title: GROseq_SH-EP-NMYCER

data_processing:
Library strategy: GRO-seq
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.
For GRO-seq, reads of all biological conditions (+/-4-OHT, +/-shBRCA1) were pooled and the 3’ adapter was trimmed using Cutadapt keeping at least 30 bp.
Untrimmed and trimmed reads passing the filter were then mapped to hg19 using Tophat2 and Bowtie2 including spliced reads.
bigwig files were generated using the "bamCoverage" function from DeepTools with a resolution of 1bp.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bigWig.html)

extract_protocol:
Cells were washed two times with cold 1x PBS and harvested in 1x PBS. Cells were re-suspended in 10 ml swelling buffer (10 mM Tris-HCl pH 7.5, 2 mM MgCl2, 3 mM CaCl2) and incubated for 5 min on ice. After centrifugation (400 xg, 10 min) cells were re-suspended in 10 ml swelling buffer containing 10 % glycerol. 10 ml lysis buffer (10 mM Tris-HCl pH 7.5, 2 mM MgCl2, 3 mM CaCl2, 10 % glycerol, 1 % Igepal) was added with gently swirling and incubated for 5 min on ice. The volume of cell suspension was brought to 45 ml with lysis buffer. Resultant nuclei were washed with 10 ml freezing buffer (40 % glycerol, 50 mM Tris-HCl pH 8.0, 5 mM MgCl2, 0.1 mM EDTA). The pellet was resuspended in 100 µl freezing buffer per 1x107 of nuclei.   For run-on reaction, resuspended nuclei were mixed with the same amount of run-on reaction buffer (10 mM Tris-HCl pH 8.0, 5 mM MgCl2, 300 mM KCl, 1 mM DTT, 500 µM ATP, 500 µM GTP, 500 µM Br-UTP, 2 µM CTP, 200 U/ml Superase In, 1 % N-Laurylsarcosine) and incubated 7 min at 30 °C. The reaction was blocked by adding 600 µl Trifast, thoroughly vortexing and incubating for 5 min. RNA was extracted by adding 160 µl chloroform, precipitated with ethanol and resuspended in 20 µl H2O. RNA was next subjected to DNAse treatment (Turbo DNA-free kit, Thermo fisher) for two times according to manufacturer’s protocol. RNA was fragmented using Ambion RNA fragmentation kit and end repaired by T4 PNK (NEB).  Anti-BrdU agarose beads (Santa-Cruz, 50 µl per sample) were twice washed and then blocked for 1 hour with blocking buffer (1 x binding buffer, 0.1 % polyvinylpyrrolidone, 0.1 % BSA). Beads were washed twice with binding buffer (0.25 x SSPE, 0.05 % Tween20, 37.5 mM NaCl, 1mM EDTA) and mixed with RNA in 700 µl binding buffer for 1 h on a rotating wheel. After binding, beads were washed twice with binding buffer, twice with low-salt wash buffer (0.2 x SSPE, 0.05 % Tween20, 1 mM EDTA), one with high-salt wash buffer (0.2 x SSPE, 137.5 mM NaCl, 0.05 % Tween20, 1 mM EDTA) and twice with TE with 0.05 % Tween20. Finally, RNA was eluted four times with 100 µl elution buffer (50 mM Tris pH 7.5, 150 mM NaCl, 0.1 % SDS, 20 mM DTT, 1 mM EDTA). RNA was purified with Trizol and Chloroform as described for mRNA-seq..   RNA was decapped using RppH (NEB) with 10 x NEB Thermopol buffer for 1 hour at 37 °C. Reaction was stopped by adding EDTA and incubation at 65 °C for 5 min. Afterwards RNA was extracted as described for mRNA-seq.
Library preparation was done according to manufacturer’s instructions using NEBNext Multiplex Small RNA Library Prep Kit for Illumina. Library size was tested with the Biorad Experion system and the amount of library DNA was quantified using a picogreen assay

value: BrdU (Santa Cruz, IIB5)


title: ChIPseq_2_minusOHT_BRCA1

status: Public on Mar 21 2019

type: SRA

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

library_source: genomic

data_processing:
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.
For ChIP-seq, fastq files were mapped to the human genome (hg19) using Bowtie v1.1.1. and normalized to the sample with the smallest number of mapped reads.
Peak calling was done with MACS v1.4.2 with default parameters but a p-value cutoff of 1e-6 (BRCA1) and 1e-11 (NMYC) and keep-dup parameter = 5. bedgraph files were generated using bedtools genomecov.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).

