title: MO22_sgKdm5a RPP_Tumor6

source_name: Lung Tumor 238 sgKdm5a RPP


title: CD8_033A

status: Public on Nov 16 2020

type: SRA

city: Hannover

first: Christian

middle: R

last: Schultze-Florey

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

library_source: transcriptomic

data_processing:
MIXCR (v2.1.11): alignment based on the IMGT database (22.05.2018) followed by assembling of clonotypes to correct PCR-errors.
random normalization to 20000 reads to avoid bias due to diverging sequencing depths
decompression, conversion into the FASTQ-file format, subsequent formatting
TCR repertoire analysis was based on usage of VDJtools, tcR-package
All bash and R scripts used are available at: https://github.com/MHHIMMUNOLOGY/MHHTCR_ANALYSIS
Supplementary_files_format_and_content: CDR3 sequences

molecule: total RNA

organism: Homo sapiens

source_name: CD8 from PBMC_post 1

extract_protocol:
sorted CD8+ - RNA extr - RACE - CDR3 amplification - MiSeq TRB sequencing
libraries were prepared for sequencing using standard Illumina protocols

tag: patient id

tag: sample tp, refer to stable 1 and 2 for further details

value: post 1

tag: dli sample

value: yes

tag: cell type

value: CD8 from PBMC

tag: molecule subtype

value: cDNA:CDR3 amplicon


title: CD8_033D

source_name: CD8 from PBMC_post 4

value: post 4


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G8_AD001

city: La Jolla

first: Joseph

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10 INTACT
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J P56 Mouse Brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x10^12 to 1x10^13 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: strain

tag: age

tag: tissue

value: brain

tag: source

value: ACA

tag: target

value: STR

tag: gender

value: male


title: Lung_cancer_validation_15

city: Reno

first: Musheng

last: Li

address: North Virginia Street

institute: University of Nevada, Reno

data_processing:
Our newly developed pipeline, SPORTS1.0 (https://github.com/junchaoshi/sports1.0), was used to parse the raw sequencing data.
Genome_build: hg19

source_name: PBMC

extract_protocol:
We extracted total RNA from PBMCs using TRIzol reagent (Invitrogen) and purified it with a mirVana miRNA Isolation Kit (Ambion, Thermo Fisher Scientific) according to the manufacturer’s protocol.
The sequencing libraries were constructed using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina.

tag: type

value: Lung cancer


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G7_AD012

value: AI

value: female


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H10_AD004


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G6_AD010


title: MO21_sgKdm5a RPP_Tumor5

city: Boston

first: Matthew

last: Oser

state: MA

address: 450 Brookline Avenue, Mayer 457

institute: Dana-Farber Cancer Institute

data_processing:
Basecalls
For RNA-Seq: gene counts were done using STAR (v2.5.1b) {Dobin A., etal (2013), Bioinformatics 29: 15.} and normalized gene counts (RPKM) were calculated using Cufflinks (v2.2.1) {Trapnell C., etal (2010), Nat. Biotech. 28: 511.}. Analysis was performed using the VIPER snakemake pipeline {Cornwell M., etal (2018), BMC Bioinformatics 19: 135.}
Genome_build: mm9
Supplementary_files_format_and_content: For RNA-Seq, cufflinks file shows normalized RPKM values.

source_name: Lung Tumor 840 sgKdm5a RPP

growth_protocol:
sgControl RPP or sgKdm5a RPP adenovirus that were titered diluted in PBS were intratracheally injected in H11 LSL-Cas9 mice (2-4 months of age) at 4 X 10^8 VP/mouse.
At the study endpoint, mice were euthanized and lung tumors harvested

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen #74106) per the manufacturer's instructions
Libraries were constructed as per the manufacturers instructions. For RNASeq: 500 ng RNA was used with the Illumina stranded total RNASeq protocol.

value: B6;129-Igs2tm1(CAG-cas9*)Mmw/J. Also known as H11-LSL-Cas9. Jackson Labs catalog number 026816

value: Small cell lung cancer lung tumor from mouse infected with sgKdm5a RPP adenovirus


title: Lung_cancer_validation_14


title: CD8_032G

source_name: CD8 from PBMC_donor

value: donor


title: MO20_sgKdm5a RPP_Tumor4

source_name: Lung Tumor 890 sgKdm5a RPP


title: Lung_cancer_validation_13


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G6_AD007


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H10_AD001


title: CD8_033E

source_name: CD8 from PBMC_post 5

value: post 5


title: CD8_030G


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G6_AD006


title: MO19_sgKdm5a RPP_Tumor3

source_name: Lung Tumor 843 sgKdm5a RPP


title: HFW1_Δcna1

city: Taipei

first: YI-HSUAN

last: HOU

address: Roosevelt Rd

country: Taiwan

institute: National Taiwan University

data_processing:
RNA-seq reads were processed using "Trinity v2.3.2".
Read quality was evaluated using "MultiQC v1.2".
The alignment and the alignment QC report was evaluated using "Qualimap v2"
The gene expression level is calculated by using FPKM method.
Genome_build: Fusarium oxysporum f. sp. lycopersici 4287
Supplementary_files_format_and_content: A tab-delimited text file includes FPKM. BLASTP, BLASTX, and annotation

source_name: F. oxysporum f. sp. lycopersici 4287 CNA1 single deletion mutant strain cells

growth_protocol: The F. oxysporum f. sp. lycopersici WT and calcineurin mutants spores were cultured in PDB at 25°C for 14 h with shaking at 200 rpm.

extract_protocol:
For total RNA extraction, mycelia were collected and frozen in liquid nitrogen, then grownd into powder. Transfer the powder to 1.5 mL centrifuge tube followed by adding an equal volume of TRIzol reagent (Invitrogen) and 100 μL chloroform, mixed well and centrifuged at 14,000 rpm for 5 min at 4℃. The upper phase was collected and precipitated with isopropanol by centrifuged at 14,000 rpm for 10 min at 4℃. The supernatants were discarded, and the nucleic acid pellets were serial washed by 70% and 100% ethanol. The RNA was then re-suspended with DEPC water.
The mRNA was enriched with oligo(dT) magnetic beads and shortened into approximately 200-base fragments in fragmentation buffer. The first strand of cDNA as synthesized by the use of a random hexamer, buffer, dNTPs, and RNase H, and the second by the use of DNA polymerase I. The double strand cDNAs were purified with magnetic beads. After end preparation and 3' end single nucleotide adenine addition were performed, sequencing adaptors were ligated to the fragments, and amplified by PCR. An Aglient 2100 bioanalyzer and ABI StepOnePlus real-time PCR system were used to qualify and quantify the sample library, and the library products were sequenced via an illumina HuSeq 2000 instrument.

tag: genotype

value: CNA1 single deletion mutant


title: CD8_030B

source_name: CD8 from PBMC_post 2

value: post 2


title: MO18_sgKdm5a RPP_Tumor2

source_name: Lung Tumor 237 sgKdm5a RPP


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G6_AD004


title: TB_validation_1

value: TB


title: Lung_cancer_validation_12


title: CD8_030A

value: post 1

value: yes

value: CD8 from PBMC


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G6_AD002

value: brain


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G6_AD001

value: ACA


title: CD8_030.

source_name: CD8 from PBMC_pre

value: pre

value: cDNA:CDR3 amplicon


title: Lung_cancer_validation_11

value: Lung cancer


title: MO16_sgControl RPP_Tumor8

source_name: Lung Tumor 218 sgControl RPP

value: Small cell lung cancer lung tumor from mouse infected with sgControl RPP adenovirus


title: MO17_sgKdm5a RPP_Tumor1

source_name: Lung Tumor 893 sgKdm5a RPP


title: CD8_028G

source_name: CD8 from PBMC_donr

value: donr


title: Lung_cancer_validation_10


title: MO15_sgControl RPP_Tumor7

source_name: Lung Tumor 229 sgControl RPP

value: B6;129-Igs2tm1(CAG-cas9*)Mmw/J. Also known as H11-LSL-Cas9. Jackson Labs catalog number 026816


title: CD8_033.


title: Lung_cancer_validation_9


title: MO14_sgControl RPP_Tumor6

source_name: Lung Tumor 221 sgControl RPP


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G5_AD007

value: AI

value: STR

value: male


title: CD8_028F

value: post 5


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G5_AD004

value: female


title: CD8_028D

source_name: CD8 from PBMC_post 4

value: post 4


title: Lung_cancer_validation_7


title: Lung_cancer_validation_6


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G5_AD002

source_name: C57BL/6J P56 Mouse Brain


title: MO13_sgControl RPP_Tumor5

source_name: Lung Tumor 839 sgControl RPP


title: MO11_sgControl RPP_Tumor3

source_name: Lung Tumor 233 sgControl RPP


title: Lung_cancer_validation_5

source_name: PBMC


title: Lung_cancer_validation_4


title: CD8_028.


title: CD8_028B

value: post 2


title: MO10_sgControl RPP_Tumor2

source_name: Lung Tumor 191 sgControl RPP


title: MO09_sgControl RPP_Tumor1

source_name: Lung Tumor 232 sgControl RPP


title: Lung_cancer_validation_3


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G2_AD008


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G2_AD010


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G2_AD007


title: CD8_027E

source_name: CD8 from PBMC_post 5

value: no (PB)


title: Lung_cancer_validation_8


title: Lung_cancer_validation_2


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G2_AD006


title: RNA-seq_IGF1_rep3

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

data_processing:
Sequencing reads were aligned to rat genome assembly rn5 by STAR.
The number of reads aligned to RefSeq annotated genes' exons were counted using HTSeq.
Differential gene expression analyses were performed using DEseq.
Genome_build: rn5
Supplementary_files_format_and_content: text file of gene read count values

organism: Rattus norvegicus

source_name: Primary NRVMs, IGF1 treatment, 48 hours

growth_protocol: NRVMs were treated for 48 hours. Total RNA was isolated.

extract_protocol: For RNA-seq analysis using the Illumina NovaSeq6000, 0.1-2 ug of total RNA was processed for library generation using the NuGEN Ovation RNA-seq library prep kit following the manufacturer’s protocol.

treatment_protocol: Phenylephrine (50 uM, 48 hours). IGF1 (10 nM, 48 hours).

tag: primary cell type

value: Primary cardiomyocytes


title: RNA-seq_IGF1_rep2


title: CD8_027C

source_name: CD8 from PBMC_post 3

value: post 3

value: CD8 from PBMC


title: Lung_cancer_validation_1


title: MO12_sgControl RPP_Tumor4

source_name: Lung Tumor 235 sgControl RPP


title: Control_validation_12

value: Healthy control


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G2_AD004

value: brain

value: ACA


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G2_AD012


title: CD8_028C

value: yes

value: cDNA:CDR3 amplicon


title: Control_validation_11


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G2_AD002


title: CD8_027A

source_name: CD8 from PBMC_post 1

value: post 1


title: RNA-seq_phenylephrine_rep3

source_name: Primary NRVMs, phenylephrine treatment, 48 hours


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G2_AD001


title: Control_validation_10


title: CD8_027.

source_name: CD8 from PBMC_pre

value: pre


title: CD8_027D


title: CD8_025G

source_name: CD8 from PBMC_donor

value: donor


title: RNA-seq_phenylephrine_rep1


title: RNA-seq_phenylephrine_rep2


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G1_AD010

value: AI

value: STR


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G1_AD012

value: female


title: Control_validation_9


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G1_AD006


title: Control_validation_8


title: RNA-seq_vehicle_rep3

source_name: Primary NRVMs, vehicle treatment


title: CD8_027B

source_name: CD8 from PBMC_post 2


title: RNA-seq_IGF1_rep1


title: RNA-seq_vehicle_rep2


title: CD8_025B


title: CD8_025A


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G1_AD002

value: male


title: Control_validation_7


title: CD8_025.


title: Control_validation_5


title: CD8_024G


title: RNA-seq_vehicle_rep1


title: Control_validation_4


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G12_AD012


title: Un-injured (UI) + all timepoints mixed in one sample, 10X chip channel B

city: Berkeley

first: Rebecca

middle: K.

last: Chance

department: Molecular and Cell Biology

institute: UC Berkeley

description: Krt5-Cre ER^T2 > Rosa YFP+ sorted cells

data_processing:
https://github.com/diyadas/10X-olfactory
Diya Das and Rebecca Chance built pipeline using previous collaborative work with Russell Fletcher
github.com/koenvandenberge/covid19Processing
Koen van den Berge removed some contaminants downstream of above
Genome_build: mm10

source_name: Olfactory Epithelium, YFP+

growth_protocol: olfactory epithelium anatomical dissections were extracted from mice

extract_protocol:
lysates were clarified from alive, lineage-traced YFP+ cells from the sorter
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: in the FACS facility cells that were alive (PI sorting rule) AND Keratin5 Cre ER > RosaYFP + were collected

tag: mouse strain

value: olfactory epithelium

tag: mouse age

value: 4-6 weeks

tag: animal sex (#)

value: Female (4) / Male (1)


title: CD8_024A

tag: patient id


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G12_AD010

source_name: C57BL/6J P56 Mouse Brain


title: Control_validation_3


title: CD8_024.

tag: sample tp, refer to stable 1 and 2 for further details


title: Control_validation_2


title: 14 DPI (Days Post Injury) replicate 2, one 10X chip channel

description: Krt5-Cre ER^T2 > Rosa YFP+ sorted cells

value: 6 weeks

value: Male (1)


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G12_AD006


title: Control_validation_6

value: Healthy control


title: Mouse_control

city: Edinburgh

first: Philippa

middle: TK

last: Saunders

address: 47 Little France Crescent

department: College of Medicine and Veterinary Medicine

country: United Kingdom

institute: The University of Edinburgh

data_processing:
Demultiplexing, alignment, and estimation of cell-containing partitions and associated UMIs using Cell Ranger 3.1.0
Genome_build: mm10 (Ensemble 84)
Supplementary_files_format_and_content: mtx: count matrix in sparse matrix format; barcodes.tsv: barcode ids per sample; genes.tsv: gene ids per sample

source_name: Uterus

extract_protocol:
Enzymatic digestion and FACS
Uteri were removed and mesenchymal cells isolated using FACS
10X Genomics Single cell 3' gene expression V2

value: Pdgfrb-BAC-eGFP

value: Healthy uterus

value: Mesenchymal cells

tag: Sex

value: F


title: CD8_023G

tag: dli sample

value: yes

tag: cell type

value: CD8 from PBMC

value: cDNA:CDR3 amplicon


title: Control_validation_1


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G12_AD004

tag: strain

value: brain

value: ACA


title: TB_10

value: TB


title: CD8_022D

source_name: CD8 from PBMC_post 4

value: post 4

tag: molecule subtype


title: CD8_022G

value: donor


title: 14 DPI (Days Post Injury) replicate 1, 10X chip channel A

description: Krt5-Cre ER^T2 > Rosa YFP+ sorted cells

tag: tissue

value: olfactory epithelium

value: Female (1)


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G1_AD001

tag: age

tag: source

value: STR

value: male


title: 14 DPI (Days Post Injury) replicate 1, 10X chip channel B

description: Krt5-Cre ER^T2 > Rosa YFP+ sorted cells

value: 6 weeks


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G12_AD002

tag: target

tag: gender


title: CD8_022C

value: post 3


title: 7 DPI (Days Post Injury) replicate 1, 10X chip channel B

description: Krt5-Cre ER^T2 > Rosa YFP+ sorted cells

value: 5 weeks

value: Male (2)


title: TB_8

source_name: PBMC

tag: type


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G12_AD001


title: CD8_022B

value: post 2


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G11_AD002


title: 7 DPI (Days Post Injury) replicate 1, 10X chip channel A

description: Krt5-Cre ER^T2 > Rosa YFP+ sorted cells


title: Un-injured (UI) + all timepoints mixed in one sample, 10X chip channel A

description: Krt5-Cre ER^T2 > Rosa YFP+ sorted cells

value: 4-6 weeks

value: Female (4) / Male (1)


title: CD8_022A

value: post 1

value: yes

value: CD8 from PBMC

value: cDNA:CDR3 amplicon


title: TB_7

value: TB


title: 96 HPI replicate 2, 10X chip channel A

description: Krt5-Cre ER^T2 > Rosa YFP+ sorted cells

value: 4 weeks


title: 96 HPI replicate 2, 10X chip channel B

description: Krt5-Cre ER^T2 > Rosa YFP+ sorted cells

value: olfactory epithelium


title: TB_9


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G10_AD012

value: brain

value: AI

value: female


title: TB_5


title: TB_6


title: 96 HPI replicate 1, 10X chip channel B

description: Krt5-Cre ER^T2 > Rosa YFP+ sorted cells

value: 6 weeks

value: Male (1)


title: CD8_020G

value: donor


title: 96 HPI replicate 1, 10X chip channel A

description: Krt5-Cre ER^T2 > Rosa YFP+ sorted cells


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G10_AD004

value: ACA

value: STR


title: CD8_020D

value: post 4


title: TB_3


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F7_AD010


title: CD8_020C

value: post 3


title: TB_4


title: 48 HPI replicate 2, 10X chip channel B

description: Krt5-Cre ER^T2 > Rosa YFP+ sorted cells

value: 7 weeks


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F7_AD008

value: male


title: TB_2


title: 48 HPI replicate 2, 10X chip channel A

description: Krt5-Cre ER^T2 > Rosa YFP+ sorted cells


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G11_AD001


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F7_AD007


title: TB_1


title: CD8_020B

value: post 2

value: yes

value: CD8 from PBMC


title: CD8_020A

value: post 1

value: cDNA:CDR3 amplicon


title: CD8_022.

value: pre


title: CD8_020.


title: 48 HPI replicate 1, 10X chip channel B

description: Krt5-Cre ER^T2 > Rosa YFP+ sorted cells

value: olfactory epithelium

value: Female (1)


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F7_AD006

value: brain

value: female


title: Lung_cancer_36

value: Lung cancer


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F7_AD004

value: ACA


title: 24 HPI replicate 2

description: Krt5-Cre ER^T2 > Rosa YFP+ sorted cells

value: 5 weeks

value: Female (6)


title: Lung_cancer_35


title: CD8_018A

value: no (PB)


title: Lung_cancer_34


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F7_AD002

value: STR


title: Lung_cancer_33


title: CD8_018.


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F7_AD001

value: male


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F6_AD012

value: AI


title: Lung_cancer_32


title: CD8_017B

value: post 2

value: yes


title: 24 HPI (Hours Post Injury) replicate 1

description: Krt5-Cre ER^T2 > Rosa YFP+ sorted cells

value: postnatal day 21 (P21)

value: Female (2) / Male (2)


title: Kinsella Composite-sncRNAseq-20

city: Edmonton

first: Changxi

state: Alberta

address: Agriculture/Forestry Centre

department: Agricultural, Food & Nutritional Science

country: Canada

institute: University of Alberta

data_processing:
Basecalls performed by bcl2fastq-v2.17.1.14  and the Raw sequence data were demultiplexed into individual FASTQ file each sample using Illumina bcl2fastq-v2.17.1.14
Sequence reads were assessed for sequencing quality using FASTQC ( 0.11.7)
3' adaptor triming and removal of long reads and shorter reads was performed using Cutadapt version 1.16
Other non miRNA small microRNAs were filtered out using bowtie-1.1.1 short read aligner
miRNA expression was profiled using miRDeep2 package (version 2.0.0.8)
Genome_build: UMD3.1
Supplementary_files_format_and_content: Tab delimited txt file (First colunm contains the mature micro RNA miRbase IDs and second column contains  micro RNA precusor IDs and the third column has the number of  the raw reads that were aligned and mapped to each miRNA)

organism: Bos taurus

source_name: Liver (Autopsy)

extract_protocol:
Qiagen RNeasy Plus Universal Mini Kit (Qiagen, Toronto, ON)
Illumina Truseq Small RNA Library Prep Kit (Illumina, San Diego, CA, USA)

tag: breed

value: Kinsella Composite

tag: finishing diet

value: 75% barley grain, 20% barley silage, 5% rumensin pellets

value: Liver

tag: sire

tag: rfi (residual feed intake) group

value: high-RFI


title: Kinsella Composite-sncRNAseq-19


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G12_AD008

value: brain


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F6_AD008


title: Kinsella Composite-sncRNAseq-18


title: CD8_017A

tag: patient id

value: post 1

value: CD8 from PBMC

value: cDNA:CDR3 amplicon


title: Lung_cancer_31

value: Lung cancer


title: Lung_cancer_30


title: CD8_017.

tag: sample tp, refer to stable 1 and 2 for further details

value: pre


title: 48 HPI replicate 1, 10X chip channel A

description: Krt5-Cre ER^T2 > Rosa YFP+ sorted cells

tag: mouse strain

value: olfactory epithelium

tag: mouse age

tag: animal sex (#)

value: Female (1)


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F6_AD006

tag: strain

value: ACA

value: STR

value: female


title: Kinsella Composite-sncRNAseq-17

value: low-RFI


title: CD8_016G

value: donor

tag: dli sample

value: yes

tag: cell type

tag: molecule subtype


title: Lung_cancer_28


title: Kinsella Composite-sncRNAseq-16

value: Kinsella Composite

value: 75% barley grain, 20% barley silage, 5% rumensin pellets

tag: tissue


title: CD8_016B

value: post 3


title: Lung_cancer_29


title: CD8_017G


title: Kinsella Composite-sncRNAseq-15

value: Liver


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F6_AD004

tag: age

value: brain

tag: source

tag: target


title: Kinsella Composite-sncRNAseq-14

tag: breed


title: Lung_cancer_27

tag: type


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F6_AD002

tag: gender

value: male


title: CD8_016.

value: CD8 from PBMC

value: cDNA:CDR3 amplicon


title: Lung_cancer_25

value: Lung cancer


title: CD8_016A2

value: post 2


title: CD8_016A

value: post 1


title: Kinsella Composite-sncRNAseq-13

tag: finishing diet

tag: sire

tag: rfi (residual feed intake) group


title: Kinsella Composite-sncRNAseq-12


title: Lung_cancer_26


title: Lung_cancer_24


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F6_AD007

value: AI


title: CD8_015G

tag: patient id

tag: sample tp, refer to stable 1 and 2 for further details


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F5_AD007

value: STR


title: Kinsella Composite-sncRNAseq-11

value: high-RFI


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F5_AD006

value: ACA

value: female


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F3_AD010


title: CD8_015B

value: yes


title: Kinsella Composite-sncRNAseq-10

value: Kinsella Composite


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F3_AD007


title: Kinsella Composite-sncRNAseq-09

value: 75% barley grain, 20% barley silage, 5% rumensin pellets

value: low-RFI


title: CD8_015A


title: Lung_cancer_22


title: Lung_cancer_21


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F3_AD006


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F6_AD001


title: CD8_013G

value: donor


title: Kinsella Composite-sncRNAseq-08

value: Liver


title: Lung_cancer_20


title: CD8_013F

source_name: CD8 from PBMC_post 6

value: post 6


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F3_AD004

value: brain


title: Lung_cancer_19


title: Kinsella Composite-sncRNAseq-06


title: Kinsella Composite-sncRNAseq-07


title: CD8_013E

source_name: CD8 from PBMC_post 5

value: post 5

value: CD8 from PBMC

value: cDNA:CDR3 amplicon


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F3_AD002

value: male


title: Lung_cancer_18

value: Lung cancer


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F3_AD001

value: STR


title: CD8_013D

value: post 4


title: Lung_cancer_23


title: CD8_013C

value: post 3


title: Kinsella Composite-sncRNAseq-05

value: high-RFI


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F2_AD008

value: AI


title: Lung_cancer_16


title: Kinsella Composite-sncRNAseq-04

value: Kinsella Composite


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F2_AD012

value: female


title: Lung_cancer_17


title: Kinsella Composite-sncRNAseq-03

value: 75% barley grain, 20% barley silage, 5% rumensin pellets

value: low-RFI


title: CD8_013B

value: post 2

value: yes


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F2_AD007

value: brain


title: Lung_cancer_15


title: CD8_013A

value: post 1


title: CD8_013.

value: pre

value: CD8 from PBMC


title: Kinsella Composite-sncRNAseq-02

value: Liver


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F2_AD006

value: ACA


title: Kinsella Composite-sncRNAseq-01


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F2_AD004

value: STR


title: Lung_cancer_14

value: Lung cancer


title: Charolais-sncRNAseq-20

value: Charolais


title: CD8_009G

value: donor

value: cDNA:CDR3 amplicon


title: Lung_cancer_12


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F2_AD001

value: male


title: CD8_009B


title: CD8_008G


title: Charolais-sncRNAseq-18


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F1_AD008

value: AI


title: Charolais-sncRNAseq-17

value: 75% barley grain, 20% barley silage, 5% rumensin pellets


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F1_AD007


title: Lung_cancer_9


title: Charolais-sncRNAseq-16


title: Lung_cancer_13


title: Charolais-sncRNAseq-19

value: high-RFI


title: CD8_008A

source_name: CD8 from PBMC_past 1

value: past 1


title: Lung_cancer_8


title: CD8_008.

value: yes


title: CD8_008B

value: post 2


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F1_AD010

value: brain

value: female


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F1_AD004


title: Lung_cancer_7


title: CD8_007G

value: CD8 from PBMC


title: CD8_007D

value: post 4


title: Lung_cancer_11


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F1_AD002

value: ACA


title: Lung_cancer_10


title: Lung_cancer_5


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F1_AD001

value: STR


title: Charolais-sncRNAseq-14

value: Liver

value: low-RFI


title: Charolais-sncRNAseq-12

value: Charolais


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F12_AD012


title: Lung_cancer_4

value: Lung cancer


title: CD8_007B

value: cDNA:CDR3 amplicon


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F1_AD006


title: Lung_cancer_3


title: Charolais-sncRNAseq-15


title: Lung_cancer_2


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F12_AD008

value: AI

value: male


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F12_AD010


title: CD8_007A

value: post 1


title: Charolais-sncRNAseq-11

value: 75% barley grain, 20% barley silage, 5% rumensin pellets


title: Charolais-sncRNAseq-10


title: CD8_007.

value: pre

value: yes


title: Lung_cancer_1


title: CD8_006G

value: donor


title: Lung_cancer_6


title: Charolais-sncRNAseq-09

value: high-RFI


title: Charolais-sncRNAseq-08


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F12_AD006

value: brain

value: female


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F12_AD004

value: ACA


title: CD8_006C

source_name: CD8 from PBMC_post 3

value: post 3

value: CD8 from PBMC


title: Charolais-sncRNAseq-13

value: Liver


title: CD8_007C


title: Charolais-sncRNAseq-07

value: Charolais

value: low-RFI


title: Control_13

value: Healthy control


title: Control_12


title: CD8_006A

value: cDNA:CDR3 amplicon


title: Charolais-sncRNAseq-06


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F11_AD002

value: STR

value: male


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F12_AD001


title: Control_11


title: CD8_006.


title: Charolais-sncRNAseq-05

value: 75% barley grain, 20% barley silage, 5% rumensin pellets


title: CD8_004G


title: Control_10


title: CD8_004B

value: post 2


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F10_AD008

value: AI


title: Control_9


title: Charolais-sncRNAseq-04


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F10_AD010


title: Charolais-sncRNAseq-03


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F10_AD007


title: Control_8


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F10_AD006


title: Control_7


title: CD8_004.

value: pre

value: yes


title: Control_6


title: Charolais-sncRNAseq-02


title: CD8_003G

value: donor


title: Charolais-sncRNAseq-01


title: Angus-sncRNAseq-20

value: Angus


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F10_AD004

value: brain

value: ACA

value: female


title: Control_5


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F10_AD002


title: CD8_003A

value: post 1

value: CD8 from PBMC


title: Angus-sncRNAseq-18

value: Liver


title: CD8_003.


title: Angus-sncRNAseq-19

value: high-RFI


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E8_AD012


title: CD8_004A

value: cDNA:CDR3 amplicon


title: Control_3

value: Healthy control


title: Control_2


title: Angus-sncRNAseq-17

value: low-RFI


title: Angus-sncRNAseq-15

value: 75% barley grain, 20% barley silage, 5% rumensin pellets


title: CD8_002B

value: post 2


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E8_AD008

value: AI

value: STR

value: male


title: Angus-sncRNAseq-16


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E8_AD007


title: HBBP1 shRNA2-d14

city: Beijing

first: Xu

middle: jia

last: yue

address: NO.3 Dongdan street, Beijing

country: China

institute: Peking Union Medical College

description: differentiated from CD34+ hematopoietic stem/progenitor cells at day14

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome
Gene expression levels were expected of fragments per kilobase of transcript sequence per millions base pairs mapped (FPKM) using Cufflinks v2.1.0
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for  mRNA genes in each sample

growth_protocol: The CD34+ cells were cultured in the basic Iscove’s modified Dulbecco’s medium (IMDM) supplemented with 20% BIT (v/v) (StemCell Technologies), 40 μg/ml inositol (Sigma), 10 μg/ml folic acid (Sigma), 160 μM monothioglycerol (Sigma), 90 ng/ml ferrous nitrate (Sigma), 900 ng/ml ferrous sulfate (Sigma), 2 mM L-glutamine and 1% penicillin and streptomycin (v/v).

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: From day 0 to 8, 5 ng/ml hIL-3, 100 ng/ml hSCF, 1 μM hydrocortisone (Sigma) and 3 U/ml hEPO was supplemented to the culture medium. From day 8 to 14, SCF and EPO was contained in the culture medium and only EPO was added to the culture during day 14 to 18. Cells were maintained at a density between 5 x 104 and 2 x 106 cells/ml, with medium change every 3 to 4 days.

value: cord blood derived hematopoietic progenitor cells


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E8_AD004


title: Angus-sncRNAseq-14

value: Angus


title: Angus-sncRNAseq-13


title: HBBP1 shRNA1-d14

source_name: differentiated from CD34+ hematopoietic stem/progenitor cells at day14


title: Control_4


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E8_AD006

value: brain


title: CD8_002.

value: pre

value: yes


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_F10_AD001

value: ACA


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E8_AD002


title: HBBP1 shRNA2-d8

description: differentiated from CD34+ hematopoietic stem/progenitor cells at day8


title: CD8_001G

value: donor

value: CD8 from PBMC


title: CD8_001A

source_name: CD8 from PBMC_post 1

value: post 1


title: Angus-sncRNAseq-12

value: Liver

value: high-RFI


title: HBBP1 shRNA1-d8

source_name: differentiated from CD34+ hematopoietic stem/progenitor cells at day8


title: Angus-sncRNAseq-11

value: low-RFI


title: CD8_002A

value: cDNA:CDR3 amplicon


title: CD8_001.

