title: Control 0065

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0065


title: lc_fas_6dpi_R3

status: Public on Apr 17 2019

type: SRA

city: Athens

first: Esther

last: van der Knaap

state: GA

address: 111 Riverbend Rd

department: Horticulture

country: USA

institute: University of Georgia

library_source: transcriptomic

data_processing:
Reads mapped to rRNA were filtered using bowtie2
The cleaned raw reads were then mapped to ITAG2.3 Released Tomato Genome through the Tophat2 high throughput short read aligner.
Genome_build: ITAG2.3 Released Tomato Genome
Supplementary_files_format_and_content: tab-delimited csv files include RPKM values for each gene per sample

molecule: total RNA

organism: Solanum pimpinellifolium

source_name: 6dpi floral buds

growth_protocol: Plants were grown in two-gallon pots under natural light supplemented with artificial light (16/8 hr light/dark cycle) in the greenhouse in Wooster, OH, USA, 2013.

extract_protocol:
During the collection, all inflorescences were immediately immersed in ice-cold RNAlater (QIAGEN) solution at five times the volume of the sample in order to prevent RNA degradation. After sample collection, vacuum infiltration was applied until tissues sunk to the bottom of RNAlater solution. The tissues were then stored in RNAlater at -80℃.  For the dissection, meristems and buds of different developmental stages were isolated by forceps under a dissection microscope and immediately put into a 1.5 ml eppendorf tube in 1 ml of fresh RNAlater that was kept on ice. The samples were stored at -80 ℃ prior to the RNA extraction.RNA extraction was conducted using Trizol® (Invitrogen Inc. USA) following manufacture’s recommendation.
Strand directed RNA-seq libraries of approximately 250 bp fragments were prepared following the protocol of Zhong et al., 2011.

tag: genotype

value: lc/fas double mutants

tag: background accession

tag: developmental stage

value: 6dpi floral buds


title: Control 0066

type: genomic

city: Campinas

first: Benilton

middle: Sa

last: Carvalho

state: Sao Paulo

address: Tessália Vieira de Camargo, 126

department: Medical Genetics

country: Brazil

institute: Universidade Estadual de Campinas

description: Hybridized to SNP6.0 Affymetrix

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The raw data (CEL files) were processed through SNPRMA and genotype calls obtained through CRLMM (both in the crlmm Bioconductor package)
primary data description: Alleles A and B intensities; Genotype calls (1=AA; 2=AB; 3=BB); Genotype confidence (integers: the larger, the better)

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: DNA Controle 0066

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from leukocytes of peripheral blood of 103 CM patients and 103 controls using the QIAamp DNA Blood Midi Kit (Qiagen®, Canada), following manufacturer’s instructions

tag: caso

tag: idade contínua

tag: idade mediana≤ 54

tag: sexo

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: sardas

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar


title: Control 0062

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0062


title: Control 0059

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0059


title: lc_fas_4dpi_R3

source_name: 4dpi floral buds

value: 4dpi floral buds


title: Control 0061

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0061


title: Control 0057

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0057


title: Control 0060

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0060


title: Control 0058

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0058


title: lc_fas_F&IM&2dpi_R3

source_name: floral and inflorescence meristems (F&IM) + 2dpi floral buds

value: floral and inflorescence meristems (FandIM) + 2dpi floral buds


title: Control 0055

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0055


title: lc_fas_F&IM&2dpi_R4


title: Control 0054

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0054


title: lc_fas_6dpi_R2


title: lc_fas_4dpi_R2


title: Control 0070

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0070


title: Control 0053

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0053


title: Control 0052

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0052


title: lc_fas_F&IM&2dpi_R2


title: lc_fas_4dpi_R4


title: Control 0048

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0048


title: Control 0049

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0049


title: lc_fas_6dpi_R1

source_name: 6dpi floral buds


title: Control 0051

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0051


title: lc_fas_4dpi_R1


title: Control 0047

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0047


title: lc_fas_F&IM&2dpi_R1


title: Control 0056

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0056


title: Control 0042

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0042


title: Control 0044

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0044


title: Control 0046

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0046


title: Control 0045

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0045


title: fas_4dpi_R4

source_name: 4dpi floral buds

value: fas mutant


title: Control 0040

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0040


title: fas_6dpi_R4


title: Control 0043

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0043


title: Control 0039

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0039


title: Control 0038

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0038


title: fas_F&IM&2dpi_R4

source_name: floral and inflorescence meristems (F&IM) + 2dpi floral buds


title: Control 0041

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0041


title: fas_6dpi_R3


title: fas_4dpi_R3


title: Control 0035

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0035


title: Control 0037

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0037


title: Control 0034

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0034


title: fas_F&IM&2dpi_R3


title: Control 0033

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0033


title: Control 0050

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0050


title: Control 0031

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0031


title: Control 0032

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0032


title: fas_6dpi_R2

source_name: 6dpi floral buds


title: Control 0029

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0029


title: Control 0028

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0028


title: Control 0027

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0027


title: Control 0023

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0023


title: Control 0022

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0022


title: Control 0021

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0021


title: fas_F&IM&2dpi_R2


title: fas_6dpi_R1


title: Control 0020

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0020


title: fas_4dpi_R1

source_name: 4dpi floral buds


title: Control 0024

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0024


title: Control 0026

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0026


title: Control 0025

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0025


title: Control 0036

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0036


title: Control 0019

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0019


title: lc_6dpi_R4

value: lc mutant


title: Control 0017

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0017


title: Control 0016

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0016


title: lc_4dpi_R4


title: Control 0014

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0014


title: Control 0030

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0030


title: lc_F&IM&2dpi_R4

source_name: floral and inflorescence meristems (F&IM) + 2dpi floral buds


title: fas_4dpi_R2


title: Control 0013

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0013


title: lc_6dpi_R3

source_name: 6dpi floral buds


title: Control 0012

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0012


title: lc_4dpi_R3


title: Control 0010

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0010


title: Control 0011

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0011


title: fas_F&IM&2dpi_R1


title: lc_F&IM&2dpi_R3


title: Control 0009

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0009


title: Control 0008

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0008


title: Control 0004

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0004


title: Control 0005

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0005


title: Control 0003

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0003


title: Control 0018

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0018


title: Control 0007

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0007


title: Control 0006

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0006


title: lc_4dpi_R2

source_name: 4dpi floral buds


title: lc_6dpi_R2


title: Control 0001

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0001


title: Control 0002

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0002


title: lc_4dpi_R1


title: Case 0102

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0102

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores

tag: localizacao tumor cabeca+tronco_membros

tag: breslow ≤1,5

tag: clark

tag: estagio clínico


title: Case 0103

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0103

tag: caso

tag: idade contínua


title: Case 0101

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0101

tag: idade mediana≤ 54

tag: sexo


title: lc_F&IM&2dpi_R1

source_name: floral and inflorescence meristems (F&IM) + 2dpi floral buds

tag: genotype

tag: background accession

tag: developmental stage


title: Case 0100

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0100

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: sardas


title: Case 0099

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0099

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar


title: Case 0097

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0097

tag: breslow ≤1,5

tag: clark

tag: estagio clínico


title: WT_6dpi_R4

source_name: 6dpi floral buds

value: wild type


title: WT_4dpi_R4


title: Case 0098

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0098

tag: caso

tag: idade contínua

tag: idade mediana≤ 54


title: Case 0096

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0096

tag: sexo


title: WT_F&IM&2dpi_R4

tag: genotype

tag: background accession

tag: developmental stage


title: Case 0094

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0094

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores

tag: localizacao tumor cabeca+tronco_membros


title: Case 0093

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0093

tag: cor dos cabelos

tag: sardas

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma


title: Case 0092

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0092

tag: caso

tag: queimadura solar

tag: clark

tag: estagio clínico


title: lc_F&IM&2dpi_R2

tag: genotype


title: Case 0091

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0091

tag: idade contínua

tag: idade mediana≤ 54

tag: sexo


title: lc_6dpi_R1

tag: background accession

tag: developmental stage


title: WT_4dpi_R3

source_name: 4dpi floral buds


title: WT_6dpi_R3


title: Case 0090

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0090

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores

tag: breslow ≤1,5


title: Case 0089

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0089

tag: cor dos cabelos

tag: sardas

tag: nevos poucos_muitos

tag: localizacao tumor cabeca+tronco_membros


title: WT_F&IM&2dpi_R3


title: Control 0015

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0015

tag: caso

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar


title: Case 0086

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0086

tag: idade contínua

tag: idade mediana≤ 54

tag: clark

tag: estagio clínico


title: Case 0087

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0087

tag: sexo

tag: fototipo i+ii_outros


title: WT_6dpi_R2

tag: genotype

tag: background accession

tag: developmental stage


title: Case 0085

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0085

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores

tag: breslow ≤1,5


title: 17104-02RT-01-3

city: Seattle

first: Sergei

last: Doulatov

state: WA

address: 1795 NE Pacific Street

institute: University of Washington

data_processing:
Sequencing was performed on Illumina HiSeq-4000 in the PE 2x150 format and >40 million reads were obtained per sample.
Data processing and normalization was performed with Illumina BaseSpace software.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited matrix text files include FPKM or regularized log (rlog)-transformed values for each sample

source_name: Hematopoietic progenitors

growth_protocol: iPSC-derived HPCs were cultured in SFEM medium supplemented with growth factors and doxycycline

extract_protocol:
RNA was harvested using Trizol reagent. Libraries were prepared using Illumina TruSeq stranded mRNA kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CD34+ HPCs were isolated using magentic columns prior to RNA isolation

tag: cell type

value: Hematopoietic progenitors

value: TP53 R209fs/+;del5q

tag: iPSc line

value: iPSC line 3

tag: experiment

value: Experiment 1


title: 17104-02RT-01-5

value: iPSC line 2

value: Experiment 2


title: 17104-02RT-01-4

value: iPSC line 1


title: WT_4dpi_R2


title: Case 0095

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0095

tag: caso

tag: idade contínua

tag: sardas

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar


title: Case 0083

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0083

tag: idade mediana≤ 54

tag: sexo

tag: fototipo i+ii_outros

tag: localizacao tumor cabeca+tronco_membros

tag: clark

tag: estagio clínico


title: Case 0084

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0084

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores

tag: breslow ≤1,5


title: 17104-02RT-01-2

tag: cell type

tag: genotype

tag: iPSc line

tag: experiment


title: WT_F&IM&2dpi_R2

source_name: floral and inflorescence meristems (F&IM) + 2dpi floral buds

tag: background accession

tag: developmental stage


title: Case 0082

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0082

tag: caso

tag: idade contínua

tag: idade mediana≤ 54

tag: sardas

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar


title: 17104-02RT-01-1


title: Case 0081

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0081

tag: sexo

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: localizacao tumor cabeca+tronco_membros

tag: clark

tag: estagio clínico


title: WT_6dpi_R1

source_name: 6dpi floral buds

tag: genotype

tag: background accession

tag: developmental stage


title: Case 0079

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0079

tag: caso

tag: idade contínua

tag: idade mediana≤ 54

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores

tag: breslow ≤1,5


title: 17104-02RT-01-6

tag: cell type

tag: iPSc line

tag: experiment


title: K562_sh-lncRNA-IIRX_3

city: Beijing

first: Xuefei

last: Wang

state: Beijing

address: NO.1 West Beichen Road, Chaoyang District, Beijing 100101, China

country: China

institute: nstitute of Microbiology, Chinese Academy of Sciences (CAS)

description:
pSIH_up37_5_2_2_CGGAAT_L008
RPKM-pSIH.up37.5.2.2

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic v0.32, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie 2 v2.1.0 with parameters default
Reads Per Kilo bases per Million reads (RPKM, Mortazavi et al., 2008) were calculated, and then analyzed using samtools v0.1.19 (Li et al., 2009).
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample.

