title: ChIP input for LK2_DNp63


title: ChIP input for LK2_GFP

status: Public on Sep 17 2019

type: SRA

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

country: USA

institute: Icahn School of Medicine at Mount Sinai

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 with -k 1 option
Peaks were identified by MACS
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: BED

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Cells were maintained in RPMI-1640 with 10% fetal bovine serum and 1% penicillin–streptomycin.

extract_protocol:
For H3K27ac, Sox2 and p63 ChIP, cells were cross-linked with 1% formaldehyde and lysed. Chromatin in the lysates was sonicated and histone-DNA complexes were isolated with antibodies. For Brn2 ChIP, cells were cross-linked with disuccinimidyl glutarate and formaldehyde. Nuclei were extracted, digested with micrococcal nuclease and sonicated. Then, histone-DNA complexes were isolated with ant-Brn2 antibody.
Up to 10 ng of DNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq 500 with paired-end 75bp reads.

tag: cell line

tag: cell type

value: lung squamous cell carcinoma (LUSC) cell lines

tag: chip antibody


title: Buccal swab, 101130760033_R06C02

type: genomic

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450k Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio software V2011.1 with GenomeStudio Methylation Analysis Module Version 1.9.1000 (background-subtraction, color-correction)

label: Cy5 and Cy3

source_name: buccal swab genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using the Gentra Puregene Buccal Cell Kit (Qiagen #158845) and DNA was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research).

value: buccal epithelial cells

tag: age

tag: gender

value: F


title: Brn2 MNase ChIP for LK2

value: Brn2 (Cell Signaling, #12137)


title: H3K27ac ChIP for LK2_DNp63

value: acetyl-histone H3K27  (Abcam, ab4729)


title: H3K27ac ChIP for LK2_GFP


title: Sox2 ChIP for LK2_DNp63


title: Sox2 ChIP for LK2_GFP


title: Buccal swab, 101103430141_R04C02


title: Sox2 ChIP for HCC2814


title: Buccal swab, 101103430145_R05C01


title: Buccal swab, 101103430145_R01C01

value: M


title: Buccal swab, 101103430145_R04C02


title: Buccal swab, 101103430141_R06C02


title: Sox2 ChIP for KNS62


title: Buccal swab, 101130760026_R04C01


title: Buccal swab, 101103430141_R03C02


title: Buccal swab, 101103430145_R06C02


title: Buccal swab, 101103430145_R02C01


title: Buccal swab, 101070190152_R04C02


title: Sox2 ChIP for HCC95


title: Buccal swab, 101070190152_R02C02


title: p63 ChIP for LK2_DNp63

value: p63 (Santa Cruz, sc-8431)


title: Buccal swab, 101103430141_R02C01


title: Buccal swab, 101103430141_R03C01


title: Buccal swab, 101130760026_R06C01


title: Buccal swab, 101103430145_R03C01


title: Buccal swab, 101070190058_R02C02


title: Buccal swab, 101130760026_R05C02


title: Buccal swab, 101070190058_R06C01


title: ChIP input for HCC2279


title: ChIP input for NCI-H2887


title: Buccal swab, 101070190152_R03C01


title: Sox2 ChIP for NCI-H520


title: Sox2 ChIP for LK2


title: Buccal swab, 101070190152_R04C01


title: Buccal swab, 101103430141_R05C01


title: Buccal swab, 101070190058_R05C01


title: ChIP input for EBC-1

description: ts_hw_ebc1_ab4729_input_0414_13c_S14_ALL


title: Buccal swab, 101130760026_R02C02


title: Buccal swab, 101070190058_R02C01


title: ChIP input for Calu-1

description: ts_hw_calu1_ab4729_input_0414_13c_S13_ALL


title: ChIP input for SQ-1


title: ChIP input for NCI-H520_replicate1

description: ts_hw_h520_ab4729_input_0505_12c_S22_ALL


title: Buccal swab, 101070190057_R04C02


title: ChIP input for LK2_replicate1


title: ChIP input for LC-1/SQSF


title: Buccal swab, 101070190057_R06C02


title: Buccal swab, 101070190058_R01C01


title: ChIP input for HCC2814


title: LHCNrtta25

city: Minneapolis

last: Kyba

state: MN

address: 2231 6th St SE

institute: University of Minnesota

library_source: transcriptomic

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence (Trimmomatics v0.33), then mapped to mm10 whole genome using HISAT 2 v2.0.2.
Read assignments were performed by SUBREAD featureCounts v1.4.6.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include SUBREAD assigned raw reads for each sample.

molecule: total RNA

source_name: Immortalized myoblasts

growth_protocol: Cell culture. Immortalized human myoblast LHCN-M2 cell lines and FSHD clonal cell lines were cultured in proliferation media (F10 (HyClone) supplemented with 20% FBS (PeakSerum, Ps-FB3, lot 293Q16), 2-mercaptoethanol 1X (GIBCO), 10-9 M dexamethasone (Sigma), 10 ng/mL bFGF (Peprotech), Glutamax (GIBCO) and Penicillin/Streptomycin (P/S, GIBCO) at 37°C in a 5% CO2 atmosphere.  293T, A204-iDUX4, RH30-iDUX4 and RD-iDUX4 were cultured in DMEM/F12 supplemented with 10% FBS and P/S. iC2C12-DUX4 and iC2C12-mDUX cells were cultured in DMEM (HyClone) and 20% FBS.

extract_protocol:
RNA was extracted using an RNA extraction kit (Zymo) and cDNA was made using 0.75 μg total RNA with oligo-dT primer and Verso cDNA Synthesis Kit (Thermo Scientific) following manufacturer’s instructions.
RNAseq libraries were prepared using 500 ng total RNA and KAPA mRNA Hyper Prep kit following manufacturer’s instructions. 50 base paired end sequencing was performed on an Illumina Novaseq instrument at the University of Minnesota Genomics Center.

treatment_protocol: Myogenic differentiation was initiated on confluent cell cultures with differentiating media (DMEM/F12 (Corning Cellgro), supplemented with 1X ITS (GIBCO), 1X NSAA (GIBCO), Glutamax and P/S.

tag: inducible gene

tag: treatment

value: doxycycline


title: LHCNrtta26


title: ChIP input for KNS62


title: ChIP input for HARA

value: HARA


title: LHCNDUX4doxp300w5

value: doxycycline + iP300w


title: Buccal swab, 101070190057_R06C01


title: H3K27ac ChIP for HCC2279


title: LHCNDUX4doxp300w4


title: Buccal swab, 101070190057_R01C02


title: Buccal swab, 101070190057_R03C01


title: Buccal swab, 101070190056_R04C02


title: Buccal swab, 101130760026_R02C01


title: LHCNDUX4dox3


title: Buccal swab, 101070190057_R04C01


title: H3K27ac ChIP for EBC-1


title: Buccal swab, 101070190056_R03C02


title: Buccal swab, 101070190056_R02C02


title: LHCNDUX4dox2


title: Buccal swab, 101070190056_R06C01


title: Buccal swab, 101070190056_R05C02


title: Buccal swab, 101070190057_R03C02


title: H3K27ac ChIP for NCI-H2887


title: H3K27ac ChIP for Calu-1


title: LHCNDUX4doxp300w6


title: Buccal swab, 101070190056_R04C01


title: Buccal swab, 101070190056_R03C01


title: ChIP input for HCC2450


title: LHCNDUX4dox1


title: Buccal swab, 101070190056_R01C02


title: Buccal swab, 101070190055_R05C02


title: H3K27ac ChIP for SQ-1


title: Buccal swab, 101070190003_R05C02


title: H3K27ac ChIP for HCC2450


title: Buccal swab, 101070190055_R03C02


title: Day 14 knockdown sample from cell line CD09 [D14_09_T3_1]

city: Philadelphia

first: Kai

last: Wang

state: Pennsylvania

address: 3501 Civic Center Boulevard, 5th Floor CTRB

institute: The Children's Hospital of Philadelphia Research Institute

description:
D14_9_T3
D14_09_T3_1
processed data file: Data2.txt

data_processing:
STAR was used for mapping and counting the reads.
EdgeR is used for differential expression analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: Data1.txt, Data1.txt: Tab-delimited text files include abundance measurements.

growth_protocol: The hiPSC line used for deriving neurons was generated by Sendai virus method at Rutgers University Cell and DNA Repository (RUCDR)-NIMH Stem Cell Center from cryopreserved lymphocytes (CPLs) of a 29-year-old male SCZ patient (cell ID: 07C65853) from the MGS collection. The NorthShore University HealthSystem Institutional Review Board (IRB) approved the study. hiPSCs were cultured using the feeder-free method in Geltrex (Thermofisher)-coated plates in mTeSR1 medium (StemCell). The media were changed daily, and cells were passaged as clumps every 5 days using ReLeSR (StemCell) in the presence of 5 μm ROCK inhibitor (R&D Systems). hiPSCs were characterized by positive IF staining of pluripotent stem cell markers OCT4, TRA-1-60, NANOG, and SSEA4.

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

tag: genotype/variation

value: TCF4 knockdown

value: IPSC-derived glutamatergic neurons

tag: time

value: Day 14


title: Day 14 knockdown sample from cell line CD09 [D14_09_T2_1]

description:
D14_9_T2
D14_09_T2_1
processed data file: Data2.txt


title: Buccal swab, 101070190055_R06C01


title: Buccal swab, 101070190056_R01C01


title: H3K27ac ChIP for NCI-H520_replicate2


title: Day 14 knockdown sample from cell line CD09 [D14_09_T1_1]

description:
D14_9_T1
D14_09_T1_1
processed data file: Data2.txt


title: Buccal swab, 101070190003_R05C01


title: Day 14 control sample from cell line CD09 [D14_09_C3_1]

description:
D14_9_C3
D14_09_C3_1
processed data file: Data2.txt

value: Control


title: Day 14 control sample from cell line CD09 [D14_09_C2_1]

description:
D14_9_C2
D14_09_C2_1
processed data file: Data2.txt


title: gDNA_rep105_ovarian_carcinosarcoma

city: Koto-ku

first: Osamu

last: Gotoh

state: Tokyo

address: Ariake 3-8-31

country: Japan

institute: Japanese Foundation For Cancer Research

description:
sample name:
OV488T1

hyb_protocol: Standard Illumina Protocol

scan_protocol: Arrays were imaged using iScan System using standard Illumina scanner setting.

data_processing:
The minfi package in R/Bioconductor
Normalized data matrix  (GA_illumina_methylation_CS_v1_processed.txt) includes Normalized Average Beta (background subtraction and control normalization).

source_name: ovarian carcinosarcoma

extract_protocol: Genomic DNA was extracted using the QIAamp DNA Micro Kit (Qiagen), according to the manufacturer’s instructions.