molecule: genomic DNA

organism: Homo sapiens

source_name: SH-EP-NMYCER

extract_protocol:
Cells were treated with 1% formaldehyde for 10 min at 37 °C. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA) and DNA was fragmented to a size <500 bp using a Branson sonifier. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used.
Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and purified with Qiagen gel extraction kit. DNA fragments were amplified by 18 cycles of PCR and library size was tested with the Biorad Experion system. The amount of library DNA was quantified using a picogreen assay

treatment_protocol: SH-EP-NMYCER cells were treated with 200nM 4-OHT or EtOH for 3h. Lentiviruses expressing a shRNA targeting BRCA1 were produced by transfection of pGIPZ plasmid together with the packaging plasmid psPAX.2, and the envelope plasmid pMD2.G into HEK293TN cells. Virus-containing supernatant was harvested 24 h and 48 h after transfection. SH-EP cells were infected with lentiviral supernatants in the presence of 4ug ml   1 polybrene (Sigma-Aldrich) for 24 h. Cells were selected for two days with puromycin (2 ug ml-1) and afterwards plated for the experiment. Where indicated, cells were treated with 10nM flavopiridol or 5uM etoposide for 2 h. shRNA sequences against BRCA1 (#1: TTCGCGTTGAAGAAGTACAAAA, #2: GCAGATAGTTCTACCAGTAAAA, SCR: GTGAGCGATCTCGCTTGGGCG) were taken from Fellmann et al., 2013. For the shRNA screen, SH-EP-NMYCER cells were lentivirally infected with either of two pGIPZ-based shRNA library pools. Following puromycin-selection, the cells were treated with 100 nM 4-OHT or EtOH continuously for 2 weeks.

tag: cell line

value: SH-EP-NMYCER

tag: treatment

value: EtOH

tag: shRNA

tag: antibody

value: BRCA1 (Bethyl, A300-000A)


title: RNAseq_2_minusOHT_shBRCA1#1_rep3

description: RNAseq_2_SH-EP-NMYCER_shBRCA1_countmatrix.txt

library_source: transcriptomic

data_processing:
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.
For mRNA-seq, reads were mapped to hg19 with Tophat2 and Bowtie2 with default settings.
Reads per gene were counted using the summarizeOverlaps function from the R package {GenomicRanges}.
Weakly and non-expressed genes were removed (mean count over all samples <1).
Genome_build: hg19
Supplementary_files_format_and_content: Count matrix containing Ensembl gene ID, gene symbol, gene description and counts for all samples and each gene.

molecule: total RNA

extract_protocol:
Total RNA was isolated using RNeasy mini columns (Qiagen) including on-column DNase I digestion.
mRNA was extracted using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB). Library preparation was performed with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the instruction manual. Size-selection of libraries was performed using Agencourt AMPure XP Beads (Beckman Coulter) followed by amplification with 12 PCR cycles. Afterwards libraries were quantified and the size was determinded using Experion Automated Electrophoresis System (Bio-Rad).


title: FL2_SWED-008.1_8R01C02

type: genomic

city: Uppsala

first: Lars

last: Feuk

address: Husargatan 3

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

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

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

data_processing:
GenomeStudio 2011.1
Average Beta and Unmethylated and methylated signal intensities are in Series supplementary files

label: Cy5 and Cy3

source_name: genomic DNA from frontal cortex post-mortem brain tissue

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using the QIAmp DNA Mini Kit (Qiagen, cat no./ID: 51306)

tag: tissue

value: frontal cortex

tag: gender

value: F

tag: disease state

value: schizophrenic


title: RNAseq_2_minusOHT_shBRCA1#2_rep3


title: RNAseq_2_plusOHT_shBRCA1#2_rep3


title: FL2_AN12657.1_8R01C01

value: M


title: RNAseq_2_plusOHT_shSCR_rep3

value: shSCR


title: ChIPseq_2_minusOHT_flavopiridol_BRCA1

value: flavopiridol


title: 435 shSPHK1.1 LungMet_2 [SA08]

type: RNA

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

country: USA

institute: M. D. Anderson Cancer Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were processed by Illumina GenomeStudio and probe level data were rma normalized and log transformed

label: biotin

source_name: MDA-MB-435 shSPHK1, spontaneous lung met

label_protocol: Illumina TotalPrep RNA Amplification kit (Ambion, AMIL1791). Cleanup with DNA Clean-up and Concentrator 5 columns (zymo research).

