: S4-1_S85


title: mESC, Tet2 KO; HxD OE, caRNA, RNA, r1


title: S2-3_S81

source_name: IL-3399-270, HRMVECs, 24 hours


title: S2-2_S80


title: S2-1_S79


title: mESC, Tet2 KO; FH OE, caRNA, RNA, r2


title: mESC, Pspc1 KO, caRNA, RNA, r3

value: Pspc1 KO


title: mESC, Tet2 KO; FH OE, caRNA, RNA, r1


title: AS_IL33_1_S31


title: S1-2_S77

source_name: IL-3395-270, HRMVECs, 24 hours


title: mESC, Tet2 KO; WT OE, caRNA, RNA, r3


title: mESC, Pspc1 KO, caRNA, RNA, r2


title: S1-3_S78


title: mESC, Pspc1 KO, caRNA, RNA, r1


title: S3-2_S83


title: mESC, WT, caRNA, RNA, r2


title: mESC, WT, caRNA, RNA, r3


title: Control-1_S73

source_name: Control, HRMVECs

value: No treatment


title: S1-1_S76


title: mESC, Tet2 KO; siNsun2, caRNA, RNA, r3

description:
chromatin-associated RNA
mm10.Onecodetofindthemall.elem_featureCounts_res1.txt

value: Tet2 KO, siNsun2


title: Control-3_S75


title: mESC, WT, caRNA, RNA, r1


title: mESC, Tet2 KO; siNsun2, caRNA, RNA, r1


title: mESC, Tet2 KO; siNsun2, caRNA, RNA, r2


title: PG_Adam_2_S38

data_processing:
STAR 2.7.5a alignment
htseq-count 0.6.1 tabulation
edgeR
Supplementary files format and content: hg38
Supplementary files format and content: count data

source_name: ADAM10 siRNA, HRMVECs

growth_protocol: Effect of ADAM10 depletion in human retinal microvascular endothelial cells (HRMVECs)

treatment_protocol: HRMVECs were transfected with control and ADAM10 siRNA and after 48 hours gene expression profiling was performed using 3 prime RNA sequencing.

value: ADAM10 siRNA


title: Control-2_S74


title: PG_Adam_3_S39


title: PG_C_2_S35

source_name: Control siRNA, HRMVECs

value: Control siRNA


title: PG_C_3_S36


title: PG_Adam_1_S37


title: mESC, Tet2 KO; siNC, caRNA, RNA, r3

value: Tet2 KO, siNC


title: mESC, Tet2 KO; siNC, caRNA, RNA, r1


title: PG_C_1_S34


title: mESC, Tet2 KO; siNC, caRNA, RNA, r2


title: mESC, WT; siNsun2, caRNA, RNA, r3

value: WT, siNsun2


title: mESC, WT; siNsun2, caRNA, RNA, r1


title: Replicate 12, scATAC-seq

city: Madison

first: Max

last: Frenkel

address: 433 babcock drive

institute: UW Madison

library_source: genomic single cell

data_processing:
For scATAC/Spear-ATAC libraries: Sequencing data was converted to fastq files using cellranger-atac mkfastq (10x Genomics, version 2.1.0). Reads were then aligned to the hg38 reference genome and quantified using cellranger-atac count. The current version of Cell Ranger can be accessed here:https://support.10xgenomics.com/single-cell-atac/software/downloads/latest
For dialout libraries: To filter for reads that contain the correct structure of amplicon, we grepped for 4 constants sequences that flanked the barcodes: “AAATCCAAGC”, “CCAGAGCATG”, “CAAGGTGGTT”, and “ATACTGATTC”. . We then matched each of the supposed hardcoded barcodes to one of the known hardcoded barcodes from the list that we intended to synthesize by identifying a closest match using a maximum restricted Damerau-Levenshtein distance of 3. We then generated a list of unique hardcoded barcode – random barcode pairs. We restricted that list to pairs to those that were seen more than once. Finally, we required that, for a given random barcode, more than 95% of the reads had to match to the same hardcoded barcode.
Assembly: hg38
Supplementary files format and content: Tab separated values

extract_protocol:
Nuclei were prepared according to 10X Genomics’ Nuclear Isolation for Single Cell ATAC Sequencing protocol with the following notes. IGEPAL CA-630 was used for the lysis buffer a 10% solution of which was prepared fresh on the day of nuclear isolation using 100% stock (Sigma i8896). After trypsinization and pelleting, cells were washed twice with ice cold PBS + 0.04% BSA before following the remainder of the nuclear isolation protocol. Lysis occurred for 4 minutes which previously was found to be appropriate time for cytoplasmic removal while retaining nuclear membrane architecture by DIC microscopy. Cells were resuspended in diluted nuclei buffer and triplicates were counted before proceeding with Spear-ATAC sequencing as previously published.
Library construction was performed according to 10X Genomics scATAC-seq v2 Chemistry and Spear-ATAC with the following modifications and notes. 10,000 nuclei were targeted for capture per 10X chip lane. Spear-ATAC included the following changes to the 10X scATAC library preparation protocol: the 1.2 uL per reaction of 50 uM oSP1735 oligonucleotide is spiked into the GEM generation master mix and the in-GEM PCR was increased from 12 to 15 cycles. Single-cell ATAC library fragment size distribution was analyzed by Tapestation prior to preparing enriched dial-out libraries for perturbation genotyping. The dial-out libraries were again prepared according to the Spear-ATAC protocol with the following changes: linear PCR with biotinylated oSP2053 was increased to 30 total cycles and the exponential PCR with oSP1594 and indexed P7 primers was increased to 18 total cycles. The indices on the P7 primers were increased from 8 bases to 10 bases.