extract_protocol:
Total RNAs were isolated from three independent groups of K562 cells expressing shRNA targeting lncRNA-IIRX and control cells, using TRIzol reagent (Invitrogen, Carlsbad, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: sh-rna

value: sh-lncRNA-IIRX


title: Case 0088

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0088

tag: sexo

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: sardas

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar


title: WT_4dpi_R1

source_name: 4dpi floral buds

tag: genotype

tag: background accession

tag: developmental stage


title: Case 0078

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0078

tag: caso

tag: idade contínua

tag: idade mediana≤ 54

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores

tag: localizacao tumor cabeca+tronco_membros

tag: breslow ≤1,5

tag: clark

tag: estagio clínico


title: WT_F&IM&2dpi_R1


title: Case 0076

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0076

tag: sexo

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos


title: Case 0075

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0075

tag: sardas

tag: nevos poucos_muitos

tag: queimadura solar


title: K562_sh-lncRNA-IIRX_1

description:
pSIH_up37_5_1_TAGCTT_L008
RPKM-pSIH.up37.5.1

tag: cell line

tag: sh-rna


title: Case 0073

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0073

tag: caso

tag: idade contínua

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma


title: K562_sh-luc_2

description:
pSIH_luc_2_1_ACTTGA_L008
RPKM-pSIH.luc.2.1

value: sh-luc


title: K562_sh-luc_1

description:
pSIH_luc_1_CAGATC_L008
RPKM-pSIH.luc.1


title: Case 0070

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0070

tag: idade mediana≤ 54

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores

tag: localizacao tumor cabeca+tronco_membros


title: Case 0071

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0071

tag: sexo

tag: estagio clínico


title: Case 0072

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0072

tag: fototipo i+ii_outros

tag: cor pele


title: DNA-PKcs -/- -5

city: New Yprk

first: Zhengping

last: Shao

state: New York

address: 1130 St. Nicholas Ave

department: ICG

institute: Columbia University Medical Center

library_source: genomic

data_processing:
Library strategy: HTGTS
Basecalls performed using Illumina RTA version 1.18.54
Miseq reads was first de-multiplexed by fastq-multx tool from ea-util, then adaptor sequence was further trimmed with SeqPrep utility.
Pre-processed reads were then mapped to customized mm9 genome (mm9sr) with IgH switch region (from JH4 to the last Cα exon, chr12 114, 494, 415–114, 666, 816) of the C57/BL6 replaced by the corresponding region of 129 strain in NCBI gene accession sequence AJ851868.3 using Bowtie2. The best-path searching algorithm (related to YAHA; ref. 50) was used to identify optimal sequence alignments from Bowtie2-reported top alignments (alignment score > 50).
The reads are then filtered to exclude mispriming events, germ-line (unmodified) sequence, sequential joints, and duplicated reads. A “duplicate read” is defined by bait and prey alignment coordinates within 2 nt of another read’s bait and prey alignments. To plot all of the S-region junctions, including those in the repeats but unequivocally mapped to an individual switch region, we combined the ones filtered by a mappability filter but unequivocally mapped to S regions with “good” reads passing both the mappability (both deduplicated) filters (please see ref. 28 for simulation and details on plotting). MHs are defined as regions of 100% homology between the bait and prey-break site. Insertions are defined as regions containing nucleotides that map to neither the bait and prey-break site. Blunt junctions are considered to have no MHs or insertions.
Mutation rate was calculated by custom Excel integrated VBA script. Mutations were determined by comparing the actual bait sequence of each IgH junction with the germ-line bait sequence based on the IgH sequence from 129/Sv strain (NCBI gene accession no. AJ851868.3). Only true mismatches (no insertion or deletion within 7 nt) were counted as a mutation.
Genome_build: mm9sr (to customized mm9 genome (mm9sr) with IgH switch region (from JH4 to the last Cα exon, chr12 114, 494, 415–114, 666, 816) of the C57/BL6 replaced by the corresponding region of 129 strain in NCBI gene accession sequence AJ851868.3)
Supplementary_files_format_and_content: .xlsx files generated from tab-delimited text files after analysis for reads distribution and mutation rates.

organism: Mus musculus

source_name: B cells

growth_protocol: Purified splenic B (CD43-) cells from mice carrying preassembled IgH and IgK loci (129Sv background) were cultured in RPMI mediume with cytokines (anti-CD40 (1 ng/mL; BD Pharmingen) and IL-4 (20 ng/mL; R&D)).

extract_protocol:
Genomic DNA was extracted from day 4 cultured B cells with standard DNA extraction protocol. Basically cells were washed with PBS before lysed overnight with rapid lysis buffer containing 10mM tris PH 7.5, 10mM EDTA PH8.0, 10mM NaCl, 0.5% SDS and 1mg/ml Proteinase K at 56 °C. DNA was precipated from lysed cells with isopropanol and washed with 70% EtOH before air dry and re-dissolving by 10mM tris/ 0.1mM EDTA TE buffer.
Libraries were prepared according to protocol in (Hu J, et al. Nat Protoc 11:853–871.(2016)) Linear amplifications were performed using Sμ-specific biotin primer  5′/5BiosG/CAGACCTGGGAATGTATGGT3′) and followed by nesting PCR with (5′CACACAAAGACTCTGGACCTC3′)  AflII is used to remove germ-line sequence.
high-throughput genome translocation sequencing (HTGTS). Sequenced with MiSeq 500v

treatment_protocol: Cells were cultured for 4 days and analyzed via flow cytometry before DNA extraction.

tag: cell type

value: anti-CD40 and Il4 activated B cells

tag: genotype

value: DNA-PKCS -/-

tag: strain


title: Case 0080

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0080

tag: cor olhos

tag: cor dos cabelos

tag: sardas

tag: nevos poucos_muitos

tag: queimadura solar

tag: breslow ≤1,5

tag: clark


title: Case 0069

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0069

tag: caso

tag: idade contínua

tag: idade mediana≤ 54

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma


title: Case 0067

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0067

tag: sexo

tag: fototipo i+ii_outros

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores

tag: localizacao tumor cabeca+tronco_membros

tag: estagio clínico


title: Case 0065

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0065

tag: cor pele

tag: cor olhos


title: Case 0064

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0064

tag: cor dos cabelos

tag: sardas


title: Cut_KD_H3K27Ac

city: Gainesville

first: Lei

last: Zhou

state: FL

department: Molecular Genetics and Microbiology

institute: University of Florida

data_processing:
The quality of sequencing reads were checked with FASTQC
Reads were mapped to dm6 with bowtie2
Enrichment (peaks) was identified with “macs2 callpeak —broad -t ChIP -c Input -g dm”
Sicer analysis with parameter “SICER RNAi_KD.bed Control.bed output_folder dm6 1 200 150 0.74 600 .01”
Genome_build: dm6
Supplementary_files_format_and_content: broad peak, bb

organism: Drosophila melanogaster

source_name: Neuroblast expressing wor-gal4 UAS-dsRed

growth_protocol: Embryos were collected for 16 hr. at 25°.

extract_protocol:
Dechorionated embryos were fixed in 1:1 solution of 1.8% formaldehyde and heptane for 15 min at room temperature. The fixative was quenched with a 2 min wash with 125 mM glycine in PBS with 0.1% Triton-X100 (PBS:130 mM NaCl, 7 mM Na2HPO4, 3 mM KH2PO4, pH 8.0), and then briefly rinsed with PBS 0.1% Triton-X100. Embryos were snap frozen in liquid nitrogen, and stored at −80°C. About 1g of embryos of each genotype were used for nuclei isolation as described in Bowman et al. (2014, 2013). Fixed nuclei from wor>dsRed embryos were enriched using a Bio-RAD S3e cell sorter with 561nm excitation. Nuclei were sorted at 40C in 100ul of PBS, with 1% BSA, 0.1% Triton-X and 1X protease inhibitor. wor-gal4 is expressed in the nervous system from stage 11 onwards.  The sorted nuclei represent approximately 0.5-3% of total embryonic nuclei, and were at least 50% pure, based on post-isolation assessment of ds-red by confocal microscopy.  About a million nuclei were used for chromatin preparation. After isolation chromatin was fragmented with 15U of micrococcal nuclease (MNase, Worthington Biochemical) followed by 3 min sonication in a Diagenode Bioruptor 377.  Immunoprecipitation was carried out with 2ug of H3K27me3 antibody (Active Motif 39136) or 1ug of H3K27Ac antibody (Active Motif, 39136). Input DNA was used as a control.
Single end tag libraries were prepared and sequenced on an Illumina, Hiseq2500 in high output mode at the MGH Next Generation Sequencing Core.

tag: tissue

value: Embryo

tag: cell type

value: neuroblast (sorted wor-gal:UAS-DsRed nuclei)

tag: genotype

tag: chip antibody


title: Case 0077

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0077

tag: caso

tag: idade contínua

tag: nevos poucos_muitos

tag: queimadura solar

tag: breslow ≤1,5

tag: clark


title: Control_H3K27Ac

value: Control


title: Case 0066

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0066

tag: idade mediana≤ 54

tag: sexo

tag: fototipo i+ii_outros

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores


title: DNA-PKcs PQR/PQR -2

value: DNA-PKcs PQR/PQR

tag: strain


title: Control_H3K27Me3

tag: tissue


title: Case 0074

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0074

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: sardas

tag: estagio clínico


title: Case 0062

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0062

tag: caso

tag: idade contínua

tag: nevos poucos_muitos

tag: localizacao tumor cabeca+tronco_membros


title: K562_sh-luc_3

description:
pSIH_luc_2_2_GATCAG_L008
RPKM-pSIH.luc.2.2

tag: cell line

tag: sh-rna


title: DNA-PKcs PQR/PQR -1

tag: cell type

tag: genotype


title: Case 0068

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0068

tag: idade mediana≤ 54

tag: sexo

tag: breslow ≤1,5

tag: clark


title: Case 0061

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0061

tag: fototipo i+ii_outros

tag: cor pele

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores


title: Case 0060

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0060

tag: caso

tag: idade contínua

tag: cor olhos

tag: cor dos cabelos

tag: sardas

tag: estagio clínico


title: Case 0059

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0059

tag: nevos poucos_muitos

tag: localizacao tumor cabeca+tronco_membros


title: MKN1 treated Para

type: RNA

city: Incheon

first: Seungyoon

last: Nam

state: Incheon

address: Namdong-gu, Namdongdae-ro 774-21

country: South Korea

institute: Gachon University Colleage of Medicine

description: MKN1 treated Para

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Human  2.0 ST Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix). Signal values were computed using the Affymetrix® GeneChip™ Command Console software.

data_processing: Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC).

source_name: stomach cancer cell line

label_protocol: cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: grown in RPMI-1640 (Invitrogen) and 10% fetal calf serum (Hyclone), at 37oC, under 5% CO2. Cells (2.5 × 105) were seeded and grown to 70–80% confluence

extract_protocol: total cellular mRNA was isolated using RNeasy kits (Qiagen)

treatment_protocol: treated with DMSO, 5-, or 10-µM para-, ortho-, or meta-BI6015 for 48 hours

tag: cell line

tag: agent

value: Para


title: Case 0058

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0058

tag: idade mediana≤ 54

tag: sexo

tag: breslow ≤1,5

tag: clark


title: MKN1 treated Meta

description: MKN1 treated Meta

value: Meta


title: MKN1 treated Ortho

description: MKN1 treated Ortho

value: Ortho


title: Case 0057

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0057

tag: fototipo i+ii_outros

tag: cor pele

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma


title: Case 0063

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0063

tag: caso

tag: idade contínua

tag: queimadura solar

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores


title: Case 0053

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0053

tag: cor olhos

tag: cor dos cabelos

tag: sardas

tag: estagio clínico


title: chromatin IP with RNA Pol II in Panx KD OSCs

city: Vienna

first: Jakob

last: Schnabl

state: Vienna

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institute of Molecular Biotechnology

description:
Panx_OSC KD_ChIP_Pol II
chromatin immunoprecipitation with RNA Pol II in Panx KD OSCs

data_processing:
reads were trimmed by removal of the adaptor sequences and to a length of 6-50 bases
reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using Bowtie (release 1.2.2) with 0 mismatches were excluded
reads were mapped to the Drosophila melanogaster TE consensus using Bowtie (release 1.2.2) with 3 mismatches or 0 mismatches for genome wide analysis
Genome_build: dm6
Supplementary_files_format_and_content: all mapping and unique mapping bigwig files for sense and antisense

source_name: OSCs

growth_protocol: OSCs were grown at 27º C, 2.5% CO2

extract_protocol:
Chromatin immunoprecipitation (ChIP) was carried out according to Lee et al. (2006)
with NEBNext Ultra DNA Library Prep Kit Illumina (NEB)

tag: cell type

value: OSC

tag: genotype

value: Panoramix knockdown

tag: chip antibody

value: anti-RNA Polymerase II, 8WG16 (Abcam Cat# ab817)


title: Cut_KD_H3K27Me3

tag: tissue


title: Case 0055

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0055

tag: idade mediana≤ 54

tag: sexo

tag: nevos poucos_muitos

tag: localizacao tumor cabeca+tronco_membros

tag: breslow ≤1,5

tag: clark


title: K562_sh-lncRNA-IIRX_2

description:
pSIH_up37_5_2_1_CGTACG_L008
RPKM-pSIH.up37.5.2.1

tag: cell line

tag: sh-rna


title: chromatin IP with RNA Pol II in Nxf2 KD#1 OSCs

description:
Nxf2_1_OSC KD_ChIP_Pol II
chromatin immunoprecipitation with RNA Pol II in Nxf2 KD#1 OSCs

value: Nxf2#1 knockdown


title: chromatin IP with RNA Pol II in Piwi KD OSCs

description:
Piwi_OSC KD_ChIP_Pol II
chromatin immunoprecipitation with RNA Pol II in Piwi KD OSCs

value: Piwi knockdown


title: AGS treated Meta

description: AGS treated Meta

value: AGS

tag: agent


title: chromatin IP with RNA Pol II in control KD OSCs

description:
ctrl_OSC KD_ChIP_Pol II
chromatin immunoprecipitation with RNA Pol II in control KD OSCs

value: control knockdown


title: Case 0052

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0052

tag: caso

tag: idade contínua

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores


title: Case 0051

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0051

tag: cor dos cabelos

tag: sardas

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar

tag: estagio clínico


title: Case 0050

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0050

tag: idade mediana≤ 54

tag: sexo

tag: nevos poucos_muitos

tag: localizacao tumor cabeca+tronco_membros

tag: breslow ≤1,5


title: Case 0049

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0049

tag: caso

tag: clark


title: chromatin IP with H3K9me3 in Nxf2 KD#2 OSCs

description:
Nxf2_2_OSC KD_ChIP_H3K9me3
chromatin immunoprecipitation with H3K9me3 in Nxf2 KD#2 OSCs

tag: cell type

tag: genotype

value: Nxf2#2 knockdown

tag: chip antibody

value: anti-H3K9me3 antibody produced in rabbit (Active Motif Cat# 39161)


title: AGS treated Ortho

description: AGS treated Ortho

tag: cell line

tag: agent


title: Case 0056

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0056

tag: idade contínua

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: sardas

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores


title: Case 0048

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0048

tag: idade mediana≤ 54

tag: sexo

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar

tag: estagio clínico


title: MKN1 treated DMSO

description: MKN1 treated DMSO

value: DMSO


title: Case 0054

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0054

tag: caso

tag: localizacao tumor cabeca+tronco_membros


title: chromatin IP with H3K9me3 in Nxf2 KD#1 OSCs

description:
Nxf2_1_OSC KD_ChIP_H3K9me3
chromatin immunoprecipitation with H3K9me3 in Nxf2 KD#1 OSCs

tag: cell type

tag: genotype

tag: chip antibody


title: SNU668 treated Meta

description: SNU668 treated Meta

tag: cell line

tag: agent


title: Case 0046

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0046

tag: idade contínua

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: breslow ≤1,5

tag: clark


title: SNU668 treated Para

description: SNU668 treated Para


title: AGS treated Para

description: AGS treated Para


title: Case 0043

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0043

tag: idade mediana≤ 54

tag: sexo

tag: sardas

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores


title: chromatin IP with RNA Pol II in Nxf2 KD#2 OSCs

description:
Nxf2_2_OSC KD_ChIP_Pol II
chromatin immunoprecipitation with RNA Pol II in Nxf2 KD#2 OSCs

tag: cell type

tag: genotype

tag: chip antibody


title: Case 0045

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0045

tag: caso

tag: idade contínua

tag: queimadura solar

tag: localizacao tumor cabeca+tronco_membros

tag: estagio clínico


title: chromatin IP with H3K9me3 in Panx OSCs

description:
Panx_OSC KD_ChIP_H3K9me3
chromatin immunoprecipitation with H3K9me3 in Panx OSCs


title: Case 0044

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0044

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: breslow ≤1,5


title: chromatin IP with H3K9me3 in control KD OSCs

description:
ctrl_OSC KD_ChIP_H3K9me3
chromatin immunoprecipitation with H3K9me3 in control KD OSCs


title: chromatin IP with H3K9me3 in Piwi KD OSCs

description:
Piwi_OSC KD_ChIP_H3K9me3
chromatin immunoprecipitation with H3K9me3 in Piwi KD OSCs


title: Case 0042

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0042

tag: idade mediana≤ 54

tag: sexo

tag: sardas

tag: nevos poucos_muitos

tag: clark


title: input DNA used for chromatin IP in Nxf2 KD#2 OSCs

description:
Nxf2_2_OSC KD_ChIP_inp
input DNA used for chromatin immunoprecipitation in Nxf2 KD#1 OSCs

tag: cell type

tag: genotype


title: SNU668 treated DMSO

description: SNU668 treated DMSO

source_name: stomach cancer cell line

tag: cell line

tag: agent


title: Case 0047

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0047

tag: caso

tag: idade contínua

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores


title: AGS treated DMSO

description: AGS treated DMSO


title: Case 0041

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0041

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: localizacao tumor cabeca+tronco_membros

tag: estagio clínico


title: Case 0040

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0040

tag: idade mediana≤ 54

tag: sexo

tag: sardas

tag: nevos poucos_muitos

tag: breslow ≤1,5

tag: clark


title: input DNA used for chromatin IP in Nxf2 KD#1 OSCs

description:
Nxf2_1_OSC KD_ChIP_inp
input DNA used for chromatin immunoprecipitation in Nxf2 KD#1 OSCs

source_name: OSCs

tag: cell type

tag: genotype

tag: chip antibody


title: SNU668 treated Ortho

description: SNU668 treated Ortho

tag: cell line

tag: agent


title: input DNA used for chromatin IP in Panx KD OSCs

description:
Panx_OSC KD_ChIP_inp
input DNA used for chromatin immunoprecipitation in Panx KD OSCs


title: SNU216 treated Ortho

description: SNU216 treated Ortho


title: SNU216 treated Meta

description: SNU216 treated Meta


title: SNU216 treated Para

description: SNU216 treated Para


title: Case 0039

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0039

tag: caso

tag: idade contínua

tag: fototipo i+ii_outros

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores


title: Mouse Liver Male XY 5

city: Lexington

first: Eric

middle: M

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

description: RMA expression value derived from Partek software; transcript-level analysis

hyb_protocol: Samples were hybridized with the Affymetrix Mouse Transcriptome Array 1.0 (MTA-1.0) and scanned at the UK Genomics Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Expression Console (Affymetrix) and Partek for background correction, normalization, and log 2 RMA signal intensity calculation at the transcript level. Data analysis and statistical evaluations were performed with The Institute for Genomic Research (TIGR) Multi-experiment Viewer (MEV) for two-way ANOVA calculations and Excel for log 2 fold change and protected Fisher's Least Significant Difference tests. For prestatistical filtering, probesets with a log 2 signal intensity > 4.2 on at least 2/19 arrays were included. Among these, in cases where more than one probe set was annotated to the same official gene symbol, the probe set with the highest average signal intensity across all arrays was retained for statistical analysis.

source_name: Liver Male XY

label_protocol: Extracted RNA was labeled and hybridized to Affymetrix Mouse Transcriptome Array 1.0 (MTA-1.0; one array per subject) according to the manufacturer’s instructions. WT cDNA Synthesis and Amplification kit and WT Sense Target Labelling and Control Reagents (Affymetrix) were used

extract_protocol: Animals were euthanized with ketamine/xylazine mixture (100/10 mg/ kg, injected intraperitoneally) in saline, and livers were removed in 3-4 minutes. ~100 mg of liver tissue was placed in RNA later solution (Ambion) and then RNA was extracted using Rneasy (Qiagen). Extracted RNA quality (RNA Integrity Number- RIN) was assayed by Agilent 2100 bioanalyzer.  Harvested samples: N = 19; [RIN]: overall average 9.55 ± 0.05 – p > 0.29; two-way ANOVA main effect of Sex p = 0.25; main effect of chromosome p = 0.13; interaction p = 0.42, disambiguated RIN values per array are provided (see characteristics: RNA Integrity Number).

treatment_protocol: 24-28 week old Ldlr-/- male and female mice with an XX or XY chromosomal complement that were surgically gonadectomized at 8-12 weeks of age and then fed a Western high fat diet for 16 weeks (n = 5 female XX, n = 5 female XY, n = 4 male XX, n = 5 male XY) prior to tissue harvesting.

tag: age

value: 24-28 week old

tag: genotype/variation

value: Ldlr-/-

tag: strain

tag: tissue

value: Liver

tag: Sex

value: Male

tag: sex chromosome complement

value: XY

tag: rna integrity number


title: SNU216 treated DMSO

description: SNU216 treated DMSO


title: Case 0038

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0038

tag: idade mediana≤ 54

tag: sexo

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: sardas

tag: nevos poucos_muitos

tag: localizacao tumor cabeca+tronco_membros

tag: breslow ≤1,5

tag: clark

tag: estagio clínico


title: Mouse Liver Male XY 4

tag: age

tag: genotype/variation


title: input DNA used for chromatin IP in Piwi KD OSCs

description:
Piwi_OSC KD_ChIP_inp
input DNA used for chromatin immunoprecipitation in Piwi KD OSCs

tag: cell type

tag: genotype

tag: chip antibody


title: input DNA used for chromatin IP in control KD OSCs

description:
ctrl_OSC KD_ChIP_inp
ctrl_OSC KD_ChIP_inp


title: Mouse Liver Male XY 3

tag: strain

tag: tissue

tag: Sex

tag: sex chromosome complement

tag: rna integrity number


title: SNU601 treated Meta

description: SNU601 treated Meta

tag: cell line

tag: agent

value: Meta


title: small RNAs (18-29 nt) from Nxf2 KD#2 OSCs with 2S rRNA depletion

description:
Nxf2_2_OSC KD_sRNAseq
sRNA_counts.txt

data_processing:
reads were trimmed by removal of the adaptor sequences and to a length of 6-50 bases
reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using Bowtie (release 1.2.2) with 0 mismatches were excluded
reads were mapped with 0 mismatches for genome wide analysis using Bowtie (release 1.2.2)
Reads mapping to rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were removed from the analysis
Genome_build: dm6
Supplementary_files_format_and_content: all mapping and unique mapping bigwig files for sense and antisense

extract_protocol:
RNA was isolated with TRIzol reagent according to the manufacturer’s instructions
small RNAs were PAGE selected and 3' and 5' linkers was ligated. 1st strand cDNA synthesis was performed using SuperScript II (Invitrogen) and the library was amplified using the Kapa HiFi Library Amp real time Kit (Peqlab) with Illumina TruSeq compatible primers.

tag: rna fraction

value: total RNA


title: SNU601 treated Para

description: SNU601 treated Para

value: Para


title: Case 0037

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0037

tag: caso

tag: idade contínua

tag: idade mediana≤ 54

tag: sexo

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: sardas

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores

tag: localizacao tumor cabeca+tronco_membros


title: Case 0035

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0035

tag: breslow ≤1,5

tag: clark

tag: estagio clínico


title: small RNAs (18-29 nt) from Nxf2 KD#1 OSCs with 2S rRNA depletion

description:
Nxf2_1_OSC KD_sRNAseq
sRNA_counts.txt

tag: genotype

tag: rna fraction

tag: cell type

value: OSC


title: SNU601 treated Ortho

description: SNU601 treated Ortho

tag: cell line

tag: agent

value: Ortho


title: Mta3_flox_flox_2.rnaseq

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

data_processing:
Reads were  quality-trimmed with TrimGalore! and  aligned to the mouse reference genome (GRCm38/mm10) and ERC spike-ins using TopHat2 guided by ENSEMBL 86 gene models. Read counts per ENSEMBL 86 transcript were obtained using FeatureCounts.
Supplementary_files_format_and_content: Processed data files contain counts per ENSEMBL 86 transcript obtained by featureCounts

source_name: embryonic stem cells

growth_protocol: Mouse embryonic stem cells (ESCs) were grown on gelatin-coated plates in 2i/LIF conditions as described (Ying et al., 2008).

extract_protocol:
Total RNA was purified using RNeasy Mini Kit (Qiagen) including on-column DNase treatment.
Libraries for sequencing were prepared using the NEXTflex Rapid Directional RNA-seq kit or SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

treatment_protocol: ES cells were induced to differentiate towards a neuroectoderm fate by removal of two inhibitors and LIF and culturing in N2B27 media as described (Ying et al., 2008).

tag: strain

tag: tissue

value: embryonic stem cells

tag: genotype/variation

tag: culture conditions


title: Mta3_flox_flox_3.rnaseq


title: SNU601 treated DMSO

description: SNU601 treated DMSO


title: Mouse Liver Male XY 1

tag: age

tag: Sex

tag: sex chromosome complement

tag: rna integrity number


title: Mouse Liver Male XX 3

source_name: Liver Male XX

value: XX


title: Mouse Liver Male XY 2


title: Mta3_flox_flox_1.rnaseq


title: Case 0036

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0036

tag: caso

tag: idade contínua

tag: idade mediana≤ 54

tag: sexo

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: sardas

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores

tag: localizacao tumor cabeca+tronco_membros


title: small RNAs (18-29 nt) from control KD OSCs with 2S rRNA depletion

description:
ctrl_OSC KD_sRNAseq
sRNA_counts.txt

tag: genotype

tag: rna fraction

tag: cell type


title: Case 0032

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0032

tag: caso

tag: idade contínua

tag: breslow ≤1,5

tag: clark

tag: estagio clínico


title: small RNAs (18-29 nt) from Panoramix KD OSCs with 2S rRNA depletion

description:
Panx_OSC KD_sRNAseq
sRNA_counts.txt

value: Panoramix knockdown


title: small RNAs (18-29 nt) from Piwi KD OSCs with 2S rRNA depletion

description:
Piwi_OSC KD_sRNAseq
sRNA_counts.txt

value: Piwi knockdown


title: Case 0033

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0033

tag: idade mediana≤ 54

tag: sexo

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos


title: Mta3_del_del_3.rnaseq

tag: strain

tag: tissue

tag: genotype/variation

tag: culture conditions


title: Mta3_del_del_2.rnaseq


title: Case 0034

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0034

tag: cor dos cabelos

tag: sardas

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores

tag: localizacao tumor cabeca+tronco_membros


title: Mta2_WT.3.rnaseq


title: small RNAs (18-29 nt) from Nxf2 KD ovaries with 2S rRNA depletion

description:
Nxf2_GLKD_sRNAseq
sRNA_counts.txt

source_name: adult ovary

growth_protocol: Flies were kept at strandard conditions at 25º C.

tag: developmental stage

value: 4-6 days old adult females

tag: genotype

value: Nxf2 knockdown

tag: rna fraction

value: ovary


title: Mouse Liver Male XX 1

tag: age

value: 24-28 week old

tag: Sex

tag: sex chromosome complement

tag: rna integrity number


title: Mta3_del_del_1.rnaseq

tag: strain

tag: tissue

tag: genotype/variation


title: Mta2_WT.2.rnaseq

tag: culture conditions


title: Mouse Liver Male XX 4

value: Ldlr-/-


title: Mouse Liver Male XX 2

value: Liver


title: small RNAs (18-29 nt) from Piwi KD ovaries with 2S rRNA depletion

description:
Piwi_GLKD_sRNAseq
sRNA_counts.txt


title: Case 0031

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0031

tag: caso

tag: idade contínua

tag: idade mediana≤ 54

tag: sexo

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: sardas

tag: nevos poucos_muitos

tag: breslow ≤1,5

tag: clark

tag: estagio clínico


title: small RNAs (18-29 nt) from control KD ovaries with 2S rRNA depletion

description:
w_GLKD_sRNAseq
sRNA_counts.txt

tag: developmental stage

tag: genotype

value: control knockdown

tag: rna fraction


title: small RNAs (18-29 nt) from Panoramix KD  ovaries with 2S rRNA depletion

description:
Panx_GLKD_sRNAseq
sRNA_counts.txt

tag: tissue


title: Case 0028

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0028

tag: caso

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores

tag: localizacao tumor cabeca+tronco_membros


title: total RNAs from Nxf2 KD#2 in OSCs with polyA selection replicate3

description: Nxf2_2_OSC KD_polyA_RNAseq-rep3

data_processing:
reads were trimmed by removal of the adaptor sequences and to a length of 6-50 bases
reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using Bowtie (release 1.2.2) with 0 mismatches were excluded
reads were mapped to the Drosophila melanogaster genome using STAR (v.2.5.2b)
reads mapping to rRNA, tRNA, mitoRNA were excluded
Genome_build: dm6
Supplementary_files_format_and_content: all mapping and unique mapping bigwig files for sense and antisense

molecule: polyA RNA

extract_protocol:
RNA was extracted using Trizol
Libraries were prepared using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB)

value: Nxf2#2 knockdown

tag: cell type

value: total RNA with polyA selection


title: total RNAs from Nxf2 KD#2 in OSCs with polyA selection replicate2

description: Nxf2_2_OSC KD_polyA_RNAseq-rep2


title: Case 0030

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0030

tag: idade contínua

tag: idade mediana≤ 54

tag: sexo

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos


title: Mouse Liver Female XY 5

source_name: Liver Female XY

tag: age

tag: genotype/variation

tag: strain

tag: Sex

value: Female

tag: sex chromosome complement

value: XY

tag: rna integrity number


title: Case 0027

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0027

tag: caso

tag: sardas

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar

tag: breslow ≤1,5

tag: clark

tag: estagio clínico


title: Mouse Liver Female XY 2

tag: tissue


title: Mouse Liver Female XY 4


title: Mouse Liver Female XY 1


title: Mouse Liver Female XY 3


title: Case 0029

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0029

tag: idade contínua

tag: idade mediana≤ 54

tag: sexo

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores

tag: localizacao tumor cabeca+tronco_membros


title: Mouse Liver Female XX 4

source_name: Liver Female XX

tag: age

tag: genotype/variation

tag: strain

tag: Sex

tag: sex chromosome complement

tag: rna integrity number


title: Case 0024

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0024

tag: caso

tag: sardas

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar

tag: breslow ≤1,5

tag: clark

tag: estagio clínico


title: Mta2_WT.1.rnaseq

tag: tissue

tag: culture conditions


title: Mta2_KO.3.rnaseq


title: Mta2_KO.2.rnaseq


title: Case 0026

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0026

tag: idade contínua

tag: idade mediana≤ 54

tag: sexo

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores

tag: localizacao tumor cabeca+tronco_membros


title: total RNAs from Nxf2 KD#1 in OSCs with polyA selection replicate3

description: Nxf2_1_OSC KD_polyA_RNAseq-rep3

source_name: OSCs

tag: genotype

value: Nxf2#1 knockdown

tag: cell type

value: OSC

tag: rna fraction


title: total RNAs from Nxf2 KD#2 in OSCs with polyA selection replicate1

description: Nxf2_2_OSC KD_polyA_RNAseq-rep1


title: Mta2_KO.1.rnaseq

source_name: embryonic stem cells

tag: strain

value: embryonic stem cells

tag: genotype/variation


title: Case 0025

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0025

tag: caso

tag: sardas

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar

tag: breslow ≤1,5

tag: clark

tag: estagio clínico


title: total RNAs from Nxf2 KD#1 in OSCs with polyA selection replicate2

description: Nxf2_1_OSC KD_polyA_RNAseq-rep2


title: Case 0023

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0023

tag: idade contínua

tag: idade mediana≤ 54

tag: sexo

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos


title: Mta1_flox_flox_3.rnaseq

tag: strain

tag: tissue

tag: genotype/variation

tag: culture conditions


title: TOP2_ACF_ULS1_R2_IN

city: St Andrews

first: Helder

last: Ferreira

address: North Haugh

department: Biology

country: United Kingdom

institute: University of St Andrews

data_processing:
Reads were mapped to the S. cerevisiae W303 genome (Matheson et al., 2017) using BWA (Li and Durbin, 2010) with default parameters for paired end sequences
Indexed BAM files were quality filtered using samtools view (Li et al., 2009) with a quality filter of 28 and a -F FLAG value of 1796.  QualiMap (Okonechnikov et al., 2016) was used to check the quality of alignment in both the unfiltered and quality filtered BAM files.  Replicate correlation was checked using Pearson’s correlation, calculated using deepTools multiBamSummary and plotCorrelation (Ramírez et al., 2016). Replicates or inputs (within one genotype) were pooled using samtools merge with default parameters. The resulting file was then sorted using samtools sort and indexed using samtools index, all with default parameters (Li et al., 2009).
Peak calling was carried out using MACS2 subcommands (Zhang et al., 2008).  PCR duplicates were filtered using macs2 filterdup.  IP pileup track was generated using macs2 pileup, extending reads to the average fragment size.  IP pileup track was generated using macs2 pileup, extending reads to the average fragment size.  INP local lambda track was generated using macs2 pileup (-B), generating three tracks where reads were extended in both directions by half the average fragment size (termed “d”), 500bp (termed “1kb_slocal”), or 2500bp (termed “5kb_llocal”).  1kb_slocal and 5kb_llocal were normalised to “d” sized fragments using macs2 bdgopt (-m multiply).  All tracks were combined to generate “local lambda” background track using macs2 bdgcmp (-m max), also normalising to maximum background noise (number of reads in INP x average fragment length / genome size) using macs2 bdgopt (-m max).  IP and local lambda were normalised to counts per million (CPM) using macs2 bdgopt (-m multiply).  A p-value statistical track was generated using macs2 bdgcmp (-m ppois).  Peak calling was carried out using macs2 bdgpeakcall with a p-value cut-off of 0.1.  IP/INP fold enrichment tracks were generated using macs2 bdgcmp.
Differential analysis compares signal at peak regions between different datasets.  To do this, the peaks called in all Top2/Uls1 datasets must be combined to give a list of the regions at which we will be completing differential analysis. This is completed using bedtools intersectBed and mergeBed (Quinlan and Hall, 2010).
Transcription start site analysis. Analysis was carried out using the R based packages rtracklayer, ChIPseeker and Genomic Features (Lawrence, 2013; Lawrence et al., 2009; R Core Team, 2018; Yu et al., 2015).  The input files for this analysis were our MACS2 peak files.
Repetitive region analysis. This analysis uses unfiltered reads where reads which map to multiple regions have not been removed. This analysis is slightly difficult in that you cannot use signal height to define whether the ChIPed protein is binding or not as the more repetitive the sequence, the higher the signal will be. However, if a pairwise comparison of two datasets within a repetitive region is carried out and one dataset shows significantly higher enrichment than the other, then it can be logically assumed that there is enrichment of the ChIPed protein within the “higher” dataset.  Analysis was carried out at subtelomeric loci (+/- 5kb from each chromosome end), tRNA (as within genome reference), TKP/TY transposons (as within genome reference), Y’ elements (as within genome reference) and the rDNA locus. We identified a partial fragment of the rDNA locus within our W303 reference by using blastn (Altschul et al., 1990) to search the sequence for a single rDNA repeat from within chromosome 12 in the S288C reference (Engel et al., 2013), aligning to the sequence of chromosome 12 within our W303 reference. According to SGD (Stanford University, 2012), the sequence of a single rDNA repeat within the S288C reference is on Chromosome 12 at 459,797-468,931. The top hit from this blast search within our W303 reference is on Chromosome 12 at 478,018-478,813, containing the sequence of part of the 35S rDNA locus. First, a .bed file was generated containing the coordinates of all the regions within one repetitive region, for instance the 141 tRNA genes within our W303 reference. This was made within excel and saved as a tab delimited file. Data tracks were then generated with signal extracted at each repetitive region using intersectBed (Quinlan and Hall, 2010) and a peak list containing the SUM score under each peak in each dataset using the following commands for each dataset:
Genome_build: A whole-genome sequence for the W303 strain of S. cerevisiae was published by Matheson et al. (2017), containing 16 nuclear chromosomes, the mitochondrial genome and additional plasmids present in the sequenced strain. We were unable to obtain a copy of the Matheson genome annotation so generated our own. Initial annotation was carried out by inputting the W303_LYZE genome sequence (Genbank GCA_002163515.1, Assembly name ASM216351v1) into the Yeast Genome Annotation Pipeline (YGAP, Proux-Wéra et al., 2012).  We used this as a basis for our genome annotation, using BLASTn (Altschul et al., 1990) to identify any ORFs which were not annotated by YGAP.  YGAP identified 5634 ORFs, with 6600 present in the S288C reference, the gold standard of genome references in yeast (Saccharomyces Genome Database, version R64-2-1, Engel et al., 2013). 141 tRNA genes were identified, with 299 being present in the S288C reference. Where an unidentified gene had high similarity to Y prime helicase elements, this was labelled as “Y’ element” (54 items), and where it had high similarity to gag pol genes, this was labelled as “TKP/TY” (86 items). Any elements that could not be identified were labelled as “unknown” (4/5634 ORFs). Gene lengths were checked against S288C and a note was made for each gene as to whether they were the same or not, with 524/5634 differing in size in W303 compared to S288C. Additional information for each ORF was extracted from the YGP S288C reference using excel, including gene names, aliases and gene ontology information.  ARS were identified using Biopython BioSeqIO (Cock et al., 2009), searching for variants of the consensus sequence for ARS (ATTTATATTTA, TTTTATATTTA, ATTTATGTTTA, TTTTATGTTTA, ATTTATATTTT, TTTTATATTTT, ATTTATGTTTT, TTTTATGTTTT), finding 333 ARS. Centromeric sequences were identified by blasting the nucleotide sequence of the S288C CEN1-16. CEN5 was identified by blasting for conserved centromeric elements CDEI and CDEIII as it had little homology to S288C CEN5.
Supplementary_files_format_and_content: bedgraph files. IP pileup track was generated using macs2 pileup, extending reads to the average fragment size.  INP local lambda track was generated using macs2 pileup (-B), generating three tracks where reads were extended in both directions by half the average fragment size (termed “d”), 500bp (termed “1kb_slocal”), or 2500bp (termed “5kb_llocal”).  1kb_slocal and 5kb_llocal were normalized to “d” sized fragments using macs2 bdgopt (-m multiply).  All tracks were combined to generate “local lambda” background track using macs2 bdgcmp (-m max), also normalizing to maximum background noise (number of reads in INP x average fragment length / genome size) using macs2 bdgopt (-m max).  IP and local lambda were normalized to counts per million (CPM) using macs2 bdgopt (-m multiply).

organism: Saccharomyces cerevisiae

source_name: Budding yeast

growth_protocol: yeast grown in 50ml YPD rich media to exponential phase

extract_protocol:
To each yeast pellet add 300μl homogenization beads (0.5mm diameter, Thistle Scientific 11079105) and 200μl lysis buffer (50mM Hepes pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, protease inhibitors). Bead beat 5 x 30 seconds at power setting 6.5 (FastPrep), placing samples on ice for 5 minutes between each cycle. Pierce tube with a 26G needle and place tube inside a 5ml u-shaped tube, spinning lysis material into U-shaped tube by centrifugation at 2,000 rpm for 2 minutes at 4°C. Re-suspend any pelleted material and dilute in a further 300μl lysis buffer, taking this to a new Eppendorf tube. Centrifuge at 15,000 rpm for 15 minutes at 4°C, remove supernatant and resuspend pellet in 300μl lysis buffer, transferring to a 1.5ml Bioruptor tube (Diagenode, C30010016). Shear chromatin using Bioruptor, 10 cycles of 30s on/off (DNA should be sheared to fragments of 250-500bp). Centrifuge at 8,000 rpm for 5 minutes at 4°C. 60μl of the supernatant is then taken as input (40μl for DNA purification, 20μl to check protein levels), with the rest being added to antibody bound beads which are incubated for 3 hours at 4°C. Beads are washed in 1ml lysis buffer twice for 5 minutes and 1ml wash buffer once for 5 minutes (100mM Tris pH 8, 250mM NaCl, 0.5% NP-40, 0.5% Na-deoxycholate, 1mM EDTA, protease inhibitors) before elution in 60μl TE/1% SDS at 65°C for 15 minutes. Magnetic beads are collected using a magnetic rack, and supernatant removed to a new tube. 20μl is used to check protein levels, and 40μl kept for DNA purification. 1% SDS is added to input, 0.5μl RNase A (10mg/ml) is added to both input and IP DNA, and both samples are un- crosslinked overnight at 65°C in a PCR machine. 0.5μl Proteinase K (20mg/ml) is added after uncrosslinking and samples incubated for 1 hour at 65°C. DNA is purified using Quaigen QIAquick PCR purification kit (Quaigen, 28106) as per specifications, eluting in 50μl H2O.
Due to the low quantity of DNA present after immunoprecipitation, to ensure there is enough sample DNA for amplification and sequencing two experimental replicates are combined before ChIP-seq library preparation. Step 1 of library preparation allows repair of DNA ends. To 80μl pooled DNA, add 20μl MMX1 (1x T4-ligase buffer with ATP, 0.4mM dNTPs, 15 units T4 DNA polymerase, 10 units Klenow DNA polymerase, 30 units T4 polynucleotide kinase) and incubate for 60 minutes at 20°C. DNA is purified by addition of a 1:1 v/v of AMPure XP magnetic beads, incubating for 5 minutes before washing twice with 200μl 70% EtOH using a magnetic rack. Residual EtOH is removed before elution of DNA in 41μl H2O. Step 2 of library preparation adds an additional adenine nucleotide to DNA ends to which adapters will later be ligated. To 41μl DNA, add 9μl MMX2 (1x Klenow buffer, 2mM dATP, 15 units Klenow exo-), incubating for 30 minutes at 37°C. DNA is purified as in step 1 using a 1:1 v/v of Agencourt AMPure XP magnetic beads, eluting in a final volume of 20μl H2O. Step 3 of library preparation ligates adapters onto DNA which are used later as a template for PCR amplification of ChIPed DNA fragments to generate the final tagged DNA library. Adapter is ordered as two oligonucleotides (HFO424/425, Illumina paired end adapter sequence). HFO425 is phosphorylated as per manual specifications using T4 polynucleotide kinase (Thermo Fisher EK0032) before annealing to HFO424 by mixing an equimolar ratio of the two oligos and heating to 95°C for 5 minutes, reducing the temperature by 5°C every 5 minutes until reaching 25°C. Adapter is then run into a 1% agarose gel, gel purified and stored at -20°C before use. To ligate adapter to DNA, to 20μl DNA add 30μl MMX3 (8nM adapter, 1x T4 DNA ligase buffer with ATP, 400 units T4 DNA ligase), incubating overnight at room temperature. DNA is purified as in step 1 with a 1:1 v/v of Agencourt AMPure XP magnetic beads, eluting in 20μl H2O. Step 4 of library preparation amplifies the DNA samples using primers complimentary to the adapters now ligated onto each DNA molecule, with each primer also containing an additional unique sequence tag which is used to identify each sample after sequencing of the DNA. Details of the primers used can be found in Table 6–6. For each sample, 3 PCR reactions are set up containing 3μl DNA and 47μl MMX4 (1X HF buffer, 3 units Phusion DNA polymerase, 0.3μM oligos (HFO426 and sequencing primer), 0.4μM dNTPs, 200mM Trehalose). The PCR is carried out by denaturing for 3 mins at 98°C before 16-20 cycles of amplification (98°C 15 secs, 60°C 25 secs, 68°C 1 min) and a final step at 68°C for 5 mins. The three PCRs are then pooled and ran on a TAE gel containing 1% agarose and 0.5μg/ml EtBr. Once the gel has ran long enough to separate free adapter from amplified DNA, bands are cut from the gel at a size of 600bp and under, avoiding contamination with adapter. DNA is purified from the gel using Quaigen MiniElute columns (Quaigen, 28006) as per kit specifications except gel was melted at 37°C, eluting from the column in 10μl EB. DNA concentration was quantified via Qubit using 1:199 DNA:Qubit dsDNA High Sensitivity assay working solution (Invitrogen, Q32854, as per kit specifications). DNA quality and mean fragment size were checked on a TapeStation, running samples onto D1000 ScreenTape with D1000 reagents (Agilent, 5067-5582, 5067-5583).

treatment_protocol: exposed to 0, 100uM (Uls1 ChIP) or 250uM (Top2 ChIP) acriflavine (ACF) for 2 hours, before crosslinking with 1% formaldehyde for 10 mins and quenched in 125mM glycine for 10 mins

tag: affinity tag

value: HA

tag: treatment

value: ACF

tag: chip antibody


title: Mta1_flox_flox_2.rnaseq


title: Mta1_flox_flox_1.rnaseq


title: Case 0022

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0022

tag: caso

tag: sardas

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores

tag: localizacao tumor cabeca+tronco_membros

tag: breslow ≤1,5


title: TOP2_ACF_ULS1_R1_IN


title: total RNAs from Panoramix KD in OSCs with polyA selection replicate3

description: Panx_OSC KD_polyA_RNAseq-rep3

tag: genotype

value: Panoramix knockdown

tag: cell type

tag: rna fraction


title: TOP2_ACF_ULS1_R2_IP

description: TOP2_ACF_ULS1_pooled_IP_srtd_dupfilt_pileup_NORMALISED_CPM_FE.bedgraph

value: HA (Roche, ROAHAHA)


title: Case 0021

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0021

tag: idade contínua

tag: idade mediana≤ 54

tag: sexo

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: clark

tag: estagio clínico


title: Mta1_del_del_3.rnaseq

tag: strain

tag: tissue

tag: genotype/variation

tag: culture conditions


title: Mouse Liver Female XX 5

tag: age

tag: Sex

tag: sex chromosome complement

value: XX

tag: rna integrity number


title: TOP2_ACF_ULS1_R1_IP

tag: affinity tag

tag: treatment

tag: chip antibody


title: total RNAs from Panoramix KD in OSCs with polyA selection replicate2

description: Panx_OSC KD_polyA_RNAseq-rep2

tag: genotype

tag: cell type

tag: rna fraction


title: Mouse Liver Female XX 2


title: Mouse Liver Female XX 1


title: Mouse Liver Female XX 3


title: Mta1_del_del_2.rnaseq


title: TOP2_YPD_ULS1_R2_IN

value: YPD


title: Mta1_del_del_1.rnaseq


title: TOP2_YPD_ULS1_R2_IP

description: TOP2_YPD_ULS1_pooled_IP_srtd_dupfilt_pileup_NORMALISED_CPM_FE.bedgraph


title: Case 0018

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0018

tag: caso

tag: idade contínua

tag: idade mediana≤ 54

tag: sexo

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: sardas

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores

tag: localizacao tumor cabeca+tronco_membros

tag: breslow ≤1,5


title: Case 0020

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0020

tag: clark

tag: estagio clínico


title: Case 0019

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0019

tag: caso

tag: idade contínua


title: total RNAs from Piwi KD in OSCs with polyA selection replicate3

description: Piwi_OSC KD_polyA_RNAseq-rep3

tag: genotype

value: Piwi knockdown

tag: cell type

tag: rna fraction


title: total RNAs from Panoramix KD in OSCs with polyA selection replicate1

description: Panx_OSC KD_polyA_RNAseq-rep1


title: Diff48.MtaKO2_2.rnaseq

source_name: 48 hour differentiating embryonic stem cells

tag: strain

tag: tissue

tag: genotype/variation

tag: culture conditions

value: 48h in N2B27 without inhibitors or LIF


title: Diff48.MtaKO2_1.rnaseq

value: 48 hour differentiating embryonic stem cells


title: TOP2_YPD_ULS1_R1_IP

tag: affinity tag

tag: treatment

tag: chip antibody


title: total RNAs from Nxf2 KD#1 in OSCs with polyA selection replicate1

description: Nxf2_1_OSC KD_polyA_RNAseq-rep1


title: Case 0017

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0017

tag: idade mediana≤ 54

tag: sexo

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: sardas

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores


title: Case 0016

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0016

tag: caso

tag: idade contínua

tag: localizacao tumor cabeca+tronco_membros

tag: breslow ≤1,5

tag: clark

tag: estagio clínico


title: total RNAs from Piwi KD in OSCs with polyA selection replicate1

description: Piwi_OSC KD_polyA_RNAseq-rep1

tag: genotype

tag: cell type

tag: rna fraction


title: Diff48.MtaKO1_2.rnaseq

tag: strain

tag: tissue

tag: genotype/variation

tag: culture conditions


title: TOP2_ACF_WT_R2_IN

tag: affinity tag

tag: treatment

tag: chip antibody


title: TOP2_ACF_WT_R1_IN


title: Case 0015

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0015

tag: idade mediana≤ 54

tag: sexo

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: sardas

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores


title: Diff48.MtaKO1_1.rnaseq

tag: strain

tag: tissue

tag: genotype/variation


title: total RNAs from control KD in OSCs with polyA selection replicate3

description: ctrl_OSC KD_polyA_RNAseq-rep3

tag: genotype

value: control knockdown

tag: cell type

tag: rna fraction


title: Case 0014

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0014

tag: caso

tag: idade contínua

tag: idade mediana≤ 54

tag: sexo

tag: localizacao tumor cabeca+tronco_membros

tag: breslow ≤1,5

tag: clark

tag: estagio clínico


title: TOP2_ACF_WT_R2_IP

description: TOP2_ACF_WT_pooled_IP_srtd_dupfilt_pileup_NORMALISED_CPM_FE.bedgraph

tag: affinity tag

tag: treatment

tag: chip antibody


title: Diff48.Ctrl2_2.rnaseq

tag: strain

value: Control

tag: culture conditions


title: TOP2_YPD_ULS1_R1_IN


title: total RNAs from control KD in OSCs with polyA selection replicate2

description: ctrl_OSC KD_polyA_RNAseq-rep2

value: total RNA with polyA selection


title: total RNAs from control KD in OSCs with polyA selection replicate1

description: ctrl_OSC KD_polyA_RNAseq-rep1


title: Case 0013

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0013

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: sardas

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores


title: total RNAs from Piwi KD in OSCs with polyA selection replicate2

description: Piwi_OSC KD_polyA_RNAseq-rep2

tag: genotype

tag: cell type

tag: rna fraction


title: TOP2_ACF_WT_R1_IP

tag: affinity tag

tag: treatment


title: Diff48.Ctrl2_1.rnaseq

tag: strain

tag: tissue

tag: genotype/variation


title: TOP2_YPD_WT_R2_IN

tag: chip antibody


title: total RNAs from Nxf2 KD#2 in OSCs with rRNA depletion

description: Nxf2_2_OSC KD_rRNA dep_RNAseq

value: Nxf2#2 knockdown

value: total RNA with rRNA depletion


title: Diff48.Ctrl1_2.rnaseq

tag: culture conditions


title: total RNAs from Nxf2 KD#1 in OSCs with rRNA depletion

description: Nxf2_1_OSC KD_rRNA dep_RNAseq

value: Nxf2#1 knockdown


title: total RNAs from Panoramix KD in OSCs with rRNA depletion

description: Panx_OSC KD_rRNA dep_RNAseq

value: OSC


title: Case 0011

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0011

tag: caso

tag: idade contínua

tag: idade mediana≤ 54

tag: sexo

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: localizacao tumor cabeca+tronco_membros

tag: breslow ≤1,5

tag: clark

tag: estagio clínico


title: TOP2_YPD_WT_R2_IP

description: TOP2_YPD_WT_pooled_IP_srtd_dupfilt_pileup_NORMALISED_CPM_FE.bedgraph

tag: affinity tag

tag: treatment


title: Diff48.Ctrl1_1.rnaseq

tag: strain

tag: tissue

tag: genotype/variation


title: TOP2_YPD_WT_R1_IP

tag: chip antibody


title: ESC-2iL.MtaKO2_2.rnaseq

value: embryonic stem cells

tag: culture conditions


title: ESC-2iL.MtaKO2_1.rnaseq


title: Case 0009

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0009

tag: caso

tag: idade contínua

tag: idade mediana≤ 54

tag: sardas

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores


title: total RNAs from Piwi KD in OSCs with rRNA depletion

description: Piwi_OSC KD_rRNA dep_RNAseq

source_name: OSCs

tag: genotype

tag: cell type

tag: rna fraction


title: ESC-2iL.MtaKO1_2.rnaseq

source_name: embryonic stem cells

tag: strain


title: Case 0008

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0008

tag: sexo

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: localizacao tumor cabeca+tronco_membros

tag: breslow ≤1,5

tag: clark

tag: estagio clínico


title: total RNAs from Nxf2 KD ovaries with rRNA depletion

description: Nxf2_GLKD_rRNA dep_RNAseq

source_name: adult ovary

tag: developmental stage

value: 4-6 days old adult females

value: Nxf2 knockdown

tag: tissue

value: ovary


title: ULS1_ACF_WT_R2_IN

source_name: Budding yeast

tag: affinity tag

value: FLAG

tag: treatment

value: ACF

tag: chip antibody


title: Case 0007

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0007

tag: caso

tag: idade contínua

tag: idade mediana≤ 54

tag: sardas

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores


title: total RNAs from Panoramix KD ovaries with rRNA depletion

description: Panx_GLKD_rRNA dep_RNAseq

tag: genotype

value: Panoramix knockdown

tag: rna fraction


title: Case 0006

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0006

tag: sexo

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: localizacao tumor cabeca+tronco_membros

tag: breslow ≤1,5

tag: clark

tag: estagio clínico


title: ESC-2iL.Ctrl2_2.rnaseq

tag: strain

tag: tissue

tag: genotype/variation

tag: culture conditions


title: ULS1_ACF_WT_R2_IP

description: ULS1_ACF_WT_pooled_IP_srtd_dupfilt_pileup_NORMALISED_CPM_FE.bedgraph

tag: affinity tag

tag: treatment

tag: chip antibody

value: FLAG (Sigma, F3165)


title: ULS1_ACF_WT_R1_IN


title: total RNAs from Piwi KD ovaries with rRNA depletion

description: Piwi_GLKD_rRNA dep_RNAseq

tag: developmental stage

tag: genotype

value: Piwi knockdown

tag: rna fraction


title: TOP2_YPD_WT_R1_IN

value: HA

value: YPD


title: ESC-2iL.Ctrl2_1.rnaseq

value: Control


title: Case 0005

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0005

tag: caso

tag: idade contínua

tag: idade mediana≤ 54

tag: sexo

tag: fototipo i+ii_outros

tag: cor pele

tag: sardas

tag: nevos poucos_muitos

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores


title: Case 0004

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0004

tag: cor olhos

tag: cor dos cabelos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar

tag: localizacao tumor cabeca+tronco_membros

tag: breslow ≤1,5

tag: clark

tag: estagio clínico


title: ULS1_YPD_WT_R2_IN

tag: affinity tag

tag: treatment

tag: chip antibody


title: total RNAs from control KD ovaries with rRNA depletion

description: w_GLKD_rRNA dep_RNAseq

tag: developmental stage

tag: genotype

value: control knockdown

tag: tissue

tag: rna fraction


title: ESC-2iL.Ctrl1_2.rnaseq

tag: strain

tag: genotype/variation

tag: culture conditions


title: Case 0003

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0003

tag: caso

tag: idade contínua

tag: idade mediana≤ 54

tag: sexo

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: sardas

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores


title: ESC-2iL.Ctrl1_1.rnaseq

tag: tissue


title: total RNAs from Nxf2-TH ovaries with rRNA depletion

description: Nxf2_KO_TH_rRNA dep_RNAseq

tag: developmental stage

tag: genotype

value: Nxf2 trans-heterozygous mutant

tag: rna fraction


title: total RNAs from control KD in OSCs with rRNA depletion

description: ctrl_OSC KD_rRNA dep_RNAseq

tag: cell type

value: total RNA with rRNA depletion


title: ULS1_YPD_WT_R1_IN

tag: affinity tag

tag: treatment

tag: chip antibody


title: ULS1_YPD_WT_R2_IP

description: ULS1_YPD_WT_pooled_IP_srtd_dupfilt_pileup_NORMALISED_CPM_FE.bedgraph


title: Case 0002

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0002

tag: caso

tag: idade contínua

tag: idade mediana≤ 54

tag: sexo

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar

tag: localizacao tumor cabeca+tronco_membros

tag: clark

tag: estagio clínico


title: Filtered_air_sample_7-7

first: James

middle: William

last: MacDonald

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

data_processing:
Sample libraries were sequenced on the Illumina HiSeq 2500. Sequences were processed by discarding the low quality reads using Illumina’s base call quality filter, and raw reads were trimmed of adapter sequences and flanking low quality base reads using the trimmomatic read trimmer, discarding any reads less than 25nt. Reads were aligned to the mm10 genome using the Bismark aligner. Output from Bismark is bedGraph format consisting of five lines; CHR, START, END, %METHYLATION, COUNT METHYLATED, COUNT UNMETHYLATED.
Genome_build: mm10
Supplementary_files_format_and_content: Processed files consist of Bismark bedGraph coverage files.

source_name: Neonatal cardiomyocytes

extract_protocol:
DNA was isolated from frozen p0 isolated cardiomyocytes using Qiagen (Germantown; MD, USA) DNeasy Blood and Tissue kit, according to the manufacturer’s protocol.
500ng of DNA was digested overnight with MspI (New England BioLabs Inc., Ipswich, MA, USA) and then directly prepared with the KAPA Hyper Library prep protocol (KAPA Biosystems, Wilmington, MA, USA). Samples were then adapter-ligated using SeqCap Adapters (Roche-Nimblegen, Pleasanton, CA, USA), and cleaned using a 2.5X post-ligation Agencourt AMPure XP bead cleanup (Beckman Coulter, Indianapolis, IN). Size selection was performed to a size range of 160bp-340bp on a 2% Pippin Prep gel (Sage Science, Beverly, MA, USA), followed by bisulfite conversion using the Zymo EZ DNA Methylation Lightning kit (Zymo Research, Irvine, CA, USA).  The converted DNA was then put back into the KAPA Hyper Library prep protocol at the library amplification step, and amplification was performed with 19 PCR cycles using 2X KAPA Hifi HotStart Uracil+ ReadyMix (KAPA Biosystems, Wilmington, MA, USA).  Post-amplification cleanup was performed with 0.8X Agencourt AMPure XP beads (Beckman Coulter).  Library size distributions were validated using the Agilent High Sensitivity D1000 ScreenTape run on an Agilent 2200 TapeStation (Agilent Technologies, Inc., Santa Clara, CA, USA).  Additional library QC, blending of pooled indexed libraries, and cluster optimization was performed using Life Technologies- Invitrogen Qubit® 2.0 Fluorometer (Life Technologies-Invitrogen, Carlsbad, CA, USA).

tag: tissue

value: Neonatal cardiomyocytes

value: Filtered air


title: total RNAs from homozygous Nxf2-mutant#2 ovaries with rRNA depletion

description: Nxf2_KO_g2_rRNA dep_RNAseq

tag: developmental stage

value: Nxf2 mutant #2


title: Filtered_air_sample_7-4


title: ULS1_YPD_WT_R1_IP


title: total RNAs from homozygous Nxf2-mutant#1 ovaries with rRNA depletion

description: Nxf2_KO_g1_rRNA dep_RNAseq

value: 4-6 days old adult females

tag: genotype

value: Nxf2 mutant #1


title: ULS1_ACF_WT_R1_IP


title: ESC-2iL.MtaKO1_1.rnaseq

tag: strain

value: embryonic stem cells

tag: genotype/variation

tag: culture conditions


title: Case 0001

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0001

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: sardas

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores

tag: breslow ≤1,5


title: Filtered_air_sample_7-3

tag: treatment


title: total RNAs from Piwi-TH ovaries with rRNA depletion

description: Piwi_KO_TH_rRNA dep_RNAseq

value: Piwi trans-heterozygous mutant

value: ovary

tag: rna fraction


title: total RNAs from Panoramix-TH ovaries with rRNA depletion

description: Panx_KO_TH_rRNA dep_RNAseq

value: Panx trans-heterozygous mutant

tag: tissue


title: total RNAs from w1118 ovaries with rRNA depletion

description: w1118_rRNA dep_RNAseq

tag: developmental stage

value: wt control


title: Diesel_exhaust_sample_7-7

value: Diesel exhaust


title: 5GB1_FM21_TR2

first: Mitchell

last: Pesesky

address: 616 NE Northlake Place

description: methane growth, batch culture

data_processing:
Alignment was performed using BWA version 0.7.12-r1044 using the BWA-MEM algorithm and default parameters
The alignments were post-processed into sorted BAM files with SAMTools version 1.2-232-g87cdc4a
Reads were attributed to open reading frames (ORFs) using the htseq-count tool from the ‘HTSeq’ framework version 0.8.0 in the ‘intersection-nonempty’ mode
Differential abundance analysis was performed with DESeq2 1.2.10 and R 3.3.1.
Genome_build: AOTL01000000
Supplementary_files_format_and_content: TPM

organism: Methylotuvimicrobium buryatense

source_name: Bioreactor culture

growth_protocol: Samples for RNAseq analysis were taken from batch culture bioreactor experiments grown on either methane or methanol with pH control and continuous methane and air flow, which have been described previously (Gilman et al. 2015). Samples were taken at late log phase.

extract_protocol:
RNA was isolated and RNA-seq data analysis was carried out as described previously (de la Torre, A. et al. 2015)
RNA sequencing and library construction was performed by GENEWIZ (South Plainfield, NJ, USA) using Illumina HiSeq2500 1x50 (single ended) reads.


title: Diesel_exhaust_sample_7-1


title: 5GB1_FM21_TR1

description: methane growth, batch culture


title: pRRLsCITED2imCherryshMir PU.1 [9744534127_E]

city: Groningen

first: Hein

last: Schepers

state: Groningen

address: Hanzeplein 1

department: Internal Medicine

country: Netherlands

institute: University Medical Center Groningen

description: pRRLsCITED2imCherryshMir PU.1

hyb_protocol: Standard Illumina scanning protocol

scan_protocol: Illumina i-Scan reader

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R, and subsequently filtered for expression values >0.6 and <17.58

source_name: CB derived CD34+

label_protocol: Standard Illumina hybridization protocol

growth_protocol: CB CD34+ cells were isolated by Miltenyi miniMACS column. Cells were prestimulated in HPGM with 100 ng/ml KITL, FLT3L and TPO for 12 hrs. Cells were transduced with control, CITED2 overexpression lentivectors, shRNA PU.1 lentivectors or both,  in two rounds over 48 hrs. Transduced cells were sorted after which RNA was isolated for Illumina beadchip arrays HT12 v4

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell type

value: CB derived CD34+

tag: protocol

value: pRRLsCITED2imCherryshMir PU.1


title: Diesel_exhaust_sample_6-7


title: 5GB1_FM20_TR3

description: methane growth, batch culture

tag: strain


title: 5GB1_FM23_TR3

description: Methanol growth, batch culture


title: Case 0012

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Paciente 0012

tag: caso

tag: idade contínua

tag: idade mediana≤ 54

tag: sexo

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar

tag: localizacao tumor cabeca+tronco_membros

tag: clark

tag: estagio clínico


title: Diesel_exhaust_sample_5

data_processing:
To process sequences, Illumina RTA-generated BCL files were converted to FASTQ files and sequence read and base quality were checked using the FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) and FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Sequences were aligned to mm10 with reference transcriptome Ensembl v67 using Tophat (26). Lane level bam data files were merged using the Picard MergeSamFiles tool and suspected PCR duplicates were marked, not removed, in the alignment files using the Picard MarkDuplicates tool (http://broadinstitute.github.io/picard/). Local realignment was performed around indels, and base quality score recalibration was run using GATK tools. Variant detection was performed with the GATK Unified Genotyper version 2.6.5, and aligned data were used for isoform assembly and quantitation with Cufflinks. Fragment counts were generated using the featureCounts function in the Bioconductor Rsubread package.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data consist of tab-delimited counts per gene for each sample. The first column contains the NCBI Gene ID, and the remaining columns are counts for each gene per sample.

extract_protocol:
RNA was purified from frozen p0 isolated NCMs using Trizol (Thermo Fisher Scientific, Waltham, MA, USA), following the manufacturer’s protocol. Ribosomal RNA was depleted by poly-A enrichment, and sample libraries were created using the TruSeq Stranded mRNA kit (Illumina, San Diego, CA)
Each library was barcoded using the Illumina adapters, and amplified with 13 cycles of PCR. Library concentrations were quantified using the Quant-it dsDNA Assay (Life Technologies, Carlsbad, CA). Libraries were normalized and pooled based on Agilent 2100 Bioanalyzer results (Agilent Technologies, Santa Clara, CA), and the pools were sequenced on an Illumina HiSeq 2500.


title: 5GB1_FM18_TR3

description: Methanol growth, batch culture


title: Filtered_air_sample_6-6


title: Diesel_exhaust_sample_3


title: Diesel_exhaust_sample_6-3


title: pRRLsimCherryshMirSCR [9744534103_A]

description: pRRLsimCherryshMirSCR

value: pRRLsimCherryshMirSCR


title: 5GB1_FM18_TR2

description: Methanol growth, batch culture


title: pRRLsCITED2imCherryshMir SCR [9744534068_D]

description: pRRLsCITED2imCherryshMir SCR

value: pRRLsCITED2imCherryshMir SCR


title: Mta3FLAG_2i_2_Input

data_processing:
Reads were aligned to the mouse reference genome (UCSC GRCm38/mm10) using bowtie (version 0.12.8) and the arguments -m 1 -v 1 allowing for uniquely mapping reads only.
Peaks were called using MACS2 version 2.1.0 with the default Q-value of < 0.05.
Genome_build: UCSC GRCm38/mm10
Supplementary_files_format_and_content: Processed data files contain genome-wide ChIP-seq read counts (RPKM- normalized). Files were converted to UCSC genome browser bigWig format.

extract_protocol:
Chromatin immunoprecipitations were carried out as previously outlined (Reynolds et al., 2012).
ChIP-seq libraries were prepared using the NEXTflex Rapid DNA-seq kit (Illumina)

tag: culture conditions

tag: chip antibody

value: input

tag: genotype/variation

value: Mta3-FLAG knocked in to the endogenous Mta3 locus


title: Mta3FLAG_2i_2_2

value: anti-FLAG


title: pRRLsimCherryshMirPU1 [9744534103_G]


title: Mta3FLAG_2i_2_1


title: pRRLsCITED2imCherryshMir SCR [9744534068_C]

description: pRRLsCITED2imCherryshMir SCR


title: pRRLsimCherryshMirSCR [9744534103_L]

description: pRRLsimCherryshMirSCR


title: Tumor_11659

city: Gothenburg

first: Toshima

middle: Z.

last: Parris

address: Medicinaregatan 1G, 6th floor

department: Department of Oncology

country: Sweden

institute: University of Gothenburg

description: Genomic DNA extracted from breast tumors was genotyped using Infinium Omni2.5-8 v1.3 Genotyping BeadChips (Illumina)

hyb_protocol: Illumina protocol

scan_protocol: Standard Illumina iScan N240 scanning protocol

data_processing:
GenomeStudio Software V2011.1
B allele frequency
Log R ratio

label: cy3 and cy5

source_name: Human breast tumor

label_protocol: Illumina protocol

extract_protocol: Genomic DNA was isolated from fresh-frozen tissue specimens using the Wizard Genomic DNA extraction kit, including proteinase K treatment followed by phenol chloroform purification

tag: 8p11-p12 amplification

value: Amplified

tag: age

tag: pt status

tag: lymph node status

tag: er status

value: pos

tag: pgr status

value: neg

tag: her2 status


title: Mta3FLAG_2i_1_Input

tag: cell type

tag: strain


title: Tumor_11378


title: Diesel_exhaust_sample_7

tag: tissue

value: Neonatal cardiomyocytes

tag: treatment


title: Tumor_11372


title: Tumor_11315


title: pRRLsimCherryshMirPU1 [9744534068_F]

tag: protocol


title: Filtered_air_sample_4

value: Filtered air


title: pRRLsCITED2imCherryshMir PU.1 [9744534103_K]

description: pRRLsCITED2imCherryshMir PU.1


title: Filtered_air_sample_3


title: Mta3FLAG_2i_1_2

value: embryonic stem cells


title: Filtered_air_sample_6


title: Tumor_10823


title: Filtered_air_sample_2


title: Tumor_10569


title: Tumor_10415


title: Mta2GFP_2i_2_Input

value: Mta2-GFP knocked in to the endogenous Mta2 locus


title: Tumor_10408


title: Mta2GFP_2i_2_2

value: Anti-GFP


title: Mta2GFP_2i_2_1


title: Tumor_10400


title: Tumor_10068


title: OSCC_K37

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

country: Germany

institute: UK Ulm

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio software (v2011.1; methylation modul 1.9.0; Illumina, Inc.). The GA_illumina_methylation_MatrixSignalIntensities.txt contains unmethylated and methylated signal intensities.

label: Cy5 and Cy3

source_name: OSCC

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using Qiagen QIAmp Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction

tag: subject status

value: oral squamous cell carcinoma (OSCC)

tag: Sex

value: male

tag: age [years]

tag: smoking

value: yes

tag: alcohol


title: OSCC_K13

value: female


title: Mta2GFP_2i_1_3

source_name: embryonic stem cells

tag: culture conditions

tag: chip antibody

tag: genotype/variation


title: Mta3FLAG_2i_1_1


title: OSCC_K8

value: no


title: Tumor_9494

tag: 8p11-p12 amplification

tag: age

tag: pt status

tag: lymph node status


title: Mta2GFP_2i_1_Input

tag: cell type


title: OSCC_K35


title: OSCC_K39


title: Tumor_9493

tag: er status

tag: pgr status

tag: her2 status


title: Mta2GFP_2i_2_3

tag: strain


title: Case 0010

description: Hybridized to SNP6.0 Affymetrix

data_processing:
The raw data (CEL files) were processed through SNPRMA and genotype calls obtained through CRLMM (both in the crlmm Bioconductor package)
primary data description: Alleles A and B intensities; Genotype calls (1=AA; 2=AB; 3=BB); Genotype confidence (integers: the larger, the better)

source_name: DNA Paciente 0010

extract_protocol: Genomic DNA was extracted from leukocytes of peripheral blood of 103 CM patients and 103 controls using the QIAamp DNA Blood Midi Kit (Qiagen®, Canada), following manufacturer’s instructions

tag: caso

tag: idade contínua

tag: idade mediana≤ 54

tag: sexo

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: sardas

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar

tag: localizacao tumor cabeca+membros superiores_tronco+membros inferiores

tag: localizacao tumor cabeca+tronco_membros

tag: breslow ≤1,5

tag: clark

tag: estagio clínico