growth_protocol: MDA-MB-435 cells were cultured and grown in Dulbecco modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 0.1% penicillin-streptomycin under humidified conditions with 5% CO2 at 37C

extract_protocol: Total RNA from cells was isolated by using Trizol reagent (Invitrogen) according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Small hairpin RNA constructs targeting the SPHK1 3’ untranslated region were cloned into the pGIPZ lentiviral vector and selected with puromycin (2 µg/ml) to obtaine stable clones. Non-silencing shRNA was used as a control. Established cell lines were injected under mouse mammary fat pad and spontaneous lung metastases harvested.

tag: cell line injected

value: MDA-MB-435 breast cancer cell lines (SPHK1 knockdown)

tag: tissue source

value: spontaneous lung metastasis


title: ChIPseq_2_minusOHT_etoposide_BRCA1

value: etoposide


title: RNAseq_2_minusOHT_shSCR_rep3


title: RNAseq_2_plusOHT_shBRCA1#1_rep2


title: RNAseq_2_plusOHT_shBRCA1#1_rep3


title: RNAseq_2_minusOHT_shBRCA1#2_rep2


title: 435 shSPHK1.1 LungMet_1 [SA07]


title: FL2_AN08951.1_7R05C01


title: RNAseq_2_plusOHT_shSCR_rep2


title: FL2_AN10477.3_7R06C02

value: control


title: 435 shSPHK1.1 MFP_2 [SA16]

source_name: MDA-MB-435 shSPHK1, mammary fat pad injection

value: mammary fat pad (MFP) in situ

value: MFP in situ


title: 435 shSCR LungMet_2 [SA06]

source_name: MDA-MB-435 shRNA control, spontaneous lung met

value: MDA-MB-435 breast cancer cell lines (shRNA control)


title: 435 shSCR LungMet_1 [SA05]


title: RNAseq_2_minusOHT_shSCR_rep2


title: FL2_AN14913.1_7R04C02


title: 435 shSCR MFP_1 [SA13]

source_name: MDA-MB-435 shRNA control, mammary fat pad injection


title: RNAseq_2_minusOHT_shBRCA1#1_rep1


title: FL2_A186/93.1_7R04C01


title: RNAseq_2_plusOHT_shBRCA1#1_rep1


title: 435 shSCR MFP_2 [SA14]


title: FL2_AN13227.1_7R06C01


title: FL2_SWED-003.1_7R05C02


title: FL2_AN10450.1_7R03C02


title: RNAseq_2_minusOHT_shBRCA1#2_rep1


title: RNAseq_2_plusOHT_shSCR_rep1


title: RNAseq_2_plusOHT_shBRCA1#2_rep2


title: FL2_SWED-004.1_7R03C01


title: RNAseq_2_minusOHT_shSCR_rep1


title: FL2_SD001/07.1_7R02C02


title: CAL-1 control  IFN Beta treated at 12hr rep 2 with R848 + recombinant vaccinia virus B18R protein

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description:
CAL-1 control  IFN Beta treated at 12hr rep 2 with 1ug/mL R848 (Invitrogen) +   1ug/mL recombinant vaccinia virus B18R protein
X011_SG_Savan_02_11_R848.B18R_CAL.1.pDC_12hr_RNA_Total_run03_S4

data_processing:
Constructed libraries were sequenced on an NextSeq 500 Illumina platform, producing 2x75nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).
Quality control of the primary sequencing data was performed using FastQC (version 0.11.3) and included adapter trimming using cutadapt (version 1.8.3).
Reads were aligned using STAR (version 2.4.0)
Genome_build: Human genome (ENSEMBL, GRCh37)
Supplementary_files_format_and_content: We mapped reads to the human reference genome (GRCh37) from Illumina's igenomes using STAR. After mapping, we assigned aligned read counts from BAM files to exons and genes using the python package HT-Seq.  HT-Seq provided the most accurate way of aligning read counts to overlapping exons. Reads that mapped to multiple positions were removed. Raw counts were normalized using the voom function in limma.
Supplementary_files_format_and_content: normalized count matrix