tag: patient diagnosis

value: ovarian carcinosarcoma

value: Female

tag: anatomical site

value: Ovary


title: gDNA_rep106_ovarian_carcinosarcoma

description:
sample name:
OV507T1


title: gDNA_rep101_ovarian_carcinosarcoma

description:
sample name:
OV328T1


title: H3K27ac ChIP for NCI-H520_replicate1

value: lung squamous cell carcinoma (LUSC) cell lines


title: gDNA_rep102_ovarian_carcinosarcoma

description:
sample name:
OV333T1


title: Buccal swab, 101070190055_R04C01

value: buccal epithelial cells


title: gDNA_rep107_ovarian_carcinosarcoma

description:
sample name:
OV594T1


title: Buccal swab, 101070190055_R02C01

value: F


title: H3K27ac ChIP for LK2_replicate2


title: H3K27ac ChIP for LK2_replicate1


title: LHCNrtta24


title: gDNA_rep100_ovarian_carcinosarcoma

description:
sample name:
OV267T1


title: gDNA_rep99_ovarian_carcinosarcoma

description:
sample name:
OV241T1


title: gDNA_rep97_ovarian_carcinosarcoma

description:
sample name:
OV216T1


title: Day 14 control sample from cell line CD09 [D14_09_C1_1]

description:
D14_9_C1
D14_09_C1_1
processed data file: Data2.txt


title: Buccal swab, 101070190003_R06C01


title: gDNA_rep95_uterin_carcinosarcoma

description:
sample name:
GY129T1

source_name: uterin carcinosarcoma

value: uterine carcinosarcoma

value: Uterus


title: Buccal swab, 101070190003_R01C02


title: Day 14 knockdown sample from cell line CD07 [D14_07_T3_1]

description:
D14_7_T3
D14_07_T3_1
processed data file: Data2.txt


title: gDNA_rep94_uterin_carcinosarcoma

description:
sample name:
GY127T1


title: gDNA_rep92_uterin_carcinosarcoma

description:
sample name:
GY125T1


title: H3K27ac ChIP for HCC2814

value: acetyl-histone H3K27  (Abcam, ab4729)


title: Buccal swab, 100994770128_R01C02


title: Buccal swab, 100994770128_R06C01

value: M


title: gDNA_rep96_ovarian_carcinosarcoma

description:
sample name:
OV075T1


title: Day 14 knockdown sample from cell line CD07 [D14_07_T2_1]

description:
D14_7_T2
D14_07_T2_1
processed data file: Data2.txt


title: H3K27ac ChIP for KNS62


title: H3K27ac ChIP for LC-1/SQSF


title: Buccal swab, 101070190055_R04C02


title: gDNA_rep91_uterin_carcinosarcoma

description:
sample name:
GY122T1


title: Day 14 knockdown sample from cell line CD07 [D14_07_T1_1]

description:
D14_7_T1
D14_07_T1_1
processed data file: Data2.txt


title: Buccal swab, 101070190003_R04C01


title: gDNA_rep90_uterin_carcinosarcoma

description:
sample name:
GY118T1


title: gDNA_rep108_ovarian_carcinosarcoma

description:
sample name:
OV667T1


title: gDNA_rep89_uterin_carcinosarcoma

description:
sample name:
GY117T1


title: gDNA_rep88_uterin_carcinosarcoma

description:
sample name:
GY105T1


title: Day 14 control sample from cell line CD07 [D14_07_C3_1]

description:
D14_7_C3
D14_07_C3_1
processed data file: Data2.txt


title: H3K27ac ChIP for HARA


title: H3K27ac ChIP for HCC95


title: gDNA_rep86_uterin_carcinosarcoma

description:
sample name:
GY099T1


title: Day 14 control sample from cell line CD07 [D14_07_C2_1]

description:
D14_7_C2
D14_07_C2_1
processed data file: Data2.txt


title: gDNA_rep84_uterin_carcinosarcoma

description:
sample name:
GY094T1


title: Buccal swab, 100994770128_R03C01


title: Day 3 knockdown sample from a schizophrenia individual [ITF2_day_3_3_1]

description:
D3_K3
ITF2_day_3_3_1
processed data file: Data1.txt

tag: disease state

value: Schizophrenia

value: IPSC-derived neural progenitor cells

value: Day 3


title: Buccal swab, 101070190055_R03C01


title: gDNA_rep83_uterin_carcinosarcoma

description:
sample name:
GY092T1


title: gDNA_rep81_uterin_carcinosarcoma

description:
sample name:
GY090T1


title: Day 3 knockdown sample from a schizophrenia individual [ITF2_day_3_1_1]

description:
D3_K1
ITF2_day_3_1_1
processed data file: Data1.txt

value: TCF4 knockdown


title: gDNA_rep82_uterin_carcinosarcoma

description:
sample name:
GY091T1


title: gDNA_rep78_uterin_carcinosarcoma

description:
sample name:
GY087T1


title: Day 3 knockdown sample from a schizophrenia individual [ITF2_day_3_2_1]

description:
D3_K2
ITF2_day_3_2_1
processed data file: Data1.txt


title: gDNA_rep79_uterin_carcinosarcoma

description:
sample name:
GY088T1


title: gDNA_rep80_uterin_carcinosarcoma

description:
sample name:
GY089T1


title: gDNA_rep85_uterin_carcinosarcoma

description:
sample name:
GY097T1


title: gDNA_rep77_uterin_carcinosarcoma

description:
sample name:
GY084T1


title: gDNA_rep76_uterin_carcinosarcoma

description:
sample name:
GY083T1


title: Day 14 knockdown sample from a schizophrenia individual [ITF2_day_14_3_1]

description:
D14_K3
ITF2_day_14_3_1
processed data file: Data1.txt

value: IPSC-derived glutamatergic neurons


title: CFPAC1.JunBKO.ATAC

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

data_processing:
Reads were pre-processing (filtering, quality trimming and adapter clipping) using Trimmomatic (version 0.38) (PMID:24695404),  then single-end with min 36-bp reads length were aligned to human genome build GRCh38/hg38 using Bowtie2 v2.2.6 (PMID: 22388286) with “–very-sensitive” preset of parameters. Reads that did not align to nuclear genome or aligned to mitocondrial genome were removed. PCR duplicates were removed using samtools. Then read positions were corrected for transposon insertion offset as described in (PMID:24097267).
Peak calling was performed using MACS2 with the “--nomodel”, “--extsize 146”,  “--qvalue 0.05”, "--nolambda" and "--keep-dup all" flags and arguments
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: *.narrowPeak, list of the peaks called by MACS2

growth_protocol: IMDM supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep

extract_protocol: 50000 cells were pelleted by centrifugation and re-suspended in 50 µl of cold lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP40, 0.1% Tween-20 and 0.01% Digitonin). After incubation on ice for three minutes, lysis was washed out by adding 1 mL of lysis buffer without NP40 and digitonin. Nuclei were pelleted by centrifugation for 10 min at 500g, 4 ºC.  The supernatant was discarded and nuclei were re-suspended in 50 µl of reaction buffer containing 1 µl of Tn5 transposase (made in house),  10 ul of 5x transposase buffer (50mM Tris-HCl, pH 8.4 and 25mM MgCl2), 16.5 µl PBS, 0.5 µl of 1% digitonin, 0.5 µl of 10% Tween-20. The reaction was incubated at 37ºC for 30 minutes with 600 RPM mixing. Then 5 µl of clean up buffer (900mM NaCl, 300mM EDTA), 2ul of 5% SDS and 2 µl of Proteinase K (20 µg/µl) (New England Biolabs) were added and incubated for 30 min at 40 ºC. Tagmented DNA was isolated using SPRI beads (2x) and amplified by PCR. Fragments smaller than 600 bp were isolated using SPRI cleanup and libraries where sequenced on an Illumina NextSeq500 platform.

tag: cell line background

value: Pancreatic Ductal Adenocarcinoma (PDAC) cell line

value: Cells electroporated with ribonucleoprotein complexes containing Cas9 protein and crRNA:trCRA targeting JunB


title: CFPAC1.JunKO.ATAC

value: Cells electroporated with ribonucleoprotein complexes containing Cas9 protein and crRNA:trCRA targeting Jun


title: CFPAC1.FOXA1KO.ChIP.FOXA2.Rep2

description: Chromatin IP against FOXA2

data_processing:
Reads were pre-processing (filtering, quality trimming and adapter clipping) using Trimmomatic (version 0.38),  then single-end 50-bp reads were aligned to human genome build GRCh38/hg38 using Bowtie2 v2.2.6 with “–very-sensitive” preset of parameters. Reads that did not align to nuclear genome or aligned to mitocondrial genome were removed. PCR duplicates were removed using samtools.
Peak calling was performed using MACS2 (version 2.1.0.20150731) with the “--nomodel”, “--extsize 200” and “--pvalue 0.001” flags and arguments. Each IP was compared to input DNA.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: *.narrowPeak, list of the peaks called by MACS2

extract_protocol: ChIP lysates were generated from 50x10^6 cells. Cells were fixed in 1% formaldehyde for 10min. Lysate was immunoprecipitated with 10ug of antibody. Antibodies were pre-bound overnight to 100ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by AMPure XP SPRI (Beckman Coulter) and quantified using Quantifluor (Promega). ChIP DNA was prepared for HiSeq2000 or NextSeq500 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, PCR with index primers and purification. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction. Library preparation is carried out on SPRIworks Fragment Library System.

value: CFPAC1 genome-edited clonal cell line

value: Anti-FOXA2 (Antibody sc-6554 Lot. A1014)

value: Isolation of clonal cell line by dilution of CFPAC1 cells infected with lentiCRIPSv2 plasmid (Addgene #52961) carring the expression of wt Cas9 and a guide RNA targeting FOXA1 gene


title: gDNA_rep75_uterin_carcinosarcoma

description:
sample name:
GY081T1

value: Female


title: gDNA_rep74_uterin_carcinosarcoma

description:
sample name:
GY080T1


title: Day 14 knockdown sample from a schizophrenia individual [ITF2_day_14_1_1]

description:
D14_K1
ITF2_day_14_1_1
processed data file: Data1.txt

value: Day 14


title: CFPAC1.FOXA1KO.ChIP.FOXA2.Rep1

description: Chromatin IP against FOXA2


title: Buccal swab, 100994770128_R05C02

value: buccal epithelial cells


title: gDNA_rep72_uterin_carcinosarcoma

description:
sample name:
GY078T1

value: uterine carcinosarcoma

value: Uterus


title: Day 3 control sample from a schizophrenia individual [ctrl_day_3_3_1]

description:
D3_Ctrl3
ctrl_day_3_3_1
processed data file: Data1.txt

value: Control


title: gDNA_rep71_uterin_carcinosarcoma

description:
sample name:
GY077T1


title: Buccal swab, 101070190003_R02C01

value: M


title: CFPAC1.FOXA2KO.ChIP.FOXA2.Rep2

description: Chromatin IP against FOXA2

value: Isolation of clonal cell line by dilution of CFPAC1 cells electroporated with plasmid pX330A_D10A-1x4 containing Cas9 nickase (Multiplex CRISPR/Cas9 Assembly System Kit; Addgene # 1000000055) and guides targeting FOXA2 gene.