title: Replicate 11, scATAC-seq


title: mESC, WT; siNC, caRNA, RNA, r3

value: WT, siNC


title: mESC, WT; siNsun2, caRNA, RNA, r2


title: Replicate 9, scATAC-seq


title: mESC, WT; siNC, caRNA, RNA, r2


title: Replicate 8, scATAC-seq


title: mESC, WT; siNC, caRNA, RNA, r1


title: Replicate 5, scATAC-seq


title: mESC, Pspc1 KO, DNA, 5mC-IP, MeDIP, r3

description: mESC_Pspc1KOvsWT_MEDIPS.meth.input.padj0.1.output.txt

data_processing:
Raw reads were trimmed with Trimmomatic (version 0.39) and then mapped to mouse genome (mm10) or human genome (hg38), together with Drosophila melanogaster chromatin (Spike-in Chromatin), using bowtie2 (version 2.4.1) with default mode, where multiple alignments are searched and the best one is reported. Mapped reads were deduplicated using a Picard tool ‘MarkDuplicates’ (version 2.26.2) (http://broadinstitute.github.io/picard/).
Differentially methylated regions were identified using MEDIPS with the following settings: diff.method = 'edgeR', p.adj = 'bonferroni', MeDIP = True, CNV = False, minRowSum = 10. Regions with an adjusted P-value less than 0.1 were defined as significantly differentially methylated regions.
Assembly: mm10 (mouse)
Supplementary files format and content: Peaks

extract_protocol:
Genomic DNA was extracted from cells using Monarch® Genomic DNA Purification Kit (NEB, T3010S). DNAs were subjected to another round of RNase A digestion following DNA clean & concentrator (Zymo Research, D4014)
Library construction was performed using the kit xGen™ Methyl-Seq Lib Prep (IDT, 10009860) according to the manufacturer's instructions.
5mC-MeDIP-seq

treatment_protocol: siRNA transfections in leukemic cells were performed with SG Cell Line 4D-Nucleofector™ X Kit L (Lonza, V4XC-3024) or SF kit (V4XC-2012) using programs recommended by the manufacturer. siRNA transfections in mESCs were performed using Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen, 13778100) following the standard protocol. Gene overexpression in mESCs were performed by using the piggyBac transposase system with a hygromycin selection marker. Stable expression clones were selected by applying hygromycin B to the culture system for two weeks.

value: IP


title: Replicate 6, scATAC-seq


title: Replicate 7, scATAC-seq


title: mESC, Pspc1 KO, DNA, 5mC-IP, MeDIP, r2


title: Replicate 3, scATAC-seq


title: mESC, Pspc1 KO, DNA, 5mC-IP, MeDIP, r1


title: mESC, WT, DNA, 5mC-IP, MeDIP, r2

value: WT


title: Replicate 10, scATAC-seq


title: Replicate 1, scATAC-seq


title: mESC, WT, DNA, 5mC-IP, MeDIP, r3


title: Replicate 4, scATAC-seq


title: mESC, Pspc1 KO, DNA, Input, MeDIP, r3

value: Input


title: mESC, Pspc1 KO, DNA Input, MeDIP, r2


title: K562, TET2KO shMBD6, caRNA, rep3

data_processing:
Raw reads were trimmed with Trimmomatic (version 0.39), then aligned to mouse (mm10) or human (hg38) genome and their corresponding transcriptome using HISAT2 (version 2.2.1).
Annotation files (version M19 for mouse, and version v29 for human in gtf format) were obtained from GENCODE database (https://www.gencodegenes.org/). Reads were counted for each GENCODE annotated gene using HTSeq (version 0.12.4).
Assembly: mm10 (mouse) or hg38 (human)
Supplementary files format and content: raw counts for each Sample

source_name: bone marrow

growth_protocol: shCtrl or shMBD6 K-562 cells were kept in RPMI-1640 (Gibco, 61870036) with 10% fetal bovine serum (FBS, Gibco) and 1 μg/mL puromycin (Gibco, A1113803) at 37 °C and 5% CO2. All mESCs were kept in DMEM (Gibco, 11995065) supplemented with 15% Stem Cell Qualified Fetal Bovine Serum, Heat Inactivated (Gemini Bio Products, 100-525), 1 × L-glutamine (Gibco, 25030081), NEAA (Gibco, 25030081), LIF (MilliporeSigma, ESG1107), 1 × β-mercaptoethanol (Gibco, 21985023), 3 μM CHIR99021 (STEMCELL Technologies, 72052) and 1 μM PD0325901 (STEMCELL Technologies, 72182) at 37 °C and 5% CO2. The medium was replaced every day. ES cells were passaged on gelatin-coated plates twice to clear feeder cells before experiments.

extract_protocol:
Fractionation of mESCs and K-562 was performed following the published protocol with the optimized concentration of NP-40 (Sigma) for each cell line. In brief, 5-10 million cells were harvested and washed with 1 mL cold PBS/1 mM EDTA buffer, then centrifuged at 4 °C with 500 g to collect the cell pellet. 200 μL ice-cold lysis buffer (10 mM Tris-HCl, pH = 7.4, 0.05% NP-40, 150 mM NaCl) were added to the cell pellet and incubated on ice for 5 minutes, then gently pipetted up the cell lysate over 2.5 volumes of chilled sucrose cushion (24% RNase-free sucrose in lysis buffer) and centrifuged at 4 °C with 15,000 g for 10 minutes. All the supernatant was collected as cytoplasmic fraction and the nuclei pellet was washed once by gently adding 200 μL ice-cold PBS/1 mM EDTA to the nuclei pellet without dislodging the pellet. The nuclei pellet was resuspended in 200 μL prechilled glycerol buffer (20 mM Tris-HCl, pH = 7.4, 75 mM NaCl, 0.5 mM EDTA, 0.85 mM DTT, 0.125 mM PMSF, 50% glycerol) with gentle flicking of the tube. Then equal volume of cold nuclei lysis buffer (10 mM HEPES, pH = 7.6, 1 mM DTT, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3 M NaCl, 1 M urea, 1% NP-40) was added, followed by vigorous vertexing for 5 seconds twice. The nuclei pellet mixtures were incubated for 2 minutes on ice, then centrifuged at 4 °C with 15,000 g for 2 minutes. The supernatant was collected as the soluble nuclear fraction (nucleoplasm). The pellet was gently rinsed with cold PBS/1 mM EDTA without dislodging and then collected as the chromosome-associated fraction.
Libraries were constructed with SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (TaKaRa Bio, 634411) according to the manufacturer’s instructions.

treatment_protocol: siRNA transfections in mESCs were performed according to the standard protocol of Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen, 13778150)

value: bone marrow

value: lymphoblast cell

value: TET2 knockout, MBD6 knockdown


title: mESC, Pspc1 KO, DNA, Input, MeDIP, r1

value: embryos


title: K562, TET2KO shMBD6, caRNA, rep1


title: K562, TET2KO shMBD6, caRNA, rep2


title: Replicate 2, scATAC-seq


title: K562, TET2KO shControl, caRNA, rep2

value: TET2 knockout, control


title: K562, TET2KO shControl, caRNA, rep1


title: mESC, WT, DNA, Input, MeDIP, r1

value: mESC

value: mouse embronic stem cell


title: mESC, Tet2 KO; siNsun2, DNA, 5mC-IP, MeDIP, r3

description: mESC_Tet2KO-siNsun2vssiNC_MEDIPS.meth.padj0.1.output.txt


title: mESC, WT, DNA, Input, MeDIP, r2


title: K562, TET2KO shControl, caRNA, rep3


title: mESC, Tet2 KO; siNsun2, DNA, 5mC-IP, MeDIP, r1


title: K562, TETWT shMBD6, caRNA, rep3

value: wildtype, MBD6 knockdown


title: mESC, Tet2 KO; siNsun2, DNA, 5mC-IP, MeDIP, r2

value: Tet2 KO, siNsun2


title: K562, TETWT shMBD6, caRNA, rep2


title: K562, TETWT shMBD6, caRNA, rep1


title: mESC, Tet2 KO; siNC, DNA, 5mC-IP, MeDIP, r2

description:
mESC_Tet2KO-siNsun2vssiNC_MEDIPS.meth.padj0.1.output.txt
mESC_Tet2KOvsWT-siNC_MEDIPS.meth.padj0.1.output.txt


