title: PTENERG_T_4

city: Bellinzona

first: Andrea

last: Alimonti

address: Via vela 6

department: Molecular Oncology

country: Switzerland

institute: Institute of oncology research

data_processing:
Samples were processed starting from stranded, paired ended 75bp-long sequencing reads
The overall quality of sequencing reads was evaluated using FastQC. Sequence alignments to the reference mouse genome (GRCm38) was performed using STAR (v.2.5.2a). Gene-expression was quantified at gene level by using the comprehensive annotations made available by Gencode. Specifically, we used v20 release of the Gene Transfer File (GTF).
Raw counts were further processed in the R Statistical environment and downstream differential expression analysis was performed using the DESeq2 pipeline.  Genes characterized by zero expression were removed and genes with low mean normalized counts were filtered out by the Independent Filtering feature embedded in DESeq(alpha = 0.05).
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts

source_name: Prostate tumor

growth_protocol: Polysome profiles analysis of prostate tumor was performed in six different genetic backgrounds: wild-type, Ptenpc-/-, Ptenpc-/-;TMPRSS2-ERGpc+/+,  Ptenpc-/-;CDCP1pc+/+, Ptenpc-/-;TIMP1-/- and Ptenpc-/-;Trp53pc-/-. For each genotype, three mice of 20-25 weeks of age were analyzed.

extract_protocol:
Prostate tumor tissues were quickly excised and homogenized in polysome lysis buffer (30 mM Tris-HCl, pH 7.5, 100 mM NaCl, 30 mM MgCl2, 1% sodium deoxycolate, 1% Triton X-100, 100 mg ml−1 cycloheximide, 1 mM DTT and 30 U ml−1 RNasin) by using a sterile pestle. After centrifugation at 12,000 rpm for 15 min at 4 °C, cytoplasmic extracts with equal amounts of RNA were loaded on a 15–50% sucrose gradient and centrifuged at 4 °C for 3 h 30 min at 39,000 r.p.m in a SW41Ti Beckman rotor by using a Beckman Coulter Ultracentrifuge Optima L-90K. Gradients were read at 254 nm by the BioLogic LP system (BioRad) and the fractions (1.0 ml each) were collected for subsequent RNA extraction to isolate the polysomal RNA fractions. Total and polysomal RNA fractions were incubated with 200 ug/ml proteinase K and SDS 1% for 1 h at 37 °C. RNA was extracted by phenol/chloroform 5:1 (Sigma-Aldrich; P1944) method, followed by overnight isopropanol precipitation at -80 °C, centrifugation at 14000 r.p.m. for 45 minutes and resuspension in 10 l of DEPC water. At the end of the procedure, DNAse digestion was carried out with Turbo DNase (Thermo Fisher Scientific) for 30 minutes at 37 °C and RNA purification was performed with RNA Clean and Concentrator kit (Zymo Research).
The purified RNA was measured by using Nanodrop and the quality was assessed using the Agilent 2100 Bioanalyzer. After random primer annealing, whole library preparation was performed using the Illumina TruSeq stranded total RNA with Ribozero Plus. Completed libraries were then submitted for sequencing. RNA-seq was constructed with barcodes to allow multiplexing of 12 samples per lane. Sequencing was carried out on NextSeq 500 Illumina platform.

value: Prostate tumor

value: Pten pc -/- Erg +

tag: molecule

value: total RNA


title: PTENERG_P_4

status: Public on Jun 09 2023

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type

tag: strain

tag: genotype

value: other:polysome-bound RNA


title: 39B0-2

city: West Haven

first: Sidi

last: Chen

state: CT

address: 850 West Campus Drive

country: USA

institute: Yale University

description: Biol rep2

data_processing:
Fastq files generated by sequencing were aligned and mapped using STAR with the human genome assembly version GRCh38.
Assembly: Ensembl GRCh38
Supplementary files format and content: Tab-delimited text files contain read counts after alignment.

organism: Homo sapiens

extract_protocol:
positive CAR-T cell total RNA was extracted using RNeasy Plus mini isolation kit (Qiagen).
Library preparations were performed using a NEBNext® Ultra™RNA Library Prep Kit for Illumina according to manufacturer’s instruction.

tag: treatment

value: No stimulation


title: 39D0-2

description: Biol rep2


title: Jejunum, WT3

city: Newark

last: Gao

state: NJ

address: 225 University Ave

department: Biological Sciences

institute: Rutgers Newark

data_processing:
Raw sequencing reads (fastq) were quality checked using fastQC (v0.11.3).
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic(0.36) (parameter- reads were trimmed based on base call phred score lower than 20)
Trimmed sequence reads were mapped to mm9 using HISTAT2 (v2.1.0) using default parameters
Reads were normalized in DESeq2 (Build 3.9) using default settings in R.
Assembly: mm9
Supplementary files format and content: Excel file includes FPKM values for each Sample

source_name: Jejunum

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
Purified RNA was processed using Illumina’s TruSeq RNA Library Prep kit v2 according to manufacturer's protocol.

treatment_protocol: Adult mice were treated with tamoxifen (40mg/kg) and then subsequently sacrificed at 2 days post tamoxifen administration. Jejunal tissue was collected

tag: tissue

value: Jejunum

value: WT

value: Tamoxifen (40mg/kg)


title: 39A2-1

description: Biol rep1

source_name: CAR-T

value: 2rounds of stimulation

value: CAR-T


title: B16F10_APOE2_rep4

city: New York

first: Nneoma

last: Adaku

state: NY

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
Tail sequences were trimmed with bbduk v.38.31
Reads were aligned to the mm10 mouse genome with STAR v.2.6.0
Aligned reads were counted with featureCounts
Differentially expressed transcripts were determined with DESeq2 v1.28.1
Assembly: mm10
Supplementary files format and content: csv file containing normalized count matrix

source_name: lung metastasis

growth_protocol: APOE2 and APOE3 knock-in mice were injected via lateral tail vein with 1 × 10^5 B16F10-TR-shApoe cells (in PBS)

extract_protocol:
Fifteen days after injection, lungs were taken from mice and digested with collagenase. TO-PRO-3 low/CD45-/GFP+ tumor cells from the single cells suspension were sorted on a BD FACSAria II. RNA was isolated with the Norgen Total RNA Purification Kit with on-column DNAse treatment. RNA was then concentrated with a Zymo RNA Clean & Concentrator Kit.
Libraries were constructed using QuantSeq 3' mRNA-Seq Library Prep Kit FWD (Lexogen)

value: lung metastasis

tag: cell line

value: murine melanoma


title: Jejunum, WT2


title: luminal breast cancer RANK OE, palbocicib + fulvestrant + OPG-Fc, rep2

city: Lisbon

first: Sandra

last: Casimiro

address: Av. Prof. Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular

description: 75_5 Expression

data_processing:
mapping to reference genome (GCF_000001405.38_GRCh38.p12) was performed with HISAT
mapping to the reference genes with Bowtie2
Expression levels in fragments per kilobase million (FPKM) for each sample were calculated with RSEM
Differential expressed genes (DEGs) were detected with PossionDis
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: luminal breast cancer

growth_protocol: MCF-7 PAR or MCF-7 RANK OE cells were harvested at the exponential phase of growth and resuspended at 106 cells/ml in 50% phenol-free matrigel solution (#356237, Corning). Mice were injected subcutaneously and bilaterally with 100 µl of cell suspension, directly into the flanks. Tumor growth was monitored every three days with a caliper and tumor volume calculated using the formula Tvol= 1/2(lengthxwidth2). When tumors reached approximately 100mm3.

extract_protocol:
Total RNA was extracted using the NZY Total RNA Isolation kit (#MB13402, Nzytech), according to manufacturer’s instructions. Tumor tissues preserved in RNA later (#AM7021, Thermo Fisher Scientific) at necropsy were transferred to lysis buffer with silica beads (#110791102; Biospec Products), and disrupted in a Minibeadbeater (Biospec Products) for 1-2 min.
DNBSEQ Eukaryotic Strand-specific mRNA library

treatment_protocol: Palbociclib (Palbo) 30mg/Kg/day p.o. (#PZ0199, Sigma-Aldrich) plus fulvestrant (F) 1 mgulv) 1mg/day s.c. (#S1191, Selleckchem); Palbo+Fulv+OPG-Fc 10mg/kg i.p. 3x/week (#461130, Amgen, Inc.); or vehicle (0,05 M Na Lactate (#L7900, Sigma-Aldrich) plus 95% corn oil (#C8267, Sigma-Aldrich) in 5% DMSO (#D8418-50ML, Sigma-Aldrich)

value: luminal breast cancer

value: epithelial

value: RANK (TNFRSF11A) overexpression

value: palbociclib + fulvestrant + OPG-Fc


title: 39A0-3

description: Biol rep3


title: 39D0-1

description: Biol rep1


title: PTENERG_P_3


title: PTENERG_T_3


title: Jejunum, WT1


title: 39A0-1

description: Biol rep1


title: 39A0-2

description: Biol rep2


title: luminal breast cancer RANK OE, palbocicib + fulvestrant, rep2

description: 74_4a Expression

value: palbociclib + fulvestrant


title: luminal breast cancer RANK OE, palbocicib + fulvestrant, rep3

description: 74_4b Expression


title: BMDMs, ERK5S496A, HFD_3

city: Houston

first: Shengyu

last: Li

state: TX

address: 6670 Bertner Ave, R10-109, floor 10

institute: Houston Methodist Research Insitute

data_processing:
We performed RNA sequencing (RNA-seq) for cultured BMDMs from WT and ERK5 S549A KI mice and used the TopHat program (v2.0.12) with default parameters to map all reads to the mouse genome (Mus musculus GRCm38).
Gene expression and significance of differential expression were calculated by Cuffdiff (v2.0.12). Differentially expressed genes (DEG) were defined by Cuffdiff according to Q value ≤0.05 as a threshold.
We calculated p value for each GO term with a modified Fisher’s exact test on DAVID website (https://david-d.ncifcrf.gov).
Hallmark analysis was performed by Gene Set Enrichment Analysis (GSEA v4.2.1).
Assembly: GRCm38 (mm10)
Supplementary files format and content: comma-delimited csv files include FPKM values for each Sample.

source_name: bone marrow

growth_protocol: Mice were housed in pathogen-free conditions. The Program for Animal Resources is an AAALAC certified and defined pathogen-free facility for housing mice and rats. A cage-level barrier system was used with an irradiated diet, ultra-filtered water, and heat-treated wood chip bedding. Enrichment material (nestlets) was provided. Cages and water were changed on a weekly basis. Animals were handled under a HEPA-filtered change station. Environmental parameters (ambient lighting, temperature, and humidity) were computer monitored as follows: 1) temperature: set point=22.2 °C (high limit=23.3 °C, low limit=21.1 °C), 2) humidity: set point=45% (high limit=55% and low limit=40%), 3) light cycle: 12 hours of light and 12 hours of dark, and 4) air changes 10-15 times per hour. The vivarium was staffed 7 days a week by animal caretakers, including weekends and holidays. Veterinary care and oversight were provided by a contract veterinarian who visited the facilities on a regular basis and was available for consultation by phone or email.

extract_protocol:
Trizol method
Total RNAs isolated from NRVMs were processed to generate cDNA libraries that were sequenced on the Illumina HiSeq 4000 platform.

treatment_protocol: Mice containing ERK5 S496A point mutation were generated using the CRISPR/Cas technique. We used only male mice for evaluating atherosclerosis lesions. We obtained rAAV plasmids encoding gain-of-function forms of murine PCSK9 (pAAV/D377Y-mPCSK9) from Addgene (plasmid #58376). PCSK9 expression was driven by an efficient liver-specific promoter, HCEApoE/hAAT. Viral vectors in serotype 8 capsids rAAV8-D377Y-mPCSK9 were produced by the University of North Carolina Vector Core (Chapel Hill, NC). Viral vectors (1 x 1011 titer/mouse) were delivered via a single tail vein injection into WT or ERK5 S496A mice; these animals had been challenged with an adjusted-calorie (high-fat) diet (HFD) consisting of 21% crude fat, 0.15% cholesterol, and 19.5% casein (TD.88137; Envigo, NJ) for 16 weeks and then killed by CO2 inhalation. In this AAV-PCSK9 injection model, we excluded mice when the LDL cholesterol level was below 300mg/dL after 16 weeks of HFD. The arterial tree was perfused via the left ventricle with saline containing heparin (40 USPU/mL), followed by 10% neutral-buffered formalin in PBS for 10 minutes. The full length of the aorta from the heart to the iliac bifurcation was dissected and opened along the ventral midline. En face preparations were washed in PBS, dipped in 60% isopropyl alcohol, and stained for 30 minutes with 0.3% Oil-Red-O that had been dissolved in 60% isopropyl alcohol. The aortic sinus area attached to the heart was dissected after fixation, as described earlier, and then embedded in paraffin; sections (5 µm) were cut. To quantify necrotic core formation, we made serial sections through the entire aortic valve area and stained them with hematoxylin and eosin.