growth_protocol: CAL-1 cells (1 million cells/mL) were cultured in 0.1% FBS CAL-1 media in triplicate in a 12-well tissue culture plate for 6 hours prior to stimulation with 1,000 U/mL recombinant human IFN-β (PBL Interferon Source) or 1ug/mL R848 (Invitrogen) or 1ug/mL R848 (Invitrogen) + 1ug/mL recombinant vaccinia virus B18R protein (Thermo Fisher Scientific) or mock stimulation.

extract_protocol:
RNA was extracted using RNeasy mini kit (QIAGEN) with on-column DNase treatment.
KAPA Total RNA-seq kit with Ribo Erase
Library quality was evaluated using the Qubit® 3.0 Fluorometer and the Agilent 2100 Bioanalyzer instrument. Constructed libraries were sequenced on an NextSeq 500 Illumina platform, producing 2x75nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).

treatment_protocol: CAL-1 pDC cells rested for 6 hours in 0.1% FBS CAL-1 media prior to stimulations with 1,000U/mL recombinant human IFN-β (PBL Interferon Source), 1ug/mL R848 (InvivoGen) with or without 1ug/mL recombinant vaccinia virus B18R protein (Thermo Fisher Scientific), or CpG-B (InvivoGen).

tag: time

value: IFN Beta with 1ug/mL R848 (Invitrogen) +  1ug/mL recombinant vaccinia virus B18R protein

tag: replicate


title: First Degree Relatives of patients with Celiac [C152]

city: New Delhi

first: Mitali

last: Mukerji

state: Delhi

address: Near Mathura Road, Sukhdev Vihar

department: CSIR TRISUTRA UNIT

country: India

institute: CSIR-Institute of Genomics and Integrative Biology

description:
8986311009_J_Grn.idat
Celiac family
C152

data_processing:
We have extracted the raw intensity files using GenomeStudio software and performed background correction, then applied quantile normalization (using Limma in R) to each array (Celiac Disease, FDR and Control samples) separately.
The overall pattern was expected due to the disease condition of Celiac patients, we also expected overall both FDR and Control individuals should show a similar pattern. Additionally, we have  selected only the probes that passed the criteria of minimum 6/12 samples (per array) with detection p-value <= 0.05, so that final normalized matrix used for further analysis is 13012 rows.

source_name: Multiple mucosal biopsies

label_protocol: Biotinylated cRNA were prepared with the IlluminaTotalPrep RNA Amplification Kit for Illumina arrays

extract_protocol: RNA extraction was carried out using RNeasy mini kit (Qiagen). RNA quantity and quality was estimated using RNA 6000 Nano kit on 2100 Agilent Bioanalyzer. The yield of RNA varied from 12-20µg of total RNA from 25 mg of tissue.

value: intestinal mucus

tag: group

value: FDR

tag: age

value: positive

value: Male


title: CAL-1 control  IFN Beta treated at 12hr rep 3 with R848 + recombinant vaccinia virus B18R protein

description:
CAL-1 control  IFN Beta treated at 12hr rep 3 with 1ug/mL R848 (Invitrogen) +   1ug/mL recombinant vaccinia virus B18R protein
X012_SG_Savan_02_12_R848.B18R_CAL.1.pDC_12hr_RNA_Total_run02_S4


title: RNAseq_2_plusOHT_shBRCA1#2_rep1

value: SH-EP-NMYCER


title: First Degree Relatives of patients with Celiac [C167]

description:
8986311009_L_Grn.idat
Celiac family
C167

value: Female


title: First Degree Relatives of patients with Celiac [C229]

description:
8986311009_K_Grn.idat
Celiac family
C229


title: CAL-1 control  IFN Lambda treated at 12hr rep 3

description:
CAL-1  IFN Lambda treated at 12 hours replicate number  3
X009_SG_Savan_02_9_R848_CAL.1.pDC_12hr_RNA_Total_run01_S1

value: Lambda


title: FL2_SWED-023.1_7R02C01

value: frontal cortex

value: F

value: schizophrenic


title: FL2_AN02883.1_7R01C02

value: M


title: First Degree Relatives of patients with Celiac [C144]