title: K562, TET2WT shControl, caRNA, rep2

value: wildtype, control


title: mESC, Tet2 KO; siNC, DNA, 5mC-IP, MeDIP, r3


title: K562, TET2WT shControl, caRNA, rep3


title: mESC, Tet2 KO; siNC, DNA, 5mC-IP, MeDIP, r1


title: K562, TET2WT shControl, caRNA, rep1


title: mESC, WT; siNsun2, DNA, 5mC-IP, MeDIP, r2

description: mESC_Tet2WT-siNsun2vssiNC_MEDIPS.meth.padj0.1.output.txt


title: K562, TET2KO shMBD6, mRNA, rep2

data_processing:
Raw reads were trimmed with Trimmomatic (version 0.39), then aligned to mouse (mm10) or human (hg38) genome and their corresponding transcriptome using HISAT2 (version 2.2.1).
Annotation files (version M19 for mouse, and version v29 for human in gtf format) were obtained from GENCODE database (https://www.gencodegenes.org/).
Reads were counted for each GENCODE annotated gene using HTSeq (version 0.12.4).
Assembly: mm10 for mouse and hg38 for human
Supplementary files format and content: raw counts for each Sample

growth_protocol: shNC and shMBD6 K-562 cell lines were kept in RPMI-1640 (Gibco, 61870036) with 10% fetal bovine serum (FBS, Gibco) and 1 μg/mL puromycin (Gibco, A1113803) at 37 °C and 5% CO2. For hematopoietic stem and progenitor Lin-c-Kit+ (LK) cell selection, magnetic-activated cell sorting was applied with autoMACS® Pro Separator (Miltenyi Biotec). Briefly, the lineage-positive cells (Lin+) were firstly depleted from total BM cells of 6–8 weeks old mice using the Direct Lineage Cell Depletion Kit (Miltenyi Biotec, 130-110-470), and then the lineage-negative cells (Lin-) were sorted with c-Kit (CD117) MicroBeads (Miltenyi Biotec, 130-091-224). The purity of selected cells was analyzed by flow cytometry. The LK cells were also incubated in suspension culture containing 30% FBS and 2% BSA in complete RPMI-1640 medium supplemented with 100 ng/mL mSCF, 10 ng/mL mIL-3, 50 ng/mL mTPO and 10 ng/ml mGM-CSF.

extract_protocol:
Total RNA from cells were extracted by TRIzol reagent (Invitrogen, 15596026) according to the standard protocol
Libraries were constructed with SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (TaKaRa Bio, 634411) according to the manufacturer’s instructions.

treatment_protocol: All the ASOs and plasmids were transfected into LK cells using electroporation with P3 Primary Cell 4D-Nucleofector™ X Kit S (Lonza Bioscience, Cat#V4XP-3032) by program CV-137.


title: mESC, WT; siNsun2, DNA, 5mC-IP, MeDIP, r3


title: mESC, WT; siNC, DNA, 5mC-IP, MeDIP, r3

description:
mESC_Tet2WT-siNsun2vssiNC_MEDIPS.meth.padj0.1.output.txt
mESC_Tet2KOvsWT-siNC_MEDIPS.meth.padj0.1.output.txt


title: mESC, WT, DNA, Input, MeDIP, r3


title: mESC, WT; siNsun2, DNA, 5mC-IP, MeDIP, r1


title: mESC, WT; siNC, DNA, 5mC-IP, MeDIP, r2


title: K562, TET2KO shMBD6, mRNA, rep1


title: K562, TET2KO shControl, mRNA, rep3


title: mESC, WT; siNC, DNA, 5mC-IP, MeDIP, r1


title: K562, TET2KO shControl, mRNA, rep1


title: K562, TET2WT shMBD6, mRNA, rep2


title: mHSPC, Tet2 KO; shMbd6, H2AK119ub, CUT&Tag, r2

data_processing:
Raw reads were trimmed with Trimmomatic (version 0.39) and then mapped to mouse genome (mm10) or human genome (hg38), together with Drosophila melanogaster chromatin (Spike-in Chromatin), using bowtie2 (version 2.4.1) with default mode, where multiple alignments are searched and the best one is reported.
Mapped reads were deduplicated using a Picard tool ‘MarkDuplicates’ (version 2.26.2) (http://broadinstitute.github.io/picard/).
Peaks were called using MACS2 with the default mode, except for the parameters “--broad --broad-cutoff 0.01”. For both ATAC-seq and CUT&Tag-seq, peaks that appeared in at least two biological replicates were retained for subsequent downstream analyses.
Assembly: mm10 (mouse), hg38 (human)
Supplementary files format and content: Peaks
Library strategy: CUT&Tag

extract_protocol:
Tagged DNA extraction was performed directly on cells following the instructions by the manufacturer (Active Motif, 53160) after adding equal amount of Drosophila spike-in (Active Motif, 53154).
Library construction was performed directly on cells following the instructions by the manufacturer (Active Motif, 53160) after adding equal amount of Drosophila spike-in (Active Motif, 53154).