value: bone marrow

value: bone marrow-derived macrophages (BMDMs)

value: KI

tag: Sex

value: male

value: High Fat Diet


title: BMDMs, ERK5S496A, NCD_3

value: Normal Chow Diet


title: 39B0-1

description: Biol rep1

value: No stimulation


title: luminal breast cancer RANK OE, palbocicib + fulvestrant + OPG-Fc, rep1

description: 75_2 Expression


title: luminal breast cancer RANK OE, untreated, rep3

description: 73_3 Expression

value: vehicle


title: WT_P_6

value: Prostate tumor

value: WT

value: other:polysome-bound RNA


title: PTENERG_P_1

value: Pten pc -/- Erg +


title: ex vivo MZ B cells TC 186

city: Philadelphia

first: Tian

last: Tian

state: PA

address: 3615 Civic Center Blvd

department: Center of Applied Genomics

institute: Children's Hospital of Philadelphia

data_processing:
The quality control of RNA-seq (trimming bases with quality score less than 20) and adaptor trimming of raw reads was conducted by trim_galore
Processed reads were aligned to hg38 reference genome by HISAT2
gene counts were summarized by StringTie67 with the GENCODE reference annotation

source_name: tonsil

extract_protocol:
RNA was isolated from 100,000 FACS-sorted MZ and GC B cells using Trizol Re- agent (Invitrogen), purified using the Directzol RNA Miniprep Kit (Zymo Research), and depleted of contaminating genomic DNA using DNAse I. Purified RNA was checked for quality on a Bioanlayzer 2100 using the Nano RNA Chip and samples with RIN > 7 were used for RNA-seq library preparation. RNA samples were depleted of rRNA using QIAseq Fastselect RNA removal kit (Qiagen).
Samples were then processed for the preparation of libraries using the SMARTer Stranded Total RNA Sample Prep Kit (Takara Bio USA) according to the manufacturer’s instructions.

value: tonsil

value: marginal zone B cells


title: ex vivo MZ B cells TC 184


title: ex vivo MZ B cells TC 181


title: luminal breast cancer RANK OE, untreated, rep2

description: 73_1b Expression

value: luminal breast cancer

value: epithelial

value: RANK (TNFRSF11A) overexpression


title: ex vivo MZ B cells TC 180


title: WT_P_10


title: BMDMs, WT, NCD_3

value: bone marrow


title: luminal breast cancer RANK OE, untreated, rep1

description: 73_1a Expression


title: PTENERG_T_1

value: total RNA


title: BMDMs, ERK5S496A, NCD_2

value: bone marrow-derived macrophages (BMDMs)

value: KI


title: BMDMs, ERK5S496A, HFD_2

value: male

value: High Fat Diet


title: PTENCDCP1_T_1

value: Pten pc -/- Cdcp1 pc -/-


title: ex vivo GC B cells TC 186

value: GC B cells


title: luminal breast cancer, palbocicib + fulvestrant + OPG-Fc, rep3

description: 77_4 Expression

value: palbociclib + fulvestrant + OPG-Fc


title: BMDMs, WT, HFD_2

value: WT


title: luminal breast cancer, palbocicib + fulvestrant + OPG-Fc, rep2

description: 77_3 Expression


title: luminal breast cancer, palbocicib + fulvestrant + OPG-Fc, rep1

description: 77_1 Expression


title: ex vivo GC B cells TC 184


title: luminal breast cancer RANK OE, palbocicib + fulvestrant, rep1

description: 74_2 Expression

value: palbociclib + fulvestrant


title: BMDMs, WT, NCD_2

value: Normal Chow Diet


title: ex vivo GC B cells TC 181

value: tonsil


title: PTENCDCP1_T_3

value: Prostate tumor


title: BMDMs, WT, HFD_3


title: WT_P_12

value: other:polysome-bound RNA


title: ex vivo GC B cells TC 180


title: PTENCDCP1_P_3


title: luminal breast cancer, palbocicib + fulvestrant, rep2

description: 76_5 Expression

value: luminal breast cancer

value: epithelial


title: BMDMs, ERK5S496A, HFD_1

value: bone marrow


title: BMDMs, ERK5S496A, NCD_1


title: luminal breast cancer, palbocicib + fulvestrant, rep1

description: 76_3 Expression


title: PTENCDCP1_T_2

value: total RNA


title: BMDMs, WT, HFD_1

value: bone marrow-derived macrophages (BMDMs)


title: ASD17AII, Day 5, Factorial E8 [P16902_143]

city: Solna

first: Abishek

last: Arora

state: Stockholm

address: NKS BioClinicum J9:30, Akademiska stråket 1

department: Department of Women's and Children's Health

country: Sweden

institute: Karolinska Institutet

description:
P16902_143
Gene_Counts.txt
Metadata_Ordered.csv

data_processing:
Pooling and sequencing were done on NovaSeq6000 (NovaSeq Control Software 1.6.0/RTA v3.4.4) with a 2x151 setup using 'NovaSeqXp' workflow in 'S4' mode flowcell. The Bcl to FastQ conversion was performed using bcl2fastq (v2.20.0.422) from the CASAVA software suite.
For further data processing, the best practice bioinformatics nf- core/RNAseq pipeline of the NGI was used (Ewels et al., 2020). In short, quality control of read sequences was performed with FastQC, followed by preparation for alignment using UMI-tools (extraction of unique molecular identifiers), Trim Galore! (adapter and quality trimming), BBSplit (removal of genomic contaminants) and SortMeRNA (removal of ribosomal RNA). Read alignment was completed using STAR aligner.
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-delimited text (.txt) file includes count values for each sample.
Supplementary files format and content: Comma-seperated values (.csv) file includes metadata for each sample.

growth_protocol: Patient-derived and previously established NES cells were seeded on 20 µg/mL poly-ornithine and 1 µg/mL Laminin2020 precoated tissue culture treated plates in DMEM/F12 Glutamax basal medium, supplemented with 0.05x B27, 1x N-2, 10 ng/mL recombinant human bFGF, 10 ng/mL recombinant human EGF and 10 U/mL penicillin-streptomycin, with daily media changes. Upon starting the undirected differentiation, cells were changed to a media with an increased 0.5x B27 concentration, without bFGF and EGF.

extract_protocol:
Cells were lysed and total RNA isolated with the ReliaPrep RNA Cell Miniprep kit (Promega Z6012).
The sequencing library was prepared using the Illumina TruSeq RNA RiboZero GOLD kit.

treatment_protocol: Cells were seeded for differentiation and treated with six environmental factors (lead, valproic acid, bisphenol A, ethanol, fluoxetine hydroxide and zinc dysregulation) along with untreated controls, in accordance with the described fractional factorial experimental design. Treatments were repeated every other day while changing media, for a period of 5 days.

value: Male

value: iPSC derived NES cells

value: Neuronal differentiation

tag: time

value: Day 5


title: BMDMs, WT, NCD_1

value: male


title: ASD17AII, Day 5, Factorial E7 [P16902_142]

description:
P16902_142
Gene_Counts.txt
Metadata_Ordered.csv


title: ASD17AII, Day 5, Factorial E6 [P16902_141]

description:
P16902_141
Gene_Counts.txt
Metadata_Ordered.csv


title: NSG15.TTP2.T

city: NW Washington

first: Barry

middle: I

last: Hudson

state: District of Columbia

address: 3970 Reservoir Road,

department: Oncology

institute: Georgetown University

data_processing:
Possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
Reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Read counts were calculated by using featureCounts from the Subread package v.1.5.2
Genes with a sum of counts across all conditions less than 120 were filtered out (Average count of 20 per condition)
Assembly: GRCh38 (Hg38)
Supplementary files format and content: Filtered Raw Counts

growth_protocol: orthotopically implanted primary breast tumors

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus Universal Mini kit following manufacturer’s instructions from flash frozen tissue samples.
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions

treatment_protocol: 1mg/kg, 2x/week Azeiragon or FPS-ZM1 or 1% DMSO (vehicle)

value: Triple negative breast cancer cells

value: tumor

tag: host

value: Mus musculus

value: TTP

tag: biological replicate

value: rep  2


title: PTENCDCP1_P_1

value: Prostate tumor

value: Pten pc -/- Cdcp1 pc -/-


title: PTENCDCP1_P_2

value: other:polysome-bound RNA


title: luminal breast cancer, untreated, rep1

description: 79_4 Expression

value: luminal breast cancer

value: epithelial

value: WT

value: vehicle


title: PTEN_TIMP1_P_1

value: Pten pc -/- Timp1 -/-


title: ASD17AII, Day 5, Factorial E4 [P16902_139]

description:
P16902_139
Gene_Counts.txt
Metadata_Ordered.csv

value: Male

value: iPSC derived NES cells


title: ASD17AII, Day 5, Factorial E5 [P16902_140]

description:
P16902_140
Gene_Counts.txt
Metadata_Ordered.csv

value: Neuronal differentiation

value: Day 5


title: NSG15.FPS2.T

value: Triple negative breast cancer cells

value: FPS


title: ASD17AII, Day 5, Factorial E3 [P16902_138]

description:
P16902_138
Gene_Counts.txt
Metadata_Ordered.csv


title: LW-Back_2

city: Chengdu

first: Qin

last: Zou

address: No.211, Huimin Road

country: China

institute: Sichuan Agricultural University

description: Skin, replicate 2

library_source: transcriptomic single cell

data_processing:
Cells genes were expressed in less than three cells, and cells were removed on the basis of detected genes number with a minimal of 200.  Mitochondrial gene expression was set at a threshold of 5% for per cell
Assembly: Sus scrofa11.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Sus scrofa

source_name: back skin

extract_protocol:
Single-cell transcriptome analyze from three CH pigs at six different anatomical body areas (head, ear, shoulder, back, abdomen, leg) and three LW pigs with one region (back).The fresh skin samples were thoroughly scraped off the hair and subcutaneous fat and were washed thrice with ice-cold Dulbecco’s Phosphate-Buffered Salline (1ｘDPBS).
Single-cell suspension were subjected to a series of progress, including droplet encapsulation, emulsion breakage, mRNA captured bead collection, reverse transcription, and cDNA amplification and purification, to generate barcoded libraries

tag: breed

value: Large White

value: back skin

value: Skin cells

value: female

tag: age

value: 180 days old


title: NSG15.TTP1.T

value: tumor

value: Mus musculus

value: TTP

value: rep  1


title: LW-Back_3

description: Skin, replicate 3


title: LW-Back_1

description: Skin, replicate 1


title: PTEN_TIMP1_P_3

value: Prostate tumor

value: other:polysome-bound RNA


title: NSG15.FPS1.T


title: ASD17AII, Day 5, Factorial E2 [P16902_137]

description:
P16902_137
Gene_Counts.txt
Metadata_Ordered.csv

value: Male


title: PTEN_TIMP1_T_2

value: Pten pc -/- Timp1 -/-

value: total RNA


title: luminal breast cancer, untreated, rep2

description: 79_5 Expression

value: luminal breast cancer

value: epithelial

value: WT

value: vehicle


title: CH-SH_2

description: Skin, replicate 2

source_name: shoulder skin

value: Chenghua

value: shoulder skin


title: CH-SH_3

description: Skin, replicate 3

value: Skin cells

value: female


title: PTEN_TIMP1_P_2


title: NSG15.D2.T

value: Triple negative breast cancer cells

value: tumor

value: DMSO

value: rep  2


title: ASD17AII, Day 5, Factorial E1 [P16902_136]

description:
P16902_136
Gene_Counts.txt
Metadata_Ordered.csv

value: iPSC derived NES cells

value: Neuronal differentiation

value: Day 5


title: PTEN_TIMP1_T_1

value: Prostate tumor

value: Pten pc -/- Timp1 -/-


title: AF22, Day 5, Factorial E4 [P16902_135]

description:
P16902_135
Gene_Counts.txt
Metadata_Ordered.csv

value: Female


title: PTEN_P53_P_4

value: other:polysome-bound RNA


title: PTEN_P53_P_5


title: CH-Leg_3

description: Skin, replicate 3

source_name: leg skin

value: leg skin

value: 180 days old


title: PTEN_TIMP1_T_3

value: total RNA


title: CH-SH_1

description: Skin, replicate 1

value: Chenghua

value: shoulder skin


title: CH-Leg_2

description: Skin, replicate 2

value: Skin cells

value: female


title: PTEN_P53_P_1


title: AF22, Day 5, Factorial E3 [P16902_134]

description:
P16902_134
Gene_Counts.txt
Metadata_Ordered.csv


title: AF22, Day 5, Factorial E2 [P16902_133]

description:
P16902_133
Gene_Counts.txt
Metadata_Ordered.csv


title: ChIP-seq data of MORC6-myc in pial1/2 background, T2 line3

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

library_source: genomic

data_processing:
For ChIP-seq analysis, raw reads were trimmed using trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and aligned to the TAIR10 reference genome with bowtie2 (v2.4.2) allowing zero mismatch and reporting one valid alignment for each read. The Samtools (v1.15) were used to convert sam files to bam files, sort bam files and remove duplicate reads. Track files in bigWig format were generated using bamCoverage of deeptools (v3.5.1) with RPKM normalization. Peaks were called with MACS2 (v2.1.2) and peaks frequently identified in previous ChIP-seq of Col-0 plant with M2 antibody for FLAG epitope were removed from analysis.
For RNA-seq analysis, the raw reads were aligned to the TAIR10 reference genome with bowtie2. Rsem-calculate-expression from RSEM with default settings was used to calculate expression levels. DEGs and DE-TEs were calculated with run_DE_analysis.pl from Trinity version 2.8.5 and log2 FC ≥ 1 and FDR < 0.05 were used as the cut off. RNA-seq track files in bigWig format were generated using bamCoverage of deeptools (v3.1.3) with RPKM normalization.
For WGBS analysis, the raw reads were aligned to both strands of the TAIR10 reference genome using BSMAP (v.2.74), allowing up to 2 mismatches and 1 best hit. Reads with more than 3 consecutives methylated CHH sites were removed, and the methylation level was calculated with the ratio of C/(C+T).
For BSPCR analysis, raw reads were aligned to both strands of the TAIR10 reference genome with BSMAP (v.2.90) allowing up to 2 mismatches and 1 best hit. After quality filtering, the methylation level of cytosines was calculated as the ratio of C/(C+T).
For ATAC-seq analysis, raw reads were adaptor-trimmed with trim_galore and mapped to the TAIR10 reference genome with Bowtie2 (-X 2000 -m 1). After removing duplicate reads and reads mapped to chloroplast and mitochondrial, ATAC-Seq open chromatin peaks of each replicate were called using MACS2 with parameters -p 0.01 --nomodel --shift -100 --extsize 200. Consensus peaks between replicates were identified with bedtools (version 2.26.0) intersect and differential accessible peaks were called with the R packge edgeR (version 3.30.0).
Assembly: tair10
Supplementary files format and content: .bw files are bigWig files of coverage tracks normalized with RPKM (for ChIP-seq and ATAC-seq), or methylation levels (for WGBS)
Supplementary files format and content: _methratio_type.txt files are tab-delimited text files containing methylation type and level at indicated chromosome positions.
Supplementary files format and content: .genes.results files are tab-delimited text files containing RNA-seq quantification data over genes and TEs.
Supplementary files format and content: .narrowPeak files are bed files containing position of called peaks for ChIP-seq.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: floral tissue

growth_protocol: Arabidopsis plants of the Columbia-0 (Col-0) ecotype were used in this study. All plants were grown under green house condition (16 h light/8 h dark, 22C). For ChIP-seq and ATAC-seq, floral tissues were collected from about one-month-old plants. For BS-PCR and WGBS, rossette leaves were were collected from about one-month-old plants. For RNA-seq, twelve-day-old whole seedlings grown on half MS plates were collected.

extract_protocol:
Genomic DNA for WGBS was extracted with DNeasy Plant Mini Kit (QIAGEN). Genomic DNA for BS-PCR-seq was extracted with CTAB method. RNA was extracted with Direct-zol RNA MiniPrep kit (Zymo Research).
ChIP-seq library preparation: 15 ml of unopened flower buds were collected for each ChIP and flash-frozen in liquid nitrogen. The flower tissue was ground to fine powder with Retsch homogenizer in liquid nitrogen and resuspended in nuclei extraction buffer (50 mM HEPES pH 8.0, 1 M sucrose, 5 mM KCl, 5 mM MgCl2, 0.6% Triton X-100, 0.4 mM PMSF, 5 mM benzamidine, cOmplete EDTA-free Protease Inhibitor Cocktail (Roche), 50uM MG132). For transgenic lines of MOM1-MYC and PIAL2-MYC, EGS was first added to resuspended lysate to 1.5 mM and the tissue lysate was incubated at room temperature for 10 min with rotation. Then the lysate was supplemented with formaldehyde at 1% and rotated at room temperature for another 10 min followed by adding glycine to stop crosslinking. For ChIP of all other proteins, crosslinking was performed by directly supplementing formaldehyde to 1% without adding EGS, then rotated at room temperature for 10 min followed by adding glycine to stop crosslinking. The crosslinked nuclei were isolated, lysed with Nuclei Lysis Buffer and diluted with ChIP Dilution Buffer. Then the lysate was sonicated for 22 min (30 s on/30s off) with Bioruptor Plus (Diagenode). After centrifugation, antibody for FLAG epitope (M2 monoclonal antibody, Sigma F1804, 10 ul per ChIP) or for MYC epitope (Cell Signaling, 71D10, 20 ul per ChIP) were added to the supernatant and incubated at 4 ℃ overnight with rotation. Then, Protein A and Protein G Dynabeads (Invitrogen) were added and incubated at 4 ℃ for 2 hours with rotation. After that, the beads were washed and eluted, and the eluted chromatin was reverse-crosslinked by adding 20 ul 5 M NaCl and incubating at 65 ℃ overnight followed by treatment of Proteinase K (Invitrogen) for 4 hours at 45 ℃. DNA was purified and precipitated with 3 M Sodium Acetate, GlycoBlue (Invitrogen) and ethanol at -20 ℃ overnight. After centrifugation, the precipitated DNA was washed with ice cold 70% ethanol, air dried and dissolved in 120 ul of H2O. ChIP-seq libraries were prepared with Ovation Ultra Low System V2 kit (NuGEN).
RNA-seq library preparation: Twelve-day old seedlings grown on half MS medium (Murashige and Skoog Basal Medium) were collected and flash-frozen in liquid nitrogen. RNA was extracted with Direct-zol RNA MiniPrep kit (Zymo Research) and 1ug of total RNA was used to prepare RNA-seq libraries with TruSeq Stranded mRNA kit (Illumina)
WGBS library preparation: Rosette leaves of about one-month-old Arabidopsis plants were collected for DNA extraction using DNeasy Plant Mini Kit (QIAGEN). 500 ng DNA was sheared with Covaris S2 (Covaris) into around 200bp at 4℃. The DNA fragments were used to perform end repair reaction using the Kapa Hyper Prep kit (Roche), and together with Illumina TruSeq DNA sgl Index Set A/B (Illumina) to perform adapter ligation. The ligation products were purified with AMPure beads (Beckman Coulter), and then converted with EpiTect Bisulfite kit (QIAGEN). The converted ligation products were used as templates, together with the primers from the Kapa Hyper Prep kit (Roche) and MyTaq Master mix (Bioline) to perform PCR. The PCR products were purified with AMPure beads (Beckman Coulter) and used for sequencing.
ATAC-seq library preparation: About 5 grams of unopened flower buds was collected and immediately transferred into ice-cold grinding buffer (300 mM sucrose, 20 mM Tris pH 8, 5 mM MgCl2, 5 mM KCl, 0.2% Triton X-100, 5 mM β-mercaptoethanol, and 35% glycerol). The samples were ground with Omni International General Laboratory Homogenizer on ice and then filtered through a two-layer Miracloth and a 40-µm nylon mesh Cell Strainer (Fisher). Samples were spin filtered for 10 min at 3,000 g, the supernatant was discarded, and the pellet was resuspended with 25 ml of grinding buffer using a Dounce homogenizer. The wash step was performed twice in total, and nuclei were resuspended in 0.5 ml of freezing buffer (50 mM Tris pH 8, 5 mM MgCl2, 20% glycerol, and 5 mM β-mercaptoethanol). Nuclei were subjected to a transposition reaction with Tn5 (Illumina). For the transposition reaction, 25 µl of 2x DMF (66 mM Tris-acetate pH 7.8, 132 mM K-Acetate, 20 mM Mg-Acetate, and 32% DMF) was mixed with 2.5 µl Tn5 and 22.5 µl nuclei suspension at 37°C for 30 min. Transposed DNA fragments were purified with ChIP DNA Clean & Concentrator Kit (Zymo). Libraries were prepared with Phusion High-Fidelity DNA Polymerase (NEB) in a system containing 12.5 µl 2x Phusion, 1.25 µl 10 mM Ad1 primer, 1.25 µl 10 mM Ad2 primer, 4 µl ddH2O, and 6 µl purified transposed DNA fragments.
BS-PCR library preparation: Rosette leaves of about one-month-old plants were collected and subject to DNA extraction with CTAB method followed by bisulfite DNA conversion using the EpiTect Bisulfite kit (QIAGEN) kit. Three regions of the FWA gene were amplified from the converted DNA with Pfu Turbo Cx (Agilent): Region 1 (chr4: 13038143-13038272), Region 2 (chr4: 13038356- 13038499) and Region3 (chr4: 13038568-13038695). Libraries were prepared with the purified PCR product by the Kapa DNA Hyper Kit (Roche) together with TruSeq DNA UD indexes for Illumina (Illumina) and were sequenced on Illumina iSeq 100 or HiSeq 4000 instruments.

value: floral tissue

value: one month old

value: MORC6-MYC in pial1/2 background

value: anti-myc (cell Signaling 71D10)


title: CH-Leg_1

description: Skin, replicate 1


title: AF22, Day 5, Factorial E1 [P16902_132]

description:
P16902_132
Gene_Counts.txt
Metadata_Ordered.csv

value: iPSC derived NES cells

value: Neuronal differentiation


title: ChIP-seq data of MORC6-myc in pial1/2 background, T2 line1


title: ChIP-seq data of MORC6-myc in pial1/2 background, T2 line2


title: PTEN_P_3

value: Prostate tumor

value: Pten pc -/-


title: ChIP-seq data of MORC6-myc in mom1-3 background, T2 line3

value: MORC6-MYC in mom1-3 background


title: PTEN_P_2

value: other:polysome-bound RNA


title: CH-Head_3

description: Skin, replicate 3

source_name: head skin

value: head skin


title: CTRL9II, Day 5, Factorial E8 [P16902_131]

description:
P16902_131
Gene_Counts.txt
Metadata_Ordered.csv

value: Male

value: Day 5


title: NSG15.D1.T

value: Triple negative breast cancer cells

value: tumor

value: Mus musculus

value: DMSO

value: rep  1


title: ChIP-seq data of MORC6-myc in mom1-3 background, T2 line2

value: floral tissue

value: one month old


title: CH-Head_2

description: Skin, replicate 2

value: Chenghua

value: Skin cells

value: female

value: 180 days old


title: CTRL9II, Day 5, Factorial E6 [P16902_129]

description:
P16902_129
Gene_Counts.txt
Metadata_Ordered.csv

value: iPSC derived NES cells

value: Neuronal differentiation


title: PTEN_P_1

value: Prostate tumor

value: Pten pc -/-

value: other:polysome-bound RNA


title: CTRL9II, Day 5, Factorial E7 [P16902_130]

description:
P16902_130
Gene_Counts.txt
Metadata_Ordered.csv

value: Male

value: Day 5


title: CH-Head_1

description: Skin, replicate 1

value: head skin


title: ChIP-seq data of MORC6-myc in mom1-3 background, T2 line1

value: MORC6-MYC in mom1-3 background

value: anti-myc (cell Signaling 71D10)


title: BM_T_3

source_name: Bone marrow

growth_protocol: For MDSCs polysome profiling analysis, bone marrow-differentiated MDSCs were collected and sorted in Cd11bhigh; Ly6Ghigh;Ly6Cint and Cd11bhigh; Ly6Gneg;Ly6Chigh after 5 days of differentiation. Sorted cells were plated and collected the day after for polysome profiling analysis after incubation with cycloheximide 100 mg/ml. Bone marrow from three mice was flushed from the femurs of C57BL/6 with RPMI 1640 medium. Red blood cells were lysed with ACK buffer (Gibco, Cat. A10492-01).

extract_protocol:
The cell pellet was resuspended and homogenized in polysome lysis buffer (30 mM Tris-HCl, pH 7.5, 100 mM NaCl, 30 mM MgCl2, 1% sodium deoxycolate, 1% Triton X-100, 100 mg ml−1 cycloheximide, 1 mM DTT and 30 U ml−1 RNasin).  After centrifugation at 12,000 rpm for 15 min at 4 °C, cytoplasmic extracts with equal amounts of RNA were loaded on a 15–50% sucrose gradient and centrifuged at 4 °C for 3 h 30 min at 39,000 r.p.m in a SW41Ti Beckman rotor by using a Beckman Coulter Ultracentrifuge Optima L-90K. Gradients were read at 254 nm by the BioLogic LP system (BioRad) and the fractions (1.0 ml each) were collected for subsequent RNA extraction to isolate the polysomal RNA fractions. Total and polysomal RNA fractions were incubated with 200 ug/ml proteinase K and SDS 1% for 1 h at 37 °C. RNA was extracted by phenol/chloroform 5:1 (Sigma-Aldrich; P1944) method, followed by overnight isopropanol precipitation at -80 °C, centrifugation at 14000 r.p.m. for 45 minutes and resuspension in 10 l of DEPC water. At the end of the procedure, DNAse digestion was carried out with Turbo DNase (Thermo Fisher Scientific) for 30 minutes at 37 °C and RNA purification was performed with RNA Clean and Concentrator kit (Zymo Research).
The purified RNA was measured by using Nanodrop and the quality was assessed using the Agilent 2100 Bioanalyzer. After random primer annealing, whole library preparation was performed using the Illumina TruSeq stranded total RNA with Ribozero Plus. Completed libraries were then submitted for sequencing. RNA-seq was constructed with barcodes to allow multiplexing of 12 samples per lane. Sequencing was carried out on NextSeq 500 Illumina platform.

value: Bone marrow

value: WT

value: total RNA


title: ChIP-seq data of MORC6-myc in Col-0 background, T2 line2

value: floral tissue

value: one month old

value: MORC6-MYC in Col-0 background


title: CTRL9II, Day 5, Factorial E5 [P16902_128]

description:
P16902_128
Gene_Counts.txt
Metadata_Ordered.csv


title: CTRL9II, Day 5, Factorial E4 [P16902_127]

description:
P16902_127
Gene_Counts.txt
Metadata_Ordered.csv


title: CH-Ear_2

description: Skin, replicate 2

source_name: ear skin

value: Chenghua

value: ear skin

value: Skin cells

value: female

value: 180 days old


title: CH-Ear_3

description: Skin, replicate 3


title: CH-Ear_1

description: Skin, replicate 1


title: CTRL9II, Day 5, Factorial E3 [P16902_126]

description:
P16902_126
Gene_Counts.txt
Metadata_Ordered.csv

value: iPSC derived NES cells

value: Neuronal differentiation


title: BM_T_2


title: BM_P_3

value: other:polysome-bound RNA


title: BM_P_2


title: CH-Back_3

description: Skin, replicate 3

value: back skin


title: CTRL9II, Day 5, Factorial E2 [P16902_125]

description:
P16902_125
Gene_Counts.txt
Metadata_Ordered.csv

value: Male

value: Day 5


title: BM_T_1

value: Bone marrow


title: ChIP-seq data of MORC6-myc in morc6 background, T2 line3

value: MORC6-MYC in morc6 background

value: anti-myc (cell Signaling 71D10)


title: ChIP-seq data of MORC6-myc in Col-0 background, T2 line1

value: floral tissue


title: ChIP-seq data of MORC6-myc in morc6 background, T2 line2

value: one month old


title: CTRL9II, Day 5, Factorial E1 [P16902_124]

description:
P16902_124
Gene_Counts.txt
Metadata_Ordered.csv


title: CH-Back_2

description: Skin, replicate 2


title: ASD12BI, Day 5, Factorial E8 [P16902_123]

description:
P16902_123
Gene_Counts.txt
Metadata_Ordered.csv


title: LY6G_T_6

source_name: MDSC

value: MDSC

value: WT

value: total RNA


title: CH-Back_1

description: Skin, replicate 1

value: Chenghua

value: Skin cells


title: ASD12BI, Day 5, Factorial E7 [P16902_122]

description:
P16902_122
Gene_Counts.txt
Metadata_Ordered.csv


title: CH-AB_3

description: Skin, replicate 3

source_name: abdomen skin

value: abdomen skin

value: female

value: 180 days old


title: WGBS data of suvh2/9, replicate 2

source_name: rosette leaf tissue

value: rosette leaf tissue

tag: ecotype

value: suvh2suvh9 double mutant


title: LY6G_P_6

value: other:polysome-bound RNA


title: WGBS data of suvh2/9, replicate 1


title: WGBS data of pial1/2 double mutant

value: pial1pial2 double mutant


title: ASD12BI, Day 5, Factorial E6 [P16902_121]

description:
P16902_121
Gene_Counts.txt
Metadata_Ordered.csv

value: Male

value: iPSC derived NES cells

value: Neuronal differentiation

value: Day 5


title: CH-AB_2

description: Skin, replicate 2


title: LY6G_T_3


title: ASD12BI, Day 5, Factorial E5 [P16902_120]

description:
P16902_120
Gene_Counts.txt
Metadata_Ordered.csv


title: LY6G_P_3


title: ASD12BI, Day 5, Factorial E4 [P16902_119]

description:
P16902_119
Gene_Counts.txt
Metadata_Ordered.csv


title: RNAseq of FC1242 MRTXR (replicate 1)

city: La Jolla

first: Herve

last: Tiriac

state: CA

address: 3855 Health Sciences Drive

department: Surgery

institute: UCSD Health

data_processing:
Quality control of the raw fastq files was performed using the software tool FastQC
Sequencing reads were trimmed with Trimmomatic and aligned using the STAR aligner
Read quantification was performed with RSEM
The R BioConductor packages edgeR and limma were used to implement the limma-voom method for differential expression analysis
lowly expressed genes—those not having counts per million (cpm) at least 3 in at least 3 of the samples—were filtered out and then trimmed mean of M-values (TMM)10 normalization was applied.
Assembly: GRCh38 for human and GRCm38 for mouse
Supplementary files format and content: SUIT2_RNAseq.txt (tab delimited txt file with nomalized counts)
Supplementary files format and content: FC1242_RNAseq.txt (tab delimited txt file with nomalized counts)

molecule: polyA RNA

growth_protocol: Parental human SUIT2 or mouse Fc1242 cells and MRTXR human SUIT2 or mouse Fc1242 cells were cultured in 10 cm dishes in duplicate.

extract_protocol:
Total RNA was extracted Nucleospin® RNA isolation kit (Macherey-Nagel GmbH & Co.) following the manufacturer’s instructions.
PolyA-enriched RNA libraries were prepared according to manufacturer's protocol

treatment_protocol: Cells were left untreated or treated with 60 nM MRTX1133 for 24 hours.

value: Pancreatic cancer cell

value: untreated


title: BM_P_1

value: Bone marrow

value: WT


title: ASD12BI, Day 5, Factorial E3 [P16902_118]

description:
P16902_118
Gene_Counts.txt
Metadata_Ordered.csv


title: RNAseq of FC1242 MRTXR (replicate 2)


title: ASD12BI, Day 5, Factorial E2 [P16902_117]

description:
P16902_117
Gene_Counts.txt
Metadata_Ordered.csv


title: RNAseq of FC1242 PT (replicate 2)


title: ASD12BI, Day 5, Factorial E1 [P16902_116]

description:
P16902_116
Gene_Counts.txt
Metadata_Ordered.csv


title: RNAseq of FC1242 PT (replicate 1)


title: LY6G_P_2

value: MDSC


title: CH-AB_1

description: Skin, replicate 1

value: Chenghua

value: Skin cells


title: LY6C_T_6

value: total RNA


title: LY6G_T_2


title: LY6C_P_6


title: LY6C_T_3


title: AF22, Day 5, Factorial E8 [P16902_115]

description:
P16902_115
Gene_Counts.txt
Metadata_Ordered.csv

value: Female


title: WGBS data of wild type (Col-0) plant as control for mom1-3 and suvh2/9, replicate 1

description: WGBS_WT_control_for_mom1_3suvh2suvh9_rep1

value: rosette leaf tissue

value: one month old


title: CXCR4+ / ITGβ1+_DMD_iPS1 RNA-seq

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

country: Germany

institute: Max-Planck-Institute for Molecular Biomedicine

data_processing:
illumina bcl2fastq (v2.19.1.403) used for basecalling and demultiplexing
Tophat (v2.1.1) used for alignment
HTSeq-count (v0.6.1) used for transcriptome abundance measurement
DESeq2(v1.20.0) used for differential gene expression analyses
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Skeletal Muscle progenitor cells

extract_protocol:
Cultured samples were directly lysis into RLT plus buffer and total RNA were extracted using RNeasy plus Micro Kit (Qiagen)
CXCR4+ / ITGβ1+/ DAPI- isolated through FACS sorting from 16 weeks organoids into RLT buffet supplemented with 10uM b-mercaptoethanol and RNA was harvested using the RNAeasy Micro Kit from Qiagen. Whole transcriptome Ovation Solo RNA seq Library Preparation Kit (TECAN, NuGEN) was used for the library preparation.
Cultured samples were directly lysis into RLT plus buffer and total RNA were extracted using RNeasy plus Micro Kit (Qiagen)
TruSeq Stranded Total RNA kit Gold (Illumina) or Whole transcriptome Ovation Solo RNA seq Library Preparation Kit (TECAN, NuGEN) was used for the library preparation of all samples

value: Skeletal Muscle progenitor cells

tag: differentiation stage

value: Becker iPSCs line


title: CXCR4+ / ITGβ1+_DMD_iPSCORE_65_1 RNA-seq

value: Duchenne iPSCs line


title: ChIP-seq data of Col-0 control with anti-Myc antibody, replicate 1

description:
ChIP_Col0rep1_forMORC6ChIPcompare
Control for the datasets of comparing MORC6-myc ChIP-seq in morc6 versus mom1-3 background.

value: floral tissue

tag: chip antibody

value: anti-myc (cell Signaling 71D10)


title: ChIP-seq data of Col-0 control with anti-Myc antibody, replicate 2

description:
ChIP_Col0rep2_forMORC6ChIPcompare
Control for the datasets of comparing MORC6-myc ChIP-seq in morc6 versus mom1-3 background.


title: X9c

city: Frankfurt

first: Xinlai

last: Cheng

address: Max-von-Laue-Strasse 15. R. 3.652

department: Pharmaceutical Chemistry

institute: Goethe university Frankfurt

data_processing: RNA seq was performed by Azenta

source_name: K562 cell line

growth_protocol: K562 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: RNA was extracted with Trizol reagent,  Quality control and sequencing were performed by Azenta

treatment_protocol:
Transfected with Cas9FCPF with/without sgRNA
1 µM JQ1 or 1 µM JQ1-FCPF

value: K562 cell line

value: lymphoblast cells


title: ChIP-seq data of MORC6-myc in morc6 background, T2 line1

value: MORC6-MYC in morc6 background


title: WGBS data of mom1-3, replicate 1


title: AF22, Day 5, Factorial E7 [P16902_114]

description:
P16902_114
Gene_Counts.txt
Metadata_Ordered.csv

value: iPSC derived NES cells

value: Neuronal differentiation

value: Day 5


title: WGBS data of mom1-3, replicate 2


title: WGBS data of wild type (Col-0) plant as control for mom1-3 and suvh2/9, replicate 2

description: WGBS_WT_control_for_mom1_3suvh2suvh9_rep2


title: LY6C_P_3

value: MDSC

value: WT

value: other:polysome-bound RNA


title: X9b


title: CXCR4+ / ITGβ1+_BMD_iPS1 RNA-seq


title: AF22, Day 5, Factorial E6 [P16902_113]

description:
P16902_113
Gene_Counts.txt
Metadata_Ordered.csv

value: Female


title: LY6C_T_2

value: total RNA


title: CXCR4+ / ITGβ1+_CB_CD34+ RNA-seq

value: Wild type iPSCs line


title: LY6C_P_2


title: X9a


title: X8c


title: iDF culture genomic DNA input for ChIP-seq

first: Dan

last: Filipescu

state: New York

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

description: H3K27ac ChIP in immortalized dermal fibroblasts fibroblasts 30 minutes after serum stimulation

data_processing:
ATAC-seq: Read pairs were merged and adapters removed using NGmerge v.0.3, followed by alignment to the mm10 assembly with bowtie2 v.2.4.1. Low-quality (MAPQ < 30), mitochondrial genome and duplicated reads were removed using samtools v.1.9 and genome coverage calculation for visualization purposes on the UCSC genome browser was performed using deepTools v.3.5.1 excluding blacklisted regions.
ChIP-seq: Adapters were trimmed with Trimmomatic v.0.36. Alignment, read filtering and genome coverage calculation were performed as for ATAC-seq.
CUT&RUN: Reads were processed as for ATAC-seq.
Assembly: Gencode M25 (GRCm38.p6)
Supplementary files format and content: fastq - raw Illumina reads. BigWig - aligned reads pileup produced with deeptools

source_name: Serum-starved and stimulated cultured iDF

extract_protocol:
~ 8 × 10^6 cultured iDFs after 30min serum stimulation were single-cross-linked and processed for ChIP as described in Fontanals-Cirera B, Hasson D, Vardabasso C, Di Micco R, Agrawal P, Chowdhury A, Gantz M, de Pablos-Aragoneses A, Morgenstern A, Wu P, Filipescu D, Valle-Garcia D, Darvishian F, Roe JS, Davies MA, Vakoc CR, Hernando E, Bernstein E. Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene. Mol Cell. 2017 Nov 16;68(4):731-744.e9. doi: 10.1016/j.molcel.2017.11.004. PMID: 29149598; PMCID: PMC5993436.
Libraries were constructed as described in Fontanals-Cirera B, Hasson D, Vardabasso C, Di Micco R, Agrawal P, Chowdhury A, Gantz M, de Pablos-Aragoneses A, Morgenstern A, Wu P, Filipescu D, Valle-Garcia D, Darvishian F, Roe JS, Davies MA, Vakoc CR, Hernando E, Bernstein E. Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene. Mol Cell. 2017 Nov 16;68(4):731-744.e9. doi: 10.1016/j.molcel.2017.11.004. PMID: 29149598; PMCID: PMC5993436.

value: WT and dKO combined

tag: antibody


title: AF22, Day 5, Factorial E3 [P16902_111]

description:
P16902_111
Gene_Counts.txt
Metadata_Ordered.csv


title: AF22, Day 5, Factorial E2 [P16902_110]

description:
P16902_110
Gene_Counts.txt
Metadata_Ordered.csv


title: X8b


title: Org_16wk Rep1 RNA-seq

source_name: iPSC-derived organoid

extract_protocol:
Cultured samples were directly lysis into RLT plus buffer and total RNA were extracted using RNeasy plus Micro Kit (Qiagen)
Organoids were flash frozen on dry ice, and RNA was harvested using the RNAeasy Micro Kit from Qiagen. Whole transcriptome Illumina TruSeq Stranded Total RNA Library Prep Kit Gold (Illumina) was used for the constuction of libraries
Cultured samples were directly lysis into RLT plus buffer and total RNA were extracted using RNeasy plus Micro Kit (Qiagen)
TruSeq Stranded Total RNA kit Gold (Illumina) or Whole transcriptome Ovation Solo RNA seq Library Preparation Kit (TECAN, NuGEN) was used for the library preparation of all samples

value: iPSC-derived organoid


title: X8a


title: AF22, Day 5, Factorial E1 [P16902_109]

description:
P16902_109
Gene_Counts.txt
Metadata_Ordered.csv


title: H3K27ac ChIP-seq in iDF WT cells

value: dKO

value: H3K27ac, 13-0045, Epicypher


title: H3K27ac ChIP-seq in iDF dKO cells


title: Organoids scRNA-seq

data_processing:
illumina bcl2fastq (v2.19.1.403) used for basecalling and demultiplexing
UMI-tools (v1.0.0) used for cell barcode and UMI counting
STAR (v2.7.1a) used for human reference genome (hg38) alignment
Subread featureCounts (v1.6.4) used for UMI quantification
Genome_build: hg38
Supplementary_files_format_and_content: tsv files include UMI counts for each cell barcode and genes

source_name: iPSC-derived skeletal muscle organoid

extract_protocol:
Organoid 12 weeks post differentiation dissociated into single cells upon incubation for 1hr with solution containing papain and EDTA. Upon dissociation, we estimated the cell number and viability; then cells resuspended on solution containing 0.5% BSA in PBS to reach concentration of 390 cells per ul. The cDNA  library was prepared using the Chromium Single Cell 3′ Reagent Kits (v3): Single Cell 3′ Library & Gel Bead Kit v3 (PN-1000075), Single Cell B Chip Kit (PN-1000073) and i7 Multiplex Kit (PN-120262) (10x Genomics).
RNA libraries were prepared for sequencing according to the manufacturers' instructions (10X Genomics).

value: iPSC-derived skeletal muscle organoid

value: 12 weeks


title: CTRL9II, Day 5, Factorial E8 [P16902_108]

description:
P16902_108
Gene_Counts.txt
Metadata_Ordered.csv

value: Male


title: X5c

value: K562 cell line

value: lymphoblast cells


title: Mouse #19331 spatial transcriptomics

description:
clustered_spatial_object.RData
annotated_spatial_object.RData

data_processing:
library strategy: Spatial transcriptomics
Sequencing data was mapped using spaceranger v2.0.0 using the mm10‑2020‑A transcriptome (10X Genomics) to generate spatial gene expression matrices.
Data was further processed according to the Seurat spatial vignette (https://satijalab.org/seurat/articles/spatial_vignette.html). We integrated data normalized with SCTransform v2 across the two ST samples.
Clusters were determined using a variety of resolutions and annotated using top cluster-specific genes conserved between WT and dKO cells.
Assembly: mm10-2020-A transcriptome
Supplementary files format and content: One h5 file including filtered features, one file for scale factors, one high resolution tissue image and a list of tissue positions used as input for Seurat, for each sample. One RData Seurat object containing the integrated cells across 2 samples, final clustering up to removal of clusters representing low-quality cells. One RData Seurat object containing the annotated clusters retained for further analysis.

source_name: Spatial transcriptomics of melanoma at 35 days post induction

extract_protocol:
Tissue was prepared according to 10X Genomics Visium V1 Slide - 3' Spatial guidelines. Resected BRAFV600E/PTEN-deficient melanomas were first frozen in a bath of isopentane and liquid nitrogen, stored at –80°C in a sealed container, then embedded in OCT compound. Tissue was sectioned at temperatures of -20°C for the cryostat chamber and -10°C for the specimen head, at 10 μm thickness. An optimal permeabilization time of 18 min was determined using the Visium Spatial Tissue Optimization Kit (10x Genomics).
Libraries were constructed according to the manufacturer’s guidelines for Visium Spatial (10X Genomics) followed by sequencing on a S1 NovaSeq chip (Illumina Inc.). Qubit 3 (Fisher Scientific) and 2100 Bioanalyzer (Agilent) were used for quality check of cDNA.

value: F

value: Melanoma tissue section


title: Mouse #19323 scRNA-seq

description:
19323_melanoma
scRNA-seq of melanoma single cell suspension at 35 days post induction
clustered_seurat_object.RData
annotated_seurat_object.RData

data_processing:
The output BAM file from sequencing was processed through cellranger software v7.0.1 (10X Genomics). Filtered gene-barcode matrices generated using the mm10-2020-A transcriptome (10X Genomics) were used for downstream analysis using Seurat 4.0.
Low-quality cells (less than 500 UMIs or 250 detected genes, or at least 20% mitochondrial transcripts) were removed
For each sample, data was normalized with SCTransform, regressing out cell cycle scores and mitochondrial ratio
Datasets were integrated using reciprocal PCA on the first 50 principal components with an alignment strength of 10.
Clusters were determined using a variety of resolutions and annotated using top cluster-specific genes conserved between WT and dKO cells, as well as known lineage genes for expected cell types. At final resolution (0.6), 3 clusters with a low number of significant genes, also displaying a low nuclear transcriptome complexity, were considered to represent low quality cells and were discarded. The least abundant cluster, characterized by genes of multiple lineages, likely contained doublets and was also discarded.
Assembly: mm10-2020-A transcriptome
Supplementary files format and content: Two tab-delimited text and one matrix file including raw counts values of each gene for each sample, used as input for Seurat. One RData Seurat object containing the integrated cells of all 6 samples, final clustering up to to removal of clusters representing low-quality cells. One RData Seurat object containing the annotated clusters retained for further analysis.

source_name: Melanoma single cell suspension

extract_protocol:
Resected BRAFV600E/PTEN-deficient melanomas were cut into 1-2mm fragments and digested using the Tumor Dissociation Kit, mouse (Miltenyi) in DMEM using the soft/medium protocol according to manufacturer’s instructions. RBC lysis was performed in ACK buffer for 5 minutes on ice, followed by a wash in 1X DPBS containing 0.04% BSA. We applied droplet-based scRNA-seq (Chromium, 10X Genomics) to single-cell suspensions of BRAFV600E/PTEN-deficient melanomas from 3 WT and 3 dKO mice. 6 × 10^3 cells were loaded per well for each of the 6 samples, partitioning and library preparation were performed according to manufacturer’s protocol for the Chromium 3’ Gene Expression v3 kit.
Cells were processed according to Chromium 3’ Gene Expression V3 Kit (10X Genomics) using manufacturer’s guidelines followed by sequencing on a S1 NovaSeq chip (Illumina Inc.). Qubit 3 (Fisher Scientific) and 2100 Bioanalyzer (Agilent) were used for quality check of cDNA.


title: Mouse #19333 spatial transcriptomics


title: X5a


title: CAF culture from mouse # 66391 macroH2A1 CUT&RUN 30 minutes after serum stimulation

description: MacroH2A1 CUT&RUN in cultured cancer-associated fibroblasts prior to serum stimulation

data_processing:
ATAC-seq: Read pairs were merged and adapters removed using NGmerge v.0.3, followed by alignment to the mm10 assembly with bowtie2 v.2.4.1. Low-quality (MAPQ < 30), mitochondrial genome and duplicated reads were removed using samtools v.1.9 and genome coverage calculation for visualization purposes on the UCSC genome browser was performed using deepTools v.3.5.1 excluding blacklisted regions.
ChIP-seq: Adapters were trimmed with Trimmomatic v.0.36. Alignment, read filtering and genome coverage calculation were performed as for ATAC-seq.
CUT&RUN: Reads were processed as for ATAC-seq.
Assembly: Gencode M25 (GRCm38.p6)
Supplementary files format and content: fastq - raw Illumina reads. BigWig - aligned reads pileup produced with deeptools
Library strategy: CUT&RUN

source_name: Serum-starved and stimulated cultured CAF

extract_protocol:
2 × 10^5 short-term cultured CAFs prior to or after 30min serum stimulation were processed for CUT&RUN as described in Skene PJ, Henikoff JG, Henikoff S. Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat Protoc. 2018 May;13(5):1006-1019. doi: 10.1038/nprot.2018.015. Epub 2018 Apr 12. PMID: 29651053. Cells were permeabilized with 0.0085% digitonin, incubated with antibody, and DNA cleaved with the CUTANA pAG-MNase (Epicypher).
Released DNA was processed using the NEBNext Ultra II Library Preparation Kit for Illumina (NEB), including a 14-cycle amplification step.

value: macroH2A1, ab37264, Abcam


title: X5b


title: AF22, Day 5, Factorial E5 [P16902_112]

description:
P16902_112
Gene_Counts.txt
Metadata_Ordered.csv

value: iPSC derived NES cells

value: Neuronal differentiation

value: Day 5


title: CTRL9II, Day 5, Factorial E7 [P16902_107]

description:
P16902_107
Gene_Counts.txt
Metadata_Ordered.csv


title: X3c


title: CAF culture from mouse # 66391 macroH2A1 CUT&RUN prior to serum stimulation

description: MacroH2A1 CUT&RUN in cultured cancer-associated fibroblasts 30 minutes after serum stimulation

source_name: Serum-starved cultured CAF

value: WT


title: Mouse #19332 scRNA-seq

description:
19332_melanoma
scRNA-seq of melanoma single cell suspension at 35 days post induction
clustered_seurat_object.RData
annotated_seurat_object.RData


title: CAF culture genomic DNA input for ChIP-seq

description: Input control for H3K27ac ChIP in cultured cancer-associated fibroblasts 30 minutes after serum stimulation

extract_protocol:
~ 8 × 10^6 cultured CAFs after 30min serum stimulation were single-cross-linked and processed for ChIP as described in Fontanals-Cirera B, Hasson D, Vardabasso C, Di Micco R, Agrawal P, Chowdhury A, Gantz M, de Pablos-Aragoneses A, Morgenstern A, Wu P, Filipescu D, Valle-Garcia D, Darvishian F, Roe JS, Davies MA, Vakoc CR, Hernando E, Bernstein E. Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene. Mol Cell. 2017 Nov 16;68(4):731-744.e9. doi: 10.1016/j.molcel.2017.11.004. PMID: 29149598; PMCID: PMC5993436.
Libraries were constructed as described in Fontanals-Cirera B, Hasson D, Vardabasso C, Di Micco R, Agrawal P, Chowdhury A, Gantz M, de Pablos-Aragoneses A, Morgenstern A, Wu P, Filipescu D, Valle-Garcia D, Darvishian F, Roe JS, Davies MA, Vakoc CR, Hernando E, Bernstein E. Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene. Mol Cell. 2017 Nov 16;68(4):731-744.e9. doi: 10.1016/j.molcel.2017.11.004. PMID: 29149598; PMCID: PMC5993436.


title: X3b


title: CTRL9II, Day 5, Factorial E5 [P16902_105]

description:
P16902_105
Gene_Counts.txt
Metadata_Ordered.csv


title: Org_16wk Rep2 RNA-seq

value: Wild type iPSCs line


title: CAF culture from mouse # 66383 H3K27ac ChIP-seq

description: H3K27ac ChIP in cultured cancer-associated fibroblasts 30 minutes after serum stimulation


title: Mouse #66675 scRNA-seq

description:
66675_melanoma
scRNA-seq of melanoma single cell suspension at 35 days post induction
clustered_seurat_object.RData
annotated_seurat_object.RData


title: X3a


title: CTRL9II, Day 5, Factorial E4 [P16902_104]

description:
P16902_104
Gene_Counts.txt
Metadata_Ordered.csv


title: CTRL9II, Day 5, Factorial E3 [P16902_103]

description:
P16902_103
Gene_Counts.txt
Metadata_Ordered.csv


title: Mouse #66208 scRNA-seq

description:
66208_melanoma
scRNA-seq of melanoma single cell suspension at 35 days post induction
clustered_seurat_object.RData
annotated_seurat_object.RData


title: Mouse #66691 scRNA-seq

description:
66691_melanoma
scRNA-seq of melanoma single cell suspension at 35 days post induction
clustered_seurat_object.RData
annotated_seurat_object.RData


title: CAF culture from mouse # 66391 IgG background for CUT&RUN

description: Control for macroH2A1 CUT&RUN in cultured cancer-associated fibroblasts

source_name: Mix of serum-starved +/- stimulated cultured CAF

value: Normal rabbit IgG


title: CTRL9II, Day 5, Factorial E1 [P16902_101]

description:
P16902_101
Gene_Counts.txt
Metadata_Ordered.csv


title: X6c

value: NT


title: CTRL9II, Day 5, Factorial E2 [P16902_102]

description:
P16902_102
Gene_Counts.txt
Metadata_Ordered.csv


title: X6b


title: Mouse #66193 scRNA-seq

description:
66193_melanoma
scRNA-seq of melanoma single cell suspension at 35 days post induction
clustered_seurat_object.RData
annotated_seurat_object.RData


title: CTRL9II, Day 5, Factorial E6 [P16902_106]

description:
P16902_106
Gene_Counts.txt
Metadata_Ordered.csv


title: Mouse # 66623 CAF ATAC-seq

description: ATAC-seq of cancer-associated fibroblasts sorted from melanoma tissue at 50 days post induction

source_name: Sorted CAF

extract_protocol:
5 × 10^4 sorted CAFs were processed for ATAC-seq as described in PMID: 26083756: Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature. 2015 Jul 23;523(7561):486-90. doi:10.1038/nature14590. Epub 2015 Jun 17.
Libraries were constructed as described in PMID: 26083756: Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature. 2015 Jul 23;523(7561):486-90. doi:10.1038/nature14590. Epub 2015 Jun 17. Libraries were subjected to double-sided size selection using SPRIselect beads (Beckman Coulter) at ratios of 0.55 and 1.2X prior to sequencing.

value: dKO


title: Mouse # 66626 CAF ATAC-seq


title: X6a


title: Mouse # 66620 CAF ATAC-seq


title: NEJ677_D

city: Memphis

first: Xiang

state: TN

address: 262 Danny Thomas Place

department: Computational Biology

institute: St.Jude Children's Research Hospital

description: Frozen section from high-risk hepatoblastoma-like genetic model was processed by Visium Spatial Gene expression Kit-10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Space Ranger software 1.3 ( https://support.10xgenomics.com/spatial-gene-expression/software/release-notes/1-3)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: comma-separated values and JPG
Library strategy: Spatial Transcriptomics

source_name: hepatoblastoma

extract_protocol:
Tumor tissue/normal liver tissue from mouse model harvested and frozen immediately.
10µm frozen section was cut using NX70 cryostat from Thermo Scientific. The sections were placed into visium gene expression slide, stored overnight before moving into cDNA step. The slide stained with H&E, imaged using Axio Scan- Zeiss. The cDNA and Library was generated following Visium Spatial Gene expression Kit from 10X Genomics.
Visium Spatial Gene expression Kit from 10X Genomics.

value: hepatoblastoma

tag: tissue preparation

value: Frozen section of mouse Liver


title: RME845

city: Singapore

first: Chin Yan

last: Lim

state: Singapore

address: 8A Biomedical Grove

country: Singapore

institute: A*STAR Skin Research Labs

data_processing:
Sequence quality was analyzed FASTQC
Reads were mapped to the hg19 reference genome using bowtie2
Counts per gene was obtained using featureCounts
Read counts for differential gene expression analysis was normalized using DESeq2 Pipeline
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: NT,Differentiated,single-end

extract_protocol:
Total RNA was subjected to polyadenylation (polyA) selection using the Poly(A) Purist MAG kit
100ng of the polyA selected RNA was used for library preparation using the NEBNext® Ultra™ II Directional RNA Library Prep kit (New England Biolabs, Cat no. E7760L)

tag: cell type

value: Keratinocyte

value: keratinocyte differentiation

value: Differentiated


title: NEJ654_D


title: iDF dKO serum 30 min replicate 2 RNA-seq

description: RNA-seq of cultured immortalized dermal fibroblasts prior to and after serum stimulation

data_processing:
Raw reads were quasi-mapped to the Gencode M25 (GRCm38.p6) gene set using salmon v.1.2.1 (Patro et al., 2017).
Assembly: Gencode M25 (GRCm38.p6)
Supplementary files format and content: fastq - raw Illumina reads; sf - table of gene expression counts and TPM generated by salmon

source_name: Cultured immortalized dermal fibroblasts

growth_protocol: DMEM, 10% FBS, 1X Pen/Strep, 37ºC in 5% CO2

extract_protocol: Cultured cells were lysed directly in their culture vessel in QIAzol. After addition of chloroform (Sigma) and centrifugation, RNA was isolated from the aqueous phase using an RNEasy Micro kit (QIAGEN).

treatment_protocol: Cells were grown to confluence, then starved in 0.5% serum for 24h, then treated with 10% serum for 30 minutes

value: M


title: RA FLSs, SCHA1

city: Guangzhou

first: lin

last: wei

state: Guangdong

address: No. 58, Zhongshan Second Road

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and iscurrently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. Genes with a P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes gene expression counts of each sample

source_name: synovial tissues

extract_protocol:
Total RNA was isolated by TRIzol reagent. RNA degradation and contamination was monitored on 1% agarose gels. Total RNA was quantified using the NanoPhotometer spectrophotometer.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. 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. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H - ). 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. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: disease state

value: rheumatoid arthritis

value: synovial tissues

value: rheumatoid fibroblast-like synoviocytes

value: SCH


title: NEJ687_C


title: RA FLSs, SCHA2

tag: genotype


title: RME842

tag: treatment


title: RA FLSs, SCHA3

tag: tissue


title: CAF culture from mouse # 66391 H3K27ac ChIP-seq

value: H3K27ac, 13-0045, Epicypher


title: iDF dKO serum 30 min replicate 1 RNA-seq


title: NEJ723_A


title: Mouse # 66624 CAF ATAC-seq


title: NEJ638_C


title: RA FLSs, DMSO3

value: DMSO


title: iDF dKO serum 0 min replicate 2 RNA-seq

treatment_protocol: Cells were grown to confluence, then starved in 0.5% serum for 24h


title: RA FLSs, DMSO2

value: WT


title: RME840

source_name: NT,Confluent,single-end

tag: cell line

value: Confluent


title: RA FLSs, DMSO1


title: WT_CNS_1_TCR

city: Boston

first: Linglin

last: Huang

state: MA

address: 60 Fenwood Road, HBTM 10016F

department: Neurology

institute: Brigham and Women’s Hospital

data_processing:
Base-calling was performed using NovaSeq Control Software v1.7.5 (RTA v3.4.4).
The cellrange_workflow in Cumulus (https://cumulus.readthedocs.io/en/stable/cellranger/index.html) was used to preprocess the data. Specifically, 10x Genomics CellRanger 6.0.1 was for BCL to fastq demultiplexing, read alignment (mm10 reference genome for RNA-seq reads and cellranger GRCm38_vdj_v5.0.0 for TCR-seq reads), RNA and hashtag UMI count matrix computation, TCR config identification, and empty droplets filtering.
Cell quality control, doublet detection, tissue origin correction and cell annotation were performed as described in the manuscript. Cleaned and annotated data are available as SingleCellExperiment R objects.
Assembly: mm10
Supplementary files format and content: tumor_rna_cleaned.rds holds a Seurat R object containing RNA-seq expression as a matrix in the RNA assay, cell hashtag data as a matrix in the HTO assay, and cell annotation (including TCR information) in meta.data.
Supplementary files format and content: eae_rna_cleaned.rds holds a Seurat R object containing RNA-seq expression as a matrix in the RNA assay, cell hashtag data as a matrix in the HTO assay, and cell annotation (including TCR information) in meta.data.

source_name: CNS

growth_protocol: C57BL/6J wildtype and B6.129S4-Pglyrp1tm1.1Lky/J mice were obtained from the Jackson Laboratory.

extract_protocol:
For the isolation of TILs, tumor tissue was dissociated with collagenase D (2.5mg/ml) at 37 degrees Celsius for 20 min, followed by centrifugation through a discontinuous Percoll gradient (GE Healthcare). 1,000 living CD8+ T cells (CD45+ TCRß+ CD8) were FACS-sorted immediately into TCL buffer (QIAGEN) supplemented with 1% ß-mercaptoethanol (Sigma Aldrich). To obtain cells from draining lymph nodes, lymph nodes were mashed through a 40 µm strainer. In the EAE experiment, mice (8-12 weeks old) sex-matched were immunized subcutaneously into the flanks with an emulsion containing the MOG35-55 peptide (100µg/mouse, Genemed Synthesis) and M. tuberculosis H37Ra extract (5mg/ml, Becton Dickinson) in CFA (200ul/mouse, Becton Dickinson). Pertussis toxin (100ng/mouse, List Biological Laboratories) was administered intravenously on days 0 and 2. For the isolation of lymphocytes from EAE mice, mice were sacrificed, and perfusion was performed intracardially with PBS. To obtain cells from  the CNS, the forebrain and cerebellum were dissected and together with the spinal cord were flushed out with PBS using hydrostatic pressure. CNS tissue was cut into small pieces with a razor blade and digested with collagenase D (2.5mg/ml, Roche Diagnostics) at 37 degrees Celsius for 20 min. Mononuclear cells were isolated by passing the tissue through a 40 µm strainer, followed by centrifugation through a Percoll gradient (37% and 70%). Lastly, the mononuclear cells were obtained from the interphase, washed, and used for further analysis.
The cell populations of interest were sorted by FACS for sequencing. For cell hashing, the cells were incubated for 30 min on ice in flow buffer with the TotalSeqTM-antibody pool (Biolegend) at 1:1000 final dilution for each antibody, followed by a total of three washes with flow buffer. Following the manufacturer’s instructions (10x Genomics), the samples were then separated into droplet emulsions using the Chromium Single Cell 5' V2 Solution. The library preparations of the scRNA-seq, including TCR-seq and 5' feature barcoding libraries were performed according to manufacturer’s instructions (10x Genomics) using the NextGem 5' v2 Dual Index protocol. Libraries were pooled to 4nM.

treatment_protocol: MC38-OVA (0.5x10^6) cells  were subcutaneously injected into the right flank of mice.

value: CNS

value: CD45+ leukocytes

value: induced EAE


title: RME843


title: NEJ634_A

last: Chen

value: hepatoblastoma


title: MCTX-Control-3_MeRIP

city: Shanghai

first: Xiaoyang

last: Dou

address: 320 Yue Yang Road

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

data_processing:
Raw reads were trimmed with Trimmomatic-0.39, then aligned to human genome and transcriptome (hg38) using HISAT (version 2.1.0) with ‘--rna-strandness RF’ parameters.
Mapped reads were separated by strands with samtools (version 1.9) and m6A peaks on each strand were called using MACS (version 2) with parameter ‘-nomodel, --keep-dup 5, -g 2.052e9, --tsize 60 -extsize 150’ separately.
Assembly: hg38
Supplementary files format and content: Tab-delimited peak locations together with peak summit, pvalue and qvalue reported by MACS2 for each sample.

source_name: human post-mortem motor cortex

growth_protocol: iPSCs were maintained in mTeSR media on Matrigel, following the Cedars-Sinai Standard Operating Procedure (SOP, https://www.cedars-sinai.edu/content/dam/cedars-sinai/research/documents/biomanufacturing/complete-ipsc-culturing-protocol-rev-4-2020.pdf). iPSCs were differentiated into spinal neurons using the direct induced motor neuron protocol. All cells were maintained at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from cells using TRIzol (Thermo Fisher). Ribosomal RNAs were further depleted from total RNA by RiboMinus Eukaryote Kit v2 (Thermo Fisher Scientific). m6A-immunoprecipitation (m6A-IP) was performed using the EpiMark N6-Methyladenosine Enrichment Kit (New England Biolabs) following the manufacturer’s protocols.
Library preparation was performed using the SMARTer Stranded Total RNA-Seq Kit v2 (Takara).