description:
8986311009_I_Grn.idat
Celiac family
C144


title: CAL-1 control  IFN Beta treated at 12hr rep 3

description:
CAL-1  IFN Beta treated at 12 hours replicate number  3
X006_SG_Savan_02_6_IFNB_CAL.1.pDC_12hr_RNA_Total_run01_S2

value: Beta


title: CAL-1 control  IFN Lambda treated at 12hr rep 1

description:
CAL-1  IFN Lambda treated at 12 hours replicate number  1
X007_SG_Savan_02_7_R848_CAL.1.pDC_12hr_RNA_Total_run02_S2


title: FL2_SD004/10.1_7R01C01

value: control


title: CAL-1 control  IFN Beta treated at 12hr rep 2

description:
CAL-1  IFN Beta treated at 12 hours replicate number  2
X005_SG_Savan_02_5_IFNB_CAL.1.pDC_12hr_RNA_Total_run03_S2


title: FL2_AN08194.1_6R06C02


title: CAL-1 control  mock treated at 12hr rep 3

description:
CAL-1  mock treated at 12 hours replicate number  3
X003_SG_Savan_02_3_mock_CAL.1.pDC_12hr_RNA_Total_run02_S1

value: mock


title: First Degree Relatives of patients with Celiac [C134]

description:
8986311009_G_Grn.idat
Celiac family
C134


title: First Degree Relatives of patients with Celiac [C123]

description:
8986311009_F_Grn.idat
Celiac family
C123


title: CAL-1 control  IFN Beta treated at 12hr rep 1

description:
CAL-1  IFN Beta treated at 12 hours replicate number  1
X004_SG_Savan_02_4_IFNB_CAL.1.pDC_12hr_RNA_Total_run01_S3


title: CAL-1 control  IFN Beta treated at 12hr rep 1 with R848 + recombinant vaccinia virus B18R protein

description:
CAL-1 control  IFN Beta treated at 12hr rep 1 with 1ug/mL R848 (Invitrogen) +   1ug/mL recombinant vaccinia virus B18R protein
X010_SG_Savan_02_10_R848.B18R_CAL.1.pDC_12hr_RNA_Total_run02_S3


title: First Degree Relatives of patients with Celiac [C94]

description:
8986311009_D_Grn.idat
Celiac family
C94


title: CAL-1 control  mock treated at 12hr rep 2

description:
CAL-1  mock treated at 12 hours replicate number  2
X002_SG_Savan_02_2_mock_CAL.1.pDC_12hr_RNA_Total_run03_S1


title: First Degree Relatives of patients with Celiac [C135]

description:
8986311009_H_Grn.idat
Celiac family
C135


title: CAL-1 control  IFN Lambda treated at 12hr rep 2

description:
CAL-1  IFN Lambda treated at 12 hours replicate number  2
X008_SG_Savan_02_8_R848_CAL.1.pDC_12hr_RNA_Total_run03_S3


title: RNAseq_plusOHT_shSCR_rep3

description: RNAseq_SH-EP-NMYCER_shBRCA1_countmatrix.txt

data_processing:
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.
For mRNA-seq, reads were mapped to hg19 with Tophat2 and Bowtie2 with default settings.
Reads per gene were counted using the summarizeOverlaps function from the R package {GenomicRanges}.
Weakly and non-expressed genes were removed (mean count over all samples <1).
genome_build: hg19
Supplementary_files_format_and_content: Count matrix containing Ensembl gene ID, gene symbol, gene description and counts for all samples and each gene.

growth_protocol: Neuroblastoma cells were grown in RPMI-1640 (Sigma). Medium was supplemented with 10% fetal calf serum (Biochrom) and penicillin/streptomycin (Sigma).