value: HSPC

value: hematopoietic stem and progenitor Lin-c-Kit+ (LK) cell

value: Tet2 KO, shMbd6


title: mHSPC, Tet2 KO; shMbd6, H2AK119ub, CUT&Tag, r1


title: mHSPC, Tet2 KO; shMbd6, H2AK119ub, CUT&Tag, r3


title: K562, TET2WT shMBD6, mRNA, rep1


title: K562, TET2KO shMBD6, mRNA, rep3


title: K562, TET2WT shMBD6, mRNA, rep3


title: K562, TET2WT shControl, mRNA, rep3


title: K562, TET2WT shControl, mRNA, rep1


title: mHSPC, Tet2 KO; shNC, H2AK119ub, CUT&Tag, r2

value: Tet2 KO, shNC


title: K562, TET2KO shControl, mRNA, rep2


title: K562, TET2WT shControl, mRNA, rep2


title: mHSPC, Tet2 KO; shNC, H2AK119ub, CUT&Tag, r1


title: K562, WT, caRNA, m5C-IP, rep3

data_processing:
Raw reads were trimmed with Trimmomatic (version 0.39), then aligned to mouse (mm10) or human (hg38) genome and transcriptome using HISAT2 (version 2.1.0).
Annotation files (version M19 for mouse, and version v29 for human in gtf format) were downloaded from GENCODE database (https://www.gencodegenes.org/).
Mapped reads were separated by strands with samtools (version 1.16.1) and m5C peaks on each strand were called using MACS2 (version 2) with parameter ‘--nomodel, --keep-dup all, -g 7e8, -extsize 150’ separately. In this regard, the genome size was estimated based on reads coverage obtained from input samples. Significant peaks with q < 0.01 identified by MACS2 were considered.
Assembly: mm10 for mouse and hg38 for human
Supplementary files format and content: raw counts for each Sample, peaks in mESCs (except for input samples)
Library strategy: MeRIP-Seq

growth_protocol: WT K-562 cells were kept in RPMI-1640 (Gibco, 61870036) with 10% fetal bovine serum (FBS, Gibco) and 1 μg/mL puromycin (Gibco, A1113803) at 37 °C and 5% CO2. mESCs were kept in DMEM (Gibco, 11995065) supplemented with 15% Stem Cell Qualified Fetal Bovine Serum, Heat Inactivated (Gemini Bio Products, 100-525), 1 × L-glutamine (Gibco, 25030081), NEAA (Gibco, 25030081), LIF (MilliporeSigma, ESG1107), 1 × β-mercaptoethanol (Gibco, 21985023), 3 μM CHIR99021 (STEMCELL Technologies, 72052) and 1 μM PD0325901 (STEMCELL Technologies, 72182) at 37 °C and 5% CO2. The medium was replaced every day. ES cells were passaged on gelatin-coated plates twice to clear feeder cells before experiments.

extract_protocol:
Total RNAs from whole cell or the chromatin-associated fractions were randomly fragmented by incubation at 94 °C for 4 minutes using 1× fragmentation buffer (NEB E6186A). Fragmentation was stopped by adding 1× Stop Solution. Spike-in RNAs were added to each sample. Four microgram anti-m5C antibody (Diagenode, MAb-081-100) was conjugated with 30 μL of protein G beads (Invitrogen, 1003D) in 300 μL IP buffer (10 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.05% Triton X-100 (v/v)) for two hours at 4 °C on a rotating wheel. The same procedure was performed for a control reaction using mouse IgGs (Abcam ab37355). Bead-antibody complexes were washed three times with IP buffer and finally brought to 250 μL with IP buffer. After heat denaturation and quick chill on ice, 10-μg samples of RNA were added to the bead-antibody complexes and incubated with 1 μL SUPERase•In™ RNase Inhibitor (Invitrogen, AM2694) overnight at 4 °C on a rotating wheel. After several washes with IP buffer, RNA was incubated in 100 μL elution buffer (5 mM Tris-HCl pH 7.5, 1 mM EDTA, 0.05% SDS, and 200 μg Proteinase K (Invitrogen 25530049)) for 1 hour at 50 °C. Beads were removed by centrifugation in a microcentrifuge, and the supernatant was purified with RCC-5 without size selection.
Libraries were constructed with SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (TaKaRa Bio, 634411) according to the manufacturer’s instructions.

value: wildtype

tag: antibody

value: m5C (Diagenode, #MAb-081-100)


title: mHSPC, Tet2 KO; shNC, H2AK119ub, CUT&Tag, r3


title: K562, WT, caRNA, Input, rep3


title: mESC, Tet2 KO; siNsun2, H2AK119ub, CUT&Tag, r1


title: K562, WT, caRNA, m5C-IP, rep2


title: mHSPC, WT; shNC, H2AK119ub, CUT&Tag, r2

value: WT, shNC


title: K562, WT, caRNA, m5C-IP, rep1

value: bone marrow


title: mHSPC, WT; shNC, H2AK119ub, CUT&Tag, r1


title: mESC, Tet2 KO; siMbd6, H2AK119ub, CUT&Tag, r3

value: Tet2 KO, siMbd6


title: mESC, Tet2 KO; siNsun2, H2AK119ub, CUT&Tag, r3


title: mESC, Tet2 KO; siNsun2, H2AK119ub, CUT&Tag, r2


title: K562, WT, caRNA, Input, rep1

value: lymphoblast cell


title: K562, WT, caRNA, Input, rep2


title: K562, TET2 KO, H2AK119ub, CUT&Tag, rep2

data_processing:
Raw reads were trimmed with Trimmomatic (version 0.39) and then mapped to mouse genome (mm10) or human genome (hg38) using bowtie2 (version 2.4.1) with default mode, where multiple alignments are searched and the best one is reported.
Peaks were called using HOMER (version 4.9) in histone mode with reads deduplicated by using ‘-tbp 1’ parameter.
Assembly: mm10 for mouse and hg38 for human
Supplementary files format and content: Peaks
Library strategy: CUT&Tag

growth_protocol: K-562 cell lines were kept in RPMI-1640 (Gibco, 61870036) with 10% fetal bovine serum (FBS, Gibco) and 1 μg/mL puromycin (Gibco, A1113803) at 37 °C and 5% CO2. For hematopoietic stem and progenitor Lin-c-Kit+ (LK) cell selection, magnetic-activated cell sorting was applied with autoMACS® Pro Separator (Miltenyi Biotec). Briefly, the lineage-positive cells (Lin+) were firstly depleted from total BM cells of 6–8 weeks old mice using the Direct Lineage Cell Depletion Kit (Miltenyi Biotec, 130-110-470), and then the lineage-negative cells (Lin-) were sorted with c-Kit (CD117) MicroBeads (Miltenyi Biotec, 130-091-224). The purity of selected cells was analyzed by flow cytometry. The LK cells were also incubated in suspension culture containing 30% FBS and 2% BSA in complete RPMI-1640 medium supplemented with 100 ng/mL mSCF, 10 ng/mL mIL-3, 50 ng/mL mTPO and 10 ng/ml mGM-CSF. All mESCs were kept in DMEM (Gibco, 11995065) supplemented with 15% Stem Cell Qualified Fetal Bovine Serum, Heat Inactivated (Gemini Bio Products, 100-525), 1 × L-glutamine (Gibco, 25030081), NEAA (Gibco, 25030081), LIF (MilliporeSigma, ESG1107), 1 × β-mercaptoethanol (Gibco, 21985023), 3 μM CHIR99021 (STEMCELL Technologies, 72052) and 1 μM PD0325901 (STEMCELL Technologies, 72182) at 37 °C and 5% CO2. The medium was replaced every day. ES cells were passaged on gelatin-coated plates twice to clear feeder cells before experiments.