value: human post-mortem motor cortex

value: Non-neurologic control


title: RME837

value: Keratinocyte

value: keratinocyte differentiation


title: iDF WT serum 30 min replicate 2 RNA-seq

tag: Sex

value: M


title: iDF WT serum 30 min replicate 1 RNA-seq


title: iDF dKO serum 0 min replicate 1 RNA-seq

value: dKO


title: WT_CNS_1_FBC


title: MCTX-Control-2_MeRIP


title: RME836

tag: time


title: iDF WT serum 0 min replicate 2 RNA-seq


title: MCTX-C9-ALS-3_MeRIP

value: fALS


title: RME833

value: Subconfluent


title: iDF WT serum 0 min replicate 1 RNA-seq


title: RME841

value: Differentiated


title: KO_CNS_1_TCR

value: Pglyrp1 KO


title: KO_CNS_1_FBC


title: MCTX-Control-1_MeRIP


title: Mouse # 66559 CAF RNA-seq

description: RNA-seq of cancer-associated fibroblasts sorted from melanoma tissue at 50 days post induction

source_name: Sorted cancer-associated fibroblasts

extract_protocol: Sorted cells were centrifuged and resuspended in QIAzol. After addition of chloroform (Sigma) and centrifugation, RNA was isolated from the aqueous phase using an RNEasy Micro kit (QIAGEN).

value: F


title: WT_CNS_1_GEX

value: WT


title: RME832


title: KO_CNS_1_GEX


title: RME838

value: Confluent


title: Mouse # 66558 CAF RNA-seq


title: MCTX-C9-ALS-1_MeRIP


title: MCTX-C9-ALS-2_MeRIP

value: fALS/FTD


title: WT_LN_2_TCR

source_name: lymph nodes

value: lymph nodes

value: CD45+ leukocytes

value: Inplanted MC38-OVA tumors


title: RME831


title: MCTX-Control-3_Input

value: human post-mortem motor cortex


title: Mouse # 66555 CAF RNA-seq


title: RME830

value: NT


title: WT_LN_2_FBC


title: RME835

source_name: NT,Subconfluent,single-end

value: Keratinocyte


title: Mouse # 66554 CAF RNA-seq


title: MCTX-Control-2_Input

value: Non-neurologic control


title: RME828

value: keratinocyte differentiation


title: MCTX-Control-1_Input


title: RME827


title: Mouse # 66566 CAF RNA-seq


title: WT_LN_1_TCR


title: Mouse # 66565 CAF RNA-seq


title: WT_LN_2_GEX


title: MCTX-C9-ALS-2_Input


title: RME826


title: WT_LN_1_FBC


title: Mouse # 66561 CAF RNA-seq

value: M


title: Mouse # 66562 CAF RNA-seq


title: RME825


title: RME823


title: WT_LN_1_GEX


title: MCTX-C9-ALS-3_Input

value: fALS


title: Mouse # 65678 tumor-infiltrating CD8 RNA-seq

description: RNA-seq of CD8+ T cells sorted from melanoma tissue at 50 days post induction

source_name: Sorted CD8+ T cells

value: dKO


title: KO_LN_2_TCR


title: RME821


title: Mouse # 65677 tumor-infiltrating CD8 RNA-seq


title: RME822


title: iPSN-Ctrl-4_MeRIP

source_name: iPSC-derived neuron

value: iPSC-derived neuron


title: KO_LN_2_GEX

value: Pglyrp1 KO


title: iPSN-Ctrl-3_MeRIP


title: Mouse # 65675 tumor-infiltrating CD8 RNA-seq


title: iPSN-Ctrl-2_MeRIP


title: RME820

value: Subconfluent


title: KO_LN_1_TCR


title: Mouse # 65674 tumor-infiltrating CD8 RNA-seq


title: iPSN-Ctrl-1_MeRIP


title: KO_LN_1_FBC


title: Mouse # 65668 tumor-infiltrating CD8 RNA-seq

value: WT


title: MCTX-C9-ALS-1_Input


title: iPSN-C9-3_MeRIP

value: patient-derived


title: Mouse # 65666 tumor-infiltrating CD8 RNA-seq


title: iPSN-C9-2_MeRIP


title: RME818


title: iPSN-C9-4_MeRIP


title: RME816


title: KO_LN_1_GEX


title: WT_Tum_2_FBC

source_name: MC38-OVA colon carcinoma

value: MC38-OVA colon carcinoma


title: Mouse # 65662 tumor-infiltrating CD8 RNA-seq

value: F


title: KO_LN_2_FBC

value: lymph nodes

value: CD45+ leukocytes


title: ATAC_237_O5_luminal-rep1

city: Duarte

first: Parijat

last: Senapati

address: 1500 E. Duarte Rd

institute: Beckman Research Institute, City of Hope

data_processing:
Raw sequencing reads were trimmed using Trim Galore (https://github.com/FelixKrueger/TrimGalore) (version 0.4.5) to remove adapters.
Trimmed reads were aligned to the human reference genome (hg19) using bowtie with the --best -k 1 -X 2000 --mm --chunkmbs 1024 parameters.
Unmapped reads, mates as well as low quality reads and secondary alignments were removed using samtools. PCR duplicates were identified using Picard and removed using samtools. The reads were shifted by 4 bases on the sense strand and 5 bases on the anti-sense strand to account for Tn5 bias. Reads from technical replicates were pooled to generate pseudoreplicates. Peaks were called using MACS2 version 2.1.1.20160309 using -p 0.01 --nomodel --shift -37 --extsize 73 --SPMR --keep-dup all --call-summits as parameters. Peak calls from technical replicates and pseudo-replicates were compared using IDR to get the most conservative set of peaks for each sample.
Genome_build: hg19
Supplementary_files_format_and_content: Narrowpeak format

source_name: Mammary luminal epithelial cells

growth_protocol: Cells were grown in M87A medium with cholera toxin and oxytocin at 0.5 ng/ml and 0.1nM, respectively. Cells were stained with anti-human CD133-PE (Biolegend, clone 7) and anti-human CD271 (Biolegend, clone ME20.4) by following standard flow cytometry protocol. Luminal epithelial cells were enriched with Aria III (Becton Dickinson) as CD133+/CD271- fractions.

extract_protocol:
50,000 live FACS sorted young and old LEPs were used for Tn5 transposition in duplicates using the Omni-ATAC method
Tn5 tagged DNA were barcoded using the Nextera indexes and PCR amplified

tag: facs sort group

value: luminal cells


title: iPSN-C9-1_MeRIP


title: WT_Tum_2_GEX

value: Inplanted MC38-OVA tumors


title: WT_Tum_1_TCR


title: iPSN-Ctrl-4_Input


title: Mouse # 65020 melanoma RNA-seq

city: New York

description: RNA-seq of bulk melanoma tissue at 50 days post induction

source_name: Bulk melanoma tissue

extract_protocol: Snap-frozen tumors were disrupted in QIAzol reagent (QIAGEN) by milling with zirconia beads (Fisher). After addition of chloroform (Sigma) and centrifugation, RNA was isolated from the aqueous phase using an RNEasy Mini kit (QIAGEN).

tag: batch


title: Mouse # 65041 melanoma RNA-seq


title: ATAC_191L_O3_luminal-rep1


title: RME817

value: Keratinocyte


title: WT_Tum_1_FBC


title: iPSN-Ctrl-3_Input

value: Non-neurologic control


title: Mouse # 65664 tumor-infiltrating CD8 RNA-seq


title: ATAC_117R_O1_luminal-rep1


title: iPSN-Ctrl-2_Input


title: Mouse # 64661 melanoma RNA-seq


title: Mouse # 64660 melanoma RNA-seq


title: ATAC_117R_O1_luminal-rep2


title: Mouse # 64982 melanoma RNA-seq


title: iPSN-Ctrl-1_Input


title: KO_Tum_2_TCR


title: ATAC_112R_O2_luminal-rep1


title: WT_Tum_2_TCR


title: Mouse # 64808 melanoma RNA-seq


title: iPSN-C9-3_Input


title: ATAC_237_O5_luminal-rep2


title: WT_Tum_1_GEX


title: Mouse # 64805 melanoma RNA-seq


title: ATAC_168R_Y7_luminal-rep2


title: KO_Tum_1_TCR


title: iPSN-C9-2_Input


title: ATAC_191L_O3_luminal-rep2


title: ATAC_168R_Y7_luminal-rep1


title: iPSN-C9-1_Input


title: Mouse # 64803 melanoma RNA-seq


title: KO_Tum_1_FBC


title: Mouse # 65018 melanoma RNA-seq


title: iPSN-Ctrl-4_6h

data_processing:
Raw reads were trimmed with Trimmomatic-0.38 and aligned to human genome and transcriptome (hg38) and external RNA Control Consortium (ERCC) RNA spike-in control (Thermo Fisher Scientific) with ‘--rna-strandness RF’  parameters.
Reads on each GENCODE annotated gene were counted using HTSeq and then normalized to counts per million (CPM) using edgeR.
Assembly: hg38
Supplementary files format and content: read counts for each sample

extract_protocol:
Total RNA was extracted from cells using TRIzol (Thermo Fisher).
RNAs were subjected to NEBNext Ultra II Directional RNA Library Prep (New England Biolabs) coupled with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).

value: actinomycin D treatment 6 hour


title: KO_Tum_2_FBC


title: ATAC_112R_O2_luminal-rep2


title: iPSN-C9-4_Input


title: Mouse # 64799 melanoma RNA-seq

value: M


title: ATAC_160_Y3_luminal-rep2


title: Mouse # 64747 melanoma RNA-seq


title: ATAC_160_Y3_luminal-rep1


title: ATAC_172L_Y2_luminal-rep2


title: KO_Tum_2_GEX


title: iPSN-Ctrl-4_0h

value: actinomycin D treatment 0 hour


title: iPSN-Ctrl-3_6h


title: Mouse # 64727 melanoma RNA-seq


title: KO_Tum_1_GEX


title: ATAC_240L_Y1_luminal-rep2


title: iPSN-Ctrl-4_3h

value: actinomycin D treatment 3 hour


title: iPSN-Ctrl-3_0h

value: iPSC-derived neuron


title: NEJ677

description:
tissue-NEJ677
Single Cells_NEJ677
Single cells was captured and cDNA processed by 3' Single Gene expression kit V3.1- 10X Genomics

data_processing: Cell Ranger 6.0 used to generate Fastq, end count and matrix files that used further analyzes.

source_name: liver tissue

extract_protocol: cDNA and Library was prepared following 3' Single cell Expression V3 from 10X Genomics.

value: liver

value: hepatoblastoma murine model


title: NEJ723

description:
tissue-NEJ723
Single Cells_NEJ723
Single cells was captured and cDNA processed by 3' Single Gene expression kit V3.1- 10X Genomics


title: NEJ709

description:
tissue-NEJ634
Single Cells_NEJ634
Single cells was captured and cDNA processed by 3' Single Gene expression kit V3.1- 10X Genomics


title: NEJ687

description:
tissue-NEJ687
Single Cells_NEJ687
Single cells was captured and cDNA processed by 3' Single Gene expression kit V3.1- 10X Genomics


title: NEJ654

description:
tissue-NEJ654
Single Cells_NEJ654
Single cells was captured and cDNA processed by 3' Single Gene expression kit V3.1- 10X Genomics


title: TyrRS rep1 input

first: Xiang-Lei

last: Yang

address: 10550 North Torrey Pines Road BCC-110

department: Molecular Medicine

institute: Scripps Research

data_processing:
Reads were quality filtered and adapter trimmed with trimgalore.
ENCODE 3 ChIP-Seq pipeline (ENCODE Project Consortium, 2012) was followed for read mapping and peak calling.
reads were aligned to hg19 with Bowtie2 (Langmead and Salzberg, 2012) and duplicates were removed using picard tools and samtools (Li et al., 2009).
TyrRS binding sites in the genome in comparison to a control input were identified using MACS (Zhang et al., 2008).
Genome_build: hg19
Supplementary_files_format_and_content: peak

growth_protocol: HEK-293 (human embryonic kidney) cells were purchased from ATCC. HEK-293 were grown in DMEM (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Gibco) and penicillin/streptomycin (Gibco). Cultures were maintained at 37°C in a humidified atmosphere under 5% CO2.

extract_protocol:
Cells were fixed with formaldehyde (1% final concentration) for 10 min at room temperature. The reaction was stopped by adding 125 mM glycine. ChIP assays were performed according to the protocol of ChIP-IT Express Enzymatic kit (Active Motif) using ChIP-grade antibody against V5 (Thermo Fisher Scientific, R960CUS), IgG (Cell signaling technology, #5415),
Libraries were prepared and sequenced by the Next Generation Sequencing Core at Scripps Research, La Jolla, California
TF-ChIP-seq

treatment_protocol: Cells were grown to 70-80% confluence before treatments.

value: human embryonic kidney


title: TyrRS rep2

value: Thermo Fisher Scientific, R960CUS


title: TyrRS rep2 input


title: iPSN-Ctrl-2_6h


title: iPSN-Ctrl-2_3h


title: TyrRS rep1


title: WGBS data of mom2-2 mutant

data_processing:
For ChIP-seq analysis, raw reads were trimmed using trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and aligned to the TAIR10 reference genome with bowtie2 (v2.4.2) allowing zero mismatch and reporting one valid alignment for each read. The Samtools (v1.15) were used to convert sam files to bam files, sort bam files and remove duplicate reads. Track files in bigWig format were generated using bamCoverage of deeptools (v3.5.1) with RPKM normalization. Peaks were called with MACS2 (v2.1.2) and peaks frequently identified in previous ChIP-seq of Col-0 plant with M2 antibody for FLAG epitope were removed from analysis.
For RNA-seq analysis, the raw reads were aligned to the TAIR10 reference genome with bowtie2. Rsem-calculate-expression from RSEM with default settings was used to calculate expression levels. DEGs and DE-TEs were calculated with run_DE_analysis.pl from Trinity version 2.8.5 and log2 FC ≥ 1 and FDR < 0.05 were used as the cut off. RNA-seq track files in bigWig format were generated using bamCoverage of deeptools (v3.1.3) with RPKM normalization.
For WGBS analysis, the raw reads were aligned to both strands of the TAIR10 reference genome using BSMAP (v.2.74), allowing up to 2 mismatches and 1 best hit. Reads with more than 3 consecutives methylated CHH sites were removed, and the methylation level was calculated with the ratio of C/(C+T).
For BSPCR analysis, raw reads were aligned to both strands of the TAIR10 reference genome with BSMAP (v.2.90) allowing up to 2 mismatches and 1 best hit. After quality filtering, the methylation level of cytosines was calculated as the ratio of C/(C+T).
For ATAC-seq analysis, raw reads were adaptor-trimmed with trim_galore and mapped to the TAIR10 reference genome with Bowtie2 (-X 2000 -m 1). After removing duplicate reads and reads mapped to chloroplast and mitochondrial, ATAC-Seq open chromatin peaks of each replicate were called using MACS2 with parameters -p 0.01 --nomodel --shift -100 --extsize 200. Consensus peaks between replicates were identified with bedtools (version 2.26.0) intersect and differential accessible peaks were called with the R packge edgeR (version 3.30.0).
Assembly: tair10
Supplementary files format and content: .bw files are bigWig files of coverage tracks normalized with RPKM (for ChIP-seq and ATAC-seq), or methylation levels (for WGBS)
Supplementary files format and content: _methratio_type.txt files are tab-delimited text files containing methylation type and level at indicated chromosome positions.
Supplementary files format and content: .genes.results files are tab-delimited text files containing RNA-seq quantification data over genes and TEs.
Supplementary files format and content: .narrowPeak files are bed files containing position of called peaks for ChIP-seq.

source_name: rosette leaf tissue

extract_protocol:
Genomic DNA for WGBS was extracted with DNeasy Plant Mini Kit (QIAGEN). Genomic DNA for BS-PCR-seq was extracted with CTAB method. RNA was extracted with Direct-zol RNA MiniPrep kit (Zymo Research).
ChIP-seq library preparation: 15 ml of unopened flower buds were collected for each ChIP and flash-frozen in liquid nitrogen. The flower tissue was ground to fine powder with Retsch homogenizer in liquid nitrogen and resuspended in nuclei extraction buffer (50 mM HEPES pH 8.0, 1 M sucrose, 5 mM KCl, 5 mM MgCl2, 0.6% Triton X-100, 0.4 mM PMSF, 5 mM benzamidine, cOmplete EDTA-free Protease Inhibitor Cocktail (Roche), 50uM MG132). For transgenic lines of MOM1-MYC and PIAL2-MYC, EGS was first added to resuspended lysate to 1.5 mM and the tissue lysate was incubated at room temperature for 10 min with rotation. Then the lysate was supplemented with formaldehyde at 1% and rotated at room temperature for another 10 min followed by adding glycine to stop crosslinking. For ChIP of all other proteins, crosslinking was performed by directly supplementing formaldehyde to 1% without adding EGS, then rotated at room temperature for 10 min followed by adding glycine to stop crosslinking. The crosslinked nuclei were isolated, lysed with Nuclei Lysis Buffer and diluted with ChIP Dilution Buffer. Then the lysate was sonicated for 22 min (30 s on/30s off) with Bioruptor Plus (Diagenode). After centrifugation, antibody for FLAG epitope (M2 monoclonal antibody, Sigma F1804, 10 ul per ChIP) or for MYC epitope (Cell Signaling, 71D10, 20 ul per ChIP) were added to the supernatant and incubated at 4 ℃ overnight with rotation. Then, Protein A and Protein G Dynabeads (Invitrogen) were added and incubated at 4 ℃ for 2 hours with rotation. After that, the beads were washed and eluted, and the eluted chromatin was reverse-crosslinked by adding 20 ul 5 M NaCl and incubating at 65 ℃ overnight followed by treatment of Proteinase K (Invitrogen) for 4 hours at 45 ℃. DNA was purified and precipitated with 3 M Sodium Acetate, GlycoBlue (Invitrogen) and ethanol at -20 ℃ overnight. After centrifugation, the precipitated DNA was washed with ice cold 70% ethanol, air dried and dissolved in 120 ul of H2O. ChIP-seq libraries were prepared with Ovation Ultra Low System V2 kit (NuGEN).
RNA-seq library preparation: Twelve-day old seedlings grown on half MS medium (Murashige and Skoog Basal Medium) were collected and flash-frozen in liquid nitrogen. RNA was extracted with Direct-zol RNA MiniPrep kit (Zymo Research) and 1ug of total RNA was used to prepare RNA-seq libraries with TruSeq Stranded mRNA kit (Illumina)
WGBS library preparation: Rosette leaves of about one-month-old Arabidopsis plants were collected for DNA extraction using DNeasy Plant Mini Kit (QIAGEN). 500 ng DNA was sheared with Covaris S2 (Covaris) into around 200bp at 4℃. The DNA fragments were used to perform end repair reaction using the Kapa Hyper Prep kit (Roche), and together with Illumina TruSeq DNA sgl Index Set A/B (Illumina) to perform adapter ligation. The ligation products were purified with AMPure beads (Beckman Coulter), and then converted with EpiTect Bisulfite kit (QIAGEN). The converted ligation products were used as templates, together with the primers from the Kapa Hyper Prep kit (Roche) and MyTaq Master mix (Bioline) to perform PCR. The PCR products were purified with AMPure beads (Beckman Coulter) and used for sequencing.
ATAC-seq library preparation: About 5 grams of unopened flower buds was collected and immediately transferred into ice-cold grinding buffer (300 mM sucrose, 20 mM Tris pH 8, 5 mM MgCl2, 5 mM KCl, 0.2% Triton X-100, 5 mM β-mercaptoethanol, and 35% glycerol). The samples were ground with Omni International General Laboratory Homogenizer on ice and then filtered through a two-layer Miracloth and a 40-µm nylon mesh Cell Strainer (Fisher). Samples were spin filtered for 10 min at 3,000 g, the supernatant was discarded, and the pellet was resuspended with 25 ml of grinding buffer using a Dounce homogenizer. The wash step was performed twice in total, and nuclei were resuspended in 0.5 ml of freezing buffer (50 mM Tris pH 8, 5 mM MgCl2, 20% glycerol, and 5 mM β-mercaptoethanol). Nuclei were subjected to a transposition reaction with Tn5 (Illumina). For the transposition reaction, 25 µl of 2x DMF (66 mM Tris-acetate pH 7.8, 132 mM K-Acetate, 20 mM Mg-Acetate, and 32% DMF) was mixed with 2.5 µl Tn5 and 22.5 µl nuclei suspension at 37°C for 30 min. Transposed DNA fragments were purified with ChIP DNA Clean & Concentrator Kit (Zymo). Libraries were prepared with Phusion High-Fidelity DNA Polymerase (NEB) in a system containing 12.5 µl 2x Phusion, 1.25 µl 10 mM Ad1 primer, 1.25 µl 10 mM Ad2 primer, 4 µl ddH2O, and 6 µl purified transposed DNA fragments.
BS-PCR library preparation: Rosette leaves of about one-month-old plants were collected and subject to DNA extraction with CTAB method followed by bisulfite DNA conversion using the EpiTect Bisulfite kit (QIAGEN) kit. Three regions of the FWA gene were amplified from the converted DNA with Pfu Turbo Cx (Agilent): Region 1 (chr4: 13038143-13038272), Region 2 (chr4: 13038356- 13038499) and Region3 (chr4: 13038568-13038695). Libraries were prepared with the purified PCR product by the Kapa DNA Hyper Kit (Roche) together with TruSeq DNA UD indexes for Illumina (Illumina) and were sequenced on Illumina iSeq 100 or HiSeq 4000 instruments.

value: rosette leaf tissue

value: one month old


title: NEJ638

description:
tissue-NEJ638
Single Cells_NEJ638
Single cells was captured and cDNA processed by 3' Single Gene expression kit V3.1- 10X Genomics


title: WGBS data of aipp3-1 mutant


title: ATAC_172L_Y2_luminal-rep1


title: IgG control input


title: iPSN-Ctrl-2_0h


title: IgG control

value: Cell signaling technology, #5415


title: iPSN-C9-4_6h

value: patient-derived


title: ATAC_240L_Y1_luminal-rep1

value: luminal cells


title: NEJ634


title: iPSN-Ctrl-3_3h


title: WGBS data of wild type (Col-0) plant as control for aipp3-1 and mom2-2


title: WGBS data of phd1-3 mutant


title: PFCR34, AD_alcohol, 3xTg-AD

city: Bologna

first: Chiara

last: Cabrelle

address: Via Irnerio, 49

country: Italy

institute: University of Bologna

description: 10x Genomics

data_processing:
Raw 10x Genomics reads from 16 samples (n=4 3xTg-AD and WT mice with and without histories of repeated alcohol intoxication) were aligned on the Mus musculus genome version mm10 (downloaded on 13 August 2021) using Cell Ranger v.6.1.1 based on the STAR aligner.
Assembly: mm10
Supplementary files format and content: Tab-separated values file with rawcounts

source_name: Prefrontal cortex

extract_protocol:
Male 3xTg-AD mice were sacrificed under deep isoflurane anesthesia and freshly dissected brain regions were snap-frozen and processed for snRNA-Seq by Singulomics (New York City, NY) using the 10x Genomics Chromium gene expression platform.
Chromium Next GEM Single Cell 3ʹ Kit v3.1 (dual index)
snRNA-seq

value: alcohol

value: Prefrontal cortex

tag: strain

value: 22 weeks


title: WGBS data of wild type (Col-0) plant as control for phd1-3


title: PFCR33, AD_alcohol, 3xTg-AD

description: 10x Genomics

tag: age


title: iPSN-C9-4_3h


title: WGBS data of fwa control plant

value: fwa


title: PFCR31, AD_alcohol, 3xTg-AD

description: 10x Genomics


title: WGBS data of PIAL2-ZF T2 plant in fwa background

value: PIAL2-ZF in fwa


title: RPMI_8226_DMSO_H3K27me3_spikein

first: Chao

last: Lu

address: 1130 Saint Nicholas Ave

department: Genetics & Development

institute: Columbia University Medical Center

data_processing:
Basecalls performed using Illumina CASAVA version 1.7
For RNA-seq samples, reads of DLBCL cell lines were mapped to the human genome assembly hg38 using HISAT2 (v2.1.0). The mapped reads count of each gene was measured by featureCounts (v1.6.1). For CUT&Tag samples, reads were mapped to the human genome assembly hg38 using HISAT2 (v2.1.0). Potential PCR duplicates were removed by the function "MarkDuplicates" (parameter: REMOVE_DUPLICATES=true) of Picard (v2.23.1).
Assembly: hg38
Supplementary files format and content: For RNA-seq samples, tab-delimited text files include reads count values for each gene in each sample. For CUT&Tag samples, bigwig files normalized to count per million reads.
Library strategy: CUT&Tag

source_name: Cell line

extract_protocol:
CUT&Tag was performed as described previously (nature communications, 2019).
CUT&Tag was performed as described previously (nature communications, 2019).

value: MM cell line

value: Treated by DMSO


title: RPMI_8226_DMSO_MLL1


title: RPMI_8226_DMSO_MEN1


title: PFCR28, ctrl, WT

description: 10x Genomics

value: control


title: RPMI_8226_EPZ6438_72hr_MLL1

value: Treated by EPZ6438


title: iPSN-C9-3_3h

value: iPSC-derived neuron

value: actinomycin D treatment 3 hour