value: shSCR


title: FL2_SD037/09.1_6R05C02


title: 435 shSPHK1.1 MFP_1 [SA15]

value: MDA-MB-435 breast cancer cell lines (SPHK1 knockdown)

value: mammary fat pad (MFP) in situ

value: MFP in situ


title: CAL-1 control  mock treated at 12hr rep 1

description:
CAL-1  mock treated at 12 hours replicate number  1
X001_SG_Savan_02_1_mock_CAL.1.pDC_12hr_RNA_Total_run01_S4


title: FL2_AN12137.1_6R05C01


title: RNAseq_plusOHT_shSCR_rep2


title: RNAseq_minusOHT_shSCR_rep2

value: EtOH


title: RNAseq_plusOHT_shSCR_rep1


title: First Degree Relatives of patients with Celiac [C76]

description:
8986311009_B_Grn.idat
Celiac family
C76

value: intestinal mucus

value: FDR

value: positive


title: First Degree Relatives of patients with Celiac [C95]

description:
8986311009_E_Grn.idat
Celiac family
C95

value: Male


title: FL2_AN03874.1_6R04C02


title: RNAseq_minusOHT_shSCR_rep1

value: SH-EP-NMYCER


title: FL2_A331/94.1_6R04C01

value: frontal cortex


title: RNAseq_plusOHT_shBRCA1#2_rep3


title: RNAseq_plusOHT_shBRCA1#2_rep1


title: RNAseq_plusOHT_shBRCA1#2_rep2


title: First Degree Relatives of patients with Celiac [C92]

description:
8986311009_C_Grn.idat
Celiac family
C92


title: Control [C73]

description:
8691758032_L_Grn.idat
Control
C73

value: negative


title: FL2_AN12940.1_6R06C01

value: schizophrenic


title: RNAseq_minusOHT_shBRCA1#2_rep3


title: RNAseq_minusOHT_shBRCA1#2_rep1


title: RNAseq_minusOHT_shBRCA1#2_rep2


title: First Degree Relatives of patients with Celiac [C28]

description:
8986311009_A_Grn.idat
Celiac family
C28

value: Female


title: RNAseq_plusOHT_shBRCA1#1_rep3


title: Control [C157]

description:
8691758032_K_Grn.idat
Control
C157


title: FL2_AN00216.1_6R02C02

value: M


title: FL2_AN04122.4_6R03C01

value: F

value: control


title: Control [C141]

description:
8691758032_J_Grn.idat
Control
C141


title: FL2_AN07617.1_6R02C01


title: RNAseq_plusOHT_shBRCA1#1_rep1


title: Control [C78]

description:
8691758032_I_Grn.idat
Control
C78


title: RNAseq_minusOHT_shBRCA1#1_rep3


title: RNAseq_plusOHT_shBRCA1#1_rep2


title: RNAseq_minusOHT_shBRCA1#1_rep2


title: Control [C146]

description:
8691758032_H_Grn.idat
Control
C146


title: RNAseq_minusOHT_shBRCA1#1_rep1


title: ChIPseq_plusOHT_shBRCA1#1_input

data_processing:
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.
For ChIP-seq, fastq files were mapped to the human genome (hg19) using Bowtie v1.1.1. and normalized to the sample with the smallest number of mapped reads.
Peak calling was done with MACS v1.4.2 with default parameters but a p-value cutoff of 1e-6 (BRCA1) and 1e-11 (NMYC) and keep-dup parameter = 5. bedgraph files were generated using bedtools genomecov.
genome_build: hg19
Supplementary_files_format_and_content: bedgraph files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).


title: Control [C74]

description:
8691758032_G_Grn.idat
Control
C74


title: FL2_AN11287.1_6R01C02


title: FL2_SWED-020.1_6R03C02


title: ChIPseq_plusOHT_shSCR_RNAPIIA10

value: shSCR

value: RNAPII (A10, Santa Cruz, sc-17798)


title: FL2_A152/95.1_6R01C01


title: ChIPseq_minusOHT_shSCR_RNAPIIA10


title: FL2_AN17188.3_5R06C02


title: Control [C136]

description:
8691758032_F_Grn.idat
Control
C136


title: ChIPseq_minusOHT_shBRCA1#2_RNAPIIA10


title: FL2_AN15717.2_5R06C01


title: ChIPseq_plusOHT_shSCR_RNAPIIpSer2

value: RNAPII (pSer2, Abcam,  ab5095)


title: ChIPseq_plusOHT_shBRCA1#2_RNAPIIA10


title: Control [C71]

description:
8691758032_E_Grn.idat
Control
C71


title: FL2_AN10477.1_5R05C02


title: ChIPseq_plusOHT_shBRCA1#1_RNAPIIpSer2


title: ChIPseq_plusOHT_shSCR_RNAPIIN20

value: RNAPII (N20, