title: AD025D2_S10

description: Day2 after VZV post vitamin D

value: Day2 after VZV


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A6_AD001

status: Public on Nov 17 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

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: PTLp

tag: target

value: STR

tag: gender

value: female


title: singleCell_spheroid_plate1_A16_S180

city: Stanford

first: Rachel

last: Agoglia

address: 371 Jane Stanford Way

institute: Stanford University

library_source: transcriptomic

data_processing:
Remove sequencing adapters with SeqPrep version 1.2
Map reads to GRCh38 and PanTro5 with STAR version 2.5.1b
Remove duplicate reads withSamtools version 0.1.19 with randomized discarding of duplicates
Remove reads which exhibit mapping bias with WASP (Hornet)
Count allele specific and total reads
Genome_build: Human: GRCh38; Chimpanzee: PanTro5
Supplementary_files_format_and_content: Counts matrix with total and allele-specific raw read counts (rows are genes, there are 3 columns per sample: total, human and chimpanzee read counts); matrix text files are provided for samples mapped on both the human and chimpanzee genomes; text files with sample meta data are also included for each data set

molecule: polyA RNA

organism:
Pan troglodytes
Homo sapiens

source_name: iPSC-derived cortical spheroid

extract_protocol:
Qiagen Rneasy Mini Kit with on-column DNAse digestion (Qiagen)
Illumina TruSeq Stranded mRNA library prep kit (Illumina)

tag: cell type

value: iPSC-derived cortical spheroid

tag: cell line

tag: differentiation id

tag: age (days)


title: AD023S6_S5

city: Lancaster

first: Barbara

middle: Bo-Ju

last: Shih

address: Bailrigg

department: Biomedical and Life Sciences

country: United Kingdom

institute: Lancaster University

description: 6 hours after saline post vitamin D

data_processing:
RNA-seq data was aligned to GRCh38 genome assembly using hisat2 using the parameters --known-splicesite-infile and --dta
Samtools was used to select for reads with paired mates.
Stringtie was used for transcriptome assembly and gene counts.
Gene level FPKM (Fragments Per Kilobase of transcript per Million) was estimated with Ballgown.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file; gene count

molecule: total RNA

organism: Homo sapiens

source_name: skin biopsy

extract_protocol:
Skin biopsy specimens were collected from the injection site 72 hours after injection with VZV antigen or 6 hour after normal saline injection. Normal (uninjected) skin from the same site was collected as a control. This was done before and after vitamin D supplementation within the same individuals. Frozen tissue was homogenized, and total RNA was extracted from bulk tissue homogenates by using the RNeasy Mini Kit (Qiagen, Hilden, Germany)
Kappa Hyperprep kit (Roche Diagnostics)

tag: supplementation

value: post vitamin D

tag: treatment

value: 6 hours after saline

value: skin


title: singleCell_spheroid_plate1_A14_S178


title: AD023N_S4

description: unmanipulated skin post vitamin D

value: unmanipulated skin


title: singleCell_spheroid_plate1_A13_S177


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A5_AD004

value: male


title: AD023D2_S6

description: Day2 after VZV post vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A5_AD002


title: singleCell_spheroid_plate1_A12_S176


title: singleCell_spheroid_plate1_A11_S175


title: WT 5

city: Houaton

first: Ali

middle: J

last: Marian

state: Texas

address: 6770 Bertner Ave DAC C900a

department: Centre for Cardiovascular Genetics

institute: UTHSC, Houston

data_processing:
Fastq files where trimmed using TrimGalore!.
Trimmed files were aligned using HISAT2.
Genes were quantified using featureCount.
Genome_build: GRCM38
Supplementary_files_format_and_content: The processed data file is in a comma seperated format and contains the final featureCount generated count matrix.

source_name: Freshly isolated Cardiac Myocytes

extract_protocol:
RNA-Sequencing (RNA-Seq):  Total RNA was isolated from cardiac myocytes of 2-week old WT and Myh6-Cre:LmnaF/F mice. RNA-seq was performed on the on ribosome-depleted RNA.
Samples with a RNA Integrity Number (RIN) read out of more than 8 were used to prepare sequencing library using the Illumina TruSeq stranded total RNA library preparation kit. The samples were sequenced on the Illumina HiSeq 4000 instrument using the paired-end sequencing reagents to generate 100 base pair runs.

value: Freshly isolated Cardiac Myocytes

tag: genotype

value: Control


title: KO 1

value: Myocyte-Specific Lamin A/C Null Mice (Myh6-cre:LmnaF/F)


title: KO 4


title: KO 3


title: KO 2


title: WT 6


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A4_AD001


title: KO 4 BRD4 ChIP

data_processing:
Data was trimmed for low quality sequence using trimGalore.
Data was mapped using bowtie 2.3.4.3 to the mouse genome.
Peaks were called using MACS v2.1.1
Super-enhancers were called using Rose v0.1.
Genome_build: USCS mm10

source_name: Cardiac myocytes

extract_protocol:
Isolated myocytes were resuspended in PBS immediately after the last step of calcium reintroduction. Formaldehyde at 1% concentration was added onto the tube to cross-link the cells and tube was placed on a rocker at room temperature for 5 minutes. Then, glycine at 125mM concentration was added to the tube, which was rocked on ice for 5 more minutes. Cells were then washed 3 times in PBS and then lysed using a dounce on ice in a cell lysis buffer (5mM Na-butyrate, 10mM HEPES pH8.0, 85mM KCl, 0.6% NP-40, protease and phosphatase inhibitors). The lysates were centrifugated for 5 minutes at 2,000 rpm at 4ºC, resuspended in a cell lysis buffer and incubated on ice for 10 minutes. The percentage of free nuclei was assessed visually, the suspension was centrifugated, and resuspended in nuclear lysis buffer (50mM TrisHCl pH8.0, 10mM EDTA, 1% Triton X-100, 0.8% SDS, protease and phosphatase inhibitors). It was then homogenized and incubated for 10 minutes on ice with regular flicking, before being transferred to sonication tubes. The sonication was performed on a Bioruptor Pico for 20 cycles 30sec ON/30sec OFF cycles at +4ºC. The sheared chromatin was then collected after centrifugation for 10 minutes at +4ºC at 13,000 rpm, diluted 10-fold with ChIP dilution buffer (16.7mM TrisHCl, 1.2mM EDTA, 140mN NaCl, 1.1% Triton X-100 protease and phosphatase inhibitors). A 10% input was collected before adding 6µg of an anti-BRD4 antibody to the remaining chromatin. After overnight immunoprecipitation, a mixture of sepharose A/B beads, pre-blocked with 1% BSA, was added onto the tube for 1 hours. Immunoprecipitates were then washed sequentially with a Low Salt buffer (0.1% SDS, 1%TritonX-100, 2mM EDTA, 20mM TrisHCl pH8.0, 150mM NaCl), High Salt buffer (0.1% SDS, 1%TritonX-100, 2mM EDTA, 20mM TrisHCl pH8.0, 500mM NaCl), LiCl buffer  (1% NP-40, 1% Na-Deoxycholate, 1mM EDTA, 10mM TrisHCl pH8.0, 250mM LiCl), and then twice in TE buffer (10mM TrisHCl pH 8.0, 1mM EDTA). Chromatin elution was collected in 1% SDS, 10mM EDTA, 50mM TrisHCl pH 8.0 at +65ºC for 15 minutes with agitation. The supernatant was then agitated at +65 ºC overnight at room temperature with 200mM final of NaCl. Chromatin was treated with RNAse A for 2 hours at +37ºC, proteinase K for 1 hour at +55ºC and DNA was then extracted using Phenol/chloroform process followed by ethanol precipitation.
Kapa Hyper Kit

value: Cardiac myocytes

tag: antibody

value: anti-BRD4 antibody


title: singleCell_spheroid_plate1_A10_S174


title: WT 3


title: AD018N_S2

description: unmanipulated skin post vitamin D


title: AD012S6_S13

description: 6 hours after saline post vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A12_AD004


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A12_AD006


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A12_AD002


title: AD012N_S16

description: unmanipulated skin post vitamin D


title: WT 2


title: WT 1


title: KO 3 BRD4 ChIP


title: AD012D2_S14

description: Day2 after VZV post vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A5_AD001


title: KO 3 Input

value: input


title: AD011S6_S11

description: 6 hours after saline post vitamin D


title: WT 4


title: AD018S6_S3

description: 6 hours after saline post vitamin D


title: AD018D2_S4

description: Day2 after VZV post vitamin D

value: Day2 after VZV


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A11_AD004

value: brain


title: KO 4 Input


title: KO 2 BRD4 ChIP


title: SPI2_TR1

city: Freiburg

first: Florian

last: Eggenhofer

address: Georges Köhler Allee 106

department: Institute for Informatics

country: Germany

institute: University of Freiburg

description: Total RNA,  rRNA depletion, and size selection (26-34 nt)

data_processing:
Basecalling with RTA 2.4.11
Trimming performed with cutadapt 2.1 (HRIBO 1.4.3)
rRNA filtering with samtools 1.9 (HRIBO 1.4.3)
Mapping with segemehl 3.4 (HRIBO 1.4.3)
Coverage file creation with HRIBO 1.4.3
Genome_build: ASM21085v2
Supplementary_files_format_and_content: wig files were generated with single nucleotide mapping and converted to bigwig

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: SPI2 TR1

extract_protocol:
see molecule, above
sRNA protocol for Illumina Nextseq500

treatment_protocol: Cultures were not treated with chloramphenicol and harvested by rapid filtration/chilling

tag: sample type


title: KO 2 Input


title: SPI1_RBP1

description: Ribosome mRNA footprints, ribosomes and footprints created by MNase digestions were harvested and size-selected (26-34 nt)

source_name: SPI1 RBP1

value: LB broth OD 2.0 SPI1-inducing


title: KO 1 BRD4 ChIP


title: SPI1_TR1

source_name: SPI1 TR1


title: AD011D2_S12

description: Day2 after VZV post vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A11_AD002

value: PTLp

value: STR


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A11_AD006


title: AD010S6_S5

description: 6 hours after saline post vitamin D


title: KO 1 Input


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A11_AD001

value: female


title: LB0.4_RBP1

source_name: LB0.4 RBP1

value: LB broth OD600 0.4


title: AD010N_S4

description: unmanipulated skin post vitamin D

value: post vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A10_AD006


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A12_AD001


title: WT 4 BRD4 ChIP


title: SPI2_RBP1

source_name: SPI2 RBP1


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A10_AD004


title: LB0.4_TR1

source_name: LB0.4 TR1


title: AD010D2_S6

description: Day2 after VZV post vitamin D

value: skin


title: WT 4 Input


title: AD011N_S10

description: unmanipulated skin post vitamin D

value: unmanipulated skin


title: Visium_ONT

city: New York

first: Anoushka

last: Joglekar

state: NY

address: 413 E 69th St

department: Dept. of Neurogenetics

institute: Weill Cornell Medicine

description: spatial sequencing

data_processing:
Illumina basecaller
PacBio IsoSeq basecaller
Oxford Nanopore Guppy basecaller
10X sequencing output processed with 10X cellranger v3
Cellranger output analyzed with Seurat v3
PacBio long read mapping done with STARlong
ONT long read mapping done with minimap2
Long read output processed with custom pipelines - Github
website with downloadable plots of the processed data: www.isoformAtlas.com
github repository with code: https://github.com/noush-joglekar/scisorseqr/
Genome_build: mm10
Supplementary_files_format_and_content: cellranger output for single-cell expression data
Supplementary_files_format_and_content: PacBio gff files: files were generated by mapping and aligning reads to the reference genome, and each line refers to an exon for a specific read. We selected reads that were uniquely mapped, spliced, and had consensus splice-sites. The files include 'hg19' but were  from mm10 alignment.

source_name: Saggital section

extract_protocol: As per recommendations of each individual platform

value: Brain

tag: brain region

value: Saggital section

tag: developmental stage


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A10_AD002

tag: strain


title: AD009S6_S11

description: 6 hours after saline post vitamin D

value: 6 hours after saline


title: WT 3 BRD4 ChIP

value: Control


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A10_AD001

tag: age


title: AD009N_S10

description: unmanipulated skin post vitamin D

tag: tissue


title: WT 3 Input

value: Cardiac myocytes


title: AD009D2_S12

description: Day2 after VZV post vitamin D


title: bulk_spheroid_RA8_D200_Hy2-16

value: iPSC-derived cortical spheroid


title: bulk_spheroid_RA9_D150_Hy2-9


title: AD006S6_S5

description: 6 hours after saline post vitamin D


title: bulk_spheroid_RA9_D150_Hy2-16


title: WT 2 Input

value: input


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H9_AD012

tag: source

value: RSP


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H9_AD010

value: brain

tag: target


title: WT 1 BRD4 ChIP

value: anti-BRD4 antibody


title: bulk_spheroid_RA9_D150_Hy1-29


title: AD006D2_S6

description: Day2 after VZV post vitamin D

value: Day2 after VZV


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H9_AD007

value: STR

tag: gender

value: male


title: WT 1 Input

tag: cell type


title: bulk_spheroid_RA8_D151_Hy2-9

tag: cell line


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H7_AD010

value: female


title: ATACseq in EB-Day4[D0+RA+SAG][NoDox] replicate 2

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

data_processing:
Basecall conversion to fastq files was performed using Picard v 2.8.2
Alignment: Paired-end ATAC-seq reads were mapped to the mouse mm10 genome using Bowtie 2.2.2 (Langmead et al., 2009).
Domain Calls: Genome-wide ATAC-seq derived accessible domains were called using DomainFinder in the SeqCode project   (https://github.com/seqcode/seqcode-core/blob/master/src/org/seqcode/projects/seed/DomainFinder.java).
Genome_build: mm10

source_name: ES-derived embryoid bodies+4D RA+SAG control

growth_protocol: mESC lines were cultured in 2-inhibitors based medium (Advanced DMEM/F12:Neurobasal (1:1) medium (Gibco), supplemented with 2.5% ESC-grade fetal bovine serum (vol/vol, Corning), N2 (Gibco), B27 (Gibco), 2mM L-glutamine (Gibco), 0.1 mM β-mercaptoethanol (Gibco), 1000 U/mL leukemia inhibitory factor (Millipore), 3μM CHIR (BioVision) and 1 μM PD0325901 (Sigma)) on 0.1% gelatin (Millipore) coated plates at 37 °C, 8% CO2.

extract_protocol:
Cells were collected prior to TF induction (day 2 of RA/SAG differentiation) and 48h after Doxycycline (Dox) treatment. 50,000 cells were aliquoted and washed twice in 1 × PBS (cold). Cell pellets were resuspended in 10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, and freshly added 0.1% NP-40 (vol/vol), and centrifuged at 4 °C. Pellets were resuspended in 25 µL of 2 × TD buffer, 2.5 µL TDE1 (Nextera DNA sample preparation kit, FC-121–1030) and 22.5 µL of water and incubated at 37 °C for 30 min. The sample was purified using the MinElute PCR purification kit (Qiagen, 28004).
A quantitative PCR reaction with 1 × SYBR Green (Invitrogen), custom-designed primers and 2 × NEB MasterMix (New England Labs, M0541) was performed to determine the optimal number of PCR cycles (one-third of the maximum measured fluorescence) (Buenrostro, Giresi, Zaba, Chang, & Greenleaf, 2013). PCR enrichment of the library was performed with custom-designed primers and 2 × NEB MasterMix (New England Labs, M0541). The libraries were purified using the MinElute PCR purification kit. High Sensitivity DNA ScreenTape (Agilent, 5067-5584) was used to verify the fragment length distribution of the library. Library quantification was performed using the KAPA library amplification kit on the Roche Lightcycler 480.

treatment_protocol: Embryoid bodies (EBs) were obtained by plating trypsinized (Gibco) mESCs in AK medium (Advanced DMEM/F12:Neurobasal (1:1) medium (Gibco), 7% KnockOut SR (vol/vol) (Gibco), 2 mM L-glutamine, 0.1 mM ß-mercaptoethanol and penicillin–streptomycin (Gibco),) at 37 °C, 5% CO2 (day -2). On day 0, EBs were split 1:2 and AK medium was replenished and supplemented with 1 μM all-trans retinoic acid and 0.5 μM smoothened agonist (SAG) (Millipore, 566660). TF induction was performed by adding 3 μg/mL of Doxycycline (Sigma, D9891) on day 2. For ATAC-seq experiments, 3.5x10^5 mESCs were plated in 100mm suspension dishes (Corning).

tag: strain genotype/variation

value: EB + 4 Days RA + SAG

value: Embryoid Bodies


title: bulk_spheroid_RA8_D151_Hy2-16

tag: differentiation id

tag: age (days)


title: ATACseq in EB-Day4[D0+RA+SAG][NoDox] replicate 1

tag: treatment


title: bulk_spheroid_RA8_D200_Hy2-9


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H7_AD007


title: bulk_spheroid_RA8_D151_Hy1-29


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H6_AD012


title: WT 2 BRD4 ChIP

tag: genotype


title: SPCA_WGS

city: Cambridge

first: Sonia

last: Iyer

state: MA

address: 455 Main Street

institute: Whitehead Institute

description:
SPCA
Supplemental Figure 2A-B

data_processing:
Paired-end reads were trimmed with Trimmomatic (v0.38, with options ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 MINLEN:36).
Trimmed read pairs were mapped to the GRCm38 (mm10) genome with 'bwa mem' (using default parameters).
Copy number alterations were predicted with Control-FREEC (v11.6, with options ploidy=2 breakPointThreshold=0.8 window = 50000) with a GEM mappability file.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Gzipped bedgraph files contain copy number (2^median ratio, as predicted by Control-FREEC).

source_name: cell lines

extract_protocol:
Cell lines mentioned above were used for whole-genome sequencing analysis. DNA was extracted from cells using the Purelink Genomic DNA Mini kit (Life Technologies, K182001), following the manufacturer's instructions. The samples were sent to NYU Langone's Genome Technology Center for low pass whole-genome sequencing.  The input for all library preps was 300ng.  Five PCR cycles were run for each sample.
Illumina Nextera Flex kit (96 sample kit, catalog number 20018705 & 200187708), using 1/4 scaled reactions
Whole-genome sequencing

treatment_protocol: The cells were not treated with any  agents

value: Fallopian tube

tag: genotype of the cell line inoculated

value: p53-/-R172H Ccne1OE Akt2 OE SMARCA4 OE


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H6_AD007


title: bulk_spheroid_RA7_D150_Hy2-16


title: BPCA_WGS

description:
BPCA
Supplemental Figure 2A-B

value: p53-/-R172H Ccne1OE Akt2 OE Brd4 short isoform OE


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H9_AD008


title: WT  plants

type: RNA

city: Taichung

first: chen

middle: wei

last: han

address: No.250 Kuo-Kuang Rd

department: Institute of Biotechnology, NCHU

country: Taiwan

institute: National Chung Hsing University Institute of Biotechnology CHY LAB

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Arabidopsis thaliana

source_name: WT

label_protocol: Agilent Low RNA Labeling Kit

growth_protocol: Wild type (Arabidopsis COL-0) and35S::ERF19 transgenic plants (Col-0)  grown in 16/8 hrs light/dark regime at 23 ºC. When plants flowering the whole inflorescence floral were cut for RNA extraction.

extract_protocol: Total RNA were extracted by Trizol and QIAGEN RNeasyPlant mini kit

treatment_protocol: Trangenic Arabidopsis

tag: cultivar

value: WT

value: whole flower


title: bulk_spheroid_RA9_D100_Hy2-9


title: AD006N_S4

description: unmanipulated skin post vitamin D

tag: supplementation

value: post vitamin D

value: unmanipulated skin

value: skin


title: 35S::ERF19 transgenic plants

source_name: 35S::ERF19 transgenic plants

value: ERF19 was expressed by 35S promoter


title: PCA_WGS

description:
PCA
Supplemental Figure 2A-B

value: p53-/-R172H Ccne1OE Akt2 OE


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H5_AD010

value: brain

value: RSP


title: KPCA.A_WGS

description:
KPCA.A
Supplemental Figure 2A-B

value: p53-/-R172H Ccne1OE Akt2 OE KRASG12V (Clone A)


title: bulk_spheroid_RA9_D100_Hy2-16

value: iPSC-derived cortical spheroid


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H5_AD008

value: STR

value: male


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H4_AD012

value: female


title: Sox10 Dom/Dom Rep4

city: Hongkong

first: Taida

last: Huang

address: 39 Area

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Sacral NCCs were obtained by culturing the neural tube explant isolated from E9.5 mouse embryos

hyb_protocol: Probes were hybridized to GeneChip mouse Gene 1.0 ST Arrays  for 18 hours according to the manufacturer’s instruction.

scan_protocol: Hybridized arrays were processed by the GeneChip Fluidics System and scanned by the GeneChip Scanner.

data_processing: The results were tabulated in files which showed a single intensity value for each probe region delineated by a grid on each array image and were imported into Partek Genomics Suite for probe set summarization and statistical analyses. Robust Multichip Analysis (RMA) was performed to obtain a single intensity value representing transcript abundance for each probe set. By normalizing and log arithmetically transforming array data, this analysis thus allowed comparisons between arrays and stabilized the variance across the arrays. Analysis of Variance (ANOVA) was used to calculate a p value for evaluating statistical significance of the difference.

label: biotin

source_name: Sacral NCCs from Dom mouse embryos

label_protocol: After extraction of total RNA from the cells, biotinylated probes were prepared from 250ng total RNA using the Ambion® WT Expression Kit coupled with the GeneChip WT Terminal Labeling and Controls Kit.