title: gDNA_rep70_uterin_carcinosarcoma

description:
sample name:
GY076T1


title: Day 3 control sample from a schizophrenia individual [ctrl_day_3_2_COM_1]

description:
D3_Ctrl2
ctrl_day_3_2_COM_1
processed data file: Data1.txt

value: Schizophrenia

value: IPSC-derived neural progenitor cells

value: Day 3


title: gDNA_rep68_uterin_carcinosarcoma

description:
sample name:
GY074T1


title: gDNA_rep67_uterin_carcinosarcoma

description:
sample name:
GY073T1


title: Day 14 knockdown sample from a schizophrenia individual [ITF2_day_14_2_1]

description:
D14_K2
ITF2_day_14_2_1
processed data file: Data1.txt

value: TCF4 knockdown

value: IPSC-derived glutamatergic neurons


title: gDNA_rep66_uterin_carcinosarcoma

description:
sample name:
GY072T1


title: CFPAC1.FOXA2WT.ChIP.FOXA2.Rep1

description: Chromatin IP against FOXA2

value: CFPAC1 clonal cell line

value: Pancreatic Ductal Adenocarcinoma (PDAC) cell line

value: Isolation of clonal cell line by dilution of CFPAC1 cells infected with lentiCRIPSv2 plasmid (Addgene #52961)


title: CFPAC1.FOXA2KO.ChIP.FOXA2.Rep1

description: Chromatin IP against FOXA2

value: CFPAC1 genome-edited clonal cell line

value: Anti-FOXA2 (Antibody sc-6554 Lot. A1014)


title: Day 14 control sample from a schizophrenia individual [ctrl_day_14_3_1]

description:
D14_Ctrl3
ctrl_day_14_3_1
processed data file: Data1.txt

value: Day 14


title: Buccal swab, 100994770128_R05C01

value: buccal epithelial cells


title: CFPAC1.FOXA2KO.ChIP.FOXA1

description: Chromatin IP against FOXA1


title: gDNA_rep64_uterin_carcinosarcoma

description:
sample name:
GY069T1

value: uterine carcinosarcoma

value: Female


title: gDNA_rep73_uterin_carcinosarcoma

description:
sample name:
GY079T1

value: Uterus


title: CFPAC1.WT.Rep3.ATAC

value: Cells electroporated with Cas9 protein


title: gDNA_rep61_uterin_carcinosarcoma

description:
sample name:
GY063T1


title: Day 14 control sample from a schizophrenia individual [ctrl_day_14_1_1]

description:
D14_Ctrl1
ctrl_day_14_1_1
processed data file: Data1.txt

value: Control


title: Day 14 control sample from a schizophrenia individual [ctrl_day_14_2_1]

description:
D14_Ctrl2
ctrl_day_14_2_1
processed data file: Data1.txt

value: Schizophrenia


title: CFPAC1.FOXA1KO.ChIP.FOXA1

description: Chromatin IP against FOXA1

value: Isolation of clonal cell line by dilution of CFPAC1 cells infected with lentiCRIPSv2 plasmid (Addgene #52961) carring the expression of wt Cas9 and a guide RNA targeting FOXA1 gene


title: gDNA_rep60_uterin_carcinosarcoma

description:
sample name:
GY057T1


title: CFPAC1.FOXA1WT.ChIP.FOXA1

description: Chromatin IP against FOXA1


title: PANC1.ovHNF1B.ChIP.HNF1B

data_processing:
Reads were pre-processing (filtering, quality trimming and adapter clipping) using Trimmomatic (version 0.38),  then single-end 50-bp reads were aligned to human genome build GRCh38/hg38 using Bowtie2 v2.2.6 with “–very-sensitive” preset of parameters. Reads that did not align to nuclear genome or aligned to mitocondrial genome were removed. PCR duplicates were removed using samtools.
Peak calling was performed using MACS2 (version 2.1.0.20150731) with the “--nomodel”, “--extsize 200” and “--qvalue 0.05” flags and arguments. Each IP was compared to input DNA.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: *.narrowPeak, list of the peaks called by MACS2

source_name: Chromatin IP against HNF1B

growth_protocol: DMEM supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep

treatment_protocol: PANC1 cells infected with pScalps_Puro vector (Addgene #99636) carring HNF1B expression

value: HNF1B overexpressing CFPAC1 cell line

value: Anti-HNF1B (HPA2083)


title: Day 3 control sample from a schizophrenia individual [ctrl_day_3_1_1]

description:
D3_Ctrl1
ctrl_day_3_1_1
processed data file: Data1.txt

value: IPSC-derived neural progenitor cells

value: Day 3


title: gDNA_rep59_uterin_carcinosarcoma

description:
sample name:
GY030T1


title: gDNA_rep57_uterin_carcinosarcoma

description:
sample name:
GY027T1


title: PANC1.ovHNF1B.ChIP.FOXA2

source_name: Chromatin IP against FOXA2

value: Pancreatic Ductal Adenocarcinoma (PDAC) cell line

value: HNF1B overexpressing PANC1 cell line

value: Anti-FOXA2 (Antibody sc-6554 Lot. A0715)


title: gDNA_rep58_uterin_carcinosarcoma

description:
sample name:
GY029T1


title: gDNA_rep56_uterin_carcinosarcoma

description:
sample name:
GY022T1


title: gDNA_rep63_uterin_carcinosarcoma

description:
sample name:
GY067T1


title: PANC1.Empty.ChIP.FOXA2

treatment_protocol: PANC1 cells infected with pScalps_Puro vector (Addgene #99636)

value: Empty vector overexpressing PANC1 cell line


title: Intermediate Repeat 3: 18.3_inter

first: Edward

last: Lee

state: PA

address: 613A Stellar Chance Laboratories; 422 Curie Blvd

institute: University of Pennsylvania

data_processing:
Adapter sequences were removed and reads were trimmed using Cutadapt v1.11
Reads were aligned to the human genome (hg38) using STAR v2.6.1
Reads per gene were counted using STAR v2.6.1 (--quantMode GeneCounts) with gencode v29 annotation
DeSeq2 v1.22 was used to call differentially expressed genes between short and intermediate repeat samples
Genome_build: GRCh38
Supplementary_files_format_and_content: ReadsPerGene.out.tab files are tab delimited files containing raw read counts for each transcript generated using STAR quantMode function
Supplementary_files_format_and_content: Degenes_All_table_combinedLanes.csv is a comma separated file with the output from DeSeq2 analysis containing all differentially expressed genes (including non-significant genes) between short and intermediate repeat cell lines. Negative log fold change values indicate decreased expression in intermediate lines compared to short repeat lines

source_name: iPSC derived Neural Progenitor Cell

growth_protocol: iPSCs were maintained in mTeSR1 (STEMCELL Technologies); NPCs were generated using protocol in Shi et al 2012 (Nature Protocols).

extract_protocol:
RNA was extraced with Rneasy kit (Qiagen) with on-column DNAse digestion
Illumina TruSeq Stranded mRNA kit was used with Ribo-zero rRNA removal kit

treatment_protocol: iPSCs were edited with CRISPR/Cas9 according to Ran et al 2013 (Nature Protocols)

tag: tissue

value: iPSC derived Neural Progenitor Cell

tag: c9orf72 repeat size

tag: day post neural induction

value: Day 12


title: gDNA_rep53_uterin_carcinosarcoma

description:
sample name:
EN683T1

value: uterine carcinosarcoma


title: gDNA_rep62_uterin_carcinosarcoma

description:
sample name:
GY066T1

value: Female


title: Intermediate Repeat 2: 20.5_inter


title: gDNA_rep55_uterin_carcinosarcoma

description:
sample name:
GY007T1

value: Uterus


title: gDNA_rep51_uterin_carcinosarcoma

description:
sample name:
EN650T1


title: gDNA_rep52_uterin_carcinosarcoma

description:
sample name:
EN676T1


title: Intermediate Repeat 1: 17.8_inter


title: gDNA_rep50_uterin_carcinosarcoma

description:
sample name:
EN626T1


title: gDNA_rep49_uterin_carcinosarcoma

description:
sample name:
EN623T1


title: gDNA_rep48_uterin_carcinosarcoma

description:
sample name:
EN618T1


title: PC3 cells treated with DMSO

type: RNA

city: Tianjin

first: Xingkang

last: Jiang

address: Hexi

department: Urology

country: China

institute: Tianjin Institute of Urology

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by lowess normalization.

source_name: Prostate cancer cells

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: Human PCa cell lines PC3 were cultured in RPMI-1640 medium (Gibco) with 10% fetal bovine serum (Hyclone) and 100U/ml penicillin-streptomycin (Hyclone). These cell lines were maintained at 37℃ and 5% CO2 in a humidified incubator.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: APS was purchased from Sigma-Aldrich.PC3 cells were treated with APS at 10mg/mL and negative control for 48h.

tag: Sex

value: Male

value: Prostate cancer cells

value: control


title: CFPAC1.Empty.ChIP.FOXA2

treatment_protocol: CFPAC1 cells infected with pScalps_Puro vector (Addgene #99636)

value: Empty vector overexpressing CFPAC1 cell line


title: CFPAC1.ovHOXB8.ChIP.FOXA2

treatment_protocol: CFPAC1 cells infected with pScalps_Puro vector (Addgene #99636) carring Flag-HOXB8 expression

value: HOXB8 overexpressing CFPAC1 cell line


title: gDNA_rep46_uterin_carcinosarcoma

description:
sample name:
EN599T1


title: Short Repeat 2: 14.3_short


title: PC3 cells treated with APS

tag: cell line

value: APS


title: Short Repeat 1: PBWT_short


title: gDNA_rep44_uterin_carcinosarcoma

description:
sample name:
EN566T1


title: gDNA_rep45_uterin_carcinosarcoma

description:
sample name:
EN571T1


title: CFPAC1.ovHOXB8.ChIP.HOXB8

source_name: Chromatin IP against Flag-HOXB8

tag: cell type

value: Anti-Flag (Sigma M2 F3165 lot. SLBN8915V)


title: CFPAC1.HNF1BKO.ATAC.Rep1

treatment_protocol: Isolation of clonal cell line by dilution of CFPAC1 cells infected with lentiCRIPSv2 plasmid (Addgene #52961) carring the expression of wt Cas9 and a guide RNA targeting HNF1B gene

value: CFPAC1 genome-edited clonal cell line


title: CFPAC1.HNF1BWT.ATAC.Rep2

treatment_protocol: Isolation of clonal cell line by dilution of CFPAC1 cells infected with lentiCRIPSv2 plasmid (Addgene #52961)

value: Pancreatic Ductal Adenocarcinoma (PDAC) cell line

value: CFPAC1 clonal cell line


title: gDNA_rep40_uterin_carcinosarcoma

description:
sample name:
EN505T1


title: gDNA_rep41_uterin_carcinosarcoma

description:
sample name:
EN525T1


title: Short Repeat 3: 18.5_short


title: CFPAC1.HNF1BKO.ATAC.Rep2


title: CFPAC1.HNF1BWT.ATAC.Rep1


title: WZG-N1_RNA&lncRNA&circRNA-Seq

city: Shenyang

first: Zhun

last: Luo

state: Liaoning

address: 155 Nanjing North Street

department: Infectious Diseases

institute: the First Affiliated Hospital, China Medical University

description:
Expression_circularRNA.xlsx
All_Differentially_Expressed_circularRNA.xlsx
Differentially_Expressed_circularRNA.xlsx
Expression_Gene.xlsx
All_Differentially_Expressed_Genes.xlsx
Differentially_Expressed_Genes.xlsx

data_processing:
Basecalls performed using solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8)
We used the StringTie software (v1.2.3) to estimate the abundance of the gene level and transcript level, referring to the official database information, then to calculate FPKM the gene or transcript level separately and to find the difference using Ballgown software.
Sequenced reads was filtered through Solexa CHASTITY, and to match to the corresponding reference genome HG19, by Hisat2 software（v2.0.4）
Genome_build: HG19
Supplementary_files_format_and_content: xlsx files include CPM or FPKM values for each sample.

source_name: adjacent tissue of hepatocellular carcinoma

growth_protocol: HCC and their adjacent paired tissues were obtained from 3 patients who were diagnosed with HCC during hepatic resection in the First Affiliated Hospital of China Medical University

extract_protocol:
The whole RNA of HCC and their adjacent paired tissues was harvested using Trizol reagent.Total RNA of the sample was subjected to test the RNA integrity using agarose gel electrophoresis, then quantified and examined by NanoDrop ND-1000 1-2 ug of total RNA was selected for each sample for sequencing library construction.
The total RNA was processed by NEBNext® Poly(A) mRNA Magnetic Isolation Module (or rRNA removal by RiboZero Magnetic Gold Kit) to enrich mRNA, and the product RNA was used for construction Library, via KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Sequencing libraries, denatured by 0.1 M NaOH to generate single-stranded DNA, as amplified in situ Illumina cBot (TruSeq SR Cluster Kit v3-cBot-HS (# GD-401-3001, Illumina)). The ends of the generated fragments was used to run 150 Cycles by the Illumina HiSeq 4000 Sequencer.
RNA libraries were prepared for sequencing using standard Illumina Hiseq protocols.

