title: Spiny projection neurons, R62Hemi_Nme1OX, rep5

first: Myriam

last: Heiman

address: 77 Massachusetts Ave., Bldg 46-4285

department: Brain and Cognitive Sciences

institute: Massachusetts Institute of Technology

description: snRNA

data_processing:
Basecalls converted to FASTQ with Cellranger v3.1.
FASTQ aligned, demultiplexed, and sorted with Cellranger v3.1 using pre-mRNA annotated GRCm38 reference that included EGFP.
Genome_build: GRCm38
Supplementary_files_format_and_content: Sparse matrices (MTX) containing unique molecular identifier counts of each gene per cell.

source_name: Striatum

extract_protocol:
Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol.  The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA.
Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual.

value: R62 mouse model of HD

value: Striatum

tag: cell type

value: spiny projection neurons

tag: virus


title: Spiny projection neurons, R62Hemi_Nme1OX, rep2

status: Public on Jan 30 2020

type: SRA

city: Cambridge

state: Massachusetts

country: USA

description: snRNA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: disease state

tag: tissue

tag: genotype


title: Spiny projection neurons, R62Hemi_Nme1OX, rep1

description: snRNA


title: Spiny projection neurons, R62Hemi_Nme1OX, rep3

description: snRNA


title: Spiny projection neurons, R62Hemi_CtlOX, rep5

description: snRNA

value: CtlOX


title: Spiny projection neurons, R62Hemi_CtlOX, rep1

description: snRNA


title: Spiny projection neurons, R62Hemi_CtlOX, rep3

description: snRNA


title: Spiny projection neurons, R62Hemi_CtlOX, rep2

description: snRNA


title: Spiny projection neurons, R62Hemi_CtlOX, rep4

description: snRNA


title: Spiny projection neurons, NonCar_Nme1OX, rep4

description: snRNA

value: NonCar


title: Spiny projection neurons, NonCar_Nme1OX, rep5

description: snRNA


title: Spiny projection neurons, NonCar_CtlOX, rep5

description: snRNA


title: Spiny projection neurons, NonCar_Nme1OX, rep3

description: snRNA


title: Spiny projection neurons, NonCar_CtlOX, rep4

description: snRNA


title: Spiny projection neurons, NonCar_Nme1OX, rep2

description: snRNA


title: Spiny projection neurons, NonCar_CtlOX, rep1

description: snRNA


title: Spiny projection neurons, NonCar_CtlOX, rep2

description: snRNA


title: Rosi_rep1_66

city: Philadelphia

first: Yachen

last: Shen

address: 3400 Civic Center Blvd, Philadelphia, PA 19104

institute: University of Pennsylvania

description:
LFD + Rosi
Rosi_rep1_66

data_processing:
Raw sequenced reads were filtered to retain only high-quality reads. In addition, ribosomal reads and repeats were eliminated by NGSC. Remaining reads were processed with RNA-Seq Unified Mapper (RUM)
RUM aligns reads to the set of known transcripts included in RefSeq, UCSC known genes, and ENSEMBL transcripts, and the genome, and outputs feature-level quantitation (transcript, exon, and  intron).
To analyze global gene expression profiles, the number of uniquely aligning read counts to mRNA transcripts in RefSeq were extracted from the RUM output and processed using a custom script to carry out differential expression analysis using Bioconductor software’s package edgeR to compute a p-value and fold-change for each transcript.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: brown adipose tissue

growth_protocol: Mice were housed at room tempature and received normal chow diet for the first 8 weeks of life.

extract_protocol:
Brown adipose tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Paired-end sequencing libraries using the NEBNext Ultra RNA library preparation kit according to the manufacturer’s instructions

treatment_protocol: Male F1 intercross progeny of C57BL/6J and 129S1SvImJ mice (Jackson Labs stock number: JAX 101043) mice received for two weeks a control low fat diet (Research Diets D12450B, n=5), or the same diet wtih 0.005% rosiglitazone (n=5), or with 0.2% fenofibrate (n=5).

tag: tag

value: brown adipose tissue

tag: age

value: 8 weeks


title: Spiny projection neurons, R62Hemi_Nme1OX, rep4

description: snRNA


title: Spiny projection neurons, NonCar_CtlOX, rep3

description: snRNA


title: X15

city: Iowa City

first: Hanna

middle: E

last: Stevens

state: IA

address: 169 Newton Road

department: Psychiatry

institute: University of Iowa

data_processing:
Reads were mapped with STAR 2.5 to mouse mm10 and a Refseq transcriptome
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each sample

source_name: Cypermethrin + No Stress_GABAergic progentitors

extract_protocol:
GAD67-GFP+ offspring brains were fixed in 4% paraformaldehyde and cryoprotected (Optimal Cutting Temperature Compound, Fisher Scientific). Laser capture microdissection (LCM) was utilized to isolate migrating GAD67-GFP+ cells from the cortical plate of fixed embryonic brain 10 µm tissue slices on metal frame PET foil slides (Leica) from one male embryo per litter (n=4 per group). Approximately 100 individual GFP+ cells were collected at the leading edge of migration from each of 10 tissue sections, giving approximately 1,000 cells per sample. RNA was isolated from the tissue using the RecoverAll Total Nucleic Acid Isolation kit (Thermo Fisher Scientific, AM1975)
Libraries were prepared using the Trio RNAseq kit (Nugen)

treatment_protocol: CD1 dams were treated with 10mg/kg alpha-cypermethrin or corn oil vehicle via oral gavage each morning from gestational days 11 to 14. Mice receiving either treatment were split into non-stressed (NS) or prenatal stress (PS) groups. On days 12 and 13, mice in the prenatal stress treatment groups were subjected to three, 45-minute sessions of restraint stress under bright light as previously described, the first episode 30 min after gavage. On gestational day 14, all dams received a final dose of cypermethrin or vehicle 90 minutes prior to euthanasia, followed by a final round of restraint stress in the stressed groups, ending 15 min prior to euthanasia.

tag: strain

value: Embryonic Day 14.5

tag: Sex

value: male

tag: treatment

value: Cypermethrin + non-stressed (NS)

value: Embryonic brain

value: Neural progenitor cells


title: X16

source_name: Vehicle + No Stress_GABAergic progentitors

value: Vehicle + non-stressed (NS)


title: X11

source_name: Vehicle + Stress_GABAergic progentitors

value: Vehicle + prenatal stress (PS)


title: X13


title: X12

source_name: Cypermethrin + Stress_GABAergic progentitors

value: Cypermethrin + prenatal stress (PS)


title: X7


title: X10


title: X9


title: X8


title: X3


title: X5


title: X4


title: X6


title: X1


title: X2


title: Gcr2p_mutant_BMH1_TDH3

city: St. Louis

first: Jiayue

last: Liu

state: MO

address: 4515 McKinley Research Building

department: Genetics

institute: Washington University in St. Louis

library_source: genomic

data_processing:
Library strategy: Calling Cards Reporter Arrays
We use our python analysis source code for data processing. The code is available on Gitlab
Genome_build: not applicable
Supplementary_files_format_and_content: The processed data files is in CSV format each row as a synthetic promoter sequence. Columns contain transposition insertion information and read count information.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Synthetic library designed based on yeast promoters

extract_protocol:
After TF directed transposition induction and selection, plasmid DNA is extracted using Qiagen mini prep kit
We amplify all TF directed transpositions from library plasmids DNA by PCR


title: Spiny projection neurons, NonCar_Nme1OX, rep1

description: snRNA


title: HFD rep2

city: Duarte

first: Kenneth

middle: Edmund

last: Stapleton

state: CA

address: 1500 Duarte Rd

department: Diabetes Complications and Metabolism

institute: City of Hope

data_processing:
Illumina RTA 1.13.48 was used for basecalling.
Reads were mapped to the mouse genome assembly mm9 using TopHat2 aligner v2.0.10 with the following options: --library-type fr-firststrand -g 10
Cufflinks v2.1.1 and Cuffmerge software were used to generate de novo transcript assemblies.
Genome_build: mm9
Supplementary_files_format_and_content: gtf file was generated by merging Refseq mm9 annotations (retrieved 12/09/2014) with novel transcripts generated with Cufflinks v2.1.1.
Supplementary_files_format_and_content: tab-delimited text files contain raw gene counts generated with Htseq, using the provided gtf file.

source_name: Peritoneal macrophages

extract_protocol:
Total RNA was extracted using TRIzol reagent followed by DNAse I treatment (both from ThermoFisher Scientific). Total RNA was depleted of rRNA using Ribo-Zero rRNA Removal kit (Illumina).
Paired-end libraries were prepared, size selected, gel purified, and sequenced in our campus Integrative Genomics Core using an Illumina HiSeq 2000 system following manufacturer’s protocols.

value: Peritoneal macrophages

tag: diet

value: High-fat (60%kcal)


title: Gcr1p_mutant_BMH1_TDH3

value: Synthetic library designed based on yeast promoters


title: Gcr1p_reprogram


title: X14


title: Ctrl Diet rep2

value: Control


title: Tye7p_mutant_BMH1_TDH3


title: Tye7p_reprogram


title: HFD rep1


title: Ctrl Diet rep1


title: Cbf1p_reprogram


title: Cbf1p_spacing


title: Cbf1p_sensitivity


title: A375_D14_R1

city: New York

first: Hans-Hermann

last: Wessels

address: 101 Avenue of the Americas

institute: New York Genome Center

description: RfxCas13d guide RNA integration extracted from genomic DNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were demultiplexed based on Illumina i7 barcodes present in PCR2 reverse primers using bcl2fastq and by their custom in-read i5 barcode using a custom python script.
Reads were trimmed to the expected guide RNA length by searching for known anchor sequences relative to the guide sequence using a custom python script.
For the tiling screens, pre-processed reads were either aligned to the designed crRNA reference using bowtie (v.1.1.2) with parameters -v 0 -m 1 or collapsed (FASTX-Toolkit) to count perfect duplicates followed by string-match intersection with the reference to retain only perfectly matching and unique alignments. Pre-processed guide RNA sequences from the essentiality screens were aligned allowing for up to 1 mismatch (-v 1 -m 1)
Genome_build: custom crRNA library
Supplementary_files_format_and_content: txt files contain raw guide RNA counts

organism: Homo sapiens

source_name: A375 TetO-RfxCas13d cells

growth_protocol: TetO-RfxCas13d cells Cells were grown in DMEM supplemented with 10% FBS. Cas13 expression was induced with doxycycline (1µg/ml). Cells were passaged every two to three days supplemented with fresh doxycycline.

extract_protocol:
The tiling screens were terminated after 5 to 10 days. For cell surface proteins, cells were stained in batches of 1x107 cells for 30 min at 4°C (BioLegend: CD46 clone TRA-2-10 #352405 - 3µl per 1x10^6 cells; CD55 clone JS11 #311311 - 1.5µg per 1x10^6 cells; CD71 clone CYIG4 #334105 - 4µl per 1x10^6 cells). We collected unsorted samples for input guide RNA representation of approximately 1000x coverage for each sample and sorted at least another 1000x representation into the assigned bins based on their signal intensities. Cells were PBS-washed and frozen at -80°C until sequencing library preparation. In each case, the bin containing the lowest 20% represented the strongest target knock-down. For each sample, genomic DNA was isolated from cell pellets using the GeneJET Genomic DNA Purification Kit (ThermoFisher K0722) with 2x10^6 cells or less per column.
The crRNA readout was performed using two rounds of PCR. For each sample, we performed PCR1 reactions as follows: 20 µl volume with 2 ug of gDNA in each reaction limited by the amount of extracted gDNA (total gDNA ranged from 8µg to 50 ug per sample with an estimated representation of 10^6 diploid cells per ~6.6 ug gDNA. PCR1: 4µl 5x Q5 buffer, 0.02U/µl Q5 enzyme (M0491L), 0.5uM forward and reverse primers and 100ng gDNA/µl. PCR conditions: 98°C/30s, 24x[98°C/10s, 55°C/30s, 72°C/45s], 72°C/5min). We pooled the unpurified PCR1 products and used the mixture for a single second PCR reaction per sample. This second PCR adds on Illumina sequencing adaptors, barcodes and stagger sequences to prevent monotemplate sequencing issues. (PCR2: 50µl 2x Q5 master mix (NEB #M0492S), 10µl PCR1-product, 0.5uM forward and reverse PCR2-primers in 100µl. PCR conditions: 98°C/30s, 17x[98°C/10s, 63°C/30s, 72°C/45s], 72°C/5min).
Amplicons from the second PCR were pooled by screen experiment (e.g. all GFP-screen samples) in equimolar ratios (by gel-based band densitometry quantification) and then purified using a QiaQuick PCR Purification kit (Qiagen 28104). Purified products were loaded onto a 2% E-gel and gel extracted using a QiaQuick Gel Extraction kit (Qiagen 28704). The molarity of the gel-extracted PCR product was quantified using KAPA library quant (KK4824) and sequenced on an Illumina NextSeq 500 - II MidOutput 1x150 v2.5.