growth_protocol: The neural tube at sacral region caudal to somite 24 was separated by micro-dissection and cultured in DMEM/F12 containing 10% FBS.

extract_protocol: Total RNA from the sacral NCC cultures was extracted using RNeasy Micro Kit by following the manufacture’s protocol.

treatment_protocol: After 24 hours, the neural tube explants were removed and the emigrated NCCs were washed with DPBS for 2 times before RNA extraction.

tag: genotype/variation

value: homozygous Sox10 dom mutant


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H4_AD010

source_name: C57BL/6J P56 Mouse Brain

tag: strain


title: KPCA.C_WGS

description:
KPCA.C
Supplemental Figure 2A-B

value: Fallopian tube

value: p53-/-R172H Ccne1OE Akt2 OE KRASG12V (Clone C)


title: Sox10 WT Rep4

source_name: Sacral NCCs from WT mouse embryos

value: wildtype


title: KPCA_WGS

description:
KPCA
Supplemental Figure 2A-B

value: p53-/-R172H Ccne1OE Akt2 OE KRASG12V (Clone B)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H4_AD008

tag: age


title: PPNM_WGS

description:
PPNM
Supplemental Figure 2A-B

tag: tissue


title: Sox10 WT Rep3


title: bulk_spheroid_RA9_D100_Hy1-29

source_name: iPSC-derived cortical spheroid


title: bulk_spheroid_RA8_D100_Hy1-29


title: bulk_spheroid_RA8_D100_Hy2-16


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H4_AD007

tag: source


title: bulk_spheroid_RA8_D100_Hy2-9


title: bulk_spheroid_RA7_D100_Hy2-9


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H3_AD012

tag: target


title: bulk_spheroid_RA7_D100_Hy2-16


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H3_AD010

tag: gender


title: BPPNM_WGS

description:
BPPNM
Supplemental Figure 2A-B


title: KPCA.C_scRNA seq Met

description:
KPCA.C
Tumors from mice inoculated with the cell line described in characteristics: genotype of the cell line inoculated
Figure 6B-D

data_processing:
Fastq files were obtained with using "cellranger mkfastq" (Cell Ranger v3.0.1 from 10x Genomics).
Demultiplexing, mapping and gene counting were performed with "cellranger count", Cell Ranger 3.0.2 from 10x Genomics.
Mapping was done against the mouse mm10 (release refdata-cellranger-mm10-1.2.0)
Genome_build: mm10
Supplementary_files_format_and_content: filtered_gene_bc_matrices text output files from Cell Ranger count.

source_name: tumors

extract_protocol:
Tumors were removed and single-cell suspensions were used for scRNA sequencing analysis.
poly-A was selected from total RNA.  Stranded RNAseq libraries were constructed using the KAPA mRNA HyperPrep kit
scRNA-Seq

treatment_protocol: The mice were not treated with any other agents

value: Omentum

tag: days post inoculation

value: 21 days post inoculation


title: bulk_spheroid_RA7_D100_Hy1-29

tag: cell type

tag: cell line


title: KPCA_scRNA seq Met

description:
KPCA
Tumors from mice inoculated with the cell line described in characteristics: genotype of the cell line inoculated
Figure 3A-B and 6B-D

value: 35 days post inoculation


title: JJH-33

city: Daejeon

first: Ho-yeon

last: Lee

address: 125, Gwahak-ro, Yuseong-gu

country: South Korea

institute: KRIBB

data_processing:
raw reads are aligned to reference fasta file(Ensembl EquCab2 79) by STAR(2.5.2b) alignment 2PASS method.
Read counts were obtained from STAR alignment output file "ReadsPerGene'. Normalization were performed in DESeq2 process. . In order to analyze only the protein coding gene, the transcript coordinates corresponding to non-coding RNA such as rRNA, snRNA, and snoRNA was removed. (From Ensembl Transcripts ID ENSECAG00000025167 to ENSECAG00000027694)
Genome_build: EquCab2

organism: Equus caballus

source_name: Skeletal muscle

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: M. Pectoralis major


title: JJH-32

value: Extensor digitorum lateralis


title: Sox10 WT Rep2


title: Sox10 Dom/Dom Rep3


title: JJH-31

value: Extensor digitorum longus


title: Sox10 WT Rep1


title: KPCA.FST.OE_Met2 (KPCA.FST OE_rep2)

description:
Tumors from mice inoculated with the cell line described in characteristics: genotype of the cell line inoculated
Figure in publicaton: Figure 7E

data_processing:
Reads were mapped to the mouse genome (GRCm38, mm10), canonical chromosomes only, with STAR (2.7.1a), using default parameters except limiting the intron size to 50000 "--alignIntronMax   50000 " and using " --sjdbOverhang 74".
Gene counts were obtained with featureCounts v1.6.2 using "-s 2", "-p" for the paired end samples, and a gtf file from ENSEMBL version GRCm38.97.
Genome_build: GRCm38, mm10

extract_protocol:
Tumors were removed, flash frozen on dry ice, and RNA was harvested using mirVana miRNA Isolation Kit, with phenol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
poly-A was selected from total RNA.  Stranded RNAseq libraries were constructed using the KAPA mRNA HyperPrep kit

value: 45 days post inoculation

value: p53-/-R172H Ccne1OE Akt2 OE KRASG12V  FST OE (Clone B)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H3_AD008

value: brain

value: RSP


title: bulk_spheroid_RA9_D50_Hy2-9

value: iPSC-derived cortical spheroid

tag: differentiation id


title: KPCA.FST.OE_Met1 (KPCA.FST OE_rep1)

value: 44 days post inoculation


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H3_AD007

value: STR

value: male


title: JJH-30

value: Biceps femoris caudal


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H2_AD012

value: female


title: bulk_spheroid_RA9_D50_Hy1-29

tag: age (days)


title: KPCA.C_Met2 (KPCA.C_rep2)

description:
Tumors from mice inoculated with the cell line described in characteristics: genotype of the cell line inoculated
Figure in publicaton: Figure 6A

value: p53-/-R172H Ccne1OE Akt2 OE KRASG12V (Clone C)


title: bulk_spheroid_RA9_D50_Hy2-16


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H2_AD010


title: KPCA.C_Met1 (KPCA.C_rep1)

value: Omentum


title: JJH-29

value: Biceps femoris middle


title: bulk_spheroid_RA8_D50_Hy2-9


title: Sox10 Dom/Dom Rep1

value: homozygous Sox10 dom mutant


title: JJH-28

value: Biceps femoris vertebral


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H2_AD008


title: KPCA_Met3 (KPCA_rep3)

description:
Tumors from mice inoculated with the cell line described in characteristics: genotype of the cell line inoculated
Figure in publicaton: Figure 6A and 7E

value: 35 days post inoculation

value: p53-/-R172H Ccne1OE Akt2 OE KRASG12V (Clone B)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H2_AD007


title: KPCA_Met2 (KPCA_rep2)


title: JJH-27

value: Gluteus superficialis


title: JJH-26

value: Semitendinosus


title: bulk_spheroid_RA8_D50_Hy1-29


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H1_AD012

value: brain


title: KPCA_Met1 (KPCA_rep1)


title: PPNM_Met2 (PPNM_rep2)

description:
Tumors from mice inoculated with the cell line described in characteristics: genotype of the cell line inoculated
Figure in publicaton: Figure 4F

value: 53 days post inoculation


title: JJH-24

value: M.extensor carpi radialis


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H1_AD010

value: RSP


title: bulk_spheroid_SY15_D100_Hy1-29

value: iPSC-derived cortical spheroid


title: JJH-25

value: Longissimus thoracis and lumborum m.


title: bulk_spheroid_RA7_D50_Hy2-16


title: JJH-23

value: M.extensor digitorum communis


title: bulk_spheroid_SY15_D75_Hy1-29


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H12_AD010

value: STR

value: female


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H1_AD007

value: male


title: JJH-22


title: bulk_spheroid_SY15_D50_Hy1-29


title: Sox10 Dom/Dom Rep2


title: PPNM_Met1 (PPNM_rep1)

value: Omentum


title: BPPNM_Met2 (BPPNM_rep2)

value: 56 days post inoculation


title: BPPNM_Met1 (BPPNM_rep1)


title: bulk_spheroid_SY15_D25_Hy1-29


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H12_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H12_AD007


title: JJH-21


title: JJH-20


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H11_AD012


title: JJH-19


title: bulk_spheroid_RA8_D50_Hy2-16


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H11_AD010


title: JJH-18


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H11_AD008


title: JJH-17

value: M.biceps brachii


title: A16F258_44C_rep1

first: Ke

last: Chen

state: California

address: Bioengineering Department, 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Raw sequencing reads were mapped to the reference genome NC_000913.3 using Bowtie 2.3.4.3 with the following options ``-X 1000 -N 1 -3 3''.
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with the following options ``mode="IntersectionStrict", singleEnd=FALSE, ignore.strand=FALSE, preprocess.reads=invertStrand''.
Transcripts per Million (TPM) were calculated by DESeq2.
Genome_build: reference genome (NC_000913.3)
Supplementary_files_format_and_content: tab-delimited text files containing raw counts of sequencing reads for each sample

organism: Escherichia coli K-12

source_name: A16F258_44C_bacteria cells

growth_protocol: Cultures were inoculated from -80°C glycerol stocks into M9 minimal medium with 4g/L glucose supplementation, and grown aerated at 37°C overnight. Physiological adaptation was achieved by growing cell cultures exponentially over 2 passages for 5 to 10 generations at the target temperature. Next, cultures growing at the exponential growth phase were passaged to a 15 mL working volume tube and grown fully aerated until mid-log phase (OD600 ≈ 0.6) for RNA-Seq sample extraction.

extract_protocol:
3 mL of cell broth was taken at OD600~0.6 and immediately added to 2 volumes Qiagen RNAprotect Bacteria Reagent (6 mL). Then, the sample was vortexed for 5 seconds, incubated at room temperature for 5 minutes, and immediately centrifuged for 10 minutes at 5000 x g.    The supernatant was decanted, and the cell pellet was stored in the -80°C.  Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the RNeasy Plus Mini Kit (Qiagen) columns following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA Removal Kit (Gram-Negative Bacteria). The quantity was determined by Nanodrop 1000 spectrophotometer (Thermo Scientific). The quality was checked using RNA 6000 Pico Kit using Agilent 2100 Bioanalyzer (Agilent). Paired-end, strand-specific RNA-seq library was built with the KAPA RNA Hyper Prep kit (Kapa Biosystems) following manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: evolved strain adapted at 45.3C

tag: medium

value: glucose M9 minimal

tag: phase

value: mid-log phase

tag: temperature


title: A10F210_44C_rep2

source_name: A10F210_44C_bacteria cells


title: A10F210_44C_rep1


title: A9F255_44C_rep2

source_name: A9F255_44C_bacteria cells


title: JJH-16

value: Caput longum des M. triceps brachii


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H11_AD007

value: brain


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H10_AD012


title: A9F255_44C_rep1


title: A9F200_44C_rep2

source_name: A9F200_44C_bacteria cells

value: evolved strain adapted at 44.8C


title: A9F200_44C_rep1


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H10_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H10_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_H10_AD010


title: A8F232_44C_rep2

source_name: A8F232_44C_bacteria cells


title: A16F258_44C_rep2


title: A8F232_44C_rep1


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G9_AD012


title: A4F244_44C_rep2

source_name: A4F244_44C_bacteria cells


title: CIG_Sarscovid2: hABSC ALI culture with cigarette smoke and SARS-Covid2 exposure

city: Los Angeles

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

institute: University of California, Los Angeles

data_processing:
Raw sequencing data were filtered by read quality, adapter- and polyA-trimmed, and reads were aligned to a hybrid human hg38-SARS Covid2 transcriptome using the Cell Range software (10X Genomics) and the STAR aligner.
Expression counts for each gene were collapsed and normalized to unique molecular identifiers to construct a cell by gene matrix for each library, filtered to keep cells with over 2000 transcripts and genes expressed in at least 0.05% of cells.
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited digital expression matrix with cells as columns and genes as rows

source_name: nonsmoker airway basal stem cells

growth_protocol: ABSCs were seeded at 100,000 cells per well in a 1:1 mixture of media:growth factor-reduced Matrigel to grow as tracheospheres or seeded directly onto collagen-coated transwells and allowed to grow in the submerged phase of culture for 4-5 days with 500μl media in the basal chamber and 200μl media in the apical chamber. ALI cultures were then established and cultured with only 500μl media in the basal chamber.

extract_protocol:
Single cells were obtained by incubating ALI cultures in 500ul Accumax for an hour and 15 minutes. Cells were then fixed in cold methanol per the Illumina protocol and frozen at -80ºC. Cells were then rehydrated in ice cold PBS and RNAse inhibitor
Reverse transcription (RT) was performed in a 96-well thermal cycler. After RT, GEMs were harvested, and the cDNA underwent size selection with SPRIselect Reagent Kit. Indexed sequencing libraries were constructed using the Chromium Single-Cell 3’ Library Kit  for enzymatic fragmentation, end-repair, A-tailing, adapter ligation, ligation cleanup, sample index PCR, and PCR cleanup.
Cells were captured using a 10X Chromium device (10X Genomics) and libraries prepared according to the Single Cell 3’ v2 or v3 Reagent Kits User Guide

treatment_protocol:
The ALI plates (without lids) were placed inside a chamber and exposed to the smoke of a 1R3F research cigarette (University of Kentucky, Lexington, KY), which was attached to the vacuum chamber tube with a cigarette holder. The cigarette was burned 10% of its length and the smoke was introduced into the chamber via suction pump. A previously optimized treatment of 3-minute exposure/day was continued for 4 days.
ALI cultures on the apical chamber of transwell inserts were infected with SARS-CoV-2 viral inoculum (MOI of 0.1; 100 µl/well) prepared in ALI TEC media.

value: airway basal stem cells

tag: treatment

value: cigarette smoke, SARS-CoV-2

tag: technology

value: 10X Genomics Single Cell RNA Sequencing


title: Mock_Sarscovid2: hABSC ALI culture with SARS-Covid2

value: mock, SARS-CoV-2


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G9_AD010

tag: strain

value: RSP


title: CIG_Control: hABSC ALI culture with cigarette smoke exposure

value: cigarette smoke


title: hTERT RPE1 cells - H3K27me3

city: Seattle

first: Marcus

last: Woodworth

state: Washington

address: 36 Bagley Hall

department: Department of Chemistry

institute: University of Washington

description:
H3K27me3_S4_L001
250,000 cells

data_processing:
library strategy: CUT&RUN-seq
Paired-end sequencing reads were aligned separately to human (GRCh38/hg38) and yeast (SacCer_Apr2011/sacCer3) genomes using Bowtie2 with the following specifications: --local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 700.
Alignment results were converted to BAM files with SAMtools.
BAM files were converted to BED files with BEDTools.
Reads were sorted and filtered with a custom python script to remove random chromosomes (see supplementary file).
Histograms were generated with BEDTools genomecov using spiked-in yeast reads and input number of cells as scaling factors.
Genome_build: human (GRCh38/hg38) and yeast (SacCer_Apr2011/sacCer3)

source_name: retinal pigmented epithelial hTERT-immortalized cell line

growth_protocol: h-TERT RPE1 cells were cultured in Dulbecco’s modified eagle medium (DMEM, Gibco, 11995-065) supplemented with 100 units/mL of penicillin and streptomycin (Gibco, 11140-50), 1% nonessential amino acids (Gibco, 11140-050), and 10% fetal bovine serum (Gibco, 26140079), and grown to ~80% confluency. The cells were then trypsinized with 0.25% trypsin-EDTA (Gibco, 25200056).

extract_protocol:
Trypsinized RPE1 cells were bound to Concanavalin A coated magnetic beads (Bangs Laboratories, BP531), permeabilized with 0.025% (w/v) digitonin, then incubated overnight with 5 μg of either anti-H3K4me3 (Active Motif, 39159), anti-H3K27ac (Active Motif, 39133) or anti-H3K27me3 (Active Motif, 39155) at 4 °C. Cells were washed then incubated with protein A-MNase fusion protein (a gift from S. Henikoff, FHCRC) for 15 minutes at room temperature. Cells were washed again and incubated with 2 mM Calcium Chloride to induce MNase cleavage activity for 30 minutes at 0 °C. The reaction was stopped with 2× STOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 100 μg/mL RNase A and 50 μg/mL glycogen) and 0.2 pg of S. cerevisiae spike-in DNA were added to each sample. Cleaved Histone-DNA complexes were isolated by centrifugation and DNA was extracted with a NucleoSpin PCR Clean-up kit (Macherey-Nagel, 740609).
Library preparation from each CUT&RUN condition was done with a KAPA Hyper Prep Kit (VWR, 89125-040) with the PCR amplification settings adjusted to have the annealing and extension steps done simultaneously at 60 °C for 10 seconds. Library products between 200-300 base pairs were selected with Agencourt AMPure XP beads (Beckman Coulter, A63880) before being sequenced with an Illumina MiSeq system with paired-end 25 base pair sequencing read length and TruSeq primer standard for approximately 6 million reads per sample.

value: hTERT RPE1 cells

tag: cut&run antibody

value: anti-H3K27me3 (Active Motif, 39155)


title: hTERT RPE1 cells - H3K27ac

description:
H3K27ac_S3_L001
250,000 cells

value: anti-H3K27ac (Active Motif, 39133)


title: hTERT RPE1 cells - H3K4me3

description:
H3K4me3_S1_L001
250,000 cells

value: anti-H3K4me3 (Active Motif, 39159)


title: Mock_Control: hABSC ALI culture

value: mock


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G9_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

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: age

tag: tissue

value: STR

value: male


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G9_AD007

tag: source

tag: target


title: A4F244_44C_rep1

tag: genotype/variation

value: evolved strain adapted at 45.3C

value: glucose M9 minimal

value: mid-log phase


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G7_AD012

value: brain

tag: gender

value: female


title: BT245-NSD-dKO-2_H3K27me3

city: Santiago de Compostela

first: Carmen

last: Rivas

address: Avda Barcelona

department: CIMUS

country: Spain

institute: Universidad de Santiago de Compostela

description: According to manufacturer's protocol

data_processing:
Raw ChIP sequencing reads were aligned using BWA version 0.7.17 with default parameters. After alignment, we sorted the bam files using samtools, then igvtools was used to generate wig files (igvtools count -w 25 -e 200). Finally, bigWig files were obtained using wigToBigWig.
Genome_build: hg19 and dm6 for human and drosophila data, respectively
Supplementary_files_format_and_content: bigWig

source_name: brain tumor derived cell line & S2 cells (spike in)

growth_protocol: Tumor-derived cell lines were maintained in NeuroCult NS-A proliferation media (StemCell Technologies) supplemented with bFGF (10ng/mL) (StemCell Technologies), rhEGF (20 ng/mL) (StemCell Technologies) and heparin (0.0002%) (StemCell Technologies) on plates coated in poly-L-ornithine (0.01%) (Sigma) and laminin (0.01 mg/mL) (Sigma).  Drosophila S2 cells were cultured in Schneider's Drosophila Medium (Invitrogen) containing 10% heat-inactivated FBS.

extract_protocol:
Cells were fixed with 1% formaldehyde (Sigma). Fixed cell preparations were washed, pelleted and stored at -80°C. Sonication of lysed nuclei (lysed in a buffer containing 1% SDS) was performed on a BioRuptor UCD-300 for 60 cycles, 10s on 20s off, centrifuged every 15 cycles, chilled by 4°C water cooler. Samples were checked for sonication efficiency using the criteria of 150-500bp by gel electrophoresis. After the sonication, the chromatin was diluted to reduce SDS level to 0.1% and before ChIP reaction 2% of sonicated drosophila S2 cell chromatin was spiked-in the samples for quantification of total levels of histone mark after the sequencing. ChIP reaction for histone modifications was performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal ChIP-seq Kit. 25ul Protein A beads (Invitrogen) or 70ul of sheep anti-mouse IgG beads (Invitrogen) were washed and then incubated with antibodies (protein A beads with: anti-H3K27me3 (1:40, CST 9733), anti-H3K27me2 (1:50, CST 9728), anti-H3K36me2 (1:50, CST 2901), anti-H3K9me3 (1:66, Abcam ab8898); anti-mouse IgG beads with: anti-H3K27me1 (1:50, Active Motif 61015), anti-H3K36me3 (1:100, Active Motif 61021)), and 2 million cells of sonicated cell lysate combined with protease inhibitors for 10 hr, followed by 20 min wash cycle with provided wash buffers. ChIP reaction for SUZ12 was performed as follows: antibodies (anti-SUZ12 (1:150, CST 3737)) were conjugated by incubating with 40ul protein A beads at 4°C for 6 hours, then chromatin from ~4 million cells was added in RIPA buffer, incubated at 4°C o/n, washed using buffers from Ideal ChIP-seq Kit (1 wash with each buffer, corresponding to RIPA, RIPA+500mM NaCl, LiCl, TE), eluted from beads by incubating with Elution buffer for 30 minutes at room temperature. Reverse cross linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2ul RNase Cocktail at 65°C for 30 min followed by 2ul Proteinase K at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol.
Library preparation was carried out using Kapa HTP or HyperPrep Illumina library preparation reagents, according to manufacturer's instructions.

tag: cell line

tag: chip antibody

value: H3K27me3 (Cell Signaling Technology, #9733)

tag: genotype


title: A3F228_44C_rep1

source_name: A3F228_44C_bacteria cells

tag: strain background


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G7_AD010


title: BT245-NSD-dKO-2_H3K27me2

description: According to manufacturer's protocol

value: H3K27me2 (Cell Signaling Technology, #9728)


title: BT245-NSD-dKO-2_H3K36me2

description: According to manufacturer's protocol

value: H3K36me2 (Cell Signaling Technology, #2901)


title: A3F181_44C_rep2

source_name: A3F181_44C_bacteria cells

value: evolved strain adapted at 44.8C

tag: medium


title: A3F181_44C_rep1

tag: phase


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G7_AD007

value: RSP


title: Anc_42CA3_44C_rep1

source_name: Anc_42CA3_44C_bacteria cells

value: Anc

tag: temperature


title: Anc_42CA3_44C_rep2


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G5_AD012

source_name: C57BL/6J P56 Mouse Brain


title: A16F258_37C_rep1

source_name: A16F258_37C_bacteria cells


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G4_AD012


title: 1-S_UV

city: Saint Louis

first: Ryan

last: McCulla

state: Missouri

address: 3501 Laclede Ave

department: Chemistry

institute: Saint Louis University

description:
Sample - cells treated with 10uM of 1-S and UV-A irradiated for 30 minutes in a photoreactor with 8 LZC-UVA bulbs
fpkm_genename-group 2.xls
fpkm_group-2.xls
fpkm_sample-group2.xls
readcount-group2.xls
readcount_genename-group2.xls
1-S_UVvsVC_UV_DEG.xls
1-S_UVvs1-S_NoUV-DEG.xls
1-S_UVvsVC_NoUV_DEG.xls
Union for cluster-2.csv

data_processing:
QC and transcriptome data analysis :Downstream analysis was performed using a combination of programs including STAR, HTseq, Cufflink and our wrapped scripts. Alignments were parsed using Tophat program and differential expressions were determined through DESeq2/edgeR. GO and KEGG enrichment were implemented by the ClusterProfiler. Gene fusion and difference of alternative splicing event were detected by Star-fusion and rMATS software
Reads mapping to reference genome :Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
Quantification of gene expression level  :HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008).
Differential expression analysis :Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.16.5). The P values were adjusted using the Benjamini & Hochberg method. Adjusted P-value of 0.05 and absolute foldchange of 1 were set as the threshold for significantly differential expression.
Clustering  :To identify the correlation between difference, we clustered different samples using expression level FPKM to see the correlation using hierarchical clustering distance method with the function of pheatmap package in R
Genome_build: Homo_sapiens_hg19 (Sample 1,2,5,6 )  and Homo_sapiens_hg38 ( (Sample 3,4,7,8) :
Supplementary_files_format_and_content: xls files include FPKM count of each sample and DEG list for each comparison.

source_name: breast cancer cells

growth_protocol: MDA-MB-231 cell line was purchased from ATCC (Manassas,VA). The cells were incubated at 37°C in 95% relative humidity with 5% CO2. The cells were cultured in DMEM medium containing 10% FBS, and 1% L-glutamine. The cells were grown to 90% confluency and passaged by removing media, washing the cells with PBS buffer, and splitting the cells.

extract_protocol:
Following treatment protocol, cell media was aspirated and each well was washed with PBS. 350 µL of lysis buffer (included in Gen Elute™ Total RNA Purification Kit) was added. Wells were coated in lysis buffer for 5 minutes and transfered to seperate microcetrifuge tubes. 200 µL absolute ethanol was added and tubes were vortexed for 10 seconds. Columns were assembled with elution tubes and the lysates were applied directly onto seperately assembled columns. Tubes were centrifuged at 3,500 g for 1 minute. If lysate hasn't passed through the column. Centrifuge an additional minute at 14,000 g. Flowthrough was discarded. 400 µL of wash solution A was applied to each column and centrifuged for 1 minute at 3,500 g (or increased to 14,000 g as necessary). Flowthrough was discarded and the column was washed twice more with a 2 minute centrifuge time for the last wash. The columns were placed into fresh elution tubes and 50 µL of elution solution was added to each. The columns were centrifuged at 200 g for 2 minutes, followed by 14,000 g for 1 minute. The elution procedure was repeated to maximize yield. Samples were stored at -80 C until shipping at -20 C.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. The mRNA was fragmented by addition of fragmentation buffer. NEB library and strand specific libraries were then chosen. (Novogene Corporation - protocol associated with NEB library and strand specific library) Libraries were constructed using standard Illumina protocol.

treatment_protocol: "Two six well plates were plated with MDA-MB-231 cells (600,000 cells/1.8mL/well). Both plates were incubated with compounds (1-SO and 1-S) at final 10μM concentration for 24 hours (VC – 1% DMSO). One plate was irradiated with UV-A light by placing it in a Luzchem photoreactor with 8 LZC-UVA bulbs (fwhm, 325-375 nm) and another plate was kept in the dark by wrapping it in aluminium foil. After UV-exposure, RNA was extracted from these samples using Gen Elute™ Total RNA Purification Kit (Sigma Aldrich, Catalog #RNB100) and the protocol associated with the product kit. The samples were then shipped to Novogene Corporation Inc on dry ice. RNA sequencing and associated bioinformatics analysis (differential gene expression analysis) were performed by Novogene Corporation.  Heatmaps were generated using pheatmap package installed in R." - Isor A. et al., 2020 in prep

tag: passage

tag: agent


title: 1-S_No UV

description:
Sample - cells treated with 10uM of 1-S
fpkm_genename-group 2.xls
fpkm_group-2.xls
fpkm_sample-group2.xls
readcount-group2.xls
readcount_genename-group2.xls
1-S_NoUVvsVC_NoUV-DEG.xls
1-S_UVvs1-S_NoUV-DEG.xls
Union for cluster-2.csv

value: 10uM of 1-S


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G4_AD010

tag: strain


title: 1-SO_UV

description:
Sample - cells treated with 10uM of 1-SO and UV-A irradiated for 30 minutes in a photoreactor with 8 LZC-UVA bulbs
fpkm_genename-group1.xls
fpkm_group-1.xls
fpkm_sample-group1.xls
readcount-group1.xls
readcount_genename_group1.xls
1-SO_UVvsVC_No UV-DEG.xls
1-SO_UVvsVC_UV-DEG.xls
Union for cluster-1.csv


title: A10F210_37C_rep2

source_name: A10F210_37C_bacteria cells


title: A16F258_37C_rep2


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G6_AD008


title: BT245-NSD-dKO-2_Input

description: According to manufacturer's protocol


title: Baf155_CKO_EMP

city: St. Louis

first: Hyung Joo

state: MO

address: 4515 McKinley Avenue

department: Department of Genetics

institute: Washington University School of Medicine

data_processing:
Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq.
The Illumina adapter sequences were trimmed from the raw sequencing reads using cutadapt v.1.11 paired-end mode.
The trimmed reads were mapped to the mouse genome sequence by using bowtie2 version 2.3.4.1 with the following parameters: --local -k 4 -X 2000 --mm.
The ATAC peaks per replicate were identified from these insertion sites by using MACS2 version 2.1.1 callpeak function with the following parameters: -g mm --keep-dup all -B --SPMR --nomodel --extsize 73 --shift -37 -p 0.01 --call-summits.
The ATAC signal bigWig tracks were converted from the bedGraph files generated by MACS2 version 2.1.1 bdgcmp function with the following parameter: -m FE.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigWig

source_name: cKit+ cells from Baf155 CKO yolk sac

extract_protocol:
Approximately 50,000 cKIT+ cells were isolated from WT and Baf155 CKO yolk sac using FACS sorter. Cells were washed once with cold PBS, lysed in 100 µL of ATAC-seq RSB (10 mM Tris pH 7.4, 10 mM NaCl, and 3 mM MgCl2) containing 0.1% NP40, 0.1% Tween-20 and 0.01% Digitonin on ice for 3 minutes, and 1 mL of ATAC-seq RSB containing 0.1% Tween-20 was added. Then nuclei pellet was collected and resuspended in 20 µL of 2x TD buffer (20 mM Tris pH 7.6, 10 mM MgCl2, and 20% dimethyl formamide). 50,000 nuclei was transposed with 2.5 µl transposase for 30 minutes at 37 ºC for transposition. Transposed DNA fragments were immediately purified by using Zymo DNA Clean and Concentrator 5 columns.
ATAC-seq libraries were amplified by using 9 cycles of PCR amplification, and purified by using the AMPure XP Beads (Beckman Coulter) with double size selection.

value: Tie2-Cre;Baf155 CKO

value: yolk sac

tag: cell type

value: cKit+ cells


title: A10F210_37C_rep1


title: A3F228_44C_rep2


title: Baf155_WT_EMP

source_name: cKit+ cells from Baf155 WT yolk sac

value: Tie2-Cre;Baf155 WT (littermate)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G3_AD012

first: Joseph

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

tag: age

value: STR


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G4_AD007

tag: tissue

value: male


title: A9F255_37C_rep2

source_name: A9F255_37C_bacteria cells

value: evolved strain adapted at 45.3C

value: glucose M9 minimal


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G4_AD008

value: brain

tag: source


title: A9F255_37C_rep1

value: mid-log phase


title: HSJ019-K27M_WGBS

description: According to manufacturer's protocol

data_processing:
Raw reads from whole-genome bisulfite sequencing were aligned using BWA (version 0.6.1). Low-quality sequence at the 3′ ends were trimmed. After alignment, we filtered duplicated or poorly mapping reads (>2% mismatches or aberrant insert size). Samtools (version 0.1.18) in mpileup mode was applied to call CpG methylation. We used igvtools to generate the tdf files.
Genome_build: hg19
Supplementary_files_format_and_content: tdf

source_name: brain tumor derived cell line

growth_protocol: Tumor-derived cell lines were maintained in NeuroCult NS-A proliferation media (StemCell Technologies) supplemented with bFGF (10ng/mL) (StemCell Technologies), rhEGF (20 ng/mL) (StemCell Technologies) and heparin (0.0002%) (StemCell Technologies) on plates coated in poly-L-ornithine (0.01%) (Sigma) and laminin (0.01 mg/mL) (Sigma).

extract_protocol:
DNA was extracted from cell lines using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) following manufacturer instructions.
Whole-genome sequencing libraries were generated from 700 to 1000 ng of genomic DNA spiked with 0.1% (w/w) unmethylated λ DNA (Promega) previously fragmented to 300–400 bp peak sizes using the Covaris focused-ultrasonicator E210. Fragment size was controlled on a Bioanalyzer DNA 1000 Chip (Agilent) and the KAPA High Throughput Library Preparation Kit (KAPA Biosystems) was applied. End repair of the generated dsDNA with 3′ or 5′ overhangs, adenylation of 3′ ends, adaptor ligation, and clean-up steps were carried out as per KAPA Biosystems’ recommendations. The cleaned-up ligation product was then analyzed on a Bioanalyzer High Sensitivity DNA Chip (Agilent) and quantified by PicoGreen (Life Technologies). Samples were then bisulfite converted using the Epitect Fast DNA Bisulfite Kit (Qiagen) according to the manufacturer’s protocol. Bisulfite-converted DNA was quantified using OliGreen (Life Technologies) and, based on quantity, amplified by 9–12 cycles of PCR using the Kapa Hifi Uracil + DNA polymerase (KAPA Biosystems) according to the manufacturer’s protocol. The amplified libraries were purified using Ampure XP Beads (Beckman Coulter), validated on Bioanalyzer High Sensitivity DNA Chips, and quantified by PicoGreen.


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G7_AD008

tag: target


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G3_AD010

value: female


title: HSJ019-KO2_Input

description: According to manufacturer's protocol

value: H3.3 (H3F3A) K27M-KO by introducing frameshift indel to the H3F3A allele carrying K27M mutation and leaving wild-type allele


title: 1-SO_No UV

description:
Sample - cells treated with 10uM of 1-SO
fpkm_genename-group1.xls
fpkm_group-1.xls
fpkm_sample-group1.xls
readcount-group1.xls
readcount_genename_group1.xls
1-SO_No UVvsVC_No UV-DEG.xls
Union for cluster-1.csv

value: 10uM of 1-SO


title: A9F200_37C_rep2

source_name: A9F200_37C_bacteria cells

tag: genotype/variation

value: evolved strain adapted at 44.8C


title: DIPGXIII-K27M_WGBS

description: According to manufacturer's protocol

value: SU-DIPGXIII


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G3_AD008

value: RSP

tag: gender


title: HSJ019-KO2_H3K27me2

description: According to manufacturer's protocol

tag: cell line

value: H3K27me2 (Cell Signaling Technology, #9728)


title: HSJ019-KO_WGBS

description: According to manufacturer's protocol


title: A8F232_37C_rep2

source_name: A8F232_37C_bacteria cells


title: BT245-KO_WGBS

description: According to manufacturer's protocol


title: HSJ019-KO2_H3K27me3

description: According to manufacturer's protocol

tag: chip antibody

value: H3K27me3 (Cell Signaling Technology, #9733)


title: bulk_spheroid_RA16_D200_H21792

first: Rachel

address: 371 Jane Stanford Way

institute: Stanford University

data_processing:
Remove sequencing adapters with SeqPrep version 1.2
Map reads to GRCh38 and PanTro5 with STAR version 2.5.1b
Remove duplicate reads withSamtools version 0.1.19 with randomized discarding of duplicates
Remove reads which exhibit mapping bias with WASP (Hornet)
Count allele specific and total reads
Genome_build: Human: GRCh38; Chimpanzee: PanTro5
Supplementary_files_format_and_content: Counts matrix with total and allele-specific raw read counts (rows are genes, there are 3 columns per sample: total, human and chimpanzee read counts); matrix text files are provided for samples mapped on both the human and chimpanzee genomes; text files with sample meta data are also included for each data set

source_name: iPSC-derived cortical spheroid

extract_protocol:
Qiagen Rneasy Mini Kit with on-column DNAse digestion (Qiagen)
Illumina TruSeq Stranded mRNA library prep kit (Illumina)

value: iPSC-derived cortical spheroid

tag: differentiation id

tag: age (days)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G1_AD012


title: HSJ019-KO2_H3K27me1

description: According to manufacturer's protocol

value: H3K27me1 (Active Motif, #61015)

tag: genotype


title: A8F232_37C_rep1

tag: strain background

tag: medium

tag: phase


title: bulk_spheroid_RA16_D200_H20961


title: HSJ019-KO1_Input

description: According to manufacturer's protocol


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G1_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G1_AD007


title: A4F244_37C_rep2

source_name: A4F244_37C_bacteria cells

tag: temperature


title: bulk_spheroid_RA16_D200_H20682


title: HSJ019-KO1_H3K27me3

description: According to manufacturer's protocol


title: bulk_spheroid_RA13_D201_H20961


title: DIPGXIII-KO_WGBS

description: According to manufacturer's protocol


title: A3F228_37C_rep2

source_name: A3F228_37C_bacteria cells

tag: strain


title: A4F244_37C_rep1


title: bulk_spheroid_RA13_D201_H20682

tag: cell type


title: A3F228_37C_rep1


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G12_AD010

tag: age


title: HSJ019-KO1_H3K9me3

description: According to manufacturer's protocol

source_name: brain tumor derived cell line & S2 cells (spike in)

value: H3K9me3 (Abcam, #ab8898)


title: bulk_spheroid_RA16_D151_H21792


title: A9F200_37C_rep1


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G3_AD007

tag: tissue

value: STR


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G12_AD007

tag: source

value: male


title: A3F181_37C_rep2

source_name: A3F181_37C_bacteria cells


title: A3F181_37C_rep1


title: HSJ019-KO1_H3K27me2

description: According to manufacturer's protocol


title: HSJ019-KO2_H3K36me2

description: According to manufacturer's protocol

value: H3K36me2 (Cell Signaling Technology, #2901)


title: HSJ019-KO1_H3K27me1

description: According to manufacturer's protocol


title: Anc_42CA3_37C_rep2

source_name: Anc_42CA3_37C_bacteria cells

value: Anc

value: evolved strain adapted at 45.3C

value: glucose M9 minimal


title: bulk_spheroid_RA14_D155_H21792


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G12_AD012

value: brain

tag: target

value: female


title: Anc_42CA3_37C_rep1

tag: genotype/variation

value: mid-log phase


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G11_AD010

tag: gender


title: bulk_spheroid_RA14_D155_H20961

tag: cell line


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G12_AD008


title: HSJ019-K27M3_Input

description: According to manufacturer's protocol

tag: chip antibody


title: A16F258_30C_rep2

source_name: A16F258_30C_bacteria cells


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G11_AD007

source_name: C57BL/6J P56 Mouse Brain


title: A16F258_30C_rep1


title: HSJ019-K27M3_H3K36me2

description: According to manufacturer's protocol


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G11_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G11_AD012


title: bulk_spheroid_RA16_D102_H21792

tag: differentiation id


title: bulk_spheroid_RA16_D151_H20682

tag: age (days)


title: HSJ019-K27M3_H3K27me2

description: According to manufacturer's protocol

tag: genotype


title: A10F210_30C_rep2

source_name: A10F210_30C_bacteria cells

tag: strain background


title: HSJ019-KO1_H3K36me3

description: According to manufacturer's protocol

value: H3K36me3 (Active Motif, #61021)

value: H3.3 (H3F3A) K27M-KO by introducing frameshift indel to the H3F3A allele carrying K27M mutation and leaving wild-type allele


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G10_AD012

value: RSP


title: bulk_spheroid_RA16_D151_H20961


title: HSJ019-K27M3_H3K27me3

description: According to manufacturer's protocol


title: A10F210_30C_rep1

tag: medium


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G10_AD010


title: bulk_spheroid_RA16_D102_H20682


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_G10_AD007


title: bulk_spheroid_RA16_D102_H20961


title: HSJ019-KO1_H3K36me2

description: According to manufacturer's protocol


title: HSJ019-K27M3_H3K9me3

description: According to manufacturer's protocol


title: A9F255_30C_rep2

source_name: A9F255_30C_bacteria cells

tag: phase


title: bulk_spheroid_RA13_D100_H21792


title: A9F255_30C_rep1

tag: temperature


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_F9_AD012

tag: strain


title: bulk_spheroid_RA14_D155_H20682

tag: cell type


title: HSJ019-K27M3_H3K27me1

description: According to manufacturer's protocol


title: bulk_spheroid_RA13_D100_H20961


title: bulk_spheroid_RA13_D100_H20682


title: DIPGXIII-KO1-r2_H3K36me3

description: According to manufacturer's protocol

value: SU-DIPGXIII


title: DIPGXIII-KO1-r2_Input

description: According to manufacturer's protocol


title: A9F200_30C_rep2

source_name: A9F200_30C_bacteria cells

value: evolved strain adapted at 44.8C


title: A9F200_30C_rep1


title: bulk_spheroid_RA16_D52_H21792

value: iPSC-derived cortical spheroid


title: DIPGXIII-K27M5_H3K36me3

description: According to manufacturer's protocol


title: bulk_spheroid_RA16_D52_H20961


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_F9_AD007

tag: age


title: A8F232_30C_rep1

source_name: A8F232_30C_bacteria cells


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_F7_AD012

tag: tissue


title: BT245-KO2-r3_SUZ12

description: According to manufacturer's protocol

value: SUZ12 (Cell Signaling Technology, #3737)


title: A8F232_30C_rep2


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_F9_AD008

tag: source


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_F7_AD010

tag: target


title: bulk_spheroid_RA16_D52_H20682


title: bulk_spheroid_RA13_D50_H21792


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_F7_AD008


title: BT245-KO1-r2_H3K36me3

description: According to manufacturer's protocol


title: A4F244_30C_rep2

source_name: A4F244_30C_bacteria cells

tag: genotype/variation


title: A4F244_30C_rep1


title: bulk_spheroid_RA13_D50_H20961


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_F9_AD010

tag: gender


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_F7_AD007


title: BT245-K27M3-DMSO-r2_Input

description: According to manufacturer's protocol

tag: cell line


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_F4_AD007


title: A3F228_30C_rep2

source_name: A3F228_30C_bacteria cells


title: bulk_spheroid_RA13_D50_H20682


title: bulk_spheroid_RA19B_D35_H21792


title: BT245-K27M3-DMSO-r2_SUZ12

description: According to manufacturer's protocol

tag: chip antibody


title: BT245-KO2-r3_Input

description: According to manufacturer's protocol


title: BT245-K27M3-DMSO_H3K36me3

description: According to manufacturer's protocol


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_F1_AD010


title: bulk_spheroid_RA19B_D35_H20961

tag: differentiation id


title: RNA-hNeurosphere-H9-UTXKO replicate 5

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
Basecalls performed using CASAVA
Paired-end 100-cycle sequencing was performed on HiSeq 2000 or HiSeq 4000 sequencers (Illumina). RNA-sequencing was mapped as described previously (Downing et al., 2012), and HTSeq (version 0.6.1p1) (Anders et al., 2015) was used to obtain gene-level counts and estimated CPM based on GENCODE (v24lift37) (Harrow et al., 2012).
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: raw reads count by HTSEQ

source_name: Cell Line

growth_protocol: H7/WA07 (WiCell) and H9/WA09 cells (WiCell) were grown on Matrigel with reduced growth  factors (ThermoFisher Scientific, #354230) in mTeSR1 medium (STEMCELL Technologies,  #85850) at 37°C and 5% CO2. For neural differentiation, ES cells were seeded onto  AggreWell800 plates (STEMCELL Technologies, #34811) and fed with neural induction medium  (STEMCELL Technologies, #05835) to form uni-sized embryoid bodies (EBs).

extract_protocol:
RNA was purified with the GeneJET RNA purification kit (ThermoFisher Scientific, K0732). The cDNA was reverse transcribed from 300 ng of RNA, using SuperScript IV reverse transcriptase (ThermoFisher Scientific, #18090050) with random hexamers. RT reactions were performed in triplicate to minimize variability.
total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s directions (Illumina, San Diego, Ca.) Paired end 100 cycle sequencing was performed on HiSeq 2000 or HiSeq 4000 sequencers according to the manufacturer’s directions (Illumina.)

treatment_protocol: On day 5, EBs were re-plated onto Matrigel-treated 6-well plates. Neural differentiation (STEMCELL  Technologies, #08500) started from day 11 to day 16. On day 17, cells were treated with  Accutase® (STEMCELL Technologies) and seeded and fed with neuronal maturation medium  (STEMCELL Technologies, #08510) till days 22–24. For Neurosphere, Human NSCs were treated with accutase (STEMCELL Technologies, Cat. No. 07920),  dissociated into single cells, and plated in low-attachment 6-well plates (Fisher Scientific,  #CLS3471) at 10,000-25,000 cells/6-well densities. For serial passages, neurospheres after 6-8  days of culturing were dissociated to single cells with accutase treatment and plated in neural  expansion media.

value: Human Neurosphere H9


title: A3F181_30C_rep1

city: La Jolla

source_name: A3F181_30C_bacteria cells


title: bulk_spheroid_RA19B_D35_H20682

city: Stanford

tag: age (days)


title: Anc_42CA3_30C_rep2

source_name: Anc_42CA3_30C_bacteria cells

value: evolved strain adapted at 42C


title: RNA-hNeurosphere-H9-UTXKO replicate 4


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_F12_AD012

last: Ecker

value: STR


title: bulk_spheroid_RA19A_D35_H21792

last: Agoglia

source_name: iPSC-derived cortical spheroid


title: bulk_spheroid_SY15_D100_C3649

organism: Pan troglodytes


title: RNA-hNeurosphere-H9-UTXKO replicate 2


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_F12_AD007

value: male


title: bulk_spheroid_RA19A_D35_H20682


title: bulk_spheroid_RA19A_D35_H20961


title: RNA-hNeurosphere-H9-UTXKO replicate 3


title: A3F228_30C_rep1


title: RNA-hNeurosphere-H9-UTXKO replicate 1


title: bulk_spheroid_SY15_D75_C3649


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_F1_AD008


title: bulk_spheroid_RA19B_D25_H21792


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_F11_AD007


title: RNA-hNeuronMat-H9-WT replicate 3

value: Human Neuronal Maturation Cell H9


title: bulk_spheroid_SY15_D50_C3649


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_F10_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_F1_AD012


title: bulk_spheroid_RA19B_D25_H20961


title: RNA-hNeuronMat-H9-WT replicate 2


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_F1_AD007


title: bulk_spheroid_RA19B_D25_H20682


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_F10_AD008


title: bulk_spheroid_SY15_D25_C3649


title: Anc_42CA3_30C_rep1

value: Anc


title: RNA-hNeuronMat-H9-UTXKO replicate 3

value: Human Neuronal Maturation Cell H9 UTXKO


title: bulk_iPSC_P29_1_Hy2-9

source_name: induced pluripotent stem cells

value: induced pluripotent stem cells

tag: passage #


title: bulk_iPSC_P29_2_Hy2-9


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E9_AD012

value: brain

value: female


title: A3F181_30C_rep2

tag: strain background

value: glucose M9 minimal

value: mid-log phase


title: bulk_spheroid_RA19A_D25_H21792


title: INPUT-hNSC-H9-WT-forK4me3K27ac

description: H3K27Ac-AB2-hNSC-H9-WT.hg19.narrowPeak.gz

data_processing:
Basecalls performed using CASAVA
Single-end reads of 50bp were mapped human genome hg19(GRCh37-lite) by BWA (version  0.7.12-r1039, default parameter), duplicated reads were then marked with Picard(version  2.6.0-SNAPSHOT) and only non-duplicated reads have been kept by samtools (parameter “-q  1 -F 1024” version 1.2).
We followed ENCODE guideline for quality control of our data. For peak calling of H3K27ac, H3K4me3, we used MACS2(version 2.1.1.20160309). To assure the  replicability, we first finalized reproducible peaks for each group as only retained a peak if it called with stringent cutoff(macs2 -q 0.05) in one sample and at least called with lower  cutoff(macs2 -q 0.5) in the other sample. Peaks for H3K27me3 were called by reproducible peaks between SICER(V1.1) and MACS2. Correlation plots indicated the libraries are  reproducible between biological replicates.
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: Peaks

extract_protocol:
Cells were harvested in PBS. Cytoplasmic fractions were extracted using buffer A with 1×  protease inhibitors and 1 mM DTT. Nuclear pellets were cross-linked by 1.1% formaldehyde in  buffer B with 1× protease inhibitors and 1 mM DTT; washed; and lysed in lysis buffer 3 with 1×  protease inhibitors, 1 mM DTT, and 1 mM PMSF. The fixed and lysed nuclear extract was  sonicated with Bioruptor® Pico (Diagenode) 10 times for 15 s each, with 45-s intervals.  Chromatin was added to Dynabeads™ (Life Technologies) prebound with 4 μg of antibodies.  For UTX chromatin immunoprecipitation (ChIP), chromatin and antibodies were incubated  overnight, followed by 4 h of recapture with Dynabeads™ the next day.
After incubation, beads were washed and immunoprecipitates were eluted. DNA from eluates was recovered by the  GeneJET FFPE DNA purification kit (ThermoFisher Scientific, #K0882).Libraries are prepared and sequenced at the St. Jude Hartwell Center.

treatment_protocol: On day 5, EBs were re-plated onto Matrigel-treated 6-well plates. Neural differentiation (STEMCELL  Technologies, #08500) started from day 11 to day 16. On day 17, cells were treated with  Accutase® (STEMCELL Technologies) and seeded and fed with neuronal maturation medium  (STEMCELL Technologies, #08510) till days 22–24.

value: Human Neural Stem Cells H9


title: bulk_spheroid_RA19A_D25_H20961


title: bulk_spheroid_RA19A_D25_H20682


title: bulk_iPSC_P26_2_Hy2-16


title: INPUT-hNSC-H9-WT-forK27me3


title: RNA-hNeuronMat-H9-UTXKO replicate 2


title: bulk_iPSC_P26_1_Hy2-16


title: INPUT-hNSC-H9-UTXKO-forK4me3K27ac

description: H3K27Ac-AB2-hNSC-H9-UTXKO.hg19.narrowPeak.gz

value: Human Neural Stem Cells H9 UTXKO


title: bulk_spheroid_RA19B_D15_H21792


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E9_AD010

value: RSP


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E9_AD007


title: bulk_iPSC_P23_Hy1-29


title: INPUT-hNSC-H7-WT-forK4me3K27ac

description: H3K27Ac-AB2-hNSC-H7-WT.hg19.narrowPeak.gz

value: Human Neural Stem Cells H7


title: bulk_iPSC_P22_Hy1-29


title: bulk_spheroid_RA19B_D15_H20682

value: iPSC-derived cortical spheroid


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E7_AD012


title: INPUT-hNSC-H7-UTXKO-forK4me3K27ac

description: H3K27Ac-AB2-hNSC-H7-UTXKO.hg19.narrowPeak.gz

value: Human Neural Stem Cells H7 UTXKO


title: bulk_iPSC_P21_Hy1-25


title: bulk_spheroid_RA19A_D15_H21792


title: bulk_iPSC_P22_Hy1-25


title: bulk_spheroid_RA19A_D15_H20682


title: bulk_spheroid_RA19A_D15_H20961


title: H3K4me3-AB2-hNSC-H7-UTXKO

description: H3K4me3-AB2-hNSC-H7-UTXKO.hg19.narrowPeak.gz


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E7_AD007


title: H3K4me3-AB2-hNSC-H9-WT

description: H3K4me3-AB2-hNSC-H9-WT.hg19.narrowPeak.gz


title: H3K4me3-AB2-hNSC-H9-UTXKO

description: H3K4me3-AB2-hNSC-H9-UTXKO.hg19.narrowPeak.gz


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E7_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E6_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E7_AD010


title: bulk_iPSC_P35_H20961


title: H3K4me3-AB2-hNSC-H7-WT

description: H3K4me3-AB2-hNSC-H7-WT.hg19.narrowPeak.gz


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_F10_AD007


title: bulk_iPSC_P33_H20682


title: bulk_spheroid_RA19B_D15_H20961


title: H3K27me3-AB1-hNSC-H7-UTXKO

description: H3K27me3.hNSC-UTXKO.Rep.SharpBroad.bed.gz


title: N4a_2

city: Birmingham

first: Daniel

middle: J.

last: Gibbs

address: Edgbaston

department: School of Biosciences

institute: University of Birmingham

data_processing:
Data cleaned with in-house Novogene perl scripts
Reference genome was built using Bowtie v2.2.3 a
Cleaned paired-end  reads were aligned to the reference genome using TopHat v2.0.12
Reads were mapped to each gene and counted using HTSeq v0.6.1
Differential expression analysis for the not4a mutant compared to Col-0 (WT) (three biological replicates per genotype) was performed using the DESeq R package (1.18.0)
Genome_build: TAIR 10
Supplementary_files_format_and_content: A textfile of raw gene read counts in all three Wild-type and not4a mutant biological replicates

source_name: Whole seedlings

growth_protocol: Seeds were sowed on half MS media, stratified for two days and then grown vertically under long day light conditions (16 hour light 8 hour dark cycle) at 22°C for 10 days

extract_protocol:
Whole seedlings were flash frozen in liquid Nitrogen, ground and RNA extracted with Qiagen RNAeasy kit
RNA libraries were prepared for sequencing using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)

tag: ecotype

tag: genotype

value: not4a -/-

value: 10 day old

value: whole seedling


title: N4a_3


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E9_AD008

value: STR

value: male


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E6_AD008


title: bulk_iPSC_P28_H21792


title: H3K27Ac-AB2-hNSC-H9-WT


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E6_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E6_AD007


title: bulk_iPSC_P20_Hy1-30


title: N4a_1


title: bulk_iPSC_P19_Hy1-30


title: H3K27Ac-AB2-hNSC-H9-UTXKO


title: bulk_iPSC_P26_H20682


title: WT_3

value: Wild-type


title: bulk_iPSC_P28_H20961

value: induced pluripotent stem cells


title: WT_2


title: H3K27Ac-AB2-hNSC-H7-WT


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E5_AD010

value: brain


title: WT_1


title: 20_LW3

status: Public on Nov 16 2020

city: Orebro

first: Anders

middle: M.

last: Wirén

address: Sodra Grev Rosengatan 42b

department: Clinical research centre

country: Sweden

institute: Region Orebro lan

data_processing:
Reads were filtered and only those which did not contain Ns, adapter sequences and did not have low sequence complexity (dinucleotide motifs constituting more than 70% of read length, single nucleotide motifs constituting more than 50% of read length) were included in further analysis (on average 93% of total number of reads across samples)
For comparison purposes, the reads in every sample were resampled to a fixed total (the method is called subsampling normalization)
Reads mapped to the Bombus terrestris genome (Bter_1.0, RefSeq assembly accession: GCF_000214255.1) using PatMan (Prüfer et al. 2008), full length, one mismatch allowed.
The expression levels were obtained as indicated in Mortazavi et al. 2008
The differential expression was determined using confidence intervals on replicates. The DE amplitude was calculated using offset fold change, with offset=20
Genome_build: Bter_1.0 (https://www.ncbi.nlm.nih.gov/assembly/294348)
Supplementary_files_format_and_content: csv file containing normalized expression levels for features (genes and novel transcripts) designated by feature-ids of format Accession.version_start-position-on-sequence_stop-position-on-sequence. Example: NC_015762.1_10000432_10107258

organism: Bombus terrestris audax

source_name: Whole larvae_Late instar larvae_Worker destined

growth_protocol: Queen-destined and Worker-destined female larvae were harvested from eight Bombus terrestris colonies. These were separated into early-instar queen-destined larvae from the first and second larval instars (EQ), early-instar worker destined larvae from the first and second larval  instars (EW) , mid-instar queen-destined larvae from the third larval instar (MQ), mid-instar worker-destined larvae from the third larval instar (MW), late-instar queen-destined larvae from the fourth larval instar (LQ), late-instar queen-destined larvae from the fourth larval instar (LQ) .

extract_protocol:
TotalRNA was extracted from each larva using Tri-reagent (Thermofisher Scientific) according to the manusfacturers protocol. The RNA was then dnase treated with the TURBO DNAfree kit (Thermofisher Scientific) to remove any DNA contamination.
standard mRNA-seq conducted by The Genome Analysis Centre (Norwich, UK) on an Illumina HiSeq 2500 sequences using Illumina TruSeq adapters

tag: developmental stage

value: Late instar larvae

tag: caste fate

value: Worker destined

tag: Sex

value: female

value: whole larvae


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E5_AD008

tag: strain

tag: age


title: 19_LW2

tag: tissue


title: bulk_iPSC_P25_H21792

tag: cell type


title: 13_MW3

source_name: Whole larvae_Middle instar larvae_Worker destined

value: Middle instar larvae


title: 18_LW1


title: 14_LQ1

source_name: Whole larvae_Late instar larvae_Queen destined

value: Queen destined


title: 16_LQ3

description: Excluded from analysis due to too few reads.


title: 15_LQ2


title: 12_MW2


title: 09_MQ3

source_name: Whole larvae_Middle instar larvae_Queen destined


title: 10_MQ4


title: 17_LQ4


title: 07_MQ1


title: 05_EW2

source_name: Whole larvae_Early instar larvae_Worker destined

value: Early instar larvae


title: 08_MQ2


title: 06_EW3


title: 04_EW1


title: 02_EQ2

source_name: Whole larvae_Early instar larvae_Queen destined


title: 03_EQ3


title: 01_EQ1


title: H3K27Ac-AB2-hNSC-H7-UTXKO


title: T24 control_A

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

data_processing:
FASTQ file sequenced by DNBseq using Phred +33 quality system
Adapter clipping was performed using Cutadapt (v2.8) with default settings.
RNA-Seq reads’ alignment was performed using STAR (v2.7.3a) on GRCh38 reference genome.
The gene read quantification was performed using HTSeq-count (v0.11.2).
The gene annotation used for quantification was Ensembl version 99.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts

source_name: T24 control

growth_protocol: HT1376 and T24 cell lines were purchased from ATCC. The cells were grown in Dulbecco's modified eagle medium (DMEM) supplemented with 10% feta bovine serum and penicillin/streptomycin. Cells were free of mycoplasma contamination and were genotyped and authenticated. Cells were grown in 5% CO2 atmosphere incubator at 37˚C.

extract_protocol:
Total RNA from cells was isolated using the NucleoSpin RNA II kit (740955, BIOKE) using the manufacturer's instructions. Thereafter, RNA samples were processed for transcriptomic sequencing and analysis.
BGISEQ-500 RNA-Seq Library protocol (SOP-SS-027) was followed. mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads. mRNA molecules were fragmented into small pieces using fragmentation reagent after reaction a certain period in proper temperture. First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adapters were ligated to the ends of these 3’ adenylated cDNA fragments. PCR process was applied to amplify the cDNA fragments with adapters from previous step. PCR products were purified with Ampure XP Beads (AGENCOURT), and dissolved in EB solution. Library was validated on the Agilent Technologies 2100 bioanalyzer.
DNBSEQ- RNASeq-PolyA – BGI index

treatment_protocol: TRAF4 was knocked down using short-haripin RNAs (shRNAs) in HT1376 using lentiviral transduction. Cells transduced with empty vector (pLKO.1) was used as control. After transduction, cells were grown in puromycin containing media for selection. Four independent experimental replicates were used for each condition. For T24 cell line, stable over-expression of Myc-TRAF4 or empty vector (Myc-tag) cells were generated in a similar manner. Again here, four independent experimental replicates were used.

tag: tag

value: Bladder cancer cell line

tag: genotype/variation

value: control with myc-tag over-expression


title: HT1376 sh5 (TRAF4)_C

source_name: HT1376 sh5 (TRAF4)

value: shRNAs targetting TRAF4


title: T24 control_B


title: HT1376 sh5 (TRAF4)_D


title: HT1376 sh5 (TRAF4)_B


title: 11_MW1

description: Excluded from analysis due to outlier status based on poor clustering in multidimensional scaling analysis


title: HT1376 sh4 (TRAF4)_D

source_name: HT1376 sh4 (TRAF4)


title: HT1376 sh5 (TRAF4)_A


title: HT1376 sh4 (TRAF4)_A


title: HT1376 control_D

source_name: HT1376 control

value: control with empty vector (pLKO.1)


title: HT1376 sh4 (TRAF4)_C


title: HT1376 sh4 (TRAF4)_B


title: HT1376 control_C


title: HT1376 control_B


title: HT1376 control_A


title: CNFPA NF-2018-022

city: México City

last: Marrero-Rodriguez

state: México City

address: Av. Cuauhtémoc 330, Col. Doctores

department: Unidad de Investigacion Medica en Enfermedades Endocrinas

country: Mexico

institute: Instituto Mexicano del Seguro Social

description:
CNFPA
Adenomas-NF-2018-022
CNFPA

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Clariom D Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 7G GeneChip scanner.

data_processing: The data was analyzed with RMA using Partek Genomic Suite default analysis settings .

label: Biotin

source_name: Pituitary gland

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip WT Pico Reagent Kit,  Affymetrix).

growth_protocol: Not applicable

extract_protocol: miRNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: With no previous treatment


title: CNFPA NF-2018-024

description:
CNFPA
Adenomas-NF-2018-024
CNFPA


title: CNFPA NF-2018-035

description:
CNFPA
Adenomas-NF-2018-035
CNFPA


title: CNFPA NF-2018-031

description:
CNFPA
Adenomas-NC-2018-031
CNFPA


title: CNFPA NF-2016-013

description:
CNFPA
Adenomas-NF-2016-013
CNFPA


title: CNFPA NF-2018-034

description:
CNFPA
Adenomas-NF-2018-034
CNFPA


title: CNFPA NF-2016-015

description:
CNFPA
Adenomas-NF-2016-015
CNFPA


title: CNFPA NF-2018-025

description:
CNFPA
Adenomas-NC-2018-025
CNFPA


title: CNFPA NF-2018-026

description:
CNFPA
Adenomas-SA-2018-026
CNFPA


title: CNFPA NF-2018-029

description:
CNFPA
Adenomas-NF-2018-029
CNFPA


title: CNFPA NF-2018-017

description:
CNFPA
Adenomas-'NF-2018-017
CNFPA


title: CNFPA NF-2018-013

description:
CNFPA
Adenomas-NF-2018-013
CNFPA


title: CNFPA NF-2018-015

description:
CNFPA
Adenomas-NF-2018-015
CNFPA


title: GH Adenomas AC-2017-007

description:
GH Adenomas
Adenomas-AC-2017-007
GH Adenomas


title: GH Adenomas AC-2018-009

description:
GH Adenomas
Adenomas-AC-2018-009
GH Adenomas


title: CNFPA NF-2018-037

description:
CNFPA
Adenomas-NF-2018-037
CNFPA


title: GH Adenomas AC-2018-001

description:
GH Adenomas
Adenomas-AC-2018-001
GH Adenomas


title: GH Adenomas AC-2018-007

description:
GH Adenomas
Adenomas-AC-2018-007
GH Adenomas


title: GH Adenomas AC-2018-003

description:
GH Adenomas
Adenomas-AC-2018-003
GH Adenomas


title: GH Adenomas AC-2018-006

description:
GH Adenomas
Adenomas-AC-2018-006
GH Adenomas


title: CNFPA NF-2017-005

description:
CNFPA
Adenomas-NC-2017-005
CNFPA


title: CNFPA NF-2018-001

description:
CNFPA
Adenomas-NF-2018-001
CNFPA


title: CNFPA NF-2018-018

description:
CNFPA
Adenomas-SA-2018-018
CNFPA


title: CNFPA NF-2018-036

description:
CNFPA
Adenomas-SA-2018-036
CNFPA


title: GH Adenomas AC-2018-008

description:
GH Adenomas
Adenomas-AC-2018-008
GH Adenomas


title: GH Adenomas AC-2018-005

description:
GH Adenomas
Adenomas-AC-2018-005
GH Adenomas


title: GH Adenomas AC-2018-002

description:
GH Adenomas
Adenomas-AC-2018-002
GH Adenomas


title: ACTH Adenomas CU-2016-002

description:
ACTH Adenomas
Adenomas-CU-2016-002
ACTH Adenomas


title: CNFPA NF-2018-016

description:
CNFPA
Adenomas-NF-2018-016
CNFPA


title: ACTH Adenomas CU-2014-002

description:
ACTH Adenomas
Adenomas-CU-2014-002
ACTH Adenomas


title: PRL Adenomas PRL-2018-002

description:
PRL Adenomas
Adenomas-PRL-2018-002
PRL Adenomas


title: ACTH Adenomas CU-2017-002

description:
ACTH Adenomas
Adenomas-CU-2017-002
ACTH Adenomas


title: ACTH Adenomas CU-2018-001

description:
ACTH Adenomas
Adenomas-CU-2018-001
ACTH Adenomas


title: T24 (TRAF4)_C

source_name: T24 (TRAF4)

value: TRAF4 over-expressed


title: T24 control_D


title: T24 (TRAF4)_B


title: T24 (TRAF4)_A