value: liver

tag: tnm stage

value: I


title: WZG-C1_RNA&lncRNA&circRNA-Seq

source_name: hepatocellular carcinoma tissue

value: hepatocellular carcinoma tissue

tag: age


title: gDNA_rep42_uterin_carcinosarcoma

description:
sample name:
EN556T1

tag: gender


title: gDNA_rep43_uterin_carcinosarcoma

description:
sample name:
EN558T1


title: gDNA_rep38_uterin_carcinosarcoma

description:
sample name:
EN486T1


title: HXR-N1_RNA&lncRNA&circRNA-Seq

value: adjacent tissue of hepatocellular carcinoma

value: IVA


title: gDNA_rep47_uterin_carcinosarcoma

description:
sample name:
EN617T1

value: uterine carcinosarcoma

value: Female


title: CFPAC1.FOXA1-KDFOXA2-KD.Rep3

description:
processed data file:
CFPAC1.FOXAKD.genes.counts.txt
CFPAC1.FOXA1FOXA2KD.genes.edgeR_results.txt

data_processing:
Reads were pre-processing (filtering, quality trimming and adapter clipping) using Trimmomatic (version 0.38), then single-end reads with a minimum of 36 bp were aligned to human genome build GRCh38/hg38 using TopHat2 (version 2.1.0) with the option “--b2-very-sensitive”. Only uniquely mapped reads were retained.
Gene expression counts were estimated using featureCounts (Rsubread version 1.6.1), summarized across all exons as annotated in the GENCODE v28, with option “largestOverlap”.
Differentially expressed genes in biological triplicates of wild-type vs. FOXA1/2-KD in CFPAC1 cell lines or wild-type vs. FOXA2-KO in PANC1 cell lines were identified using EdgeR R-package v3.2.2.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: *.gene.counts.txt files contain raw read counts for each samples. *.edgeR_results.txt files contain differentially expressed genes for each comparison.

source_name: CFPAC1 silenced

extract_protocol: 10^6 cells are lysed and processed according to SMART-Seq2 protocol. Briefly, 10 ng of poly-A containing mRNA molecules are copied into first strand cDNA by reverse transcription and template-switching using oligo(dt) primers and LNA-containing template-switching oligo (TSO). cDNA is pre-amplified using limited number of cycles, purified and tagmented with Tn5 transposase. cDNA fragments generated after tagmentation are gap-repaired, enriched by PCR and purified to create the final cDNA library for HiSeq 2000 Illumina sequencing.

treatment_protocol: CFPAC1 cells transfected with FOXA1 siRNA (SANTA CRUZ, sc-37030) and FOXA2 siRNA (SANTA CRUZ, sc-35569)

tag: transfected with


title: gDNA_rep36_uterin_carcinosarcoma

description:
sample name:
EN472T1

value: Uterus


title: HXR-C1_RNA&lncRNA&circRNA-Seq


title: gDNA_rep35_uterin_carcinosarcoma

description:
sample name:
EN445T1


title: CFPAC1.FOXA1-KDFOXA2-KD.Rep2

value: FOXA1 siRNA (SANTA CRUZ, sc-37030) and FOXA2 siRNA (SANTA CRUZ, sc-35569)


title: DYT-N1_RNA&lncRNA&circRNA-Seq


title: gDNA_rep34_uterin_carcinosarcoma

description:
sample name:
EN442T1


title: CFPAC1.FOXA1-KDFOXA2-KD.Rep1


title: gDNA_rep33_uterin_carcinosarcoma

description:
sample name:
EN437T1


title: gDNA_rep31_uterin_carcinosarcoma

description:
sample name:
EN362T1


title: gDNA_rep39_uterin_carcinosarcoma

description:
sample name:
EN496T1


title: gDNA_rep29_uterin_carcinosarcoma

description:
sample name:
EN321T1


title: UNT.9576.ClontechV4

first: Gregory

middle: Robert

last: Grant

address: 3400 Civic Center Blvd.

department: Genetics

description: FINAL_master_list_of_gene_counts_MIN.V4.txt

data_processing:
RNA-Seq data were aligned to the mouse genome build mm9 by GSNAP.v2018-07-04.
Data were normalized at the gene-level, using a resampling strategy, the code is available at https://github.com/itmat/Normalization (-v0.8.5b-beta)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file from gene-level normalization contains counts from unique reads that only map to one gene.

organism: Mus musculus

source_name: Liver

growth_protocol: Twelve-week old male C57/B6J mice were acquired from Jackson Labs.

extract_protocol:
Mice were sacrificed and liver samples were dissected and snap-frozen in liquid nitrogen. RNA was extracted from the liver tissue using TRIzol and Qiagen Rneasy Kit, according to manufacturers’ protocols.
Illumina TruSeq: Total RNA from each liver sample was prepared for sequencing using the Illumina: TruSeq Stranded mRNA Sample Preparation Kit. 200 ng of RNA was used to prepare the RNA libraries. The libraries were sequenced on Illumina HiSeq 2500. Depths of 16-34 million paired-end 125 bp reads were generated for each sample. (GSE98562)    Takara Bio SMARTer: Total RNA from each liver sample was prepared for sequencing using the Takara Bio SMARTer: SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian. 1.7-2.6 ng of RNA was used to prepare the RNA libraries. The libraries were sequenced on Illumina HiSeq 4000. Depths of 30-44 million paired-end 150 bp reads were generated for each sample. The libraries were reproduced to repeat the experiment and ensure reproducibility.    Takara Bio SMART-Seq: Total RNA from each liver sample was prepared for sequencing using the Takara Bio SMART-Seq: SMART-Seq® v4 Ultra® Low Input RNA Kit. 0.8-1.3 ng of RNA was used to prepare the RNA libraries. The libraries were sequenced on Illumina HiSeq 4000. Depths of 15-30 million paired-end 150 bp reads were generated for each sample.

treatment_protocol: Four hours prior to tissue collection, mice were treated with either 20 µg/Kg of IL-1B or saline.

tag: treatment

value: saline

tag: strain

value: Twelve-week

value: male


title: DYT-C1_RNA&lncRNA&circRNA-Seq


title: CFPAC1.FOXA2-KD.Rep3

description:
processed data file:
CFPAC1.FOXAKD.genes.counts.txt
CFPAC1.FOXA2KD.genes.edgeR_results.txt

treatment_protocol: CFPAC1 cells transfected with control siRNA-A (Santa Cruz, sc-37007) and FOXA2 siRNA (SANTA CRUZ, sc-35569)


title: gDNA_rep37_uterin_carcinosarcoma

description:
sample name:
EN482T1


title: gDNA_rep28_uterin_carcinosarcoma

description:
sample name:
EN320T1


title: gDNA_rep30_uterin_carcinosarcoma

description:
sample name:
EN325T1


title: gDNA_rep25_uterin_carcinosarcoma

description:
sample name:
EN250T1


title: UNT.9574.ClontechV4


title: gDNA_rep26_uterin_carcinosarcoma

description:
sample name:
EN288T1


title: UNT.9575.ClontechV4


title: gDNA_rep23_uterin_carcinosarcoma

description:
sample name:
EN204T1


title: CFPAC1.FOXA1-KD.Rep3

description:
processed data file:
CFPAC1.FOXAKD.genes.counts.txt
CFPAC1.FOXA1KD.genes.edgeR_results.txt

treatment_protocol: CFPAC1 cells transfected with control siRNA-A (Santa Cruz, sc-37007) and FOXA1 siRNA (SANTA CRUZ, sc-37030)


title: ILB.9583.ClontechV4

value: IL-1 Beta


title: gDNA_rep22_uterin_carcinosarcoma

description:
sample name:
EN195T1


title: CFPAC1.FOXA1-KD.Rep2

value: control siRNA-A (Santa Cruz, sc-37007) and FOXA1 siRNA (SANTA CRUZ, sc-37030)


title: gDNA_rep21_uterin_carcinosarcoma

description:
sample name:
EN193T1


title: ILB.9582.ClontechV4


title: gDNA_rep20_uterin_carcinosarcoma

description:
sample name:
EN191T1


title: gDNA_rep19_uterin_carcinosarcoma

description:
sample name:
EN175T1


title: CFPAC1.FOXA2-KD.Rep2

value: control siRNA-A (Santa Cruz, sc-37007) and FOXA2 siRNA (SANTA CRUZ, sc-35569)


title: gDNA_rep18_uterin_carcinosarcoma

description:
sample name:
EN154T1


title: ILB.9579.ClontechV4


title: CFPAC1.FOXA2-KD.Rep1

value: Pancreatic Ductal Adenocarcinoma (PDAC) cell line


title: CFPAC1.WT.Rep3

description:
processed data file:
CFPAC1.FOXAKD.genes.counts.txt

source_name: CFPAC1 transfected

treatment_protocol: CFPAC1 cells transfected with control siRNA-A (Santa Cruz, sc-37007)

value: control siRNA-A (Santa Cruz, sc-37007)


title: gDNA_rep24_uterin_carcinosarcoma

description:
sample name:
EN205T1


title: UNT.9576.ClontechPico

description: FINAL_master_list_of_gene_counts_MIN.sense.Pico.R.txt


title: gDNA_rep104_ovarian_carcinosarcoma

description:
sample name:
OV381T1

value: ovarian carcinosarcoma

value: Ovary


title: gDNA_rep17_uterin_carcinosarcoma

description:
sample name:
EN152T1


title: CFPAC1.JunKO_JunBKO.ATAC

value: Cells electroporated with ribonucleoprotein complexes containing Cas9 protein and crRNA:trCRA targeting Jun and JunB


title: CFPAC1.WT.Rep2


title: gDNA_rep103_ovarian_carcinosarcoma

description:
sample name:
OV343T1


title: UNT.9575.ClontechPico


title: UNT.9574.ClontechPico


title: gDNA_rep98_ovarian_carcinosarcoma

description:
sample name:
OV227T1


title: gDNA_rep93_uterin_carcinosarcoma

description:
sample name:
GY126T1


title: PANC1.FOXA2-KO.Rep3

description:
processed data file:
PANC1.FOXA2KO.genes.counts.txt
PANC1.FOXA2KO.genes.edgeR_results.txt

source_name: PANC1 genome-edited transfected

treatment_protocol: PANC1 cells transfected with multiplex CRISPR/Cas9 assembly system kit (Addgene #1000000055) modified with the insertion of the Puromycin resistance gene and driving the expression of the Cas9-nickase and different pairs of gRNAs designed to target the DNA binding domain of FOXA2


title: CFPAC1.WT.Rep1


title: ILB.9583.ClontechPico


title: gDNA_rep16_uterin_carcinosarcoma

description:
sample name:
EN151T1


title: gDNA_rep14_uterin_carcinosarcoma

description:
sample name:
EN136T1


title: gDNA_rep87_uterin_carcinosarcoma

description:
sample name:
GY101T1


title: PANC1.FOXA2-KO.Rep2

value: multiplex CRISPR/Cas9 assembly system kit (Addgene #1000000055) modified with the insertion of the Puromycin resistance gene and driving the expression of the Cas9-nickase and different pairs of gRNAs designed to target the DNA binding domain of FOXA2


title: CFPAC1.FOXA1-KD.Rep1


title: ILB.9582.ClontechPico


title: gDNA_rep54_uterin_carcinosarcoma

description:
sample name:
EVE016T1


title: gDNA_rep11_uterin_carcinosarcoma

description:
sample name:
EN088T1


title: gDNA_rep13_uterin_carcinosarcoma

description:
sample name:
EN128T1


title: PANC1.FOXA2-KO.Rep1


title: ILB.9579.ClontechPico


title: gDNA_rep32_uterin_carcinosarcoma

description:
sample name:
EN432T1


title: gDNA_rep15_uterin_carcinosarcoma

description:
sample name:
EN145T1


title: PANC1.WT.Rep3

source_name: PANC1 transfected

treatment_protocol: PANC1 cells transfected with plasmid pX330A_D10A-1x4 containing Cas9 nickase. (Multiplex CRISPR/Cas9 Assembly System Kit; Addgene # 1000000055) modified with the insertion of the Puromycin resistance gene.


title: gDNA_rep27_uterin_carcinosarcoma

description:
sample name:
EN296T1


title: gDNA_rep10_uterin_carcinosarcoma

description:
sample name:
EN083T1


title: PANC1.WT.Rep1

value: plasmid pX330A_D10A-1x4 containing Cas9 nickase. (Multiplex CRISPR/Cas9 Assembly System Kit; Addgene # 1000000055) modified with the insertion of the Puromycin resistance gene.


title: PANC1.WT.Rep2


title: gDNA_rep12_uterin_carcinosarcoma

description:
sample name:
EN092T1

value: uterine carcinosarcoma


title: gDNA_rep9_uterin_carcinosarcoma

description:
sample name:
EN058T1

value: Female


title: CFPAC1.ChIP.FOXA2.Rep2

description: Chromatin IP against FOXA2

extract_protocol: ChIP lysates were generated from 50x10^6 cells. Cells were either fixed in 1% formaldehyde for 10min (for FOXA2, HOXB8, JUNB and FOXA3 ChiP-seq) or with a double cross-linking protocol consisting in 45 minutes of 2 mM DSG followed by 10 minutes in 1% formaldehyde for FOS ChIP-seq.  Lysate was immunoprecipitated with 10ug of antibody. Antibodies were pre-bound overnight to 100ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by QIAquick columns (Qiagen) and quantified using PicoGreen (Invitrogen). ChIP DNA was prepared for HiSeq 2000 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, PCR with index primers and purification. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction. Library preparation is carried out on SPRIworks Fragment Library System.

value: original CFPAC1 cell line

tag: antibody

value: Anti-FOXA2 (Antibody sc-6554 Lot. A0715)


title: gDNA_rep7_uterin_carcinosarcoma

description:
sample name:
EN043T1

tag: patient diagnosis

value: Uterus


title: gDNA_rep4_uterin_carcinosarcoma

description:
sample name:
EN025T1

tag: anatomical site


title: PANC1.ChIP.HOXB8

description: Chromatin IP against Flag-HOXB8

treatment_protocol: PANC1 cells infected with pScalps_Puro vector (Addgene #99636) carring Flag-HOXB8 expression

value: HOXB8 overexpressing PANC1 cell line

value: Anti-Flag (Sigma M2 F3165 lot. SLBN8915V)


title: Regenerating cardiomyocytes rep3

city: Charlestown, MA

first: Raz

last: Ben-Yair

state: MA

address: 13th st.

department: CVRC

institute: MGH

data_processing:
Reads from three replicates of uninjured (“uninjured”) and 5 days
post injury (“5 dpa”) heart samples were aligned against the GRCz10 genome assembly
of the Zebrafish, ENSEMBL 89 annotation using STAR v. 2.5.3a in paired-end mode
with parameters --runThreadN 16 --runMode alignReads --outFilterType BySJout --
outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --
outFilterMismatchNmax 999 --alignIntronMin 10 --alignIntronMax 1000000 --
alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --quantMode
TranscriptomeSAM . The resulting Aligned.toTranscriptome.out.bam files were postprocessed
using RSEM v. 1.3.0 using following flags --paired-end --calc-ci --alignments
-p 8 --forward-prob 0. Posterior mean estimates of counts, RPKM and TPM were
retrieved for each gene in each sample.
Differential expression analysis between uninjured and 5 dpa samples was performed
using DESeq2 in the R statistical environment (v. 3.3.3) on protein-coding genes
(according to ENSEMBL’s biotype assignments).
Supplementary_files_format_and_content csv files are a DEseq2 estimations of changes in read density of protein coding genes (according to ENSEMBL release 89’s biotype assignments) between experimental groups.
Supplementary_files_format_and_content: IGVtools utility 'count' was used on aligned bam files to compute the average alignment over 164 base windows across the genome and generate binary tiled data (.tdf) files (Thorvaldsdottir et al. 2013).

organism: Danio rerio

source_name: Cardiac ventricle tissue

extract_protocol: Ventricle apexes were removed and cleared of injury tissue, then dissociated using the Miltenyi neonate heart dissociation kit, pelleted and resuspended in PBS/serum. Cell suspensions were strained on a 50 micron nylon mesh and immediately FACS-sorted directly into RLT lysis buffer (RNeasy micro-prep RNA extraction kit, Qiagen). RNA integrity and concentration were checked on a Fragment Analyzer (Advanced Analytical).  cDNA samples were generated using the Ovation low input v2 kit (Nugen) according to the manufacturer’s.  The resulting cDNA samples were then end-repaired and adaptor-ligated using the SPRI-works Fragment Library System I (Beckman Coulter Genomics) and indexed during amplification. Libraries were quantified using the Fragment Analyzer (Advanced Analytical) and qPCR before being loaded for paired-end sequencing 2X40 nt using the Illumina HiSeq 2000.

value: Cardiac ventricle apex

tag: batch

value: 5 days post ventricular apex resection


title: gDNA_rep6_uterin_carcinosarcoma

description:
sample name:
EN042T1


title: PANC1.ChIP.FOXA2.Rep2

description: Chromatin IP against FOXA2

treatment_protocol: Isolation of clonal cell line by dilution of PANC1 cells transfected with plasmids pX330A_D10A-1x4 containing Cas9 nickase. (Multiplex CRISPR/Cas9 Assembly System Kit; Addgene # 1000000055).

value: PANC1 clonal cell line


title: Regenerating cardiomyocytes rep1


title: Regenerating cardiomyocytes rep2


title: gDNA_rep3_uterin_carcinosarcoma

description:
sample name:
EN019T1


title: Uninjured cardiomyocytes rep3

data_processing:
Data Processing
Reads from three replicates of uninjured (“uninjured”) and 5 days
post injury (“5 dpa”) heart samples were aligned against the GRCz10 genome assembly
of the Zebrafish, ENSEMBL 89 annotation using STAR v. 2.5.3a in paired-end mode
with parameters --runThreadN 16 --runMode alignReads --outFilterType BySJout --
outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --
outFilterMismatchNmax 999 --alignIntronMin 10 --alignIntronMax 1000000 --
alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --quantMode
TranscriptomeSAM . The resulting Aligned.toTranscriptome.out.bam files were postprocessed
using RSEM v. 1.3.0 using following flags --paired-end --calc-ci --alignments
-p 8 --forward-prob 0. Posterior mean estimates of counts, RPKM and TPM were
retrieved for each gene in each sample.
Differential expression analysis between uninjured and 5 dpa samples was performed
using DESeq2 in the R statistical environment (v. 3.3.3) on protein-coding genes
(according to ENSEMBL’s biotype assignments).
Supplementary_files_format_and_content csv files are a DEseq2 estimations of changes in read density of protein coding genes (according to ENSEMBL release 89’s biotype assignments) between experimental groups.
Supplementary_files_format_and_content: IGVtools utility 'count' was used on aligned bam files to compute the average alignment over 164 base windows across the genome and generate binary tiled data (.tdf) files (Thorvaldsdottir et al. 2013).

value: uninjured


title: M-MØ _SBBW_donor3_rep1

city: Madrid

first: Angel

middle: L

last: Corbí

state: Madrid

address: Ramiro de Maeztu 9

department: Molecular Microbiology and Infection Biology

country: Spain

institute: Consejo Superior de Investigaciones Científicas

description: M-MØ _SBBW_donor3_rep1

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at room temperature in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Data files from Feature Extraction were imported into GeneSpring® GX (Agilent Technologies). Quantile normalization was performed and expression values (log2 transformed) were obtained for each probe.

source_name: Gene expression in M-MØ after 6 hours of SB204741 and BW723C86

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the LowInputQuick Amp Labeling kit – Agilent 5190-2305 according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 5 days in the presence of 10 ng/ml M-CSF to generate M-CSF-polarized macrophages, which were later incubated for 48 hours in serum-free medium before treatments.

extract_protocol: Total RNA from each condition was extracted and purified using the RNA isolation kit (macheray-Nagel).Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.

treatment_protocol: Macrophages were treated with DMSO (Control), BW723C86 (10mM), SB204741 (1mM) or BW723C86 plus SB204741 during 6h. Before treatment, M-MØ macrophages were maintained in serum-free medium for 48 hours.

value: Monocyte-derived M-CSF macrophages

tag: donor id


title: M-MØ _SBBW_donor2_rep1

description: M-MØ _SBBW_donor2_rep1


title: 2-2-unevolved-in-xylose

city: Lakewood

first: Albert

last: Tafur Rangel

state: Colorado

address: 1617 Cole Blvd,

institute: NREL-Universidad de Los Andes-Universidad Popular del Cesar

description:
DSM 1314
Supplementary file S1, column UCellobiose2

data_processing:
Evaluate sequence quality
Trimm reads
Map reads to genome Ref Seq C. thermocellum DSM1313
Generate hitcounts
SARTools (Statistical Analysis of RNA-Seq data Tools) was used for statistical RNA-Seq analysis. Differentially expressed genes (DEGs) were identified using the DESeq2 R Package
Genome_build: NC_017304.1
Supplementary_files_format_and_content: excel file with normalized counts and differential expression

organism: Acetivibrio thermocellus

source_name: bacterial total RNA

growth_protocol: To compare the global gene expression profiles between cells grown in cellobiose vs. xylose, triplicates of the xylAB-expressing strain (KJC335) were grown in either cellobiose (5 g/L) or xylose (5 g/L) until harvest. Briefly, KJC335 was inoculated into glass tubes of 10.5 mL of CTFUD defined medium61 containing either cellobiose or xylose, and with close to 15 mL of argon gas in the headspace. The final concentrations of all components in the defined medium are: 3 g/L of sodium citrate tribasic dihydrate, 1.3 g/L ammonium sulfate, 1.5 g/L potassium phosphate monobasic, 0.13 g/L of calcium chloride dihydrate, 0.5 g/L of L-cysteine-HCl, 11.56 g/L of 3-morpholinopropane-1-sulfonic acid (MOPS) sodium salt, 2.6 g/L magnesium chloride hexahydrate, 0.001 g/L of ferrous sulfate heptahydrate, 0.001 g/L resazurin, and 5 g/L of either cellobiose or xylose. A 25 mL of 1000x vitamin solution containing 50 mg pyridoxamine HCl, 5 mg biotin, 10 mg of p-aminobenzoic acid (PABA), and 5 mg of vitamin B12 were prepared, and 1 mL of the solution was added to a liter of the defined medium. The number of cells to add from the seeding culture was calculated so that the initial OD600 was between 0.08 – 0.09 for all tubes and all cultures were harvested for total RNA purification at OD600 between 0.45 – 0.50. Carefully lining up the initial and harvest OD600 ensures that all cultures underwent the same number of doubling for comparison. The seeding culture was a fresh overnight culture also grown in defined media to minimize yeast extract carryover, and the culture was at its late log phase at inoculation. No sodium bicarbonate was added in any of the tubes.

extract_protocol:
The supernatant was discarded, and the cell pellets were lysed with lysozyme-EDTA using a Qiagen RNeasy Mini kit (Cat No./ID: 74104) following the manufacturer’s protocol. Each sample was treated with DNaseI (Qiagen, Cat No./ID: 79254) twice following the protocol in order to remove the genomic DNA in the total RNA completely. The quality of each purified total RNA sample was checked and validated by electrophoresis before it was sent out to commercial RNA-seq services for further sample processing and data analyses
Genewiz protocol . Whole transcriptome sequencing via rRNA depletion

treatment_protocol: To harvest the cells for total RNA purification, it was first chilled by swirling the anaerobic culture in dry ice/70% ethanol for 45 seconds and kept on ice for 5 minutes. The inactivated cells (1 – 1.5 mL) were then pelleted by centrifugation.

tag: carbon source

value: xylose


title: gDNA_rep65_uterin_carcinosarcoma

description:
sample name:
GY071T1


title: 2-3-unevolved-in-xylose

description:
DSM 1315
Supplementary file S1, column UCellobiose3


title: gDNA_rep1_uterin_carcinosarcoma

description:
sample name:
CX036T1


title: Uninjured cardiomyocytes rep2

tag: tissue


title: gDNA_rep2_uterin_carcinosarcoma

description:
sample name:
CX204T1


title: gDNA_rep5_uterin_carcinosarcoma

description:
sample name:
EN037T1


title: 2-3-unevolved-in-cellobiose

value: cellobiose


title: 2-1-unevolved-in-xylose

description:
DSM 1313
Supplementary file S1, column UCellobiose1


title: gDNA_rep69_uterin_carcinosarcoma

description:
sample name:
GY075T1


title: 2-2-unevolved-in-cellobiose


title: M-MØ _SBBW_donor1_rep1

description: M-MØ _SBBW_donor1_rep1


title: CFPAC1.FOXA2WT.ChIP.FOXA2.Rep2

description: Chromatin IP against FOXA2

value: CFPAC1 clonal cell line

value: Pancreatic Ductal Adenocarcinoma (PDAC) cell line

tag: chip antibody

value: Anti-FOXA2 (Antibody sc-6554 Lot. A1014)

value: Isolation of clonal cell line by dilution of CFPAC1 cells infected with lentiCRIPSv2 plasmid (Addgene #52961)


title: M-MØ _SB_donor1_rep1

description: M-MØ _SB_donor1_rep1

source_name: Gene expression in M-MØ after 6 hours of SB204741


title: M-MØ _BW_donor3_rep1

description: M-MØ _BW_donor3_rep1

source_name: Gene expression in M-MØ after 6 hours of BW723C86


title: M-MØ _SB_donor3_rep1

description: M-MØ _SB_donor3_rep1


title: M-MØ _BW_donor2_rep1

description: M-MØ _BW_donor2_rep1


title: 2-1-unevolved-in-cellobiose


title: M-MØ _Control_donor3_rep1

description: M-MØ _Control_donor3_rep1

source_name: Gene expression in M-MØ


title: M-MØ _BW_donor1_rep1

description: M-MØ _BW_donor1_rep1


title: Tibe3

city: Chengdu

first: Wenjie

last: Tang

address: NO.211 HuiMing road district, wenjiang

institute: Sichuan Agricultural University

data_processing:
Single-end reads were assigned to samples based on their unique barcode and truncated by cutting off the barcode and primer sequence.
Quality filtering on the raw reads were performed under specific filtering conditions to obtain the high-quality clean reads according to the quality-controlled process.
The reads were compared with the reference database using UCHIME algorithm to detect chimera sequences, and the chimera sequences were removed . Then, the Clean Reads finally obtained.
Sequences analysis was performed by Uparse software (Uparse v7.0. 1001) . Sequences with ≥ 97% similarity were assigned to the same OTUs. Representative sequence for each OTU was screened for further annotation.
For each representative sequence, the Silva Database (Quast et al., 2012) was used based on Mothur algorithm to annotate taxonomic information.
Genome_build: Silva Database
Supplementary_files_format_and_content: abundance of identified OTUs in each library

organism: pig gut metagenome

source_name: Tibe_colonic digesta

growth_protocol: Three Tibetan pigs from Sichuan Reservation Farm were used in current research as fecal donors. The donors were similar in age, were raised from birth in the same environment and were fed the same diet without antibiotics. Routine diagnoses for specific pathogens, including viruses and parasites, were performed before the experiment to ensure that the donors met the SAU specific pathogen-free standard for pigs (Xiao et al., 2017). Thirty-two DLY (Duroc × Landrace × Yorkshire) weaned barrows (6.55 ± 0.02 kg) were fed in the metabolic cages (1.4 m × 0.6 m × 0.8 m) with 1-sided feeder and stainless-steel nipple drinker. The room temperature was controlled at 26 ± 1℃. The basal diet was formulated to meet the nutrient requirements recommended by the National Research Council (NRC 2012), and the ingredient composition and nutrient levels are shown in supplementary material (Table S1). Piglets were randomly allotted to two groups (n = 16 per group) matched for body weight and litter origin as follows: Group FMT received capsulized fecal microbiota for 21 days (full-trial period); control group received empty capsule for 21 days; the same diet was used for all groups throughout the process.

extract_protocol:
The piglets were then euthanized by intravenous injection of chlorpromazine hydrochloride (3 mg/kg body weight). The abdomen was immediately opened. The colon segments (distal section of the colon) were sampled and fixed into 10% buffered formalin at 4 ℃ for morphometric analysis and histological injured score.
Sequencing libraries were generated using Ion Plus Fragment Library Kit 48 rxns (Thermo Scientific) following manufacturer's recommendations. The library quality was assessed on the Qubit@ 2.0 Fluorometer (Thermo Scientific).

tag: breed

value: Tibetan pig

value: 42 days

tag: sample source

value: Colonic digesta

tag: molecule subtype

value: 16S rRNA


title: Uninjured cardiomyocytes rep1


title: M-MØ _Control_donor2_rep1

description: M-MØ _Control_donor2_rep1

tag: cell type


title: Patient4_10m

city: Helsinki

first: Virginia

last: Brilhante

state: Uusimaa

address: Haartmaninkatu 8

department: Stem Cells and Metabolism Research Program

country: Finland

institute: University of Helsinki

description:
AWVM22_P10
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv

data_processing:
High throughput RNA sequencing perfomed on BGISEQ-500 platform.
Filtering of reads with adaptors, reads of low quality, and reads with high content of unknown bases.
Alignment of reads against the GRCh38 Human genome assembly using STAR 2.5.0a.
Counting of reads mapping to genes performed with htseq-count, HTSeq 0.10.0, in union overlap resolution mode.
Estimation of normalised read counts per gene and differential gene expression analysis with the Bioconductor DESeq2 1.18.1 package. Control and patient groups at three treatment time points were compared pairwisely for gene expression. When comparing control groups at different time points, or patient groups at different time points, the group-specific effect of treatment was estimated controlling for individual effects.
Genome_build: GRCh38
Supplementary_files_format_and_content: AWVM29samples.HTSeq.counts.tsv in tsv format contains raw counts of sequencing reads per gene per sample. AWVM29samples.DESeq.normCounts.csv in csv format contains normalized counts of reads per gene per sample.

source_name: vastus lateralis muscle

extract_protocol:
A Bergström needle biopsy from vastus lateralis was collected from controls at 0 and 4 months and from patients at the time points 0, 4 and 10 months. Total muscle RNA was extracted with standard TRIzol and chloroform method and purified with RNA purification kit (RNeasy; Qiagen).
Standard protocol in BGISEQ-500 workflow.

treatment_protocol: Mitochondrial myopathy patients and healthy controls were supplemented with niacin and the collection of muscle biopsies were performed in patients at the time points 0, 4 and 10 months and in controls. at 0 and 4 months

tag: individual

tag: disease state (study group)

value: Mitochondrial myopathy patient

tag: genotype

value: single mtDNA deletion

value: niacin

tag: time

value: 10 months


title: Patient1_10m

description:
AWVM31_P10
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv

tag: treatment


title: Patient2_10m

description:
AWVM19_P10
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv

value: Twinkle mutation


title: Patient4_4m

description:
AWVM21_P4
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv

value: 4 months


title: Tibe1

tag: age


title: FMT12

source_name: FMT_colonic digesta

value: Duroc x Landrace x Yorkshire piglet

value: capsulized fecal microbiota for 21 days


title: Tibe2


title: Patient3_4m

description:
AWVM24_P4
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv


title: Patient5_4m

description:
AWVM27_P4
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv


title: BafA 24h-2

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

description: BMP-induced quiescence

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: qNSC

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: NSCs were cultured in quiescence medium including BMP for 3 days to induce quiescence before treatment.

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Qiagen).

treatment_protocol: Quiescent NSCs were incubated in quiescence medium with or without 20nM Bafilomycin A for 4 and 24 hours.

tag: cell

value: quiescent neural stem cells


title: control 24h-2

description: BMP-induced quiescence


title: FMT11


title: Patient1_4m

description:
AWVM30_P4
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv


title: NHLF_siSOX11_TGF-beta

city: SAGA

first: Yasuhiro

last: Nanri

address: 5-1-1 Nabeshima

institute: Saga university

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: NHLF, SOX11 siRNA, TGF-beta

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using theRNAiso plus kit (Takara Bio) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2200 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: NHLF cell

tag: sirna

value: SOX11 siRNA


title: BafA 4h-2

description: BMP-induced quiescence


title: control 24h-1

description: BMP-induced quiescence


title: BafA 24h-1

description: BMP-induced quiescence


title: FMT9


title: NHLF_siSOX11_NS

source_name: NHLF, SOX11 siRNA, NS


title: FMT8


title: Control9_4m

description:
AWVM14_C4
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv

value: Healthy control

value: WT


title: M-MØ _Control_donor1_rep1

description: M-MØ _Control_donor1_rep1

value: Monocyte-derived M-CSF macrophages


title: Patient2_4m

description:
AWVM18_P4
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv


title: SP_WT

city: San Antonio

first: Zhenqing

last: Ye

state: TX

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Clinic sequence core using the pipeline Cassava 1.7.
Reads aligned to mouse reference genome (mm10) using Tophat (v2.0.6) with default parameters.
Raw count and RPKM were calculated using RSeQC (v2.3.6) with parameters "-d '1+-,1-+,2++,2--' -r hg19.refseq.bed12".
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *FPKM.txt: Tab-delimited text files include FPKM values for each Sample.

source_name: SPLEEN

growth_protocol: CD8+ T cells were activated with anti-CD3 and BMDC for 4 days.

extract_protocol:
RNAs were extracted using RNeasy Mini Kit.
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit.

treatment_protocol: OVA257-264 specific CD8+ T cells were sorted from tumor and spleen of B16-OVA bearing mice; OTI cells were sorted from IAV infected mice at 35 D.P.I.

tag: strain/background

tag: genotype/variation

value: Spleen

value: CD8+ T cell


title: control 4h-2

description: BMP-induced quiescence


title: NHLF_siControl_NS

source_name: NHLF, control siRNA, NS

value: siControl


title: control 4h-1

description: BMP-induced quiescence


title: BafA 4h-1

description: BMP-induced quiescence


title: MRC-5_siPeriostin_TGF-beta

source_name: MRC-5, periostin siRNA, TGF-beta

value: MRC-5 cell

value: periostin siRNA


title: NHLF_siControl_TGF-beta

source_name: NHLF, control siRNA, TGF-beta

value: control siRNA


title: NHLF_siControl_TGF-beta [AR2857]


title: NHLF_siPeriostin_TGF-beta

source_name: NHLF, periostin siRNA, TGF-beta


title: RNA-seq st. 32 replicate 3

city: Wako

first: Koh

last: Onimaru

state: Saitama

address: 312 Information Science Building, 2-1 Hirosawa

institute: Center for Biosystems Dynamics Research

description:
replicate 3
bamboo_shark_fin_average_TPM_expression_data_with_gene_symbol.txt
bamboo_shark_fin_TPM_expression_data_with_gene_symbol.txt

data_processing:
Basecalling with Illumina RTA 1.18.64
Short reads were aligned to curated, non-redundant genes in GCF_000001635.26_GRCm38.p6_rna.fna for mouse samples and a transcriptome assemble for bamboo shark samples using RSEM with bowtie2 (bowtie2 options: –no-mixed --no-discordant --gbar 1000 --end-to-end -k 200).
Transcripts per million (TPM) were calculated using RSEM and a perl script in Trinity software.
Genome_build: mm10 or a transcritopme assembly
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each species.

organism: Chiloscyllium punctatum

source_name: pectoral fin bud at st. 32

extract_protocol:
RNeasy Mini plus kit
Described in the SAMPLES section
Using >100 μg of each of the RNA samples, strand-specific single-end RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, Cat. No. RS-122-2101 and/or RS-122-2102 ). For purification, we applied 1.8x (after end repair) and 1.0x (after PCR) volumes of Agencourt AMPure XP (Beckman Coulter, Cat. No. A63880). The optimal number of PCR cycles was determined by a preliminary PCR using KAPA Library Amplification Kit (KAPA, Cat. No. KK2702) and estimated to be XXXX cycles for mouse limb buds and XXX cycles for bamboo shark fin buds. The quality of the libraries was checked by Agilent 4200 TapeStation.

value: pectoral fin bud


title: FMT7

value: 42 days

value: Colonic digesta

value: 16S rRNA


title: RNA-seq st. 32 replicate 2

description:
replicate 2
bamboo_shark_fin_average_TPM_expression_data_with_gene_symbol.txt
bamboo_shark_fin_TPM_expression_data_with_gene_symbol.txt


title: WT_TIL

source_name: TUMOR

value: Tumor


title: Control8_4m

description:
AWVM16_C4
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv

value: niacin

value: 4 months


title: WT_SP


title: Lung_KO

source_name: LUNG

value: Lung


title: Control7_4m

description:
AWVM10_C4
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv

value: Healthy control


title: Control6_4m

description:
AWVM12_C4
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv

value: WT


title: Control5_4m

description:
AWVM04_C4
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv


title: MRC-5_siControl_TGF-beta

source_name: MRC-5, control siRNA, TGF-beta


title: FMT5

value: Duroc x Landrace x Yorkshire piglet

value: capsulized fecal microbiota for 21 days


title: Bhlhe40-/-_CD8-2

value: Spleen

value: CD8+ T cell


title: FMT4


title: RNA-seq st. 32 replicate 1

description:
replicate 1
bamboo_shark_fin_average_TPM_expression_data_with_gene_symbol.txt
bamboo_shark_fin_TPM_expression_data_with_gene_symbol.txt


title: RNA-seq st. 31 replicate 3

source_name: pectoral fin bud at st. 31


title: Bhlhe40-/-_CD8-1


title: FMT3


title: Control4_4m

description:
AWVM08_C4
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv


title: Control3_4m

description:
AWVM06_C4
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv


title: Lung_WT


title: RNA-seq st. 31 replicate 2


title: RNA-seq st. 31 replicate 1


title: WT_CD8-2


title: FMT1


title: FMT2


title: WT_CD8-1


title: Patient5_0m

description:
AWVM26_P0
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv

value: Mitochondrial myopathy patient

value: single mtDNA deletion

value: control

value: 0 months


title: FMT10

value: 42 days


title: RNA-seq st. 30 replicate 2

source_name: pectoral fin bud at st. 30

value: pectoral fin bud


title: CTL12

source_name: control_colonic digesta

value: empty capsule for 21 days

value: Colonic digesta

value: 16S rRNA


title: alpha.sca.DT.2

city: Milano

first: Stefano

last: de Pretis

address: Via Olgettina, 58

institute: IRCCS San Raffaele Institute

description: Freshly sorted cells

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_quality_trimmer -Q33 -t 20 -l 10 -v -i ; fastq_masker -Q33 -q 20 -r -N -v -i
Reads were aligned on the mouse reference genome (NCBI 37, MM9) with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-inds --library-type fr-unstranded
Transcript abundance was quantified through ‘Reads Per Kilobase exon model per Million mapped reads’ (RPKM)
Genome_build: mm9
Supplementary_files_format_and_content: RPKMs

source_name: Gastrocnemius muscle

extract_protocol:
Total RNA extracted with Qiagen RNeasy micro kit (Qiagen Cat#: 74004)
Generation of libraries by Smart-Seq2 protocol (Picelli et al., 2014), with minor modifications

tag: strain

value: mdxITGAM-DTR

value: Hind-limb skeletal muscle

value: alpha7Sca1 cells

tag: agent

value: Diphtheria toxin (DT)


title: Patient4_0m

description:
AWVM20_P0
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv

source_name: vastus lateralis muscle


title: CTL11

value: Duroc x Landrace x Yorkshire piglet


title: alpha.sca.DT.1

description: Freshly sorted cells

tag: tissue


title: RNA-seq st. 30 replicate 1


title: Patient3_0m

description:
AWVM23_P0
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv

value: Twinkle mutation


title: SC.DT.2

description: Freshly sorted cells

value: satellite cells (SCs)


title: CTL10

tag: breed


title: M-MØ _SB_donor2_rep1

description: M-MØ _SB_donor2_rep1

source_name: Gene expression in M-MØ after 6 hours of SB204741

value: Monocyte-derived M-CSF macrophages

tag: donor id


title: RNA-seq st. 29 replicate 3

source_name: pectoral fin bud at st. 29


title: Control1_4m

description:
AWVM02_C4
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv

value: Healthy control

value: WT

value: niacin

value: 4 months


title: Patient2_0m

description:
AWVM17_P0
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv

value: Mitochondrial myopathy patient

value: control

value: 0 months


title: SC.DT.1

description: Freshly sorted cells


title: RNA-seq st. 29 replicate 2

value: pectoral fin bud


title: SC.crtl.2

description: Freshly sorted cells


title: RNA-seq st. 29 replicate 1


title: CTL8

value: 42 days

value: empty capsule for 21 days

tag: sample source

value: Colonic digesta

tag: molecule subtype

value: 16S rRNA


title: CTL9


title: Control9_0m

description:
AWVM13_C0
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv

tag: individual


title: Control8_0m

description:
AWVM15_C0
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv

tag: disease state (study group)


title: CTL7


title: RNA-seq st. 30 replicate 3


title: SC.crtl.1

description: Freshly sorted cells

value: mdxITGAM-DTR

value: Hind-limb skeletal muscle

tag: cell type


title: Control7_0m

description:
AWVM09_C0
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv

tag: genotype

tag: time


title: RNA-seq st. 27.5 replicate 3

description:
replicate 3
bamboo_shark_fin_average_TPM_expression_data_with_gene_symbol.txt
bamboo_shark_fin_TPM_expression_data_with_gene_symbol.txt

source_name: pectoral fin bud at st. 27.5

extract_protocol:
RNeasy Micro plus kit
Described in the SAMPLES section
Using >100 μg of each of the RNA samples, strand-specific single-end RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, Cat. No. RS-122-2101 and/or RS-122-2102 ). For purification, we applied 1.8x (after end repair) and 1.0x (after PCR) volumes of Agencourt AMPure XP (Beckman Coulter, Cat. No. A63880). The optimal number of PCR cycles was determined by a preliminary PCR using KAPA Library Amplification Kit (KAPA, Cat. No. KK2702) and estimated to be XXXX cycles for mouse limb buds and XXX cycles for bamboo shark fin buds. The quality of the libraries was checked by Agilent 4200 TapeStation.

tag: age


title: CTL6

value: Duroc x Landrace x Yorkshire piglet

tag: treatment


title: gDNA_rep8_uterin_carcinosarcoma

description:
sample name:
EN050T1

data_processing:
The minfi package in R/Bioconductor
Normalized data matrix  (GA_illumina_methylation_CS_v1_processed.txt) includes Normalized Average Beta (background subtraction and control normalization).

source_name: uterin carcinosarcoma

extract_protocol: Genomic DNA was extracted using the QIAamp DNA Micro Kit (Qiagen), according to the manufacturer’s instructions.

tag: patient diagnosis

value: uterine carcinosarcoma

tag: gender

value: Female

tag: anatomical site

value: Uterus


title: RNA-seq st. 27.5 replicate 2

description:
replicate 2
bamboo_shark_fin_average_TPM_expression_data_with_gene_symbol.txt
bamboo_shark_fin_TPM_expression_data_with_gene_symbol.txt


title: EV_WA_3

city: Pittsburgh

first: Shivendra

middle: V

last: Singh

address: 5117 Centre Avenue UPMC HCC Research Pavilion Suite 2.32A

department: Pharmacology and Chemical Biology

institute: University of Pittsburgh

description: Cells were treated with 2 µM of WA for 16 hours.

data_processing:
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. The fragments per kilobase per million mapped (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
For DESeq2 with biological replicates, differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed. Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.16.5). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 1 were set as the threshold for significantly differential expression.
Genome_build: Homo Sapiens(GRCh37/hg19)
Supplementary_files_format_and_content: FPKM represents Summary of gene expression level analysis by FPKM; Differential expression analysis

source_name: prostate cancer

growth_protocol: The 22Rv1 human prostate cancer cell lines stably transfected with pcDNA3 empty vector (EV) were plated in 10-cm dish at a density of 1.5×106 cells/dish in triplicate and incubated overnight for attachment.

extract_protocol:
The cells were harvested by trypsin treatment and total RNA was extracted using the RNeasy mini kit (Qiagen, Germantown, MD).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with DMSO (final concentration- 0.01%) or 2 µM of WA for 16 hours prior to RNA isolation and RNA-Seq analysis.

value: human prostate cancer

tag: cell line

tag: transfection

value: withaferin A


title: Control6_0m

description:
AWVM11_C0
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv

value: Healthy control

value: WT


title: RNA-seq st. 27.5 replicate 1

tag: tissue


title: Control5_0m

description:
AWVM03_C0
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv

value: control


title: EV_WA_2

value: stably transfected with pcDNA3 empty vector (EV)

tag: agent


title: RNA-seq st. 27 replicate 3

source_name: pectoral fin bud at st. 27

extract_protocol:
PicoPure™ RNA Isolation Kit
Described in the SAMPLES section
Using >100 μg of each of the RNA samples, strand-specific single-end RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, Cat. No. RS-122-2101 and/or RS-122-2102 ). For purification, we applied 1.8x (after end repair) and 1.0x (after PCR) volumes of Agencourt AMPure XP (Beckman Coulter, Cat. No. A63880). The optimal number of PCR cycles was determined by a preliminary PCR using KAPA Library Amplification Kit (KAPA, Cat. No. KK2702) and estimated to be XXXX cycles for mouse limb buds and XXX cycles for bamboo shark fin buds. The quality of the libraries was checked by Agilent 4200 TapeStation.

value: pectoral fin bud


title: EV_WA_1


title: Control4_0m

description:
AWVM07_C0
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv

value: 0 months


title: CTL5

tag: breed

value: 42 days

value: empty capsule for 21 days


title: RNA-seq st. 27 replicate 2


title: CTL2

tag: sample source

value: Colonic digesta

value: 16S rRNA


title: EV_0_2

description: Cells were treated with vehicle (DMSO) for 16 hours.