extract_protocol:
N/A
CUT&Tag libraries were constructed following the manufacturer's instructions of CUT&Tag-IT™ Assay Kit (Active Motif, 53160).

treatment_protocol: siRNA transfections in K-562 was performed according to the standard protocols of Lonza Walkersville SF Cell Line 4D-Nucleofector X Kit L (Lonza, V4XC2024) with program FF-120.

value: TET2 knockout


title: mESC, Tet2 KO; siMbd6, H2AK119ub, CUT&Tag, r1

value: embryos


title: mESC, Tet2 KO; siMbd6, H2AK119ub, CUT&Tag, r2

value: mESC


title: K562, TET2 KO, H2AK119ub, CUT&Tag, rep1


title: K562, TET2 WT, H2AK119ub, CUT&Tag, rep2


title: K562, TET2 WT, H2AK119ub, CUT&Tag, rep1


title: K562, siMBD6, H2AK119ub, CUT&Tag, rep2

value: MBD6 knockdown


title: mESC, Tet2 KO; siNC, H2AK119ub, CUT&Tag, r2

value: mouse embronic stem cell

value: Tet2 KO, siNC


title: mESC, WT; siNC, H2AK119ub, CUT&Tag, r2

value: WT, siNC


title: mESC, WT; siNC, H2AK119ub, CUT&Tag, r3


title: K562, siControl, H2AK119ub, CUT&Tag, rep2

value: control


title: K562, siMBD6, H2AK119ub, CUT&Tag, rep1


title: K562, siControl, H2AK119ub, CUT&Tag, rep1


title: mESC, Tet2 KO, H2AK119ub, CUT&Tag, r1

value: Tet2 KO


title: OM_222180_S30

city: Vienna

first: Andrea

last: Komljenovic

address: Schwarzspanierstrasse 17

country: Austria

institute: Medical University of Vienna

description: Illumina NovaSeq SP Flowcell in SR100 mode

data_processing:
Overall quality of the next-generation sequencing data was evaluated automatically and manually with fastQC v0.11.8 (Andrews 2010) and multiQC v1.7 (Ewels et al. 2016). Reads from all passing samples were adapter trimmed and quality filtered using bbduk from the bbmap package v38.69 (Bushnell 2015) and filtered for a minimum length of 17nt and phred quality of 30.
Alignment steps were performed with STAR v2.7 (Dobin et al. 2013) using samtools v1.9 (Li et al. 2009) for indexing
Assignment of features to the mapped reads was done with htseq-count v0.13
Assembly: GRCh38.p12 provided by Ensembl
Supplementary files format and content: RNAseq_human_osteoclasts_counts.txt
Supplementary files format and content: tab-delimited text file includes raw read counts mapped to genes from the human genome

extract_protocol:
Total RNA was extracted by using TRIzol Reagent (Ambion, #15596018) and quantified using Bioanalyzer with the RIN >7.
Libraries have been prepared with the QuantSeq 3’ mRNA-Seq V2 Library Prep Kit with UDI (Lexogen, Austria) according to the manufacturer’s instructions. 250 ng total RNA has been used as input and final amplification of libraries was performed with 17 PCR cycles

value: primary cells

value: stromal cells

value: osteogenic differentiation medium (OM)


title: OM_222163_S13


title: OM_222179_S29


title: mESC, WT, H2AK119ub, CUT&Tag, r1

value: WT


title: OM_222182_S32


title: mESC, WT, H2AK119ub, CUT&Tag, r2


title: OM_222181_S31


title: OM_222161_S11


title: mESC, Tet2 KO; siNC, H2AK119ub, CUT&Tag, r3


title: mESC, Tet2 KO; siNC, H2AK119ub, CUT&Tag, r1


title: mESC, WT, BAP1, CUT&Tag, r2

value: BAP (Santa Cruz, sc-28383)


title: OM_222160_S10

value: bone marrow


title: mESC, WT, DNA, 5mC-IP, MeDIP, r1

value: IP


title: mESC, WT, BAP1, CUT&Tag, r1


title: GM_222186_S36

value: growth medium (GM)


title: mESC, Tet2 KO, H2AK119ub, CUT&Tag, r3


title: OM_222159_S9


title: mHSPC, Tet2 KO; shMbd6, ATAC, r3

data_processing:
Raw reads were trimmed with Trimmomatic (version 0.39) and then mapped to mouse genome (mm10) or human genome (hg38), together with Drosophila melanogaster chromatin (Spike-in Chromatin), using bowtie2 (version 2.4.1) with default mode, where multiple alignments are searched and the best one is reported.
Mapped reads were deduplicated using a Picard tool ‘MarkDuplicates’ (version 2.26.2) (http://broadinstitute.github.io/picard/). Reads that mapped to the mitochondrial genome were discarded prior to deduplication.
Peaks were identified using MACS266 with the default mode, except for the parameters “--shift -75 --extsize 150 --nomodel --call-summits”.
Assembly: mm10 (mouse), hg38 (human)
Supplementary files format and content: Peaks

extract_protocol:
ATAC-seq was performed using a commercial kit (Active Motif, 53150) with ATAC-Seq Spike-In Control (Active Motif, 53154) following the standard protocol recommended by the manufacturer.
ATAC-seq was performed using a commercial kit (Active Motif, 53150) with ATAC-Seq Spike-In Control (Active Motif, 53154) following the standard protocol recommended by the manufacturer.