source_name: CD8 from PBMC_pre


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E7_AD001


title: Ctrl-d14


title: Control_1

value: Healthy control


title: swr1D HTZ1-GFP T=15h GFP ChIP

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

data_processing:
Illumina output reads were processed as described in (Paul et al., 2018). The ChIP-seq reads were mapped to S288C genome (Yue et al., 2017) using Bowtie (Langmead et al., 2009). Reads with up to 2 mismatches across all 51bp were considered during mapping, and reads with more than one reportable alignment were mapped to the best position and used for further analysis.
For ChIP-seq, 3' ends of the reads were extended to a final length of 200bp using MACS2 2.1.1 (https://github.com/taoliu/MACS). The input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used to create bedgraph files for further analyses.
Genome_build: S288c (Yue et al., 2017)
Supplementary_files_format_and_content: Bedgraph

organism: Saccharomyces cerevisiae

source_name: swr1D HTZ1-GFP T=15h GFP ChIP

growth_protocol: To induce meiosis and sporulation, BR strains were grown in 3.5 ml of 2X SC medium (2% glucose, 0.7% yeast nitrogen base without amino acids, 0.05% adenine, and complete supplement mixture from Formedium at twice the particular concentration indicated by the manufacturer) for 20–24 h, then transferred to 2.5 ml of YPDA (1% yeast extract, 2% peptone, 2% glucose, 0.02% adenine) and incubated to saturation for additional 8 hr. Cells were harvested, washed with 2% potassium acetate (KAc), resuspended into 2% KAc (10 ml), and incubated at 30C with vigorous shaking to induce meiosis. Both YPDA and 2% KAc were supplemented with 20 mM adenine and 10 mM uracil.

extract_protocol:
For ChIP-seq samples, 25 ml of the meiotic cells were collected at 0 hr and 15 hr time points and fixed for 30 min in 1% formaldehyde.  The formaldehyde was quenched with 125 mM glycine. Samples were processed as described in (Blitzblau et al., 2012).
Quality of all libraries was checked on 2200 Tapestation. Libraries were quantified using qPCR. The libraries were sequenced on Illumina HiSeq 2500 instruments at NYU Biology Genomics core to yield 51 bp single-end reads.

tag: background strain

tag: time

value: 15 hour

tag: genotype

value: DP841 (swr1D HTZ1-GFP)

tag: antibody

value: anti-GFP


title: swr1D HTZ1-GFP T=15h input

source_name: swr1D HTZ1-GFP T=15h input


title: Angus-sncRNAseq-09

value: 75% barley grain, 20% barley silage, 5% rumensin pellets


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E6_AD004

tag: strain

value: STR

value: female


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E5_AD012

tag: tissue

value: brain

value: AI


title: CD8_002G

source_name: CD8 from PBMC_donor

tag: dli sample

value: yes

tag: cell type

tag: molecule subtype


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E5_AD006

tag: age

tag: source

value: ACA

tag: target


title: swr1D HTZ1-GFP T=0h GFP ChIP

source_name: swr1D HTZ1-GFP T=0h GFP ChIP

value: 0 hour


title: swr1D HTZ1-GFP T=0h input

source_name: swr1D HTZ1-GFP T=0h input


title: Angus-sncRNAseq-08

tag: breed

value: Angus

tag: finishing diet


title: Angus-sncRNAseq-07

value: Liver

tag: sire

tag: rfi (residual feed intake) group


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E5_AD004

source_name: C57BL/6J P56 Mouse Brain

tag: gender


title: WT HTZ1-GFP T=15h GFP ChIP

source_name: WT HTZ1-GFP T=15h GFP ChIP

tag: background strain

value: DP840 (HTZ1-GFP)


title: Angus-sncRNAseq-06

value: low-RFI


title: MAX IP in sgMax preSC Rep2

city: Seattle

first: Haritha

last: Mathsyaraja

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutch

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4
Alignment to mm10 with Bowtie 2,  reads >700bp filtered out, samples spike-in normalized
BigWigs were created using bedtools (genomecov) and WigToBigWig scripts
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: sgMga Kras G12D Trp53 -/- lung cancer cells

growth_protocol: Tumors from Kras G12D Trp53-/- mice were dissociated and cultured to grow out lung tumor cells in vitro. They were cultured in 10% FBS containing DMEM. They were genotyped to confirm indels in MGA.  One control line (empty) and one MGA inactivated line (sgMga) were used for the study

extract_protocol:
Cells were crosslinked in formaldehyde and ChIP was performed
Libraries were constructed using the NEB Ultra II kit for Illumina according to manufacturer protocol

treatment_protocol: No treatment was performed

value: derived from Kras G12D Trp 53 -/- tumors

value: MAX IP

tag: transduction

value: sgMax preSC


title: Input control in sgMax preSC Rep2

tag: genotype

value: Input control


title: MAX IP in sgMaxpreSC Rep1

tag: antibody


title: Input control in sgMax preSC Rep1


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E8_AD001

tag: strain

value: male


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E3_AD007

tag: tissue


title: RNApolII  IP in sgCtrl preSC Rep2

value: RNApolII

value: sgCtrl preSC


title: Angus-sncRNAseq-10

source_name: Liver (Autopsy)

value: 75% barley grain, 20% barley silage, 5% rumensin pellets


title: Angus-sncRNAseq-05

value: high-RFI


title: Ctrl-d8

value: cord blood derived hematopoietic progenitor cells


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E3_AD004

value: brain

value: STR

value: female


title: Angus-sncRNAseq-04

value: Angus


title: RNApolII IP in sgCtrl preSC Rep1


title: Angus-sncRNAseq-03

value: Liver


title: MYC IP in sgCtrl preSC Rep2

value: MYC IP


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E3_AD002

value: ACA


title: WT no tag T=15h GFP ChIP

source_name: GFP ChIP for WT no tag T=15h

tag: time

value: 15 hour

value: anti-GFP


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E3_AD001


title: Angus-sncRNAseq-02

value: low-RFI


title: WT no tag T=15h input

source_name: WT no tag T=15h input


title: Angus-sncRNAseq-01


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E2_AD010

value: AI


title: WT no tag T=0h GFP ChIP

source_name: GFP ChIP for WT no tag T=0h

value: 0 hour


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E3_AD012


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E2_AD001

value: male


title: MNT IP in sgCtrl preSC Rep2

source_name: Control Kras G12D Trp53 -/- lung cancer cells

value: derived from Kras G12D Trp 53 -/- tumors

value: MNT IP

value: sgCtrl preSC


title: MNT IP in sgCtrl preSC Rep1


title: WT no tag T=0h input

source_name: WT no tag T=0h input


title: swr1D HTZ1-GFP T=15h GFP ChIP rep 2

description: PS841-15h-mab-S288CYue-2mis-S288CYue-2mis_W3_MACS2_FE.bdg.gz

source_name: swr1D HTZ1-GFP T=15h GFP ChIP rep 2

extract_protocol:
For ChIP-seq samples, 25 ml of the meiotic cells were collected at 0 hr and 15 hr time points and fixed for 30 min in 1% formaldehyde.  The formaldehyde was quenched with 125 mM glycine. Samples were processed as described in (Blitzblau et al., 2012).
Quality of all libraries was checked on 2200 Tapestation. Libraries were quantified using qPCR. The libraries were sequenced on NextSeq 500 instruments at NYU Biology Genomics core to yield 51 bp single-end reads.

value: DP841 (swr1D HTZ1-GFP)

tag: chip antibody


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E1_AD010

value: brain


title: swr1D HTZ1-GFP T=15h input rep 2

source_name: swr1D HTZ1-GFP T=15h input rep 2


title: WT HTZ1-GFP T=0h GFP ChIP

source_name: WT HTZ1-GFP T=0h GFP ChIP

value: DP840 (HTZ1-GFP)


title: WT HTZ1-GFP T=15h input

source_name: WT HTZ1-GFP T=15h input


title: swr1D HTZ1-GFP T=0h GFP ChIP rep 2

description: PS841-0h-mab-S288CYue-2mis-S288CYue-2mis_W3_MACS2_FE.bdg.gz

source_name: swr1D HTZ1-GFP T=0h GFP ChIP rep 2


title: WT HTZ1-GFP T=0h input

source_name: WT HTZ1-GFP T=0h input


title: WT-3

first: Yumeng

last: Cai

state: Be

address: Qinghua Dong Road NO.17,Beijing,China

institute: China Agriculture University

description:
processed data file:
Gene_full_table.txt

data_processing:
After the library was constructed, preliminary quantification was performed using Qubit 3.0, and the library was diluted to 1 ng/uL. Then, the insert size of the library was detected using Qsep100. After the insert size was as expected, the effective concentration of the library was accurately determined by Q-PCR. Quantification (library effective concentration > 2 nM) to ensure library quality.
Filter the data to obtain Clean Data, sequence comparison with the specified reference genome, and obtain Mapped Data for library quality evaluation such as insert length test and randomness test; perform alternative splicing analysis, new gene discovery and gene Structural level analysis such as structural optimization; analysis of expression levels of differential expression analysis, functional expression of differentially expressed genes, and functional enrichment based on the expression levels of genes in different samples or different sample groups.
The sequenced raw sequence reads (Sequenced Reads) or Raw reads, which contain low-quality reads with connectors. In order to ensure the quality of information analysis, Raw reads must be filtered to get Clean reads, and subsequent analysis is based on Clean reads. The steps for data processing are as follows:(1) removing the reader with the adapter; (2) removing N (N means that the base information cannot be determined) is greater than 1% of the reads;(3) Remove low-quality reads (the number of bases with a mass value of sQ <= 15 accounts for more than 50% of the total read).
Alignment by reference to TopHat software, reference genome link.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Solanum lycopersicum

source_name: S. lycopersicum (Micro-Tom)_WT

extract_protocol:
5 DPA, tomato fruits were collected, immediately frozen in liquid nitrogen, and total RNA was harvested using HiPure Plant RNA Kits (Magen, China). Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: treatment/genotype

value: wild type tomato

tag: Stage

value: 5 DPA

value: fruit


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E1_AD007

tag: age

tag: source

value: STR


title: MAX IP in sgCtrl preSC Rep1

value: MAX IP


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E1_AD006

value: ACA

tag: target

value: female


title: WT-1


title: WT-2


title: swr1D HTZ1-GFP T=0h input rep 2

source_name: swr1D HTZ1-GFP T=0h input rep 2


title: Input control in sgCtrl preSC Rep2

value: Input control


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E1_AD004

source_name: C57BL/6J P56 Mouse Brain


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E1_AD002


title: WT HTZ1-GFP T=0h GFP ChIP rep 2

description: PS840-0h-mab-S288CYue-2mis-S288CYue-2mis_W3_MACS2_FE.bdg.gz

source_name: WT HTZ1-GFP T=0h GFP ChIP rep 2

value: anti-GFP


title: MYC IP in sgCtrl preSC Rep1

value: MYC IP


title: NPA_C54B_H3K4me3

city: Ann Arbor

first: Maria

middle: Belen

last: Garcia-Fabiani

state: Michigan

address: 4574 MSRB II, 1150 West Medical Center Drive

department: Neurosurgery

institute: University of Michigan

description: NPAH.H3K4me3_vs_NPA.H3K4me3__PePr_chip2_sharpPeaks.bed

data_processing:
ChIP-seq data quality was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and the first 2 bases were trimmed out due to the low read quality
ChIP-seq and input reads were aligned to the mouse reference genome (mm10) using bowtie2 with default options, and the unique mapped reads were extracted.
Post-alignment QC was performed using Deeptools2 and extract uniquely mapped reads were selected
PePr (USENIX) was used to identify the differential H3K27ac, H3K27Me3, H3K4Me1, H3K4Me3 or H3K36Me3 peaks between H3.3-WT and H3.3-G34R groups using p-value < 1e-5 as the cutoff.
The identified peaks were annotated to genomic features (1 to 5 kb upstream of promoter, promoter, intron, exon, UTR, CDS, and intergenic) using annotatr package (R package version 1.0.2).
Genome_build: mm10
Supplementary_files_format_and_content: peak files, .bed format