treatment_protocol:
Doxycycline-inducible RfxCas13d-NLS human HEK293FT, double-transgenic HEK293FT-GFP or A375 cells were transduced with the respective library pooled lentiviruses in separate infection replicates ensuring at least 1000x guide representation in the selected cell pool per infection replicate using a standard spinfection protocol. We generated either 2 or 3 independent replicate experiments. After 24 hours, RfxCas13d expression was induced by addition of 1µg/ml doxycycline (Sigma D9891) and cells were selected with 1 ug/mL puromycin (ThermoFisher A1113803), resulting in ~30% cell survival. Puromycin-selection was complete ~48 post puromycin-addition. Assuming independent infection events (Poisson), we determined that ~83% of surviving cells received a single sgRNA construct. Cells were passaged every two days maintaining at least the initial cell representation and supplemented with fresh doxycycline.
The essentiality screens were started (Day 0) upon complete puromycin selection, which was at 5 days after transduction. Cells were passaged every two to three days maintaining at least the initial cell representation and supplemented with fresh doxycycline. At Day 0 (=Input) and every 7 days, we collected a >1000x representation from each sample. The HEK293FT cell screen was conducted in triplicate and cultured for 4 weeks. The A375 cell screen was conducted in duplicate and cultured for 2 weeks.

tag: cell line

value: Melanoma cells

value: Dropout

tag: sample selection

value: Day 14


title: A375_D14_R2


title: Cbf1p_affinity


title: A375_D7_R1

value: Day 7


title: A375_Input_R2

value: Selected Input

value: Input


title: HEK_R3_D21

source_name: HEK293FT TetO-RfxCas13d cells

value: human embryonic kidney cells

value: Day 21


title: HEK_R1_D21


title: HEK_R2_D21


title: HEK_R1_D27

value: Day 27


title: A375_Input_R1


title: HEK_R2_D27


title: HEK_R2_D14


title: HEK_R3_D14


title: HEK_R3_D27


title: HEK_R2_D7


title: HEK_R1_D14


title: HEK_R3_D7


title: HEK_R3_D0


title: HEK_R1_D7


title: A375_D7_R2


title: HEK_TilingScreen_CD71_input_R2

value: unsorted sample


title: HEK_TilingScreen_CD71_low_R2

value: Sorted:0-20% signal intensity

value: Low


title: HEK_TilingScreen_CD71_low_R1


title: HEK_TilingScreen_CD71_high_R2

value: Sorted:80-100% signal intensity

value: High


title: HEK_TilingScreen_CD55_input_R2


title: HEK_TilingScreen_CD55_low_R1


title: HEK_TilingScreen_CD55_low_R2


title: HEK_TilingScreen_CD55_input_R1


title: HEK_TilingScreen_CD55_high_R2


title: HEK_TilingScreen_CD46_input_R3


title: HEK_TilingScreen_CD46_low_R3


title: HEK_TilingScreen_CD55_high_R1


title: NPC1-ExpB GRO-seq

city: La Jolla

first: Meiyan

last: Wang

address: 10010 N. Torrey Pines Road

institute: The Salk Institute for biological studies

data_processing:
Library strategy: GRO-seq
fastq files were aligned using Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
samfiles were processed with HOMER (http://homer.ucsd.edu/homer/) to generated Tag directory
Expression was analyzed with HOMER with parameter (analyzeRepeats.pl rna hg19 -count genes -strand - -rpkm)
Genome_build: hg19
Supplementary_files_format_and_content: txt files containing rpkm of the transcripts

source_name: hiPSC-derived neural progenitor cells

growth_protocol: Human ESC- and iPSC-derived NPCs were cultured as described before (Yu et al., 2014; Marchetto et al., 2017).

extract_protocol:
For the run-on assay, re-suspended nuclear extract was mixed with an equal volume of run-on reaction buffer (10 mM Tris-HCl pH 8.0, 5 mM MgCl2, 300 mM KCl, 1 mM DTT, 200 U/ml RNaseOut, 1% Sarkosyl, 500 uM ATP, 500 uM GTP, 500uM CTP, and 500 uM Br-UTP) and incubated for 5 min at 30C. The reaction was stopped by adding 1mL TRIzol LS reagent (Thermo Fisher). The total nuclear RNA was extracted by acidic phenol/chloroform and precipitated by ethanol.
The library construct was done according to GRO-seq protocol described in Core, Leighton J., Joshua J. Waterfall, and John T. Lis. "Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters." Science 322.5909 (2008): 1845-1848.

value: Neural progenitor cells

tag: passage

tag: molecule subtype

value: nuclear RNA


title: 6683

city: Madison

first: Feyza

last: Engin

state: Wisconsin

address: 440 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin-Madison

description:
ClusterWT_KO_alpha_DEG_mean.txt
ClusterWT_KO_beta_DEG_mean.txt
ClusterWT_KO_delta_DEG_mean.txt

data_processing:
Cell Ranger mkfastq v3.0.0
Cell Ranger count v3.0.0
cellranger-aggr v3.0.0
Genome_build: mm10
Supplementary_files_format_and_content: txt files of differential gene expression analysis of either beta, alpha, or delta cells

source_name: Pancreatic islets

growth_protocol: Housed under a 12:12-hr light/dark cycle, with unrestricted access to food and drinking water in an animal housing facility accredited by the Association for Assessment and Accreditation of Laboratory Animal Care.

extract_protocol:
Islets were isolated using the standard collagenase/protease digestion method. The pancreatic duct was cannulated and distended with 4°C collagenase/protease solution. Islets were separated from the exocrine tissue using Histopaque-1077. Hand-picked islets were cultured overnight at 37°C in RPMI-1640 media containing 10% FBS and 1% Penicillin/Streptomycin. Cells were dissociated using accutase digestion.
RNA libraries were prepared for sequencing using standard 10X Genomics protocols

treatment_protocol: To induce Cre recombinase activity, tamoxifen was dissolved in sterilized corn oil  by shaking overnight at 37°C. The solution was protected from light, and 10 mg/ml tamoxifen was administrated via intraperitoneal injection twice every 24 hours in five consecutive days.

value: NOD/ShiLtJ

value: Pancreatic islets

value: 5 weeks old


title: HEK_TilingScreen_CD46_low_R2


title: NPC1-ExpA GRO-seq


title: HEK_TilingScreen_CD46_high_R2


title: HEK_R2_D0


title: HEK_R1_D0


title: PBMC_CITEseq

city: Toulouse

first: Jean Jacques

last: FOURNIE

address: 2 av Hubert Curien

department: oncology

country: France

institute: INSERM

data_processing:
Raw data were firstly demultiplexed using mkfastq application (Cell Ranger v3.0.2).
Fastq files were then run with count application (Cell Ranger v3.0.2) using default settings, which performs alignment (using STAR aligner), filtering and UMI counting. The UMI count table was used for further analysis.
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include UMI numbers for all genes and single cells that passed filtering

source_name: Peripheral Blood mononuclear cells stained with monoclonal antibodies to 9 cell surface markers

extract_protocol: Sequencing library was prepared following the manufacturer’s instructions (10X Genomics), with 14 cycles used for cDNA amplification and 12 cycles for library amplification

value: peripheral blood mononuclear cells (PBMCs)


title: HEK_TilingScreen_CD46_input_R2


title: HEK_TilingScreen_CD46_high_R3


title: HEK_TilingScreen_CD71_input_R1


title: HEK_TilingScreen_CD46_input_R1


title: HEK_TilingScreen_CD46_low_R1


title: HEK_TilingScreen_GFP_Bin4_R3

source_name: HEK293FT TetO-RfxCas13d EGFPd2PEST cells

value: Sorted:60-100% GFP intensity

value: Bin 4


title: HEK_TilingScreen_CD71_high_R1


title: HEK_TilingScreen_GFP_Bin2_R3

value: Sorted:20-40% GFP intensity

value: Bin 2


title: HEK_TilingScreen_GFP_Bin3_R3

value: human embryonic kidney cells

value: Sorted:40-60% GFP intensity

value: Bin 3


title: HEK_TilingScreen_CD46_high_R1


title: HEK_TilingScreen_GFP_Bin1_R3

value: Sorted:0-20% GFP intensity

value: Bin 1


title: L24

city: Harbin

first: Junchao

last: Zhao

state: HeiLongjiang

address: 600 Changjiang Road

country: China

institute: The Northeast Agricultural University

description: L24 was Vm24

data_processing:
Raw reads were filtered via SOAPnuke (v1.4.0) by removing reads containing adaptors, poly-N or low quality, and then clean reads were obtained.
Trinity (v2.0.6) was used to assemble the clean reads and Tgicl (v2.0.6) to perform clustering and eliminate redundant data in the assembled transcripts to obtain unique genes.
Clean reads were mapped to the assembled unique genes by Bowtie2 (v2.2.5) and the expression level of genes were calculated by RSEM (v1.2.8) and normalized to FPKM (Fragments per kilo base of transcript per million mapped reads).
Supplementary_files_format_and_content: csv file includes FPKM values for each Sample

organism: Lolium multiflorum

source_name: Low Cadmium

growth_protocol: The seeds of LmHC and LmLC were provided by Jingang Wang's Group at the Northeast Agricultural University in China. To obtain seedlings,the seeds were sown under sterile conditions in Petri dishes that contained MS medium and solidified with 0.8% (w⁄v) agar. Seven-day-old seedlings were transferred into Hoagland solution and grown in a sterilized, pathogen-free glasshouse. The cultures were maintained at 22-25℃ under a 16h photoperiod. The culture solution was replaced every 3d.

extract_protocol:
Ethanol precipitation protocol and CTAB-PBIOZOL reagent was used for the purification of total RNA from the plant tissue according to the manual instructions. Grind tissue samples about 80mg with liquid nitrogen into powder and transfer the powder samples in 1.5ml of preheated 65°C CTAB-pBIOZOL reagents. The samples were incubated by Thermo mixer for 15min at 65°C to permit the complete dissociation of nucleoprotein complexes. After centrifuge at 12000×g for 5min at 4°C, the supernatant was added 400ul of chloroform per 1.5ml of CTAB-pBIOZOL reagent and was centrifuged at 12000×g for 10min at 4°C. The supernatant was transferred to a new 2.0ml tube that added 700ul acidic phenol and 200ul chloroform followed by centrifuging 12000×g for 10 min at 4°C. The aqueous phase was added equal volume of aqueous phase of chloroform and centrifuged at 12000×g for 10 min at 4°C. The supernatant was added equal volume of supernatant of isopropyl alcohol and placed at -20°C for 2 hours for precipitation. After that, the mix was centrifuged at 12000×g for 20min at 4°C and then removed the supernatant. After washed with 1ml of 75% ethanol, the RNA pellet was air-dried in the biosafety cabinet and was dissolved by adding 50µL of DEPC-treated water. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: Two-week-old LmHC and LmLC seedlings were treated with 0h and 300µM CdCl2 for 24h

value: Low Cadmium

tag: time


title: L0

description: L0 was Vm0


title: HEK_TilingScreen_GFP_Input_R3

value: unsorted sample

value: Input


title: H24

description: H24 was Dg24

source_name: High Cadmium

value: High Cadmium


title: HEK_TilingScreen_GFP_Bin3_R2


title: HEK_TilingScreen_GFP_Bin4_R2


title: HEK_TilingScreen_GFP_Bin2_R2


title: HEK_TilingScreen_GFP_Input_R1


title: HEK_TilingScreen_GFP_Input_R2


title: HEK_TilingScreen_GFP_Bin4_R1


title: HEK_TilingScreen_GFP_Bin1_R1


title: HEK_TilingScreen_GFP_Bin1_R2


title: HEK_TilingScreen_GFP_Bin2_R1


title: Tumor CTX-471-AF

city: Boston

first: Vijay

last: Kuchroo

state: MA

address: 60 Fenwood Road

department: Neurology

institute: Brigham & Women's Hospital

description:
Single-cell or single nucleus RNA-Seq (10X). The count matrix is stored as an HDF5 file.
BRI-097

data_processing:
3' RNAseq (10x kit V2 chemistry)
Demultiplexing is run using Cell Ranger mkfastq (Version 2.1.0).
Cell Ranger count (Version 2.1.0) is run using the Cumulus cellranger_workflow.
Cell Ranger count (Version 2.1.0) is run to filter expression matrix to only cells containing valid& detected cellular barcodes
Genome_build: mm10
Supplementary_files_format_and_content: Filtered count matrices are in the H5 Feature Format used by 10x.

source_name: Tumor

extract_protocol:
Dissociated individual cells sorted for CD8+
3' RNAseq (10x kit V2 chemistry)

value: Tumor


title: Tumor 3H3

description:
Single-cell or single nucleus RNA-Seq (10X). The count matrix is stored as an HDF5 file.
BRI-096


title: Tumor Control

description:
Single-cell or single nucleus RNA-Seq (10X). The count matrix is stored as an HDF5 file.
BRI-095

value: Control


title: WT_Input DNA

data_processing:
Sequenced reads were aligned to the mouse reference genome (mm9) using Bowtie2.
Uniquely aligning read per genomic position was kept for further analysis by using Picard.
Peak calling was performed with HOMER and a false-discovery rate (FDR) cutoff of <0.1%, and all tag counts were normalized to 10 million reads and ≥ 4-fold tag count enrichment compared to both input control and local tag density in all subsequent analyses.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph

growth_protocol: 8 weeks mice brown adipose tissue

extract_protocol:
Lysates were clarified from sonicated nuclei and PPARs-DNA complexes were isolated with antibody.
Extracted DNA (1-5ng) was used to prepare sequencing libraries using the NEBNext ChIP-seq library preparation master mix set for Illumina (New England Biolabs, E6240S). The library was analyzed by Agilent Bioanalyzer and was sequenced by the Functional Genomics Core of the Penn Diabetes Research Center by using the Illumina HiSeq2500 (single-end 50bp)

value: 8 weeks

tag: antibody


title: KO_Input DNA


title: Pparg_WT_ChIPseq rep2

value: PPARg(Proteintech 16643-1-AP)


title: Ppara_KO_ChIPseq rep2

value: PPARa(Santa Cruz sc-398394)


title: Ppara_WT_ChIPseq rep1


title: Ppara_WT_ChIPseq rep2


title: HEK_TilingScreen_GFP_Bin3_R1

tag: cell type


title: KO3

data_processing:
Illumin BCL2fastq v2.20
Adapter trimming with Skewer v0.1.123 and parameters -m pe -q 20 -k 15 -l 25
Alignment with STAR v2.5.3a and parameters --twopassMode Basic --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes NH HI AS NM MD XS --outSAMunmapped Within --outFilterMultimapNmax 50
Expression estimation with RSEM v1.2.31 and parameters --alignments --paired-end --no-bam-output
Differential expression with edgeR v3.16.15
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Microsoft Excel files containing results of edgeR analysis

extract_protocol:
Islets were isolated using the standard collagenase/protease digestion method. The pancreatic duct was cannulated and distended with 4°C collagenase/protease solution. Islets were separated from the exocrine tissue using Histopaque-1077. RNA from hand-picked islets was extracted using RNeasy Mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: NOD/ShiLtJ

value: Pancreatic islets

value: 7 weeks old


title: KO1


title: KO2


title: KO4


title: WT3


title: WT1


title: WT2


title: H0

description: H0 was Dg0


title: Pparg_WT_ChIPseq rep1


title: Ppara_KO_ChIPseq rep1


title: RAW264.7_ASO-Mist_rep3

type: RNA

description: Gene expression from RAW 264.7 cells treated with Mist-targete GapmeR.

hyb_protocol: The chips were hybridized by Affymetrix Hybridization Oven 640 and washed by Affymetrix Fluidics Station 450 according to manufacturer's protocols.

scan_protocol: The chips were scanned by Affymetrix scanner 3000 7G using manufacturer's default settings.

data_processing: Raw Affymetrix intensity measurements of all probe sets were background-corrected, normalized, and summarized into gene level expression measurements using RMA method implemented in Partek Genomic Suite V6.6, release 6.15.0127

label: biotin

source_name: RAW 264.7 cells

label_protocol: One-Cycle target labeling was performed using 5ug of total RNA according to Affymetrix's Eukaryotic Target Labeling protocol.

extract_protocol: RNA was extracted on Rneasy columns (Qiagen) with on-column DNAse I treatment, following manufacturer's instructions.

treatment_protocol: Cells were transfected with either non-targeting control gapmer (ASO-NC) or mouse Mist-targeting (ASO-Mist) GapmeR for 48 hours.

tag: gapmer

value: Mist-targeted


title: RAW264.7_ASO-NC_rep3

description: Gene expression from RAW 264.7 cells treated with non-targeted negative control GapmeR.


title: RAW264.7_ASO-Mist_rep1


title: RAW264.7_ASO-Mist_rep2


title: M3D1_PLACEBO

city: Göttingen

first: Hannelore

last: Ehrenreich

address: Hermann Rein Straße 3

department: Clinical Neuroscience

country: Germany

institute: Max Planck Institute of Experimental Medicine

description: PLACEBO treated

data_processing:
Base calls performed with bcl2fastq (v2.15)
Drop-seq toolkit (v1.2) was used for alignment (Star v2.4.0) and processing to generate digital expression matrix, see also descriptions by https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1626795
Genome_build: mm10 (provided with Drop-seq)

molecule: polyA RNA

source_name: Hippocampus CA1

extract_protocol:
The hippocampi were dissected and sliced into 600µm sections using McIlwain Tissue chopper (Cavey Laboratory Engineering Co. Ltd). The CA1 region was digested with a working solution of Papain/DNaseI in Earle’s Balanced Salt Solution, according to manufacturer’s instructions (Worthington Biochemical Corp). The samples were then incubated at 37°C for 40min with constant agitation before gentle manual trituration. The samples were centrifuged for 10min at 200g at 4°C. After discarding the Papain/DNaseI supernatant, cells were resuspended in 1mL of sterile DMEM/F12 (Sigma) without phenol-red containing 3% fetal bovine serum (FBS; Life Technologies) and the suspension was passed through a 40µm strainer cap (Corning) to yield a uniform single-cell suspension.
according to Macosko, E. Z. et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202-1214 (2015)

treatment_protocol: P28 male mice, 1xEPO (5000IU/kg, rhEPO) or 1xPlacebo injection, sacrificed after 6 hours

value: Hippocampus CA1


title: M5D2_PLACEBO

description: PLACEBO treated


title: M2D1_EPO

description: EPO treated


title: M4D2_EPO

description: EPO treated


title: M1D1_PLACEBO

description: PLACEBO treated


title: RAW264.7_ASO-NC_rep2


title: RAW264.7_ASO-NC_rep1


title: WT4


title: M6D2_EPO

description: EPO treated


title: cel_miR_39-3p_rep2

city: Tallinn

first: Ilmatar

last: Rooda

address: Akadeemia tee 15

department: Chemistry and Biotechnology

country: Estonia

institute: Tallinn University of Technology

description: Gene expression data from KGN cell line transfected with control cel-miR-39-3p 72h.

hyb_protocol: GeneChip Human Gene 2.0 ST Arrays were hybridized for 16 hours in 45 °C incubator, rotated at 60rpm. Arrays were washed and stained using the Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 7G.

data_processing: Affymetrix microarray raw data was normalized in Expression Console, provided by Affymetrix (http://www.affymetrix.com), using the robust multi-array average (RMA) method.

source_name: KGN cell line transfected with cel-miR-39-3p 72h

label_protocol: From each sample 250 nanograms of total RNA were used to generate amplified and biotinylated sense-strand cDNA according to the GeneChip WT PLUS Reagent Kit User manual (Affymetrix, Santa Clara, CA) and scanned using GeneChip® Scanner 3000 7G

growth_protocol: KGN cell line cells were grown in L-glutamine-containing Dulbecco’s Modified Eagle’s medium with 10% fetal bovine serum  and 100 U/ml penicillin and 0,1mg/ml streptomycin on 6-well plate.

extract_protocol: Cells were lysed in QIAzol lysis reagent. For total RNA extraction RNeasy Mini Kit was used according to the user manual.

treatment_protocol: For microRNA transfection Lipofectamine RNAiMAX reagent and miRCURY LNA miRNA mimics hsa-miR-548ba, hsa-miR-7973 and control miRNA cel-miR-39-3p were used according to manufacturer´s protocol. miRNA mimics were transfected at concentration of 12,5nM and for 72 h.

value: KGN

tag: transfection


title: cel_miR_39_3p_rep3


title: hsa_miR_7973_rep3

description: Gene expression data from KGN cell line transfected with hsa-miR-7973 72h.


title: cel_miR_39_3p_rep4


title: SW1990 Side Population (SP) PAF1 CRISPR KD 1 - L001

status: Public on Jan 29 2020

city: Omaha

first: Saswati

last: Karmakar

state: NE

address: 42nd st & Emile

institute: UNMC

data_processing:
Illumina sequencing and base calls
Raw Reads: FASTQ format: 1.Quality inspection using FastQC;  2.Aligned to human reference genome (hg19) using HISAT2
non-normalized gene counts were retrieved using FeatureCounts tool
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel sheet with first 5 columns containing feature information followed by non-normalized counts

source_name: Pancreas

extract_protocol:
mirVana™ miRNA Isolation Kit was used to isolate RNA. RNA quality was checked with an Agilent Bioanalyzer (Agilent Technologies, Inc.) and all of the RINs (RNA integrity numbers) were 10.
Library preparation was achieved using Illumina TruSeq RNA Sample Preparation Kit according to the manufacturer’s protocol.

tag: tissue

value: Pancreatic ductal cancer

tag: replicate

value: technical replicate 1


title: SW1990 Side Population (SP) control 2 - L002

value: technical replicate 2


title: SW1990 Side Population (SP) PAF1 CRISPR KD 2 - L002


title: SW1990 Side Population (SP) PAF1 CRISPR KD 2 - L001


title: SW1990 Side Population (SP) PAF1 CRISPR KD 1 - L002


title: cel_miR_39-3p_rep1


title: SW1990 Side Population (SP) control 2 - L001


title: SW1990 Side Population (SP) control 1 - L001


title: SW1990 Side Population (SP) control 1 - L002


title: hsa_miR_548ba_rep1

description: Gene expression data from KGN cell line transfected with hsa-miR-548ba 72h.


title: hsa_miR_548ba_rep3

source_name: KGN cell line transfected with hsa-miR-548ba 72h


title: hsa_miR_548ba_rep4


title: hsa_miR_548ba_rep2


title: hsa_miR_7973_rep4

source_name: KGN cell line transfected with hsa-miR-7973 72h


title: hsa_miR_7973_rep2


title: hsa_miR_7973_rep1


title: PDX NB_COG-N-453X_ MYCN amp, ALK F1174L

first: Malkiel

last: Cohen

address: 455 Main St

institute: Whitehead Institute

description: PDX MYCNamp, ALKF1174L (using COG-N-453X cells) expanded 1x in NU/NU mice in DFCI

data_processing:
A meta-genome was created from the canonical chromosomes from human (GRCh38) and mouse (GRCm38) and indexed with STAR using genome annotations from Ensembl 91 and the option "--sjdbOverhang 39"
Reads were mapped to this human+mouse meta-genome with STAR (version 2.7.1a, with default parameters).
Reads mapped to genes were counted with featureCounts  (version 1.6.2) using a GTF file of Ensembl 91 gene annotations and the "-s 2" option.
Genome_build: Human (GRCh38) and mouse (GRCm38)
Supplementary_files_format_and_content: Ensembl gene ID, raw counts

source_name: Human PDX NB

extract_protocol: Libraries were prepared for RNA-Seq using KAPA Biosystems KAPA mRNA HyperPrep Kit, according to manufacturer’s directions. Briefly, total RNA (0.1-1 ug) is captured for polyadenylated sequences using oligo-dT magnetic bead. The enriched mRNA fraction is then fragmented, and first-strand cDNA is generated using random primers. Strand specificity is achieved during second-strand cDNA synthesis by replacing dTTP with dUTP, which quenches the second strand during amplification. The resulting cDNA is A-Tailed and ligated with indexed adapters. Finally, the library is amplified using a DNA Polymerase which cannot incorporate past dUTPs, effectively quenching the second strand during PCR.

tag: genotype

value: MYCNamp, ALKF1174L

tag: rna extraction method

value: Mirvana

tag: anatomic location

value: Subcutaneous


title: PDX NB_SJNBL013763_ MYCN amp, ALK WT

description: PDX MYCNamp, ALKwt (using SJNBL013763_x1 cells, St. Jude) expanded 1x in NU/NU mice in DFCI

value: MYCNamp, ALKwt


title: SH-SY5Y

description: In vitro cultured cells

source_name: Human NB cell line

value: MYCNwt, ALKF1174L

value: RNAeasy


title: NCC-xenograft-023

description: hNCCs injected sq to NSG mice +Dox

source_name: Human NCC Xenograft


title: PDX NB_SJNBL046148_MYCN amp, ALK WT

description: PDX MYCNamp, ALKwt (using SJNBL046148 cells, St. Jude) expanded 1x in NU/NU mice in DFCI


title: NCC-xenograft-009_Rep_1

description: hNCCs injected sq to NSG mice +Dox


title: NCC-xenograft-010

description: hNCCs injected sq to NSG mice +Dox


title: NCC-xenograft-008

description: hNCCs injected sq to NSG mice +Dox


title: PDX NB_COG-N-415X_ MYCN amp, ALK F1174L

description: PDX MYCNamp, ALKF1174L (using COG-N-415X cells) expanded 1x in NU/NU mice in DFCI


title: NCC-xenograft-009_Rep_2

description: hNCCs injected sq to NSG mice +Dox


title: NCC-xenograft-007

description: hNCCs injected sq to NSG mice +Dox


title: Kelly

description: In vitro cultured cells


title: hNCCs WIBR#3

description: In vitro differentiated hESC-derived cells

source_name: Human NCCs

value: wt


title: hNCCs AA

description: In vitro differentiated hiPSC-derived cells


title: SMP4_0009335_B06

type: genomic

city: Melbourne

first: TANJINA

last: KADER

state: VIC

address: 305 Grattan Street

department: Cancer Genomics

country: Australia

institute: The Sir Peter MacCallum Cancer Centre

hyb_protocol: standard affymetrix protocol

scan_protocol: standard affymetrix protocol

data_processing:
standard affymetrix protocol
Copy number values were obtained against a baseline of normal DNA samples. Raw data is only available for the single file run on OncoScan v3. The rest are available in 2 matrix files, and have slightly different numbers of probes. Each sample has 5 columns: Copy A, Copy B, Copy number, Allele ratio and Allelic difference. P1 and P2 was run on OncoScan v2.

source_name: papilloma coexisting with DCIS

label_protocol: standard affymetrix protocol

extract_protocol: up to 40x 10 micron FFPE sections were needle microdissected for epithelial cells. Total genomic DNA was isolated using the DNeasy Blood and Tissue Kit (Qiagen) using a modified protocol: Wu L, Patten N, Yamashiro CT, Chui B (2002) Extraction and amplification of DNA from formalin-fixed, paraffin-embedded tissues. Appl Immunohistochem Mol Morphol 10 (3):269-274

treatment_protocol: retrospective cases received standard care

tag: histopath subtype

value: high grade ductal carcinoma in situ

tag: p63 status

tag: er status

value: Positive

tag: her2 copy number status

value: Negative


title: CPDX_COG-N-415X_NB MYCN amp, ALK F1174L

description: PDX-derived cells, MYCNamp, ALKF1174L , From COG-N-415X

source_name: Human cells derived from PDX NB


title: shCTCF-2_ATAC_seq

city: Berkeley

first: Robert

last: Tjian

address: LKS

institute: UC Berkeley/HHMI

data_processing:
Illumina’s Bcl2tofastq2 v2.17 was used to convert BcL files to fastq files and to demultiplex the samples
ATAC-seq pair-end reads were first adapter removed by Cutadapt and mapped to mm10 genome build using Bowtie2 with the following parameters: --no-discordant --no-mixed --phred33 -X2000 –threads32.
Reads mapped to mitochondria/uncharacterized chromosomes (chrM/chrUn/random) and PCR duplicates were removed by samtools.
ATAC-seq peaks were called using the MACS2 callpeak function using the –f BAMPE parameter.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig (bw)

growth_protocol: JM8.N4 mouse ESCs from the C57BL/6N strain and their genome edited derivatives were cultured on 0.1% gelatin coated plates without feeders at 37°C and 5% CO2. The ESC medium was composed of the knockout DMEM(1X) optimized for ESCs (Thermo Fisher Scientific 10829-018), 15% ESC qualified Fetal Bovine Serum (ATCC SCRR-30-2020), 1 mM GlutaMAX (Thermo Fisher Scientific 35050-061), 0.1 mM MEM nonessential amino acids (Thermo Fisher Scientific 11140-50), 0.1 mM 2-mercaptoethanol (Thermo Fisher Scientific 21985-023),1000 units of Leukemia inhibitory factor (LIF) (Millipore) and Antibiotic-Antimycotic (Thermo Fisher Scientific 15240-062).

extract_protocol: we performed ATAC-seq on 50,000 cells which were trypsinized, washed with PBS on ice, and resuspended in the reaction mix (25 μL of 2× TD buffer, 2.5 μL of transposase, 22.5 μL of nuclease-free H2O) for 30 min at 37°C. Following transposition, genomic DNA was purified and amplified by 10-14 cycles of PCR.Both ATAC-seq samples were sequenced in Illumina HiSeq 2500 or Nextseq with 150cycle paired-end sequencing

treatment_protocol: Auxin treatment results in loss of CTCF or Rad21 through proteasomal degradation.

tag: strain

value: embryonic stem cells

value: CTCF knockdown

tag: tn5 source

value: purified in house


title: 6h_TSA_ATAC_seq

description: TSA for 6hours

source_name: TSA for 6hours

value: wild type


title: KG75IBC12

source_name: papilloma coexisting with invasive cancer

value: Grade 2 invasive cancer


title: AID_Halo_CTCF_noauxin_ATAC_seq

description: no auxin

source_name: no auxin


title: KG01_Pap1

value: atypical papillary lesion


title: AID_Halo_CTCF_auxin_washoff_ATAC_seq

description: 12hour auxin + 24 hour wash off

source_name: 12hour auxin + 24 hour wash off (CTCF depletion followed by CTCF production)


title: hNCCs AA MYCN+ALK +Dox

description: In vitro differentiated hiPSC-derived cells +Dox


title: KG8DCIS7 (pap)

value: benign papillomatosis


title: KG8_pap6 (DCIS)

value: low grade ductal carcinoma in situ


title: shCon_ATAC_seq

description: empty vector shRNA

source_name: empty vector shRNA


title: AID_Halo_CTCF_12hauxin_ATAC_seq

description: 12hour auxin

source_name: 12hour auxin (CTCF depletion)


title: shCTCF-1_ATAC_seq


title: KG-04-pap4

source_name: Pure papilloma FFPE tissue

value: benign


title: KG_01_DCIS2


title: KG-14-pap10

value: benign papilloma w usual hyperplasia


title: SMP4_0009335_B07


title: KG17Pap13


title: KG-18-pap14


title: KG-15-pap11


title: KG-02-pap3


title: hNCCs WIBR#3 MYCN+ALK +Dox

description: In vitro differentiated hESC-derived cells +Dox


title: Col5_DNA_varseq

city: Riverside

first: Xueqing

middle: Maggie

last: Lu

address: 3401 Watkins Drive, Genomics, Room 2126

department: Cell Biology

institute: University of California, Riverside

data_processing:
Library strategy: Var-seq
For Var-seq, bcl2fastq was used for converting the raw data to FASTQ format (base-calling). Quality check was performed using FASTQC package. Quality check was performed using FASTQC package.Sequence reads were mapped / aligned against the reference genome using BWA. Variant calling was performed using SamTools
For ChIP-seq, raw reads quality was first analyzed using FastQC, and any base with a quality score below 25 or N was trimmed using Sickle.  Trimmed reads were then mapped to the A. thaliana genome (TAIR 10) using BWA 0.7.15-r1140 with mem option default parameters. Uniquely mapped reads were further filtered for calculating H3K9me2 coverage in transcript, while unfiltered reads were used for calculating H3K9me2 coverage in transposable elements.
For genome browser tracks, read coverage per nucleotide is calculated using BEDTools. Coverage values were then normalized per million mapped reads.
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: Aerial parts of two-weeks old seedlings

growth_protocol: Arabidopsis seedlings were grown on soil or half-strength Murashige and Skoog (1/2 MS) solid medium containing 1% (w/v) sucrose in a growth chamber (16-h day, 8-h night, 22 °C; 100 μE m-2s-1)

extract_protocol:
Chromatin was sonicated and immunoprecipitated with respective antibody. Genomic DNA were extracted with DNeasy Plant Mini Kit from Qiagen following to the manufacturer’s instruction
ChIP-seq libraries were prepared using NEBNext Ultra II DNA library prep kit for Illumina (E7645, New England Biolabs) according to the manufacturer’s instruction. Var-seq libraby were prepared using NEBNext Ultra DNA library prep kit for Illumina (E7370, New England Biolabs) according to the manufacturer’s instruction.

value: Aerial parts of two-weeks old seedlings

value: Wild type


title: WT_NoTSA_control_ATAC_seq

description: DMSO for 6hours

source_name: DMSO for 6hours


title: edm3_DNA_varseq


title: GEMM NB Th-MYCN;ALK F1174L; #644C

city: Cambridge

description: Transgenic Th-MYCN;ALKF1174L; #644 coeliac ganglia (From R. George lab, DFCI, HMS)

source_name: GEMM NB

value: Mirvana

value: Coeliac ganglia


title: Mouse Adrenal

description: Adult adrenal gland from a wt mouse

source_name: Adult mouse adrenal gland

value: wt

value: RNAeasy

value: Adrenal gland


title: GEMM NB Th-MYCN;ALK F1174L; #392AC

description: Transgenic Th-MYCN;ALKF1174L; #392 adrenal/coeliac fused (From R. George lab, DFCI, HMS)

value: Adrenal/coeliac fused


title: GEMM NB Th-MYCN;ALK F1174L; #644A

description: Transgenic Th-MYCN;ALKF1174L; #644 adrenal (From R. George lab, DFCI, HMS)

value: Adernal


title: KG-05-pap5

value: Positive

value: Negative


title: CHB23-2

first: Christopher

last: Chan

address: 185 Cambridge St

institute: Massachusetts General Hospital

data_processing:
Sequencing was performed on Illumina HiSeq 2500 instrument, resulting in approximately 30 million of 50 bp reads per sample. Sequencing reads were mapped in a splice-aware fashion to the Ensembl annotation of the mouse GRCm37/mm9 transcriptome using STAR (Dobin et al., 2013). Read counts over transcripts were calculated using HTSeq (Anders et al., 2015), followed by the differential expression analysis using EdgeR (Robinson et al., 2010). Genes were claddified as differentially expressed based on the cutoffs of 2-fold change in expression value and false discovery rates (FDR) below 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample

source_name: Thymus

extract_protocol:
Thymuses were harvested from 2 month old animals, digested in a Liberase TH/Dnase cocktail gently until a single cell suspension was obtained. Cortical and medullary thymic epithelial cells were purified by fluorescence activated cell sorting directly into RNA lysis buffer. RNA was extracted using a Nucleospin XS RNA kit,
SMARTer Low Input RNA kit v.4 (Takara Bio)

value: medullary thymic epithelial cell

value: LXRalpha flox LXR beta flox


title: CHb23-10

value: cortical thymic epithelial cell

value: FoxN1-Cre x LXRalpha flox LXR beta flox


title: CHb23-6


title: CHb23-11


title: CHb23-5


title: CHb23-4


title: CHb23-8


title: CHb23-9


title: PA549_Tn5_ATAC_seq

value: embryonic stem cells

value: wild type

value: purified in house


title: CHb23-3


title: CHb23-7


title: CHb23-1


title: Nextera_ATAC_seq

source_name: Nextera

value: Nextera kit


title: NCH644-Ro-H3K27ac

first: Markus

last: Siegelin

state: New York

department: Pathology and Cell Biology

institute: Columbia University

description: CHIP sequencing

data_processing:
none provided by the submitter
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

source_name: NCH644 glioblastoma cell line

growth_protocol: DMEM+10%FBS+primocin for U87; GBM-MG, ready-to-use for NCH644

extract_protocol:
DNA was extracted using the SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) #9005 from Cell Signalling.
next generation sequencing (NGS) from Genewiz, New Jersey

treatment_protocol: DMEM+1.5%FBS+primocin for U87+Panobinostat 0.5uM or Romidepsin 5nM; GBM-MG, ready-to-use for NCH644+Panobinostat 0.5uM or Romidepsin 5nM

value: Glioblastoma cell line

tag: treatment

value: Romidepsin

tag: chip antibody

value: H3K27ac (Cell Signalling, 8173)


title: U87-Ro-H3K27ac

description: CHIP sequencing

source_name: U87 glioblastoma cell line


title: U87-DMSO-HDAC2

description: CHIP sequencing

value: DMSO

value: HDAC2 (Cell Signalling, 57156)


title: NCH644-DMSO-H3K27ac

description: CHIP sequencing


title: NCH644-DMSO-Rpb1

description: CHIP sequencing


title: NCH644-Pb-Rpb1

description: CHIP sequencing

value: Panobinostat


title: U87-Pb-H3K27ac

description: CHIP sequencing


title: SW1990_SP_Input

data_processing:
Adaptor sequences and low quality (Phred score < 20) ends were trimmed from sequences using Trim Galore software package (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Resulting fastq files were aligned to the human genome (GRCh38/hg38) using the sequence aligner Bowtie2 (version 2.2.3)
The software package Picard routine, MarkDuplicates, (http://broadinstitute.github.io/picard/) was used to remove sequence duplications.
BigWig files were generated using the deeptools bamCoverage routine (https://deeptools.readthedocs.io/en/develop/). Alignment of significant peaks to gene specific regions was accomplished using the bedtools routine intersect (https://bedtools.readthedocs.io/en/latest/).
Genome_build: GRCh38
Supplementary_files_format_and_content: Mean occupancy values

source_name: Pancreas

extract_protocol:
SW1990 SP cells were fixed with 0.4% formaldehyde and 1.5 mM EGS (ethylene glycol bis(succinimidyl succinate)) (Thermo Scientific Fischer), washed, harvested, and resuspended in 500 μl SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris‐HCl [pH 8.1], 1 mM PMSF, and 1 μg/ml aprotinin). Samples were sonicated and diluted in ChIP dilution buffer (0.01% SDS, 1.1% Triton X‐100, 1.2 mM EDTA, 16.7 mM Tris‐HCl [pH 8.1], 167 mM NaCl, 1 mM PMSF, and 1 μg/ml aprotinin). For input control, 10% of sonicated samples were separated. Immunoprecipitation was performed with ChIP‐grade PAF1 (Abcam) and Phf5a (Proteintech) antibody as previously described. Chromatin extracts were pulled down with protein A+G beads. The samples were washed extensively with wash buffers (low salt, high salt, LiCl, and Tris/EDTA buffers), eluted with SDS elution buffer, and subjected to reverse cross-linking and proteinase digestion. IgG antibody was used as a control for the ChIP assay.
The captured and purified DNA was prepared for high throughput sequencing using the New England Biolabs NEBNext Ultra II DNA Library Prep Kit for Illumina.

tag: cell line

value: Pancreatic ductal cancer


title: EM_HD1_NK_scRNAseq

first: Emily

last: Mace

department: Department of Pediatrics

institute: CUIMC

data_processing:
Raw FASTQ files were processed using CellRanger (v 2.0.1) in-order to map reads against the human hg38 reference genome, filter out unexpressed genes, and count barcodes and unique molecular identifiers (UMIs).
Genome_build: hg38
Supplementary_files_format_and_content: CellRanger output

source_name: sorted primary NK cells

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from fresh blood collected into EDTA-coated tubes (fisher scientific) using density gradient centrifugation (Ficoll-Paque Plus; Amersham Pharmacia Biotech). Primary human NK cells were isolated using negative magnetic bead selection (Miltenyi Biotec or Stemcell Technologies).

extract_protocol: Individually-barcoded single cell RNA-seq libraries were prepared using the Chromium Single Cell Controller and Chromium Single Cell 3′ Library & Gel Bead Kit v2 kit (10x Genomics, Pleasanton, CA). All steps were carried out according to the manufacturers’ instructions.

tag: cell type

value: NK cells

tag: passages

value: primary

tag: disease

value: healthy


title: U87-DMSO-H3K27ac

description: CHIP sequencing


title: CHb23-12


title: SW1990_SP_Pkf5a

tag: tissue


title: SW1990_SP_PD2


title: HCT116_WT_clones_methylome

city: Rehovot

first: Zohar

last: Meir

state: Shfela

address: Herzl 234

department: Mathematics & CS

country: Israel

institute: Weizmann Institute of Science

description: Capture-PBAT DNA methylation profiling HCT116 WT clones, using probe set targeting >47K loci and designed for colon cancer analysis. Names of clones match the corresponding transctripome samples

data_processing:
scRNA MARS-seq: .Read-1 files were mapped to the hg19 genome assembly using Bowtie2 (default parameters)
.Demultiplexing and UMI counting were based on 8bp of UMI and 7bp of cell-barcodes in Read-2, and performed using the pipeline described in Jaitin et al. 2014
bulk MARS-seq: .Mapping, demultiplexing and UMI counting was performed as for scRNA MARS-seq (see above)
.UMI counts of wells that were assigned to the same clone in each plate were aggregated based on 1) conversion key of well-barcode to well-position. 2) plate design template, assigning each clone-ID to a well-position
single cell whole-genome-PBAT methylome and clonal populations capture-PBAT methylome: PE 150bp reads were aligned to the GRCh37 (hg19) reference genome (UCSC, February 2009) using an in-house script based on Bowtie2 (Mukamel et al.). In cases where the two reads ends were not aligned in a concordant manner, the reads were discarded. Reads that were mapped to the same genome coordinates where marked as duplicates and were used only once. We subsample methylation of single-cells to have only one methylation call per CpG.
Supplementary_files_format_and_content: Expression datasets: UMI counts per gene per sample. Methylation: methylated and un-methylated calls per CpG
Genome_build: hg19

source_name: colorectal cancer cell line HCT-116

extract_protocol:
RNA capture for scRNA MARSseq: single-cells were FACS-sorted directly into barcoded lysis solution in 384-well MARS-seq plates, which were immediately transfered and kep at -80C. lysis solution contained UPW, 8nM poly-dT barcodes,  0.1%triton and RNAse inhibitors. RNA capture for bulk-RNA MARSseq: 1ul of each suspended clonal population transferred maunally into barcoded lysis solution in 384-well MARS-seq, assigning 2-6 wells for each clonal population which serve as technical replicates
Cells were propagated and split in tissue-culture routinely, and grown on proper media according to the manufacturer instructions
genomic material for DNA methylation assays was treatead with Proteinase K and RNAse A prior to bisulfite conversion
cDNA MARS-seq library preparation: scRNA MARS-seq library prepartion was performed as described in Jaitin et al. 2014. For bulk MARS-seq, only difference was extending the first evaportaion step at 95 degree from 3 to 4 minutes, in order to compensate for the additional volume.  10x scRNAseq: 3' single cell cDNA libraries of WT and DKO HCT116 cells were generated using Chromium™ Single Cell 3’ Library & Gel & Bead Kit v2 (PN-120237), Chromium Single cell 3' Chip Kit V2 (PN-120236) and Chromium i7 Multiplex Kit (PM-120262), following the manufacture instructions (10x Genomics®, Inc.)
whole-genome single-cell PBAT DNA methlyation profiling: single WT and DKO HCT116 cells were FACS sorted in 384-wells plates, before bisulfite-conversion and processing by the PBAT protocol (Mukamel et al, in preparation). targeted methylation profiling of clones by capture-PBAT: 8uL of each suspension of clonal population was use for PBAT-capture methylome (the other 2uL of each HCT116 clone were used for transcriptiome profiling). The full protocol is described in Mukamel et al. In brief, we have created whole-genome DNA methylation profile of each clone in a 96-wells plates according to wgPBAT. we then created balanced pools of 30-40 clones prior to hybridization to probe library designed for colon cancer analysis (Mukamel et al.), targeting nearly 50K regions and enriched for ehancers and promoters.

value: colorectal cancer cell line

tag: genotype/variation

value: Wild type

tag: molecule subtype

value: DNA methylation (5'-methylcytosine)


title: HCT116_WT_cells_methylome_wgPBAT

description: whole-genome DNA methylation profiling (using Post Busulfilte Adaptor Tagging, PBAT) of single HCT116 cells


title: HCT116_WT_longTerm_cells_transcriptome_MARSseq_day148

description: scRNA sampling of six selected single-cell-derived HCT116 clones (selected based on distributions after 10 and 18 days) as well as a control polyclonal population at different time-points (since seeding of clone founder cells)


title: HCT116_WT_longTerm_cells_transcriptome_MARSseq_day62


title: HCT116_WT_longTerm_cells_transcriptome_MARSseq_day33


title: A549_clones_transcriptome

description: bulk MARS-seq of single-cell-derived A549 clones

source_name: Adenocarcinomic human alveolar basal epithelial cell line A549


title: WI38_clones_transcriptome

description: bulk MARS-seq of single-cell-derived WI-38 clones

source_name: Embryonic lung fibroblasts cell line WI38-hTERT

value: Embryonic lung fibroblasts cell line


title: HCT116_WT_longTerm_cells_transcriptome_MARSseq_day98


title: HCT116_WT_clones_transcriptome

description: bulk MARS-seq of single-cell-derived HCT116 WT clones


title: HCT116_DKO_cells_transcriptome_10x

description: single cell RNA sequencing of polyclonal DKO population of colorectal cancer cell line HCT-116 by the 10x platform.

value: DKO (DNMT1exons3-5/exons3-5; DNMT3B-/-)


title: WI38_cells_transcriptome_MARSseq

description: single cell RNA sequencing of polyclonal  population of embryonic lung fibrobalsts cell line WI-38 by MARS-seq (Jaitin et al., 2014)


title: HCT116_WT_clones_transcriptome_longTerm_day10

description: low-depth bulk MARS-seq of single cell derived HCT116 clones, 10 days after seeding of single cells


title: Jun_DZ50

city: Wuhan

first: Leike

last: Zhang

address: Xiaohongshan road

institute: The State Key Laboratory of Virology  Wuhan Institute of Virology, CAS

data_processing:
base calling: Casava v1.8.2 was used for base calling
data filtering: NGSQCtoolkit v2.3.3 was used for data filtering
read alignment: HISAT v0.1.5 was used for read alignment
abundance measurement: StringTie v1.3.3 was used for abundance measurement
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: whole blood cells

extract_protocol:
Whole blood cells were collected and total RNA was extracted with Trizol (Tiangen, Beijing) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Invitrogen).
The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) was used to construct the libraries for sequencing.

tag: patient diagnosis

value: whole blood cells

tag: clincal status group

value: Healthy


title: Jun_DZ45


title: HCT116_WT_cells_transcriptome_10x

description: single cell RNA sequencing of polyclonal WT population of colorectal cancer cell line HCT-116 by the 10x platform.


title: HCT116_WT_cells_transcriptome_MARSseq

description: single cell RNA sequencing of polyclonal WT population of colorectal cancer cell line HCT-116 by MARS-seq (Jaitin et al., 2014)


title: K562-COP1

city: Guangzhou

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

institute: Southern Medical University

data_processing:
Library strategy: CoP-seq
Illumina Casava1.7 software used for basecalling.
CoP, ATAC-seq and HiCoP rawdata were filtered by fastp(version 0.19.6) with default parameters.
CoP and ATAC-seq reads were mapped to the hg19 (or mm10) genome assembly using bowtie2 (version 2.20.8) with parameters (-X 2000, --sensitive);
Uniq mapped CoP and ATAC-seq reads pairs were got after pcr duplication removing by Picard (version version 2.20.8) and samtools (version 1.3.1);
RPKM normalized BigWig files of CoP and ATAC-seq were generated by BEDtools (version 2.26.0);
BroadPeaks of CoP and ATAC-seq were called from Bam file by using MACS2 (version 2.1.3.3) with parameters (--nomodel, --extsize 147, -q 0.01).
HiCoP reads were aligned to the hg19 genome assembly and filtered by using HiCPro (version 2.11.1) with default parameters;
Hic file of HiCoP were transfer from HiCPro result by using Juicertools (version 1.13.02);
HiCoP interactive loops were identified by FitHiC (version 2.0.7)  with parameters (distUpThres=1000000, disLowThres=20000, noofBins=100, noOfPasses=2) at resolution 10kb.
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: bigwig files; broakpeak file (bed format); hic file;

growth_protocol: Jurkat cells were grown in RPMI-1640 medium containing 10% fetal bovine serum at 37°C and 5% CO2. K562 cells were grown in IMDM medium containing 10% fetal bovine serum at 37°C and 5% CO2, and HL-60 cells were grown in IMDM medium containing 20% fetal bovine serum at 37°C and 5% CO2.

extract_protocol:
For mouse CoP, thymus, spleen and kidney were removed,cells were filtered through nylon mech. Red cells were lysed in AcK buffer.Cells were crosslinked,lysates of CoP sample were clarified from sonicated nuclei and open chromatin were isolated with DNA purification column.
For K562 CoP, cells were crosslinked,open chromatin were isolated with DNA purification column from sonicated nuclei.
For K562 Hi-CoP, cells were crosslinked,digested and ligated. After sonication, open chromatin were isolated with DNA purification column.
For mouse ATAC, thymus was removed,cells were filtered through nylon mech. Red cells were lysed in AcK buffer.Cells were perforated and dealed with Tn5, open chromatin were isolated with DNA purification column.
The CoP libraries were prepared by either Tn5 tagmentation or linker ligation. Tagmentation was done with TransNGS Tn5 DNA Library Prep kit for Illumina following the manufacturer’s recommendations. The reaction was incubated 5 min at 55 ºC followed by adding 30μl of 2x Tn5 Digestion Mix and incubated 5min at 55ºC, then purified with MagicPure Size Selection DNA Beads and elution in21 μL of water. After that, library (20 μL)was amplified by using TransNGS Library Amplification SuperMix. Alternatively, end repair and dA tailing were done with VAHTSTM Universal End preparation Module for Illumina. DNA was purified with VAHTS DNA Clean beads. Added adapter by Quick ligase, then library was amplified with PCR amplification kit. After 5 cycles of amplification, qPCR was done to determine additional cycle number. After library amplification, purification and size selection, library concentration was detected by Qubit. The libraries were sequenced by HiseqXten-PE150 Illumina sequencing platform in Novogene Corporation Inc.
Hi-CoP libraries were prepared using in-situ HiC protocol. Dynabeads MyOne Streptavidin C1 beads was washed once with 1×Tween Washing Buffer. The beads were added to HiCoP DNA and incubated at RT for 15 min with rotation. The beads were washed by adding 200μl of 1×TWB. Heat the tubes on a Thermomixer at 55°C for 2 min with mixing. The beads were reclaimed using a magnet, supernatant was discarded. Repeat washing. End-repair and dA tailing following the in situ Hi-C protocol, adapters were added to DNA fragments. PCR amplification was performed with thirteen to nineteen cycles using Illumina primers.
ATAC library was prepared according to Vazyme's instructions accompanying the TruePrep DNA Library Prep Kit V2 for Illumina (#TD501).

value: Cell line

tag: genotype

value: wild type


title: Jun_DZ37


title: K562-COP2


title: HCT116_KO_clones_transcriptome

description: bulk MARS-seq of single-cell-derived HCT116 KO clones

value: KO (DNMT3B-/-)


title: Jun_DZ36


title: Jun_DZ44


title: Jun_DZ51


title: Jun_DZ35


title: Jun_DZ46


title: HCT116_DKO_clones_transcriptome

description: bulk MARS-seq of single-cell-derived HCT116 DKO clones


title: HCT116_DKO_cells_methylome_wgPBAT

description: whole-genome DNA methylation profiling (using Post Busulfilte Adaptor Tagging, PBAT) of single HCT116 DKO cells


title: HCT116_DKO_cells_transcriptome_MARSseq

description: single cell RNA sequencing of polyclonal DKO population of colorectal cancer cell line HCT-116 by MARS-seq (Jaitin et al., 2014)


title: Jun_DZ32


title: HCT116_WT_clones_transcriptome_longTerm_day18

description: low-depth bulk MARS-seq of single cell derived HCT116 clones, 18 days after seeding of single cells


title: H1299_clones_transcriptome

description: bulk MARS-seq of single-cell-derived NCI-H1299 clones

source_name: Non-small cell lung cancer (NSCLC) cell line NCI-H1299


title: Jun_DZ34


title: Jun_DZ31


title: Jun_DZ25


title: Jun_DZ27


title: Jun_DZ28


title: Jun_DZ3


title: Jun_DZ22


title: Jun_DZ16


title: Jun_BJ84

value: SFTS

value: AcuteRecover


title: Jun_BJ80

value: AcuteDeceased


title: Jun_BJ82


title: Jun_BJ81


title: Jun_BJ9


title: Jun_BJ85


title: Jun_DZ15


title: Jun_BJ72


title: Jun_BJ67


title: Jun_DZ11

value: Recover


title: Jun_BJ70


title: Jun_BJ68


title: Jun_BJ78


title: Jun_BJ65


title: Jun_BJ77


title: Jun_BJ66


title: Jun_BJ60


title: Jun_BJ59


title: Jun_BJ62


title: Jun_DZ30


title: Jun_DZ21


title: Jun_BJ55


title: Jun_DZ17


title: Jun_BJ56


title: Jun_BJ61


title: Jun_BJ75


title: Jun_BJ49


title: Jun_BJ46


title: Jun_BJ43


title: Jun_BJ47


title: Jun_BJ48


title: Jun_BJ45


title: Jun_BJ51


title: Jun_BJ42


title: Jun_BJ53


title: Jun_BJ37


title: Jun_BJ41


title: Jun_BJ32


title: Jun_BJ44


title: Jun_BJ38


title: Jun_BJ29


title: Jun_BJ31


title: Jun_BJ28


title: Jun_BJ58


title: Jun_BJ27


title: Jun_BJ57


title: Jun_BJ36


title: Jun_BJ24


title: Jun_BJ25


title: Jun_BJ20


title: Jun_BJ21


title: Jun_BJ23


title: Jun_BJ19


title: Jun_BJ17


title: Jun_BJ39


title: Jun_BJ13


title: Jun_BJ11


title: Jun_BJ12


title: ski3 mutant_2

city: Tokyo

first: Toshiro

last: Aigaki

address: 1-1, Minami-oosawa, Hachioji-shi

department: Biological Sciences

country: Japan

institute: Tokyo Metropolitan University

data_processing:
Illumina NovaSeq 6000 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to BDGP6 whole genome using bowtie v2.3.4.1 with default parameters and TopHat v2.3.4.1 with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using caffdiff software.
Genome_build: DGRP6
Supplementary_files_format_and_content: gene feature format files include FPKM values for each Sample

organism: Drosophila melanogaster

source_name: 3rd instar larvae

extract_protocol:
Third instar larvae were collected, flash frozen in liquid Nitrogen, and RNA was harvested using Trizol reagent. QuantiTect Reverse Transcription Kit (Cat#205311) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CantonS

value: Whole body

tag: age

value: 3rd instar larvae

value: ski3f03251 homozygote


title: Ctrl_1

value: Control


title: Ctrl_2


title: Jun_BJ16


title: TH1Minus.3

first: Sylvie

last: Guerder

address: CHU Purpan

department: Immunology

institute: INSERM

data_processing:
Trim reads were aligned  to the mouse genome using the splice-aware alignment tool : STAR v.2.6
Reads were counted and were associated with known genes.
Count reads were normalized using Deseq2 v.1.24.0
Genome_build: Mouse mm10
Supplementary_files_format_and_content: normalized counts

source_name: Immature cDC1 sorted from the Thymus

extract_protocol:
Mature (CCR7+ Esam+) and immature (CCR7- Esam-) cDC1 (F4/80-Ly6g-Ly6c-DX5-B220-CD24+ CD11b- CD11c+ cells  ) and cDC2 (B220-CD24- CD11b+ CD11c+ cells) from were FACS-sorted using BD Aria II. RNA was extracted using a RNA XS Isolation Kit (Macherey Nagel)
RNA libraries were prepared according to Illumina's instructions, using an Truseq Stranded mRNA kit.

treatment_protocol: Total CD11c+ cells were extracted with enzymatic digestion from Thymus and Spleen and positive selection using CD11c magnetic beads (Miltenyi Biotec).

value: 6-8 weeks

value: Thymus

tag: maturation state

value: Immature


title: SP1Minus.4

source_name: Immature cDC1 sorted from the Spleen

value: Spleen


title: TH2Plus.2

source_name: Mature cDC2 sorted from the Thymus

value: Mature


title: RNASeq Th1 cells 72h polarization

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

data_processing:
Sequenced reads were aligned to the mm10 genome assembly using Bowtie 2.2.6 and Tophat 2.2.1
Aligned reads are converted to BAM files using samtools. BAM files are subsequently converted to BED files using bedtools. MACS v1.4.2 is used to call peaks using the BED files. RSEM (RNA-Seq by Expectation-Maximization) and unpublished python scripts were used to calculate raw counts. RPKM (reads per kilobase per million reads) model was used to normalize gene expression values for RNA-Seq data. R package edgeR was used to identify differentially expressed genes among different conditions.
Genome_build: mm10
Supplementary_files_format_and_content:
abundance measurements for RNA-seq samples
bed files for ChIP-seq samples

source_name: spleen

growth_protocol: Naïve CD4+ T cells were purified from spleens of 7-8 week old mice using a CD4+CD62+ T cell Isolation Kit II (Miltenyi). Mouse naïve CD4+ T cells were cultured at 1e6/ml in RPMI 1640 medium containing 10 mM Hepes, 10% fetal bovine serum, 2 mM L-glutamine, and antibiotics, including 50 μM 2-ME

extract_protocol:
For ChIP-seq, 10 million Th1 cells overexpressing Trp73 or vector control cells were performed using anti-FLAG (M2) antibody (Sigma) as previously described. For RNA-seq, Trp73 overexpressed Th1 cells were isolated by FACS sorting as GFP+ cells three days after retroviral transduction, and total RNA was then extracted. RNA-Seq libraries were prepared from mRNA (isolated from 2 μg total RNA) using the KAPA kit per the manufacturer’s protocol.
After quantification by Qubit (Invitrogen), barcoded samples were mixed and sequenced on an Illumina HiSeq2000 or HiSeq3000 system.

treatment_protocol: Purified naïve CD4+ T cells were polarized under Th1 conditions for 3 days with plate-bound anti-CD3 (2 μg/ml), soluble anti-CD28 (1 μg/ml, PharMingen), 10 ng/ml mouse IL-12 (PeproTech), and 10 μg/ml of anti-mIL-4 antibody

value: Th1 cells

value: Th1, polarized 72 hours


title: RNASeq naive CD4+ T cells

value: naive CD4+ T cells


title: RNASeq Th1 TAp73 over-expression

value: TAp73 over-expression, Th1, polarized 72 hours


title: RNASeq Th1 Vector

value: Vector, Th1, polarized 72 hours


title: RNASeq Th1 DNp73 over-expression

value: DNp73 over-expression, Th1, polarized 72 hours


title: TH2Plus.1


title: TH1Plus

source_name: Mature cDC1 sorted from the Thymus


title: TH1Plus.1


title: TH2Plus


title: SP1Minus.3


title: SP2Minus.2

source_name: Immature cDC2 sorted from the Spleen


title: SP1Minus.2


title: Jun_BJ14

value: SFTS

value: whole blood cells

value: Recover


title: TH2Minus.1

source_name: Immature cDC2 sorted from the Thymus


title: TH1Minus.2


title: TH1Minus.1


title: TH2Minus.2


title: TH2Minus


title: SP2Minus.1


title: TH1Minus


title: TH1Plus.2


title: SP1Minus.1


title: ski3 mutant_1

value: CantonS

value: Whole body

value: 3rd instar larvae


title: H3C_edm3_Rep1

data_processing:
For Var-seq, bcl2fastq was used for converting the raw data to FASTQ format (base-calling). Quality check was performed using FASTQC package. Quality check was performed using FASTQC package.Sequence reads were mapped / aligned against the reference genome using BWA. Variant calling was performed using SamTools
For ChIP-seq, raw reads quality was first analyzed using FastQC, and any base with a quality score below 25 or N was trimmed using Sickle.  Trimmed reads were then mapped to the A. thaliana genome (TAIR 10) using BWA 0.7.15-r1140 with mem option default parameters. Uniquely mapped reads were further filtered for calculating H3K9me2 coverage in transcript, while unfiltered reads were used for calculating H3K9me2 coverage in transposable elements.
For genome browser tracks, read coverage per nucleotide is calculated using BEDTools. Coverage values were then normalized per million mapped reads.
Genome_build: TAIR10

source_name: Aerial parts of two-weeks old seedlings

value: Aerial parts of two-weeks old seedlings


title: SP2Minus

value: 6-8 weeks


title: H3C_WT_Rep2

value: Wild type


title: H3C_edm3_Rep2


title: SP1Minus

value: Spleen

value: Immature


title: ChIPSeq Th1 DNp73

description:
 p100.FDR0.05.Th1.DNp73.vs.vector_peaks.bed
 combined.p100.DNp73.TAp73.peaks.bed

value: Th1 cells

value: anti-FLAG (M2) antibody (Sigma)


title: ChIPSeq Th1 TAp73

description:
 p100.FDR0.05.Th1.TAp73.vs.vector_peaks.bed
 combined.p100.DNp73.TAp73.peaks.bed


title: 0004626-B11

source_name: Pure papilloma FFPE tissue

tag: histopath subtype

value: atypical papillary leison

tag: p63 status

value: Positive

tag: er status

tag: her2 copy number status

value: Negative


title: H3K9me2_edm3_Rep2


title: H3K9me2_WT_Rep2


title: H3K9me2_edm3_Rep1


title: C57-thymus-COP3

source_name: Thymocytes

tag: strain

value: thymus

value: 4-12 weeks

value: wild type


title: H3K9me2_WT_Rep1


title: CHNB022

description: human neuroblastomas from mouse-human neural crest chimeric mice model +Dox

organism:
Homo sapiens
Mus musculus

source_name: CHNB

tag: rna extraction method

value: Mirvana

tag: anatomic location

value: Retroperitoneum


title: c57-thymus-ATAC

data_processing:
Illumina Casava1.7 software used for basecalling.
CoP, ATAC-seq and HiCoP rawdata were filtered by fastp(version 0.19.6) with default parameters.
CoP and ATAC-seq reads were mapped to the hg19 (or mm10) genome assembly using bowtie2 (version 2.20.8) with parameters (-X 2000, --sensitive);
Uniq mapped CoP and ATAC-seq reads pairs were got after pcr duplication removing by Picard (version version 2.20.8) and samtools (version 1.3.1);
RPKM normalized BigWig files of CoP and ATAC-seq were generated by BEDtools (version 2.26.0);
BroadPeaks of CoP and ATAC-seq were called from Bam file by using MACS2 (version 2.1.3.3) with parameters (--nomodel, --extsize 147, -q 0.01).
HiCoP reads were aligned to the hg19 genome assembly and filtered by using HiCPro (version 2.11.1) with default parameters;
Hic file of HiCoP were transfer from HiCPro result by using Juicertools (version 1.13.02);
HiCoP interactive loops were identified by FitHiC (version 2.0.7)  with parameters (distUpThres=1000000, disLowThres=20000, noofBins=100, noOfPasses=2) at resolution 10kb.
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: bigwig files; broakpeak file (bed format); hic file;


title: C57-thymus-COP2


title: CHNB025


title: C57-thymus-COP1


title: Input-Chip

city: Nanjing

first: Zhengguang

state: Jiangsu

address: No.1 Weigang, Nanjing Agricultural University

institute: Nanjing Agricultural University

description: ck

data_processing:
Basecalls performed using Bowtie2
ChIP-seq reads were aligned to the FungiDB-39_CneoformansH99
Data were filtered using the following specifications:Mismatches of no more than two bases, of which the only matched reads (the reads matched to the only position on the genome) will be used for subsequent information analysis
peaks were called using Macs2.Based on the sequence located on the genome and its abundance, we can find those statistically significant site peaks.
Genome_build: FungiDB-39_CneoformansH99

organism: Pyricularia oryzae

source_name: Fungus mycelium

growth_protocol: MoAtf1-GFP strain and the wild type strain incubated in  the complete medium for 2 days

extract_protocol:
1. Mycelium was cultured in liquid CM for 2 days at 28℃, 160 rpm.  Day1:  2. The harvested mycelia were divided with one part being immediately frozen in liquid nitrogen for future RNA isolation and RNA-seq.  3. Cross-linking. Re-suspending ~3 g mycelia in 54 ml of Buffer A with 1% formaldehyde (~1.5 ml) in 125 ml flask for 10 min under shaking (160 rpm) at 28℃.  4. Stop cross-linking by adding 1.25 M glycine (final concentration 0.125 M), continue incubation for 5min.  5. Rinse the mycelia with a lot of water to remove formaldehyde. Mycelia were collect and dry well.  6. Grind frozen mycelia in a chilled (with LOTS of liquid N) mortar and pestle. Transfer fine powder to 20 ml cell lysis buffer and brief vortex. Stay on ice for 5 min. The following operations should keep on the ice.  7. Using four layers of filter cloth filter collecting the filtrate in a new 50 ml tube. Centrifuge at 1,350 g for 10 min at 4°C. This step is critical. Check sample by microscopy before centrifuging, make sure the filtrate contains free nuclei.   8. Discard supernatant and re-suspend pellet into 200-250ul of nuclei lysis buffer for 30 min. Keep cold.  9. DNA fragmentation. The sample should dilute 1 time with TE buffer (the concentration of SDS is 0.5%). The diluted samples sonicated with Biorupter in the following condition: 30 sec ON and 30 sec OFF at power level H for total 8 min. 4 samples were broken at one time, and the four samples were placed next to each other, each sample 100 ul.  Note: sonication is the most important step for ChIP. Conditions depend on type of sonicator. The ChIP DNA should shear to an average size of 250 bp ranging from 100-500bp.  10. Centrifuge at 12,000 rpm for 5 min at 4 °C.   11. Absorb supernatant, if proceeding to ChIP immdediately store on ice, otherwise put at -80°C immediately. 30 ul sample was divided into a new 1.5 ml tube for reverse crosslinking of the input control. The remaining sample was saved for immunoprecipitation.  Day2: Immunoprecipitation  12. The GFP-Trap® - ChromoTek was used to Immunoprecipitation, and 35 ul agarose bead for each tube. Add 1 ml of wash buffer, inverse 6 times, centrifuge at 2600 g for 3 min at 4°C, discard supernatant. Repeat one time and will be used.  13. The sample saved for immunoprecipitation was diluted 5 times again (the concentration of SDS is 0.1%). 1 ml dilution sample was added to the tube with 30 ml beads. Rotate at 4°C for 2 hours.   14. Centrifuge at 2600 g for 3min at 4°C, discard supernatant.  15. Add 1 ml of wash buffer, inverse 6 times, centrifuge at 2600 g for 3min at 4°C, pipet off supernatant. Repeat two times.  16. Add 50 ul glycine and gently beat tube for 1 min. the sample should be in cold.  17. Transfer 45 ul supernatant to a new tube and add 5 ul Tris-base - this is your ChIP’d DNA.  18. Add 5.5 ul of 2 M NaCl (the concentration of NaCl is 0.2 M) and incubate ovetnight at 65°C for reverse crosslinging. From this step, he input sample and ChIP’d DNA have same treatments.   Day 3: Purify ChIPed DNA  19. Add 1 ul of RNase A and incubate for 30 min at 37°C.  20. Add 2 ul of Proteinase K and incubate for 90 min at 42°C.  21. Add 120 ul of EtOH at -20°C for 30 min to precipitation. Centrifuge at 12,000 rpm for 10 min and dry.  22. Add 25 ul ddH2O at 37°C for 30 min. This is the final ChIP’d DNA and is named output.  23. The input and output send to company for sequencing.
prepared for sequencing using standard lllumina GA

treatment_protocol: without treatment

value: mycelium

tag: sample type

value: input


title: CHNB021

data_processing:
A meta-genome was created from the canonical chromosomes from human (GRCh38) and mouse (GRCm38) and indexed with STAR using genome annotations from Ensembl 91 and the option "--sjdbOverhang 39"
Reads were mapped to this human+mouse meta-genome with STAR (version 2.7.1a, with default parameters).
Reads mapped to genes were counted with featureCounts  (version 1.6.2) using a GTF file of Ensembl 91 gene annotations and the "-s 2" option.
Genome_build: Human (GRCh38) and mouse (GRCm38)
Supplementary_files_format_and_content: Ensembl gene ID, raw counts


title: CHNB013

value: RNAeasy


title: Atf1-Chip

value: ChIP


title: CHNB010


title: CHNB012


title: CHNB009


title: CHNB008


title: H3C_WT_Rep1

value: Aerial parts of two-weeks old seedlings

value: Wild type


title: ChIPSeq Th1 Vector

description:
 p100.FDR0.05.Th1.TAp73.vs.vector_peaks.bed
 p100.FDR0.05.Th1.DNp73.vs.vector_peaks.bed
 combined.p100.DNp73.TAp73.peaks.bed

tag: cell type

tag: treatment

value: Vector, Th1, polarized 72 hours

tag: chip antibody


title: K562-HiCoP2

value: Cell line


title: Prrx1cre_E115

city: Houston

first: Noriaki

last: Ono

state: Texas

department: School of Dentistry

institute: University of Texas Health Science Center at Houston

description:
FACS-sorted at E11.5
Sample_132331

data_processing:
The sequencing data was first pre-processed using the 10X Genomics Cell Ranger software.
For alignment purposes, we generated and used a custom genome fasta and index file by including the sequences of eGFP and tdTomato_WPRE to the mouse genome (mm10).
Further downstream analysis steps were performed using the Seurat R package.
We filtered out cells with less than 1000 genes per cell and with more than 15% mitochondrial read content.
The downstream analysis steps include normalization, identification of highly variable genes across the single cells, scaling based on number of UMI, dimensionality reduction (PCA, and UMAP), unsupervised clustering, and the discovery of differentially expressed cell-type specific markers.
Genome_build: mm10_trans_nono
Supplementary_files_format_and_content: raw_feature_bc_matrix/barcodes.tsv.gz, features.tsv.gz & matrix.mtx.gz

source_name: Hind limbs

extract_protocol:
Hind limbs were dissected and enzymatically dissociated. tdTomato+ cells were FACS-isolated. ~15,000 cells were loaded onto 10X Genomic Chromium Single Cell Solution v3
10X Genomic Chromium Single Cell 3' v3 Libraries

tag: tissue

value: Hind limbs

value: Prrx1-cre; R26R(tdTomato/+)

tag: cells

value: tdTomato+ limb bud mesenchymal cells

tag: developmental stage

value: Embryonic day 11.5


title: Lor 2w

status: Public on Jan 28 2020

city: Tampa

last: Vander Velde

state: FL

address: 12902 USF Magnolia Drive

institute: H. Lee Moffitt Cancer Center

data_processing:
Basecalls performed using bcl2fastq2
Reads were aligned to the human genome (hg38) using the BWA algorithm (default settings)
Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome.
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of p-value = 1e-7. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Genome_build: hg38
Supplementary_files_format_and_content: tsv file with position and rlog values of peaks and nearby genes

source_name: Cancer Cell Line

growth_protocol: Cells were grown in RPMI with 10% FBS

extract_protocol: H3122 cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield.

treatment_protocol: Cells were treated in .1% DMSO

tag: evolved resistance in

value: 0.5µM lorlatinib

tag: cell line

value: Histone H3K27ac antibody (pAb) (Active Motif, cat# 39133, Lot# 01518010)


title: H3122p


title: erAlec0

value: 2µM alectinib


title: erLor1

value: 2µM lorlatinib


title: NPC_H8_R_B2_P10

city: Munich

first: Tatsiana

last: Aneichyk

address: Josef-Frankl-Strasse 5A

institute: Independent Data Lab

data_processing:
Quality control (QC) assessment of sequence reads was performed using fastQC (v. 0.10.1 http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were aligned to to human reference genome Ensembl GRCh37 (v. 75) using STAR (v. 2.4.2) with its default parameter settings and --quantMode GeneCounts to generate gene counts.
Genome_build: Ensembl GRCh37 (v. 75)
Supplementary_files_format_and_content: Processed data files consist ENSEMBL gene ID and raw RNA-seq gene counts

source_name: iPSC-derived NPCs_wt

growth_protocol: iPSCs were cultured on Matrigel-coated wells using conditioned mTeSR medium (StemCell Technologies). Expandable neuronal progenitor cells (NPCs) were generated from iPSCs through differentiation by the embryoid body (EB) protocol using STEMdiff™ Neural Induction Medium (StemCell Technologies), following the manufacturer’s instructions. Terminal neuronal differentiation was achieved by plating expanded NPCs at a seeding density of 2 × 106 cells per well on polyornithine/laminin-coated plates (coated together overnight) in NPC expansion medium lacking both growth factors EGF and bFGF and heparin, with medium replacement every 3–5 days for 30 days.

extract_protocol:
RNA from cell lines was obtained by lysing 1-2 million cells using 1mL of Trizol (Invitrogen) then mixed with 1/5th volume of chloroform and centrifuged at 200g for 5 minutes. The aqueous phase was collected and processed using a RNeasy Mini column (Qiagen). cDNA was synthetized from 1µg of extracted RNA using SuperScript® III Reverse Transcriptase (ThermoFisher Scientific) with oligo(dT), random hexamers, and RNase inhibitor.
The RNAseq library was prepared as previously described (Aneichyk et al 2018).

treatment_protocol: The iPSCs (1 × 10^6 cells) were transfected with 1 µg total DNA plasmid, Cas9 expression vector pX459 (pSpCas9(BB)-2A-Puro - Addgene plasmid 48139) along with the chosen gRNAs (inserted into pGuide - Addgene plasmid 41824) and an external EGFP (enhanced green fluorescent protein) vector. For nucleofection of the gRNAs into the iPSC, the Human Stem Cell Nucleofector Kit 1 (Lonza) and Amaxa Nucleofection II device (Lonza) were used with program B-016, according to the manufacturer’s instructions. After nucleofection, iPSCs were cultured on Matrigel-coated wells using conditioned mTeSR medium (StemCell Technologies) supplemented with 10 µM ROCK inhibitor (Y-27632 dihydrochloride, Santa Cruz Biotech) and 10 ng/ml bFGF (R&D).   Three MBD5-edited cell lines with alterations in the conserved MBD domain were used in this study (Figure 4C). Cell line 1 is a compound heterozygote cell line (6het AIVG12), generated using guideRNAs 6.8 and 6.5 (Supplementary Table 2). The first allele contains a 4bp deletion (NM_018328.4(MBD5):c.66_70del), that is predicted to lead to a prematurely truncated peptide of only 80 amino acids. The second allele bears a 4bp deletion (NM_018328.4(MBD5):c.66_70del) followed by a 16bp insertion  (NM_018328.4(MBD5):c.70_86ins) that result in an in-frame insertion of four amino acids (Q9P267.3(MBD5):p.V23_G24insYTSS) and a substitution of one amino acid in the canonical protein isoform (Q9P267.3 (MBD5):p.G24C), predicting a 1498 amino acid protein from this allele. Cell lines 2 and 3 (6het AIIIB5 and 6hom AIID2) harbored heterozygous and homozygous alterations, respectively, which were formed by non-homologous end joining (NHEJ) that resulted in precise editing at the genomic target sites without further changes by the guideRNAs 6.3 and 6.8 (Supplementary Table 2). Gene editing in cell lines 2 and 3 led to the precise excision of 41bp within exon 6 (NM_018328.4(MBD5):c.23_64del), removing the initial portion of the conserved MBD domain. As this modification causes a frameshift of the open reading frame, it is predicted to result in a prematurely truncated peptide of 38 amino acids, considering the canonical MBD5 protein isoform. MBD5 protein levels could not be assessed as no suitable antibodies were found upon stringent testing of commercially available reagents. Three cell lines were used as controls, namely: a) a wild-type ( “non-treated”) 8330-8 iPSC line; b) an 8330-8 iPSC line transfected only with Cas9 (“Cas9 only”); c) a negative control, that resembles a wild-type cell line, which was transfected with CRISPR/Cas9 however no cuts in the targeted sites were obtained.

value: iPSC-derived NPCs

tag: genotype/variation

value: wild type


title: erCriz0

value: 0.5µM crizotinib


title: HAP1 + LbCas12a + Optimization Library + 6-thioguanine

city: Toronto

first: Jason

last: Moffat

state: ON

address: 686 Bay Street, Room 13.9705

department: Molecular Genetics

country: Canada

institute: University of Toronto

data_processing:
FASTQ files were pre-processed to extract Cas9 or Cas12a guide sequence using a bespoke Perl script.
The Cas12a guide was extracted from read1 files as the 23 bases preceeding 'ATCTAC', while Cas9 guide sequence was extracted from read2 files as the 20 bases proceeding 'GTTT'.
Trimmed FASTQ files were then aligned to the appropriate FASTA file using bowtie v0.12.1 using the following command line parameters:   -p 16 -v 3 -l 18 --chunkmbs 256 -t <library_file> --un unmapped.fastq --al mapped.fastq -1 <trimmed_read1.fastq> -2 <trimmed_read2.fastq> aligned.sam
The number of reads aligning to each dual-guide sequence was enumerated for each aligned .sam file, and alignment statistics were recorded.  Dual-guide IDs and counts were written to individual count files.
All individual count files were merged along with library annotations in R.

source_name: dual-guide amplicon

growth_protocol: Human HAP1 cells were maintained in low glucose (10 mM), low glutamine (1 mM) DMEM supplemented with 10% FBS and 1% Penicillin/Streptomycin. Human hTERT-RPE1 cells were maintained in DMEM with high glucose and pyruvate supplemented with 10% FBS and 1% Penicillin/Streptomycin. CGR8 mouse embryonic stem cells (mESC) were grown in gelatin-coated plates in GMEM supplemented with 100 μM β-mercaptoethanol, 0.1 mM nonessential amino acids, 2 mM sodium pyruvate, 2 mM L-glutamine, 5,000 units/mL penicillin/streptomycin, 1,000 units/mL recombinant mouse LIF and 15% ES fetal calf serum. Mouse neuroblastoma Neuro-2A (N2A) cells were grown in DMEM with high glucose supplemented with 10% FBS, sodium pyruvate, non-essential amino acids, and penicillin/streptomycin.

extract_protocol:
Genomic DNA was extracted using the Wizard Genomic DNA Purification Kit (Promega).
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Sequencing libraries were prepared in two PCR steps, the first to enrich guide-RNA regions from the genome, and the second to amplify guide-RNA and attach Illumina TruSeq adapters with i5 and i7 indices.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: non-treated; 2.5 mM thymidine; 6 µM 6-thioguanine; Torin1 treatment was performed at a concentration that causes a 60% reduction in cell growth (i.e. IC60).

tag: cas protein

tag: crispr library

value: CHyMErA Human Optimization Libary

tag: library file

tag: annotation file


title: HAP1 + AsCas12a + Optimization Library + Thymidine Block

value: double thymidine block


title: HAP1 + AsCas12a + Optimization Library + 6-thioguanine


title: ctr_b

city: Kent

first: Soumitra

last: Basu

state: Ohio

address: 203 WilIiams Hall

department: Chemistry and Biochemistry

institute: Kent State University

description: Control

data_processing:
RNA-Seq data were analyzed using CLC Genomics Workbench software v12 (Qiagen Inc) following manufacturer’s instruction (http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=RNA_seq_Small_RNA_analysis.html). Briefly, single-end RNA-Seq reads, obtained in FASTQ format, were subjected to sequence quality checks using “QC for Sequencing Reads” tool. The  reads with FRED score >20 were then aligned to the human reference genome GRCh38 assembly sequence using the default parameters of “RNA-Seq Analysis” tool. Genes and transcripts annotations provided by Ensembl (release 92) were used.
Differentially expressed genes (DEGs) between control and oxidized state were determined using “Differential Expressions in Two Groups” tool provided by CLC Genomics Workbench v12 (Qiagen Inc) . The tool uses a multifactorial statistic based on a negative binomial Generalized Linear Model.
Genome_build: human GRCh38
Supplementary_files_format_and_content: tab-delimited text files include, Total Counts, TPM, and  RPKM values for each Sample ...

source_name: human neuroblastoma (SH-SY5Y) cells

growth_protocol: Human neuroblastoma (SH-SY5Y) cells obtained from ATCC were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% (v/v) fetal bovine serum, and 1% penicillin/streptomycin at 37 °C under 5% CO2 in air. The cells were seeded in a 6-well plate (500K cells/well) and they were allowed to settle for 24 h before the treatment.

extract_protocol:
mRNA was isolated from SH-SY5Y cells using standard protocol (TRIzolTM Reagent, Invitrogen).
mRNA from SH-SY5Y cells (oxidized RNA from SNP treated cells and control RNA) were sequenced using iLumina HighSeq platform (75 base pair sequencing, 40 million reads per sample, girihlet Inc, https://www.girihlet.com/).

treatment_protocol: To determine the effect of sodium nitroprusside (SNP) on retinoic acid differentiated SH-SY5Y cells, the cells were treated with various doses of SNP for 8 h. In a single experiment, each treatment was performed in triplicate.

tag: agent


title: ctr_a

description: Control


title: OS1_a

description: Oxidized State

value: SNP


title: OS1_b

description: Oxidized State


title: NPC_GM_R_B1_P10


title: NPC_6homAIID2_R_B1_P10

source_name: iPSC-derived NPCs_del

value: MBD5-edited cell lines with alterations in the conserved MBD domain


title: Pooled Input

description: Pooled genomic DNA from other samples

value: pooled samples

value: input


title: NPC_6hetAIIIB5_R_B2_P10


title: Neuron_GM_R_B1_P14

source_name: NPC-derived neurons_wt

value: NPC-derived neurons


title: Neuron_H8_R_B2_P14


title: Neuron_6homAIID2_R_B1_P14

source_name: NPC-derived neurons_del


title: Neuron_6hetAIVG12_R_B3_P11


title: erLor0


title: Neuron_GM_P37


title: erCriz1


title: Neuron_6hetAIIIB5_R_B2_P14


title: AM2045-7_S7: Low-fat rep3

first: Mehdi

last: Pirooznia

address: 12 SOUTH DR

institute: National Institutes of Health

data_processing:
quality controls of paired-end reads were assessed using FastQC tools
Adapter sequences and low-quality bases were trimmed using Cutadapt Alignment was performed by using HISAT2
Uniquely mapped paired-end reads were used for subsequent StringTie for abundance estimation
Ballgown was employed for DEA
Genome_build: GRCm38
Supplementary_files_format_and_content: count matrix, raw count, tab delimited

source_name: DC-restricted progenitors from BM

growth_protocol: DC-restricted progenitors (Lin-/c-kit(int)/Sca1(lo)/CD115+/Flt3+; ~50,000 cells) from bone marrow (BM) compartment of high fat (60kcal % fat) & control chow (10 kcal%fat)-fed mic (n=4 per group) were flow-sorted and RNA was isolated.

extract_protocol:
DC-restricted progenitors were flow-sorted directly into lysis buffer and RNA was harvested using Arctus PicoPure RNA isolation kit, quality tested by Bioanalyzer (Agilent)for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NuGen Ovation Solo RNA-Seq System (Mouse part no 0501) protocols

treatment_protocol: The whole transcriptome was amplified and library was constructed using NuGen Ovation Solo RNASeq System; and evaluated on high-sensitivity DNAchip (Agilent) and sequenced on a HiSeq 3000 platform

tag: strain background

tag: age

value: age-&diet-matched control

tag: genotype

value: DIO-Control

value: DC-restricted progenitors from bone marrow


title: AM2045-8_S8: Low-fat rep4


title: NPC_GM_P32

tag: cell type


title: NPC_6hetAIVG12_R_B3_P10