value: HSPC

value: hematopoietic stem and progenitor Lin-c-Kit+ (LK) cell

value: Tet2 KO, shMbd6


title: mESC, WT; siNC, H2AK119ub, CUT&Tag, r1

value: embryos

value: mESC


title: mESC, WT, H2AK119ub, CUT&Tag, r3

value: mouse embronic stem cell


title: mHSPC, Tet2 KO; shMbd6, ATAC, r2


title: mHSPC, Tet2 KO; shMbd6, ATAC, r1


title: OM_222162_S12


title: GM_222184_S34


title: mESC, Tet2 KO, H2AK119ub, CUT&Tag, r2


title: GM_222183_S33


title: GM_222185_S35


title: mHSPC, Tet2 KO; shNC, ATAC, r3

value: Tet2 KO, shNC


title: GM_222168_S18


title: mHSPC, Tet2 KO; shNC, ATAC, r2


title: mHSPC, Tet2 KO; shNC, ATAC, r1


title: GM_222167_S17


title: GM_222166_S16


title: mHSPC, WT; shNC, ATAC, r2

value: WT, shNC


title: mHSPC, WT; shNC, ATAC, r1


title: GM_222165_S15


title: GM_222164_S14


title: mESC, Tet2 KO; HxD OE, ATAC, r2, set2

value: Tet2 KO, TET2 HxD OE


title: mESC, Tet2 KO; HxD OE, ATAC, r3, set2


title: 5mM_222172_S22

value: primary cells

value: OM + 5mM itaconic acid


title: mESC, Tet2 KO; HxD OE, ATAC, r1, set2


title: 5mM_222171_S21

value: stromal cells


title: mHSPC, WT; shNC, H2AK119ub, CUT&Tag, r3


title: 5mM_222170_S20


title: mESC, Tet2 KO; WT OE, ATAC, r1, set2

value: Tet2 KO, TET2 WT OE


title: 5mM_222169_S19


title: mESC, Tet2 KO; WT OE, ATAC, r2, set2


title: 5mM_222154_S4


title: 5mM_222153_S3


title: mESC, Tet2 KO; EV OE, ATAC, r3, set2

value: Tet2 KO, EV OE


title: 5mM_222152_S2

value: bone marrow


title: mESC, Tet2 KO; WT OE, ATAC, r3, set2


title: mESC, Tet2 KO; EV OE, ATAC, r1, set2


title: mHSPC, WT; shNC, ATAC, r3


title: KKU-100, shControl, replicate 3

city: Bangkok

first: Khajeelak

last: Chiablaem

state: State...

address: 270 Rama VI Road, Toong Phayathai, Ratchathewi

country: Thailand

institute: Faculty of Medicine Ramathibodi Hospital, Mahidol University

data_processing:
Quality control of RNA-Seq reads was performed using FastQC (v0.11.9).
The cleaned reads were then ready for alignment to the human reference genome (GRCh38) using the STAR (v2.5.1b) aligner, and duplicated reads were removed using the MarkDuplicates function of Picard v1.139.
Gene-level quantification of RNA-Seq reads was then determined using StringTie v2.1.6 and HT-Seq v0.6.1p1 to obtain transcripts per kilobase per million mapped reads (TPM) and raw counts, respectively.
Differential expression genes (DEGs) analysis of genes was performed by DESeq2 v1.34.0.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts, TPM, FPKM, and normalized counts for each sample

source_name: Biliary tract

growth_protocol: KKU-100 cells were cultured in Ham’s F12 medium, supplemented with 10% FBS. HuCCT1 and YSCCC were cultured in RPMI-1640 medium with 10% FBS. All cultures were supplemented with antimicrobial agents (100 U/ml penicillin, 100 μg/ml streptomycin, and 0.25 μg/ml amphotericin B), and 25 mM HEPES in a humidified 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using TRIzol reagent and RNeasy mini kit (Qiagen). 750 ng of total RNA was used for the construction of libraries.
RNA libraries for RNA sequencing using the Human TruSeq standard mRNA protocol (Illumina, Inc.) .

value: Biliary tract

value: Cholangiocarcinoma cells

value: WT


title: mESC, Pspc1 KO, ATAC, r1, set2

value: Pspc1 KO


title: KKU-100,shRNF213#2, replicate 2

value: RNF213 knockdown


title: mESC, WT, ATAC, r3, set2

value: embryos


title: KKU-100, shControl, replicate 2


title: mESC, WT, ATAC, r2, set2

value: mESC


title: mESC, Tet2 KO; EV OE, ATAC, r2, set2

value: mouse embronic stem cell


title: 5mM_222173_S23


title: KKU-100,shRNF213#2, replicate 1


title: mESC, WT, ATAC, r1, set2


title: mESC, Tet2 KO; siNsun2, ATAC, r3, set1

value: Tet2 KO, siNsun2


title: KKU-100, shControl, replicate 1


title: YSCCC, shControl, replicate 3

source_name: Liver

value: Liver

value: YSCCC


title: mESC, Tet2 KO; siNsun2, ATAC, r2, set1


title: mESC, Tet2 KO; siNsun2, ATAC, r1, set1


title: 5mM_222151_S1

value: primary cells


title: mESC, Tet2 KO; siMbd6, ATAC, r3, set1

value: Tet2 KO, siMbd6


title: mESC, Pspc1 KO, ATAC, r2, set2


title: mESC, Tet2 KO; siNC, ATAC, r3, set1

value: Tet2 KO, siNC


title: YSCCC, shControl, replicate 1


title: YSCCC, shControl, replicate 2


title: mESC, Pspc1 KO, ATAC, r3, set2


title: mESC, Tet2 KO; siNC, ATAC, r1, set1


title: mESC, WT; siNC, ATAC, r3, set1

value: WT, siNC


title: HuCCT1, shRNF213#2, replicate 3

source_name: Bile duct

value: Bile duct


title: HuCCT1, shRNF213#2, replicate 1


title: mESC, Tet2 KO; siMbd6, ATAC, r1, set1


title: HuCCT1, shControl, replicate 2


title: YSCCC, shRNF213#2, replicate 2


title: mESC, Tet2 KO; siNC, ATAC, r2, set1


title: YSCCC, shRNF213#2, replicate 3


title: mESC, Tet2 KO; siMbd6, ATAC, r2, set1


title: HuCCT1, shControl, replicate 1


title: mESC, Tet2 KO, ATAC, r3, set1

value: Tet2 KO


title: KKU-100,shRNF213#2, replicate 3

value: Biliary tract


title: YSCCC, shRNF213#2, replicate 1

value: Cholangiocarcinoma cells


title: HuCCT1, shRNF213#2, replicate 2


title: NU_MCC_051, bulk RNA

data_processing: Sequence reads were trimmed and filtered using Trim Galore! (v0.6.7) to remove low-quality reads, adapter sequences, and bases with low Phred scores. Reads were then aligned to the reference human genome (GRCh38.p13 primary assembly ) augmented with the Merkel cell polyomavirus transcriptome, using the GENCODE v32 transcript annotation with STAR (v2.7.10b) on two-pass mode.  The dataset was quality-controlled to remove significant outliers. Differential gene expression analysis was performed using DESeq2 (v1.28.1) or other appropriate software. The limma package was used to fit differential expression to a generalized linear model. Pathway analysis was conducted with GSVA and GSEA. ClusterProfiler4.0 was used to visualize resulting enrichment plots.

source_name: Merkel Cell Carcinoma (MCC)

extract_protocol:
Formalin-fixed paraffin-embedded (FFPE) tissue blocks were sectioned at a thickness of 5 μm. RNA was extracted from the FFPE tissue sections using the RNeasy FFPE Kit (Qiagen) according to the manufacturer's instructions. The extracted RNA was treated with RNase-Free DNase Set (Qiagen) to remove any genomic DNA contamination. RNA quality and quantity were assessed using a Bioanalyzer (Agilent) and Qubit fluorometer (Thermo Fisher Scientific), respectively.
RNA sequencing libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) according to the manufacturer's instructions. Briefly, 500 ng of total RNA was used for poly(A) mRNA selection, fragmentation, and cDNA synthesis. The resulting cDNA was end-repaired, adenylated, and ligated with Illumina-specific adapters. PCR amplification was then performed to enrich the adapter-ligated fragments. The final library was purified and validated for size distribution using a Bioanalyzer (Agilent) and quantified by qPCR using a Kapa Library Quantification Kit (Kapa Biosystems). Libraries were pooled at equimolar concentrations and sequenced on an Illumina NovaSeq 6000.

value: Merkel Cell Carcinoma (MCC)

value: bulk RNA


title: mESC, Tet2 KO, ATAC, r2, set1


title: HuCCT1, shControl, replicate 3

value: WT


title: mESC, WT; siNC, ATAC, r1, set1

value: embryos


title: NU_MCC_045, bulk RNA


title: NU_MCC_044.1, bulk RNA


title: mESC, Tet2 KO, ATAC, r1, set1

value: mESC


title: mESC, WT; siNC, ATAC, r2, set1

value: mouse embronic stem cell


title: mESC, WT, ATAC, r2, set1


title: mESC, WT, ATAC, r3, set1


title: NU_MCC_037, bulk RNA


title: NU_MCC_044.3, bulk RNA


title: NU_MCC_043, bulk RNA


title: mESC, WT, ATAC, r1, set1


title: dLAM3-CSF

first: Yudan

last: Chi

address: 131 Dongan Road

institute: Fudan University

description: Sorted resident macrophages from tamoxifen-induced Cx3cr1CreER:mTmG mice with LLC-LeptoM inoculation

data_processing:
Quality control of the raw sequencing data was performed using FastQC. The reads were aligned to the reference genome using HISAT2, and gene expression quantification was performed using featureCounts.
Assembly: mm10
Supplementary files format and content: FPKM values for each Sample

source_name: cerebrospinal fluid

extract_protocol:
Fluorescence-activated cell sorting (FACS) was used to prepare cell samples for bulk RNA-seq. Single cell suspensions from CSF of Cx3cr1CreER:mTmG (tamoxifen treat) LM models were prepared and stained. Cells were sorted using the MA900 Cell Sorter into DMEM medium with 10% FBS and antibiotics. CD45+CD11b+F4/80+Ly6C-GFP+ cells were sorted as dLAMs. CD45+CD11b+F4/80+GFP- and CD45+CD11b+F4/80lowLy6C+GFP- cells were sorted and mixed together as monocyte-macrophages. Total RNA from dLAMs or Mono-Macrophage was isolated with RNeasy Mini Kit (Cat#74106, Qiagen).
RNA quality and quantity was assessed by Bioanalyzer 4200 (Agilent technologies). All samples with RNA integrity (RIN) value >7 were prepared for library construction and RNA-seq on a NovaSeq 6000 platform (Illumina) using paired-end 150-bp reads, to a sequencing depth of >10 million reads per sample.

value: cerebrospinal fluid

value: resident macrophage


title: Mono-MΦ2-CSF

description: Sorted monocyte-macrophages from tamoxifen-induced Cx3cr1CreER:mTmG mice with LLC-LeptoM inoculation

value: monocyte-macrophage


title: Mono-MΦ3-CSF


title: Mono-MΦ1-CSF


title: NU_MCC_028, bulk RNA


title: NU_MCC_030, bulk RNA


title: dLAM2-CSF


title: NU_MCC_025, bulk RNA


title: NU_MCC_023, bulk RNA


title: dLAM1-CSF


title: NU_MCC_021, bulk RNA


title: Dura-LM-D12-3

data_processing:
The BD Rhapsody Complete Analysis Pipeline on the Seven Bridges Genomics cloud platform was used to process the raw sequencing data, which allowed us to obtain gene expression counts matrices for single cells. The R package Seurat (v4.3.0) was used for downstream analysis, including quality control, data normalization, data scaling and visualization. Filtering was applied in order to remove low quality cells by excluding cells expressing fewer than 300 or greater than 9,000 unique genes, as well as cells with greater than 20% mitochondrial gene expression or greater than 5% hemoglobin gene expression. Samples were then integrated after the selection of the top 3,000 most highly variable genes. Principal component analysis was conducted for dimension reduction, and an elbow plot was used to select the principal components for UMAP analysis and clustering. Unsupervised clustering was implemented by the Seurat FindNeighbors and FindClusters function, and UMAP plots were generated.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Dura

extract_protocol:
The dura was dissected from the skull, then was minced into small pieces and digested with 1 mL of 1 mg/mL Collagenase VIII (#C2139, Sigma) and 0.1 mg/mL of DNase I (#DN25, Sigma) in 5%-FBS DMEM in a water bath at 37°C for 15 minutes. The enzymes were neutralized with 5 mL 5%-FBS DMEM, and samples were filtered through a 40 μm cell strainer, followed by centrifugation at 400×g for 5 minutes at 4°C.
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol. Briefly, dura cells were loaded on BD Rhapsody Cartridge, followed by reverse transcription and exonuclease I digestion, library preparation, and sequencing on NovaSeq 6000 (Illumina) with 150-bp paired-end run.

value: Dura

value: LM

value: stage day 12


title: Dura-LM-D12-2


title: Dura-LM-D7-4

value: stage day 7


title: NU_MCC_018.1, bulk RNA


title: Dura-LM-D12-1


title: NU_MCC_017, bulk RNA


title: Dura-LM-D7-3


title: NU_MCC_035, bulk RNA


title: Dura-LM-D7-1


title: NU_MCC_016, bulk RNA


title: NU_MCC_012, bulk RNA


title: Dura-LM-D7-2


title: NU_MCC_031, bulk RNA


title: Dura-Ctrl-2

value: control


title: NU_MCC_005, bulk RNA


title: MO_MCC_095, bulk RNA


title: MO_MCC_092.2, bulk RNA


title: MO_MCC_083, bulk RNA


title: MO_MCC_092.1, bulk RNA


title: Peri-injured 14d/injured 12_SP-C mutant lung tissue (non immune)

city: Salt Lake City

first: Alessandro

last: Venosa

state: UT

department: Pharmacology and Toxicology

institute: University of Utah

description: Peri--injured region_012_CD45- "other"

data_processing:
Raw sequencing files were processed using Nanostring GeoMx NGS pipeline to generate DCC files
Sequences were aligned to mm10 genome within the NGS pipeline using NanoString oligo RTS_ID alignment
Aligned sequences were deduplicatedaccording to Nanostring oligo UNI sequences to generate final DCC
Assembly: mm10
Supplementary files format and content: 111_CTL (top) - 113_14d injured (bottom) [JPG]: tissue_hiresolution_image
Supplementary files format and content: file with barcodes, matrix, features

source_name: lung

growth_protocol: all animals were kept in a germ free facility for the duration of their lives. Food and water was provided ad libitum. Sacrifice was performed according to IACUC protocol. Lungs were perfused through the heart with saline solution (0.9% sodium chloride). Lungs were then inflated with 10% Neutral buffered formalin at steady state pressure (25cmH2O). Tissue embedding in paraffin blocks was followed by sectioning immediately prior to immunofluorescent staining (CD45, CD68, DNA). Regions of interested were selected and staining threshold standardized across of samples.

extract_protocol:
Paraffin embedded blocks were sectioned at 6um of thickness
Spatial transcriptome sequencing libraries  were prepared with NanoString Mouse Whole Transcriptome Kit (v1.0) and Reagents according to Nanostring protocols

treatment_protocol: Single oral gavage treatment with tamoxifen (175mg/kg, in corn oil) excises neomycin cassette and boosts mutant SPC mutant expression. Corn oil gavage was used for

value: lung

value: SP-CI73T mutant

tag: Sex

value: Male

tag: time point

value: day 14

value: tamoxifen treated


title: Dura-Ctrl-1


title: Injured 14d/injured 11_SP-C mutant lung tissue (non immune)

description: Injured region_011_CD45- "other"


title: MO_MCC_079.2, bulk RNA

value: Merkel Cell Carcinoma (MCC)

value: bulk RNA


title: MO_MCC_079.1, bulk RNA


title: Peri-injured 14d/injured 12_SP-C mutant lung tissue (immune)

description: Peri--injured region_012_CD68+


title: MO_MCC_085, bulk RNA


title: NU_MCC_020, bulk RNA


title: Injured 14d/injured 11_SP-C mutant lung tissue (immune)

description: Injured region_011_CD68+


title: Peri-injured 14d/injured 10_SP-C mutant lung tissue (non immune)

description: Peri--injured region_010_CD45- "other"


title: MO_MCC_071, bulk RNA


title: Peri-injured 14d/injured 10_SP-C mutant lung tissue (immune)

description: Peri--injured region_010_CD68+


title: MO_MCC_068.2, bulk RNA


title: Dura-Ctrl-3


title: Peri-injured 14d/injured 9_SP-C mutant lung tissue (non immune)

description: Peri--injured region_009_CD45- "other"


title: Peri-injured 14d/injured 9_SP-C mutant lung tissue (immune)

description: Peri--injured region_009_CD68+


title: MO_MCC_066, bulk RNA


title: MO_MCC_063, bulk RNA


title: Injured 14d/injured 8_SP-C mutant lung tissue (non immune)

description: Injured region_008_CD45- "other"


title: MO_MCC_065, bulk RNA


title: MO_MCC_064, bulk RNA


title: Injured 14d/injured 8_SP-C mutant lung tissue (immune)

description: Injured region_008_CD68+


title: Injured 14d/injured 7_SP-C mutant lung tissue (non immune)

description: Injured region_007_CD45- "other"


title: MO_MCC_061, bulk RNA


title: Injured 14d/injured 7_SP-C mutant lung tissue (immune)

description: Injured region_007_CD68+


title: MO_MCC_062, bulk RNA


title: Peri-injured 14d/injured 6_SP-C mutant lung tissue (non immune)

description: Peri--injured region_006_CD45- "other"


title: MO_MCC_075, bulk RNA


title: Peri-injured 14d/injured 6_SP-C mutant lung tissue (immune)

description: Peri--injured region_006_CD68+


title: Injured 14d/injured 5_SP-C mutant lung tissue (non immune)

description: Injured region_005_CD45- "other"


title: MO_MCC_058.1, bulk RNA


title: MO_MCC_055, bulk RNA


title: MO_MCC_056.1, bulk RNA


title: Injured 14d/injured 4_SP-C mutant lung tissue (non immune)

description: Injured region_004_CD45- "other"


title: Injured 14d/injured 5_SP-C mutant lung tissue (immune)

description: Injured region_005_CD68+


title: Injured 14d/injured 4_SP-C mutant lung tissue (immune)

description: Injured region_004_CD68+


title: MO_MCC_054.2, bulk RNA


title: healthy region 13_SP-C mutant lung tissue (non immune)

description: healthy region_013_CD45- "other"

value: control (day 0)

value: untreated


title: MO_MCC_051, bulk RNA


title: healthy region 13_SP-C mutant lung tissue (immune)

description: healthy region_013_CD68+


title: healthy region 3_SP-C mutant lung tissue (non immune)

description: healthy region_003_CD45- "other"


title: MO_MCC_049, bulk RNA


title: MO_MCC_048, bulk RNA


title: healthy region 3_SP-C mutant lung tissue (immune)

description: healthy region_003_CD68+


title: MO_MCC_046.2, bulk RNA


title: MO_MCC_046.1, bulk RNA


title: healthy region 1_SP-C mutant lung tissue (non immune)

description: healthy region_001_CD45- "other"


title: MO_MCC_044, bulk RNA


title: MO_MCC_060, bulk RNA


title: MO_MCC_042, bulk RNA


title: no template control

description: no template control


title: MO_MCC_041.2, bulk RNA


title: healthy region 1_SP-C mutant lung tissue (immune)

description: healthy region_001_CD68+


title: MO_MCC_036, bulk RNA


title: MO_MCC_035.2, bulk RNA


title: T3,tumor-PTEN

city: shanghai

first: jiaming

last: shen

address: SHANGHAI

institute: shanghai jiaotong university

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

source_name: tumor

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

value: tumor


title: MO_MCC_035.1, bulk RNA


title: C3,tumor-PBS


title: C4,tumor-PBS


title: MO_MCC_034, bulk RNA


title: C1,tumor-PBS


title: C2,tumor-PBS


title: MO_MCC_031, bulk RNA


title: MO_MCC_032, bulk RNA