value: DMSO


title: Control1_0m

description:
AWVM01_C0
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv


title: RNA-seq st. 27 replicate 1

description:
replicate 1
bamboo_shark_fin_average_TPM_expression_data_with_gene_symbol.txt
bamboo_shark_fin_TPM_expression_data_with_gene_symbol.txt


title: EV_0_3


title: EV_0_1


title: CTL1

value: Duroc x Landrace x Yorkshire piglet

tag: molecule subtype


title: CTL4


title: CTL3


title: Patient3_10m

description:
AWVM25_P10
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv

tag: individual

value: Mitochondrial myopathy patient

value: Twinkle mutation

value: niacin

value: 10 months


title: Control3_0m

description:
AWVM05_C0
AWVM29samples.HTSeq.counts.tsv
AWVM29samples.DESeq.normCounts.csv

tag: disease state (study group)


title: R106

status: Public on Sep 16 2019

city: Utrecht

first: Judith

middle: M.

last: Boer

address: Heidelberglaan 25

country: Netherlands

institute: Prinses Maxima Centrum

description: blast percentage >90%

hyb_protocol: Affymetrix hybridization kit was used including fragmentation according to Affymetrix's protocol. Arrays were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: The arrays were scanned using the Affymetrix Genechip scanner

data_processing: R-version 2.13.0 with Bioconductor packages affy version 1.30.0, vsn version 3.20.0 and biobase version 2.12.1 were used to extract data according to rma and to normalize using VSN. Combat was used to correct for different batches.

label: biotin

source_name: leukemic blast

label_protocol: 8ul 125ng/ul was used as input for the Affymetrix in vitro one cycle kit, followed by IVT labelling (Affymetrix)

growth_protocol: Primairy human leukemic cells were isolated at initial diagnosis (blast percentage >90%)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: all subtype

value: Other BCP

tag: batch

value: B


title: R101

description: blast percentage >90%


title: R103

description: blast percentage >90%

value: T-ALL


title: R104

description: blast percentage >90%


title: R98

description: blast percentage >90%


title: R96

description: blast percentage >90%


title: R99

description: blast percentage >90%


title: R100

description: blast percentage >90%


title: R102

description: blast percentage >90%


title: R95

description: blast percentage >90%


title: R93

description: blast percentage >90%


title: R94

description: blast percentage >90%


title: R107

description: blast percentage >90%


title: R88

description: blast percentage >90%


title: R92

description: blast percentage >90%


title: R105

description: blast percentage >90%


title: R97

description: blast percentage >90%


title: R84

description: blast percentage >90%


title: R83

description: blast percentage >90%


title: R87

description: blast percentage >90%


title: R86

description: blast percentage >90%


title: R90

description: blast percentage >90%


title: R85

description: blast percentage >90%


title: R91

description: blast percentage >90%


title: R89

description: blast percentage >90%


title: FMT6

source_name: FMT_colonic digesta

value: capsulized fecal microbiota for 21 days


title: R81

description: blast percentage >90%


title: R80

description: blast percentage >90%


title: R76

description: blast percentage >90%


title: R78

description: blast percentage >90%


title: R77

description: blast percentage >90%


title: R70

description: blast percentage >90%


title: R72

description: blast percentage >90%


title: R71

description: blast percentage >90%


title: R69

description: blast percentage >90%


title: R60

description: blast percentage >90%


title: R75

description: blast percentage >90%


title: R74

description: blast percentage >90%


title: R82

description: blast percentage >90%


title: R67

description: blast percentage >90%


title: R79

description: blast percentage >90%


title: R62

description: blast percentage >90%


title: R66

description: blast percentage >90%


title: R59

description: blast percentage >90%


title: R68

description: blast percentage >90%


title: R64

description: blast percentage >90%


title: R65

description: blast percentage >90%


title: R58

description: blast percentage >90%


title: R56

description: blast percentage >90%


title: R52

description: blast percentage >90%


title: R57

description: blast percentage >90%


title: R55

description: blast percentage >90%


title: R54

description: blast percentage >90%


title: R63

description: blast percentage >90%


title: R61

description: blast percentage >90%


title: R48

description: blast percentage >90%


title: R47

description: blast percentage >90%


title: R46

description: blast percentage >90%


title: R51

description: blast percentage >90%


title: R45

description: blast percentage >90%


title: R42

description: blast percentage >90%


title: R43

description: blast percentage >90%


title: R37

description: blast percentage >90%


title: R44

description: blast percentage >90%


title: R38

description: blast percentage >90%


title: R35

description: blast percentage >90%


title: R28

description: blast percentage >90%


title: R41

description: blast percentage >90%


title: R34

description: blast percentage >90%


title: R40

description: blast percentage >90%


title: R33

description: blast percentage >90%


title: R29

description: blast percentage >90%


title: R30

description: blast percentage >90%


title: R24

description: blast percentage >90%


title: R25

description: blast percentage >90%


title: R36

description: blast percentage >90%


title: R27

description: blast percentage >90%


title: R31

description: blast percentage >90%


title: R26

description: blast percentage >90%


title: R23

description: blast percentage >90%


title: R21

description: blast percentage >90%


title: R19

description: blast percentage >90%


title: R18

description: blast percentage >90%


title: R22

description: blast percentage >90%


title: R20

description: blast percentage >90%


title: R17

description: blast percentage >90%


title: R15

description: blast percentage >90%


title: R14

description: blast percentage >90%


title: R16

description: blast percentage >90%


title: R7

description: blast percentage >90%


title: R4

description: blast percentage >90%


title: R13

description: blast percentage >90%


title: A552

description: blast percentage >90%

value: E


title: R9

description: blast percentage >90%


title: A549

description: blast percentage >90%


title: R5

description: blast percentage >90%


title: R2

description: blast percentage >90%


title: A548

description: blast percentage >90%


title: R11

description: blast percentage >90%


title: R10

description: blast percentage >90%


title: A551

description: blast percentage >90%


title: R1

description: blast percentage >90%


title: A544

description: blast percentage >90%


title: A550

description: blast percentage >90%


title: R3

description: blast percentage >90%


title: A542

description: blast percentage >90%


title: R6

description: blast percentage >90%


title: A546

description: blast percentage >90%


title: A541

description: blast percentage >90%


title: R8

description: blast percentage >90%


title: A545

description: blast percentage >90%


title: A543

description: blast percentage >90%


title: A536

description: blast percentage >90%


title: A539

description: blast percentage >90%


title: A537

description: blast percentage >90%


title: A534

description: blast percentage >90%


title: A538

description: blast percentage >90%


title: A547

description: blast percentage >90%


title: A535

description: blast percentage >90%


title: A532

description: blast percentage >90%


title: A528

description: blast percentage >90%


title: A527

description: blast percentage >90%


title: A526

description: blast percentage >90%


title: A523

description: blast percentage >90%


title: A525

description: blast percentage >90%


title: A530

description: blast percentage >90%


title: A524

description: blast percentage >90%


title: A520

description: blast percentage >90%


title: A522

description: blast percentage >90%


title: A533

description: blast percentage >90%


title: A518

description: blast percentage >90%


title: A519

description: blast percentage >90%


title: A531

description: blast percentage >90%


title: A529

description: blast percentage >90%


title: R32

description: blast percentage >90%


title: A515

description: blast percentage >90%


title: R39

description: blast percentage >90%


title: A514

description: blast percentage >90%


title: A513

description: blast percentage >90%


title: A512

description: blast percentage >90%


title: A517

description: blast percentage >90%


title: A516

description: blast percentage >90%


title: A521

description: blast percentage >90%


title: A510

description: blast percentage >90%


title: A511

description: blast percentage >90%


title: A509

description: blast percentage >90%


title: A506

description: blast percentage >90%


title: A504

description: blast percentage >90%


title: A502

description: blast percentage >90%


title: A507

description: blast percentage >90%


title: A505

description: blast percentage >90%


title: A497

description: blast percentage >90%


title: A500

description: blast percentage >90%


title: A496

description: blast percentage >90%


title: A501

description: blast percentage >90%


title: A508

description: blast percentage >90%


title: A503

description: blast percentage >90%


title: A498

description: blast percentage >90%


title: A495

description: blast percentage >90%


title: A499

description: blast percentage >90%


title: A489

description: blast percentage >90%


title: A553

description: blast percentage >90%


title: A493

description: blast percentage >90%


title: A487

description: blast percentage >90%


title: A492

description: blast percentage >90%


title: A488

description: blast percentage >90%


title: A491

description: blast percentage >90%


title: A486

description: blast percentage >90%


title: A494

description: blast percentage >90%


title: A482

description: blast percentage >90%


title: A485

description: blast percentage >90%


title: A483

description: blast percentage >90%


title: A484

description: blast percentage >90%


title: A480

description: blast percentage >90%


title: A478

description: blast percentage >90%


title: A479

description: blast percentage >90%


title: A481

description: blast percentage >90%


title: A475

description: blast percentage >90%


title: A477

description: blast percentage >90%


title: A473

description: blast percentage >90%


title: A474

description: blast percentage >90%


title: A469

description: blast percentage >90%


title: A471

description: blast percentage >90%


title: A490

description: blast percentage >90%


title: A472

description: blast percentage >90%


title: A476

description: blast percentage >90%


title: A464

description: blast percentage >90%


title: A465

description: blast percentage >90%


title: A470

description: blast percentage >90%


title: A540

description: blast percentage >90%


title: A453

description: blast percentage >90%


title: A459

description: blast percentage >90%


title: A461

description: blast percentage >90%


title: A456

description: blast percentage >90%


title: A462

description: blast percentage >90%


title: A460

description: blast percentage >90%


title: A467

description: blast percentage >90%


title: A468

description: blast percentage >90%


title: A454

description: blast percentage >90%


title: A463

description: blast percentage >90%


title: A457

description: blast percentage >90%


title: A466

description: blast percentage >90%


title: A455

description: blast percentage >90%


title: A458

description: blast percentage >90%


title: A445

description: blast percentage >90%


title: A444

description: blast percentage >90%


title: A452

description: blast percentage >90%


title: A446

description: blast percentage >90%


title: A449

description: blast percentage >90%


title: A442

description: blast percentage >90%


title: A448

description: blast percentage >90%


title: A440

description: blast percentage >90%


title: A438

description: blast percentage >90%


title: A439

description: blast percentage >90%


title: A450

description: blast percentage >90%


title: A441

description: blast percentage >90%


title: A451

description: blast percentage >90%


title: A443

description: blast percentage >90%


title: A437

description: blast percentage >90%


title: A430

description: blast percentage >90%


title: A433

description: blast percentage >90%


title: A425

description: blast percentage >90%


title: A436

description: blast percentage >90%


title: A432

description: blast percentage >90%


title: A431

description: blast percentage >90%


title: A435

description: blast percentage >90%


title: A447

description: blast percentage >90%


title: A429

description: blast percentage >90%


title: A420

description: blast percentage >90%


title: A422

description: blast percentage >90%


title: A423

description: blast percentage >90%


title: A428

description: blast percentage >90%


title: A427

description: blast percentage >90%


title: A434

description: blast percentage >90%


title: A419

description: blast percentage >90%


title: A418

description: blast percentage >90%


title: A426

description: blast percentage >90%


title: A413

description: blast percentage >90%


title: A421

description: blast percentage >90%


title: A424

description: blast percentage >90%


title: A410

description: blast percentage >90%


title: A412

description: blast percentage >90%


title: A416

description: blast percentage >90%


title: A414

description: blast percentage >90%


title: A408

description: blast percentage >90%


title: A415

description: blast percentage >90%


title: A411

description: blast percentage >90%


title: A409

description: blast percentage >90%


title: A407

description: blast percentage >90%


title: A405

description: blast percentage >90%


title: A403

description: blast percentage >90%


title: A398

description: blast percentage >90%


title: A406

description: blast percentage >90%


title: A402

description: blast percentage >90%


title: A417

description: blast percentage >90%


title: A397

description: blast percentage >90%


title: A395

description: blast percentage >90%


title: A404

description: blast percentage >90%


title: A383

description: blast percentage >90%


title: A381

description: blast percentage >90%