source_name: Mouse cells derived from a Sleeping beauty-based genetically engenieered high grade glioma (HGG) mouse model encoding for H3.3-WT

growth_protocol: Primary glioma neurospheres (NS) (H3.3-G34R NS and H3.3-WT NS) were generated from our SB transposase HGG model. Briefly, tumors were harvested at the time of euthanasia by transcardial perfusion with Tyrode’s solution. The brains were excised and the tumors were identified by GFP or by GFP/Katushka expression under an epi-fluorescence stereo microscopes at the time of resection. The tumor mass was dissociated using non-enzymatic cell dissociation buffer, filtered through a 70 μm strainer and maintained in neurosphere cell medium (DMEM/F12 with L-Glutamine, B-27 supplement, N-2 supplement, penicillin-streptomycin, and Normocin 1X) at 37 °C, 5% CO2. hFGF and hEGF were added twice weekly at 1 μL (20 ng/μL each stock, 1000x formulation) per 1 mL medium. Primary cell cultures used in this study were generated from female mice.

extract_protocol:
Qiagen QIAquick PCR Purification Kit (Qiagen)
libraries were prepared at the Epigenomics Core using the TruSeq ChIP Library Preparation Kit (Illumina)

treatment_protocol: For each immunoprecipitation (IP) performed, 1x106 NS were collected, washed in HBSS, and pelleted in low bindin microtubes. A 95 μL aliquot of digestion buffer (50 mM Tris-HCl, 1mM CaCl2, 0.2% Triton X-100, pH 8.0) supplemented with 1:100 protease inhibitors was added per 1x106 NS and immediately pipetted gently up and down to lyse. Chromatin digestion was initiated by the addition of 5 μL of Micrococcal Nuclease  at 3.83 x 10-3 U/μL final concentration, for 12 minutes at 37 °C, and stopped by the addition of 10X stopping buffer (110 mM Tris-HCl, 55 mM EDTA , pH 8). The lysate was then diluted with an equal volume of X2 RIPA buffer (280 mM NaCl, 1.8% TritonX-100, 0.2% SDS, 0.2% sodium deoxycholate, 5 mM EGTA , protease inhibitor diluted 1:100). At this stage, 10% of the lysate volume was withdrawn as input. The remaining lysate was then precleared with 10 μL of Dynabeads (1:1 mixture of Protein A  and protein G ) and washed in RIPA buffer (10 mM Tris-HCl, 1 mM EDTA, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, pH 8). Samples were then incubated overnight at 4 °C with 1 μg of anti-H3K27ac antibody, anti-H3K27Me3 antibody, anti-H3K4Me1 antibody, anti-H3K4Me3 antibody, anti-H3K36Me3 antibody or anti-total mouse IgG antibody. Immunoprecipitation was performed in the following day by incubating the samples for 3 hours with 10 μL of Dynabeads (1:1 mixture of Protein A and Protein G ) in 1x RIPA, followed by washing steps with 1X RIPA (5 times, supplemented with 1:1000 dilution of protease inhibitor  ), LiCl buffer (1 time, 250 mM LiCl (10 mM Tris-HCl, 1 mM EDTA, 0.5% NP-40, 0.5 % sodium deoxycholate, pH 8, supplemented with 1:1000 dilution of protease inhibitor), and finally TE buffer (1 time, protease inhibitor-free). Immunoprecipitated chromatin was freed from histones and Dynabeads by incubating the samples 1 hour at 37°C with proteinase K at a final concentration of 0.50 mg/mL. Chromatin samples were then purified by the Qiagen QIAquick PCR Purification Kit and eluted with 50 μL of the EB buffer provided in the kit.

value: brain tumor cells

value: overexpression of NRASG12V + short hairpin for TP53 + short hairpin for ATRX

value: H3K4me1 polyclonal antibody, Diagenode, Cat#C15410003-50


title: NPA_C54B_H3K4me1

description: NPAH.H3K4me1_vs_NPA.H3K4me1__PePr_chip2_broadPeaks.bed

value: H3K4me1 polyclonal antibody, Diagenode, Cat#C15410194


title: WT HTZ1-GFP T=15h GFP ChIP rep 2

description: PS840-15h-mab-S288CYue-2mis-S288CYue-2mis_W3_MACS2_FE.bdg.gz

source_name: WT HTZ1-GFP T=15h GFP ChIP rep 2

value: 15 hour


title: NPA_C54B_Input

description: IP_vs_Input_NPA.H3K36me3__PePr_broadPeaks.bed/ IP_vs_Input_NPA.H3K27me3__PePr_broadPeaks.bed/ IP_vs_Input_NPA.H3K27ac__PePr_broadPeaks.bed/ IP_vs_Input_NPA.H3K4me3__PePr_sharpPeaks.bed/ IP_vs_Input_NPA.H3K4me1__PePr_broadPeaks.bed

value: Normal mouse IgG, Santa Cruz Biotechnology, Cat#sc-2025


title: WT HTZ1-GFP T=15h input rep 2

source_name: WT HTZ1-GFP T=15h input rep 2

value: DP840 (HTZ1-GFP)


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E1_AD001

value: brain

value: male


title: Input control in sgCtrl preSC Rep1

value: derived from Kras G12D Trp 53 -/- tumors

value: sgCtrl preSC


title: WT no tag T=15h input rep 2

description: PS421-15h-mab-S288CYue-2mis-S288CYue-2mis_W3_MACS2_FE.bdg.gz

source_name: WT no tag T=15h input rep 2


title: suc-1202

description:
processed data file:
Gene_full_table.txt
WT_vs_suc-12.annotation.txt

source_name: S. lycopersicum (Micro-Tom)_VvSUC12 overexpression

value: VvSUC12 from Vitis vinifera was overexpressed in tomato

value: 5 DPA

value: fruit


title: MAX IP in sgCtrl preSC Rep2

source_name: Control Kras G12D Trp53 -/- lung cancer cells

value: MAX IP


title: suc-2701

description:
processed data file:
Gene_full_table.txt
WT_vs_suc-27.annotation.txt

source_name: S. lycopersicum (Micro-Tom)_VvSUC27 overexpression

value: VvSUC27 from Vitis vinifera was overexpressed in tomato


title: suc-2703


title: WT HTZ1-GFP T=0h input rep 2

source_name: WT HTZ1-GFP T=0h input rep 2

value: 0 hour


title: NPA_C54B_H3K27ac

description: NPAH.H3K27ac_vs_NPA.H3K27ac__PePr_chip2_broadPeaks.bed

value: brain tumor cells

value: H3K27ac polyclonal antibody, Diagenode, Cat#C15410196


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E12_AD006

value: ACA

value: STR

value: female


title: suc-1203


title: GFP ChIP for WT no tag T=15h rep 2

source_name: GFP ChIP for WT no tag T=15h rep 2

value: 15 hour

value: anti-GFP


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E12_AD010

value: brain

value: AI


title: NPA_C54B_H3K36me3

description: NPAH.H3K36me3_vs_NPA.H3K36me3__PePr_chip2_broadPeaks.bed

value: overexpression of NRASG12V + short hairpin for TP53 + short hairpin for ATRX

value: H3K36me3 polyclonal antibody, Diagenode, Cat#C15410192


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E12_AD004


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E12_AD008

value: male


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E12_AD012


title: NPA_C54B_H3K27me3

description: NPAH.H3K27me3_vs_NPA.H3K27me3__PePr_chip2_broadPeaks.bed

value: H3K27me3 polyclonal antibody, Diagenode, Cat#C15410195


title: suc-1102

description:
processed data file:
Gene_full_table.txt
WT_vs_suc-11.annotation.txt

source_name: S. lycopersicum (Micro-Tom)_VvSUC11 overexpression

value: VvSUC11 from Vitis vinifera was overexpressed in tomato

value: 5 DPA

value: fruit


title: suc-1201

value: VvSUC12 from Vitis vinifera was overexpressed in tomato


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E12_AD002


title: NPA_C1_H3K4me3

value: brain tumor cells

value: H3K4me1 polyclonal antibody, Diagenode, Cat#C15410003-50


title: suc-1101


title: NPA_C1_H3K4me1

value: H3K4me1 polyclonal antibody, Diagenode, Cat#C15410194


title: GFP ChIP for WT no tag T=0h rep 2

description: PS421-0h-mab-S288CYue-2mis-S288CYue-2mis_W3_MACS2_FE.bdg.gz

source_name: GFP ChIP for WT no tag T=0h rep 2

value: 0 hour


title: suc-2702

value: VvSUC27 from Vitis vinifera was overexpressed in tomato


title: NPA_C1_Input

value: Normal mouse IgG, Santa Cruz Biotechnology, Cat#sc-2025


title: NPA_C1_H3K27ac

value: H3K27ac polyclonal antibody, Diagenode, Cat#C15410196


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E10_AD012

value: brain

value: STR

value: female


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E10_AD007

value: AI


title: NPA_C1_H3K36me3

value: overexpression of NRASG12V + short hairpin for TP53 + short hairpin for ATRX

value: H3K36me3 polyclonal antibody, Diagenode, Cat#C15410192


title: WT no tag T=0h input rep 2

source_name: WT no tag T=0h input rep 2


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E11_AD006

value: ACA


title: suc-1103

value: VvSUC11 from Vitis vinifera was overexpressed in tomato

value: 5 DPA


title: suvh9_gp4_IPARE_rep1

first: Shriya

last: Sethuraman

state: MI

address: 5164 Biological Sciences Building, 1105 N. University Ave.

department: Bioinformatics

data_processing:
UMI was extracted from the read 2 and appended to read 1 name using umi_tools.
The reads were then trimmed for the 3' adapters and poly(A) sequences using cutadapt with a maximum allowed error-rate of 0.05 and a minimum length cut-off of 20bps.
The trimmed reads were then mapped to the TAIR10 genome using bowtie2 allowing one mismatch.
The mapped reads were then sorted followed by removal of PCR duplicates using the umi_tools_dedup command.
The hmmlearn python package was used to split the genome based on Pol V IPARE enrichment in Col-0 compared to nrpe1 and CHHme difference between Col-0 and nrpe1, and IPARE strand bias.
The HMM output states were then filtered further to produce 3 final groups: RdDM_PolV_transcribed; nonRdDM_PolV_transcribed; nonPolV_transcribed.
The WGBS reads were mapped using Bismark allowing no mismatches. The methylation information was extracted using bismark_methylation_extractor.
genome build: TAIR10.
processed data files format and content: RdDM_PolV_transcribed_HMM_bins.bed : tab delimited bed file with the filtered HMM bins identified as RdDM-PolV transcribed.
processed data files format and content: nonRdDM_PolV_transcribed_HMM_bins.bed : tab delimited bed file with the filtered HMM bins identified as nonRdDM-PolV transcribed.
processed data files format and content: nonPolV_transcribed_HMM_bins.bed : tab delimited bed file with the filtered HMM bins identified as nonPolV transcribed.
processed data files format and content: 200bp_150bp_sliding_windows_allDatasets_coverages.bed : tab delimited bed file with the read coverages and average methylation of all datasets in each 200bp-150bp sliding window. The "NA" in methylation columns suggests there weren't sufficient reads to calculate methylation ratios (#converted Cs/Total number of Cs).

organism: Arabidopsis thaliana

source_name: 18 day-old seedlings

growth_protocol: Arabidopsis thaliana plants were grown in at 22ºC under white fluorescent light in 16h/8h day/dark cycle.

extract_protocol:
Immunoprecipitation followed by Analysis of RNA Ends (IPARE) was performed as described in the associated publication. Briefly, RNA was immunoprecipitated using an anti-NRPE1 antibody and the high throughput sequencing library was prepared using a modified template switching NanoPARE protocol.
WGBS samples: Genomic DNA was extracted from 3.5-week old Arabidopsis leaves using Dneasy Plant Mini Kit.
Library was prepared by a modified version of NanoPARE protocol (PMID: 30355603). RNA was polyadenylated with Poly(A) polymerase. The polyadenylated RNA was EtOH-precepitated. The deadenylated RNA was DNase treated with TURBO DNase. The RNA was EtOH precepitated. The RT, template switching, pre-amplification and 2nd PCR were performed as NanoPARE.
The DNA extracted for WGBS were processed with bisulfite treatment followed by 100 bp paired-end sequencing.
RIP-seq with modified NanoPARE : IPARE and WGBS

tag: ecotype

value: Columbia

tag: development stage

value: 18 day-old seedlings


title: suvh2_gp4_IPARE_rep1

description: 200bp_150bp_sliding_windows_allDatasets_coverages.bed


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E10_AD008

value: male


title: dms5-1_gp6_IPARE_rep2

description: 200bp_150bp_sliding_windows_allDatasets.bed

extract_protocol:
Immunoprecipitation followed by Analysis of RNA Ends (IPARE) was performed as described in the associated publication. Briefly, RNA was immunoprecipitated using an anti-NRPE1 antibody and the high throughput sequencing library was prepared using a modified template switching NanoPARE protocol.
WGBS samples: Genomic DNA was extracted from 3.5-week old Arabidopsis leaves using Dneasy Plant Mini Kit.
Library was prepared by a modified version of NanoPARE protocol (PMID: 30355603). RNA was polyadenylated with Poly(A) polymerase. The polyadenylated RNA was EtOH-precepitated. The deadenylated RNA was DNase treated with TURBO DNase. The RNA was EtOH precepitated. The RT, template switching, pre-amplification and 2nd PCR were performed as NanoPARE.
The DNA extracted for WGBS were processed with bisulfite treatment followed by 100 bp paired-end sequencing.


title: nrpe1_gp6_IPARE_rep5


title: NPA_B1_H3K4me1

value: brain tumor cells

value: H3K4me1 polyclonal antibody, Diagenode, Cat#C15410194


title: NPA_C1_H3K27me3

value: H3K27me3 polyclonal antibody, Diagenode, Cat#C15410195


title: NPA_B1_H3K36me3


title: drd3-3_gp6_IPARE_rep2


title: NPA_B1_Input

value: Normal mouse IgG, Santa Cruz Biotechnology, Cat#sc-2025


title: NPA_B1_H3K4me3

value: H3K4me1 polyclonal antibody, Diagenode, Cat#C15410003-50


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D9_AD007

value: brain


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E10_AD004

value: STR


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D9_AD004

value: female


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E10_AD006


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D9_AD002


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E10_AD002


title: NPA_B1_H3K27ac

value: H3K27ac polyclonal antibody, Diagenode, Cat#C15410196


title: NPAH_C2_H3K4me3

description: NPAH.H3K4me3_vs_NPA.H3K4me3__PePr_chip1_sharpPeaks.bed

source_name: Mouse cells derived from a Sleeping beauty-based genetically engenieered high grade glioma (HGG) mouse model encoding for H3.3-G34R

value: overexpression of NRASG12V + short hairpin for TP53 + short hairpin for ATRX + overexpression of mutated histone H3.3 G34R


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_E10_AD001


title: Col-0_gp5_IPARE_rep4

value: Col-0 (wild-type)


title: suvh2/suvh9_gp4_IPARE_rep1


title: Col-0_gp6_IPARE_rep5


title: drd3-3_gp5_IPARE_rep1


title: NPA_B1_H3K27me3

value: overexpression of NRASG12V + short hairpin for TP53 + short hairpin for ATRX


title: nrpe1_gp5_IPARE_rep4


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D8_AD008

value: AI


title: dms3_gp4_IPARE_rep1


title: NPAH_C2_H3K4me1

description: NPAH.H3K4me1_vs_NPA.H3K4me1__PePr_chip1_broadPeaks.bed


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D9_AD001

value: ACA


title: NPAH_C2_H3K36me3

description: NPAH.H3K36me3_vs_NPA.H3K36me3__PePr_chip1_broadPeaks.bed

value: H3K36me3 polyclonal antibody, Diagenode, Cat#C15410192


title: nrpe1_gp4_IPARE_rep3

description:
200bp_150bp_sliding_windows_allDatasets.bed
RdDM_PolV_transcribed_HMM_bins.bed
nonRdDM_PolV_transcribed_HMM_bins.bed
nonPolV_transcribed_HMM_bins.bed

value: Columbia

value: 18 day-old seedlings


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D8_AD007

value: male


title: drd1_gp4_IPARE_rep1


title: NPAH_C2_Input

description: IP_vs_Input_NPAH.H3K36me3__PePr_broadPeaks.bed/ IP_vs_Input_NPAH.H3K27me3__PePr_broadPeaks.bed/ IP_vs_Input_NPAH.H3K27ac__PePr_broadPeaks.bed/ IP_vs_Input_NPAH.H3K4me3__PePr_sharpPeaks.bed/ IP_vs_Input_NPAH.H3K4me1__PePr_broadPeaks.bed

value: brain tumor cells


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D8_AD006


title: Col-0_gp4_IPARE_rep3


title: dms5-1_gp5_IPARE_rep1


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D8_AD004


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D8_AD002


title: NPAH_C2_H3K27ac

description: NPAH.H3K27ac_vs_NPA.H3K27ac__PePr_chip1_broadPeaks.bed


title: NPAH_B9_Input


title: sgMGA4

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4
Reads of low quality were filtered out and  alignments were performed using STAR2 aligner (with hg38 reference), featureCounts was used for gene quantification
Genome_build: hg38
Supplementary_files_format_and_content: csv file include counts for all samples generated at the gene-level using Featurecounts

molecule: polyA RNA

source_name: human colon organoids

extract_protocol:
Cells were stored in Trizol and RNA extracted using the Zymogenetics directZol miniprep kit
RNA-seq libraries were prepared from total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech Laboratories, Inc., Mountain View, CA, USA) and the Nextera XT DNA Library Preparation Kit (Illumina, Inc., San Diego, CA, USA)

treatment_protocol: Human colon organoids were cultured in Intesticult medium

tag: cell type

value: epithelial enriched colon organoid population

tag: viral vector used

value: lentiCRISPRv2 sgMGA


title: nrpe1_gp3_IPARE_rep2


title: Col-0_gp3_IPARE_rep2


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D8_AD001

source_name: C57BL/6J P56 Mouse Brain

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

tag: gender


title: sgMGA2


title: NPAH_B9_H3K4me3

value: H3K4me1 polyclonal antibody, Diagenode, Cat#C15410003-50


title: sgMGA3


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D6_AD010

value: brain


title: NPAH_B9_H3K4me1

value: H3K4me1 polyclonal antibody, Diagenode, Cat#C15410194


title: NPAH_B9_H3K36me3


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D6_AD007

value: STR


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D6_AD004

value: female


title: sgMGA1


title: ago4_grp2_IPARE_rep1


title: Col-0_gp2_IPARE_rep1


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D6_AD001


title: Empty4

value: lentiCRISPRv2 empty


title: NPAH_C2_H3K27me3

description: NPAH.H3K27me3_vs_NPA.H3K27me3__PePr_chip1_broadPeaks.bed

value: overexpression of NRASG12V + short hairpin for TP53 + short hairpin for ATRX + overexpression of mutated histone H3.3 G34R

value: H3K27me3 polyclonal antibody, Diagenode, Cat#C15410195


title: NPAH_B9_H3K27ac

value: H3K27ac polyclonal antibody, Diagenode, Cat#C15410196


title: Empty3


title: NPAH_B9_H3K27me3


title: spt5l_IPARE_rep1


title: ago4_gp3_IPARE_rep2


title: spt5l_gp3_IPARE_rep2


title: nrpe1_IPARE_rep1


title: NPAH_B7_Input

value: Normal mouse IgG, Santa Cruz Biotechnology, Cat#sc-2025


title: Empty2


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D5_AD007

value: AI


title: NPAH_B7_H3K4me3


title: Empty1


title: Col-0_IPARE_rep1

value: Columbia

value: Col-0 (wild-type)


title: NPAH_B7_H3K4me1


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D5_AD006

value: ACA


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D5_AD004


title: MYC IP in Empty transduced A549 cells set#2

data_processing:
Library strategy: CUT&RUN
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4
Alignment to hg38 with Bowtie 2,  reads >700bp filtered out, samples spike-in normalized
BigWigs were created using bedtools (genomecov) and WigToBigWig scripts
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

source_name: A549 lung adenocarcinoma

growth_protocol: Human lung adenocarcinoma line A549 cells were cultured in 10% FBS containing DMEM. They were transduced with vectors (lentiCRISPRv2 Empty and sgMGA). Cells were selected using puromycin.

extract_protocol: CUT&RUN libraries were prepared for sequencing using custom protocols

treatment_protocol: Cells were bound to ConA beads and incubated with antibodies (1 million cells per antibody)

value: lung adenocarcinoma

tag: cell line

value: MYC IP

tag: transduction

value: empty


title: NPAH_B7_H3K36me3

value: brain tumor cells

tag: genotype

value: H3K36me3 polyclonal antibody, Diagenode, Cat#C15410192


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D5_AD002

tag: strain

value: brain

value: male


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D3_AD008

tag: tissue

value: STR


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D3_AD010

value: female


title: L3MBTL2 IP in Empty transduced A549 cells set#2

tag: antibody

value: L3MBTL2 IP


title: NPAH_B7_H3K27me3

value: overexpression of NRASG12V + short hairpin for TP53 + short hairpin for ATRX + overexpression of mutated histone H3.3 G34R

tag: chip antibody

value: H3K27me3 polyclonal antibody, Diagenode, Cat#C15410195


title: MAX IP in Empty transduced A549 cells set#2

value: MAX IP


title: MGA IP in Empty transduced A549 cells set#2

value: MGA IP


title: NPAH_B7_H3K27ac

value: H3K27ac polyclonal antibody, Diagenode, Cat#C15410196


title: IgG control IP in Empty transduced A549 cells set#2

value: IgG control IP


title: HA36_TKO_DNMT3A2_I715N_r2

city: Utrecht

first: Tuncay

last: Baubec

address: Padualaan 8

department: Department of Biology

country: Netherlands

institute: Utrecht University

description: WGBS

data_processing:
Sequencing reads were pre-processed and trimmed using cutadapt v1.16 and sickle v1.33
Trimmed reads were mapped against the mm9 mouse assembly using bwa-meth v0.2.0  running bwa v0.7.12-r1039
Duplicates were removed with Picard MarkDuplicates (picard-tools v1.96, http://broadinstitute.github.io/picard/) with `REMOVE_DUPLICATES=TRUE and REMOVE_SEQUENCING_DUPLICATES=TRUE` flags.
Alignments with MAPQ > 40 were used as input to methylation calling with methyldackel v0.3.0-3-g084d926 (https://github.com/dpryan79/MethylDackel) (using HTSlib v1.2.1) in `cytosine_report` mode for all cytosines in the genome both CpG and CpH contexts (`extract -q 40 --cytosine_report --CHH –CHG`).
Genome_build: mm9
Supplementary_files_format_and_content: Processed tab delimited file contains cytosine report with following information: chromosome, nucleotide position, reported methylated cytosines, reported unmethylated cytosines, sequence context, exact sequence

source_name: Mouse Embryonic Stem Cells

growth_protocol: ES cells were were cultivated on feeder cells or 0.2% gelatine coated dishes. ES cell growth medium consisted of DMEM (Invitrogen) supplemented with 15% foetal calf serum (Invitrogen), 1x non-essential amino acids (Invitrogen), 1mM L-glutamine, LIF and 0.001% beta-mercaptoethanol.

extract_protocol:
Genomic DNA extraction, followed by phenol/chloroform extraction and ethanol precipitation. RNaseA treatment was performed for 30 min at 37C
Prior library preparation unmethylated Lambda phage DNA and SssI-methylated T7 DNA were spiked-in to genomic DNA samples to control bisulphite conversion rates. For WGBS, 10ug of DNA was sonicated to ca 500bp using a Bioruptor Pico. DNA was end-repaired and A-tailed using the NEB-Ultra Illumina library preparation kit (E7370). DNA fragments were ligated to methylated adapters (NEB E7535) following the NEB Ultra protocol. After adapter removal using Ampure xp beads (Beckman Coulter), DNA was converted using the Qiagen Epitect bisulphite conversion kit following the FFT sample protocol. After conversion library PCR amplification was performed with 10 cycles following NEB Ultra kit protocol, and cleaned up using Ampure xp beads.

value: embryonic stem cells


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D5_AD008

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10 INTACT
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

value: AI


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D3_AD007


title: HA36_TKO_DNMT3A2_I715N_r1

description: WGBS


title: MYC IP in sgMGA transduced A549 cells set#1

value: lung adenocarcinoma

value: MYC IP

value: sgMGA


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D3_AD006

value: ACA


title: MYC IP in Empty transduced A549 cells set#1

value: empty


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D3_AD004

value: brain


title: NHEM_7d

type: RNA

city: Erlangen

first: Peter

last: Dietrich

address: Fahrstr. 17

institute: FAU Erlangen-Nürnberg

hyb_protocol: 3.8 µg fragmented and labeled sense-strand cDNA were hybridized to Affymetrix GeneChip Human Gene 1.0 arrays for 16 h at 45 °C in a GeneChip hybridization oven 640.

scan_protocol: GeneChips were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled the by the Affymetrix GeneChip Command Console software v3.2 (AGCC).

data_processing: log2 gene level RMA signal intensity, generated by the Affymetrix GeneChip Expression Console v1.3 software.

label: biotin

source_name: Normal human epidermal melanoytes (NHEM)

label_protocol: The Ambion WT Expression Kit Protocol was used for the preparation of biotinylated sense-strand cDNA from 300ng of total RNA, followed by fragmentation and labeling according to the Affymetrix GeneChip WT Terminal Labeling and Hybridization User Manual.

growth_protocol: standard cell culture, 8% CO2, Normoxia, Medium: NHEM-medium (PromoCell)

extract_protocol: RNA was isolated using E.Z.N.A. Micro Elute Total RNA Kit (Omega, Norcross, GA, USA)

treatment_protocol: no specific treatment

value: primary melanocytes

tag: culture

value: 7 days


title: NHEM_14d

value: 14 days


title: NHEM_14d_II


title: MGA IP in sgMGA transduced A549 cells set#1


title: M_RNA-Seq_rep2

city: Leioa

first: Iraia

middle: Maialen

last: Muñoa Hoyos

state: Bizkaia

address: Barriso Sarriena S/N

country: Spain

institute: Universidad del País Vasco

data_processing:
ChIP-Seq: FASTQC Report (v.0.11.8) was used to assess  the quality of the FASTQ files. Sequenced reads were trimmed for adaptor sequence with TrimGalore! (v.0.6.2), and mapped to mm10 whole genome usin Bowtie2 (v.2.3.5.1). Peak calling was performed using MACS (10.30 m-fold, 300 bandwidth, p-value cutoff 10^5, v.1.4.2) to detect the binding sites, and the differential binding sites were identified using DiffBinnd (v.2.12.0) package in the R statistical environment.
RNA-Seq: FASTQC Report (v.0.11.8) was used to assess  the quality of the FASTQ files. Sequenced reads were trimmed for adaptor sequence with TrimGalore! (v.0.6.2), and mapped to mm10 whole genome using hisat2 (v.2.1.0). Transcripts assembly was carried out using StringTie (v.1.3.6) and transcripts reads count was quantified using featureCounts (v.1.6.4) software. Differential expressed genes were called using edgeR (v.3.26.4)
Integrative analyises were performed using Venny tool (v.2.1.0) and the Gene Ontology Resource from GO consortium (v.14.1.0) was used to identify the biological functions.
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-Seq: Peak text files and bigwig files for peaks visualization
Supplementary_files_format_and_content: RNA-Seq: Raw counts matrix text file

source_name: mESC

growth_protocol: Mouse (Oct4-GFP) embryonic stem cells (mESCs) were cultured feeder-free in 0.1% gelatin coated dishes.  For all conditions cells were passaged in 48h intervals, using trypsin  for detachment.

extract_protocol:
Total RNA was extracted using TRIzol method. For chromatin inmmunoprecipitation lysates were sonicated and histone-DNA complexes were isolated with specific antibody.
RNA and ChIP libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For drug treatment, mESCs were grown in respective medium supplemented with %0.9 (p/v) NaCl and 10uM morphine for 24 h, for control and treatment condition respectively and collected for further experimentation (P1). After treatment removal, mESCs were seeded and maintained in culture for 48h and 96h and collected (P2 and P3) for experimentation.

value: Mouse embryonic stem cells

tag: treatment

value: YES


title: C_RNA-Seq_rep2

value: NO


title: MGA IP in Empty transduced A549 cells set#1

value: MGA IP


title: M_RNA-Seq_rep1


title: 10024_2_4_Signal

city: shanghai

first: xueqin

last: zhu

address: zhizaoju Road 639

department: Department of Oral and Maxillofacial-Head and Neck Oncology and Faculty of Oral and Maxillofacial Surgery

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

description: miRNA and mRNA expression of tongue tissue

hyb_protocol: Preparation of antisense RNA, hybridization, staining, and scanning of the Rat Genome U34 Array (Affymetrix Inc.) was performed according to the Affymetrix standard protocol.

data_processing: The GeneSpring GX software (Agilent Technologies) was used to analyze the microarray data.

source_name: normal tissue of rat tongue

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was isolated from 7 tongue SCC tumors and 7 normal tissue samples using mirVanaTM RNA Isolation Kit (Applied Bio system p/n AM1556) following homogenization.

treatment_protocol: The animal model was established as previously described. Briefly, 40 male Sprague-Dawley (SD) rats, aged 6-7 weeks, were randomly divided into two groups. In the experimental group (n=20), the rats were fed daily with dissolved 4NQO (Sigma, #N8141-5G) at a concentration of 0.02 g/l, whereas the control group (n=20) were fed distilled water only. At the end of the 36th week, all rats were sacrificed. Tumors and normal tongue tissues were collected from the experimental and control groups.

value: tongue

value: Sprague-Dawley (SD) rat

value: male

tag: disease state

value: healthy


title: 10024_2_3_Signal

description: miRNA and mRNA expression of tongue SCC

scan_protocol: Preparation of antisense RNA, hybridization, staining, and scanning of the Rat Genome U34 Array (Affymetrix Inc.) was performed according to the Affymetrix standard protocol.

source_name: SCC tumors of rat tongue

value: squamous cell carcinoma


title: MAX IP in Empty transduced A549 cells set#1

value: lung adenocarcinoma

value: MAX IP


title: C_RNA-Seq_rep1


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D2_AD012

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

tag: age

tag: source

value: AI

value: STR

value: female


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D3_AD002

value: brain

value: ACA

tag: target


title: M_H3K27me3_ChIP-Seq_rep2

value: TriMethyl-Histone H3-K27 (Rabbit pAb, Catalog number A2363, AbClonal)


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D2_AD010


title: Ethyl linoleate/oleate, rep 2

first: William

last: Swindell

address: 1500 E. Medical Center Drive

department: Dermatology

description: EL rep 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Fluorescent signal capture and quantitation was performed using GenomeStudio software with default settings.

data_processing: Microarrays were background-corrected using maximum likelihood estimation for the normal-exponential convolution model (R package: limma: function: backgroundCorrect). Quantile normalization was then applied to ensure that empirical distributions between arrays were comparable (R package: limma, function: normalizeBetweenArrays).

label: Biotin

source_name: EpiDermFT skin substitute

label_protocol: Samples were subjected to first- and second-strand reverse transcription, followed by a single in vitro transcription (IVT) amplification that incorporates biotin-labeled nucleotides using the TargetAmp-Nano Labeling Kit.

growth_protocol: EpiDermFT tissues were prepared in vitro from neonatal keratinocytes and fibroblasts (Mattek, Ashland, MA; Cat. no. EFT-412; Lot no. 17522, Kit O). Tissue cultures were handled according to the manufacturer’s instructions.

extract_protocol: RNA extraction was performed using the NucleoSpin RNA II kit (Macherey-Nagel, Bethleem, PA). The quality of extracted RNA was assayed by spectrometry and electrophoresis. DNA microarray analysis was performed using high-quality RNA with well-defined 18S and 28S RNA peaks. The average RNA integrity number (RIN) among samples was 8.37 (range: 8.1 - 8.7).

treatment_protocol: Test materials were solubilized in DMSO at 50 mg/ml and further dilutions were done in distilled water. Materials were applied on tissues at a concentration of 50 µg/ml with 0.1% DMSO as control. Test materials were applied only to the tissue surface and was not in direct contact with tissue media. The incubation time of test materials with EpiDermFT tissues was 48 hours.

value: Ethyl linoleate/oleate (EL, 50 µg/ml)


title: Isosorbide di-(linoleate/oleate), rep 1

description: IDL rep 1

value: Isosorbide di-(linoleate/oleate) (IDL, 50 µg/ml)


title: Isosorbide di-(linoleate/oleate), rep 2

description: IDL rep 2


title: L3MBTL2 IP in sgMGA transduced A549 cells set#1

value: L3MBTL2 IP

value: sgMGA


title: Ethyl linoleate/oleate, rep 1

description: EL rep 1


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D2_AD007


title: L3MBTL2 IP in Empty transduced A549 cells set#1

value: empty


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D2_AD008


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D3_AD001


title: KMT2D_KO_RNAseq_rep3

city: Houston

first: Mahinur

last: Mattohti

state: TX

address: 6670 Bertner Ave

department: Surgery

institute: Houston Methodist Research Institute

data_processing:
RNAseq reads were aligned using STAR
raw count for each gene was obtained by HTSeq-count
Genome_build: mm9
Supplementary_files_format_and_content: HTSeq count txt file

source_name: KMT2D Mutant

growth_protocol: Cells were maintained in DMEM, high glucose, GlutaMAX™ Supplement, HEPES and 1% antibiotic-antimycotic.

extract_protocol:
Total RNA was prepared from cerebellar tissues using Trizol reagent (Life Technologies). RNA samples were sequenced using the Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: KMT2D mutant mice were crossed with iBIP mice (iBIP = Tyr-CreERT2, Rosa26-rtta, TetO-BRAFV600E, PTENL/L, INK/ARFL/L; mixed genetic background of FVB and B6 (REF)) to generate iBIP;KMT2DL/+ genotype containing mice (as assessed by genotyping for all alleles). The iBIP;KMT2DL/+ males and females were mated to generate iBIP;KMT2D+/+, iBIP;KMT2DL/+, and iBIP;KMT2DL/L genotype containing cohorts. They were put on doxycycline and 4-OHT (1uM) was applied on the ears to generate auricular tumor. KMT2D WT and KO murine cells isolated from iBIP;KMT2D+/+ and iBIP;KMT2DL/L mice.

value: iBiP melanoma mouse model tumor cell

tag: genotype/variation

value: mutant


title: C_H3K27me3_ChIP-Seq_rep2

tag: cell type

value: Mouse embryonic stem cells

value: NO


title: HA36_TKO_DNMT3A2_r2

description: WGBS

extract_protocol:
Genomic DNA extraction, followed by phenol/chloroform extraction and ethanol precipitation. RNaseA treatment was performed for 30 min at 37C
Prior library preparation unmethylated Lambda phage DNA and SssI-methylated T7 DNA were spiked-in to genomic DNA samples to control bisulphite conversion rates. For WGBS, 20ug of DNA was sonicated to ca 500bp using a Bioruptor Pico. For RRBS, 20ug of DNA was digested for 18h with MspI and separated on 2% agarose gels. Digested DNA was excised at 150-250 and 250-350 bp. Sonicated and digested DNA samples for WGBS and RRBS, respectively, were end-repaired and A-tailed using the NEB-Ultra Illumina library preparation kit (E7370). DNA fragments were ligated to methylated adapters (NEB E7535) following the NEB Ultra protocol. After adapter removal using Ampure xp beads (Beckman Coulter), DNA was converted using the Qiagen Epitect bisulphite conversion kit following the FFT sample protocol. After conversion library PCR amplification was performed with 10 cycles following NEB Ultra kit protocol, and cleaned up using Ampure xp beads.

value: embryonic stem cells


title: KMT2D_KO_RNAseq_rep1


title: C_H3K27me3_ChIP-Seq_rep1


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D2_AD002

city: La Jolla

value: male


title: IgG control IP in Empty transduced A549 cells set#1

value: lung adenocarcinoma

value: IgG control IP


title: Control, rep 2

description: CTL rep 2

value: 0.1% DMSO


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D1_AD001

value: brain

value: STR


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D2_AD004

value: ACA

value: female


title: KMT2D_WT_RNAseq_rep2

source_name: KMT2D WT

value: wild type


title: KMT2D_WT_RNAseq_rep3


title: m_15742_ko

city: Montreal

first: André

last: Veillette

state: QC

address: 110 Des Pins Ouest Rm1065

department: Molecular Oncology

institute: IRCM

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to the reference mouse genome version GRCm38 (gene annotation Ensembl v98) using STAR version 2.5
Gene expressions are obtained with featureCounts v1.5
DESeq2 version 1.14.1 was used to normalize raw counts and compute differential expression between wt and ko conditions.
Genome_build: GRCm38
Supplementary_files_format_and_content: normalized count matrix from DESeq2

source_name: Germinal center B cells

growth_protocol: AID-GFP reporter mice

extract_protocol:
GFP+ cells were sorted for total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Immunized with NP(18)OVA + alum, splenocytes isolated on Day 9

value: Germinal center B cells

tag: cell population

value: AID-GFP+ cells

value: SFR KO

value: Immunized, on Day 9


title: Control, rep 1

description: CTL rep 1


title: SC273 scRNA-seq

city: Pittsburgh

first: Kathryn

last: Torok

state: Pennsylvania

address: 530 45th St, Rangos 9161 Bay1

department: Peds Rheumatology

institute: University of Pittsburgh

data_processing:
Cellranger 3.0
Seurat
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: dissociated 4mm bx skin

extract_protocol:
Miltenyi Biotec Whole Skin Dissociation Kit human
10X Genomics Single Cell RNA Seq 3 Prime V2 libraries

value: scleroderma

value: dissociated 4mm bx skin

value: RPMI

tag: status

value: Active

tag: patient


title: SC272 scRNA-seq

value: Cryostor


title: KMT2D_KO_RNAseq_rep2

value: iBiP melanoma mouse model tumor cell

value: mutant


title: m_15743_ko


title: KMT2D_WT_RNAseq_rep1


title: M_H3K27me3_ChIP-Seq_rep1

value: Mouse embryonic stem cells

value: YES

value: TriMethyl-Histone H3-K27 (Rabbit pAb, Catalog number A2363, AbClonal)


title: m_15741_ko


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D12_AD012

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

value: brain

value: AI

value: STR

tag: gender


title: SC268 scRNA-seq


title: SC267 scRNA-seq


title: KMT2D Mutant Input DNA

data_processing:
ChIPseq reads were aligned to mm9 genome using bowtie1 with max 1 mismatch, duplicated reads were removed
peaks were called using MACS14 and MACS2 using pvalue cutoff of 1e-5, and was further filtered for downstream analysis using a more stringent cutoff of 1e-9
bigwig files were generated by deeptools bamCoverage normalized by RPKM
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files contains the ChIPseq signal normalized by RPKM. Bed files contain the peaks called by MACS14

extract_protocol:
Crosslinked KMT2D WT and Mutant samples were thawed on ice and resuspended in RIPA lysis buffer supplemented with protease inhibitor, lysed the cells on ice then sheared the chromatin by sonication. After centrifuge, the clean sonicated cell lysate mixed with protein G magnetic dynabeads (Invitrogen) coupled to antibodies described above and incubated over night at 4 degrees. Samples was washed 5 times with cold RIPA, twice with high salt RIPA, twice with LiCl buffer, twice with TE, and then eluted in elution buffer. The eluate was reverse crosslinked at 65C. Solid-phase reversible immobilization (SPRI) cleanup steps were performed. Beads were washed twice on the magnet with 70% ethanol and then air-dried. The DNA was eluted in EB buffer.
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and Bioanalyzer 1000 before multiplexing.


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D12_AD007

value: male


title: m_15736_wt

value: Germinal center B cells

value: AID-GFP+ cells

tag: genotype

value: wildtype


title: KMT2D Mutant H3K27me3_ChIPseq


title: m_15734_wt

tag: strain

value: Immunized, on Day 9


title: SC223 scRNA-seq

value: scleroderma

tag: tissue

value: dissociated 4mm bx skin


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D12_AD006

value: ACA

value: female


title: KMT2D Mutant H3K4me3_ChIPseq

value: iBiP melanoma mouse model tumor cell


title: SC222 scRNA-seq

value: Cryostor

value: Active


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D12_AD004


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D12_AD002


title: KMT2D Mutant H3K79me2_ChIPseq

value: mutant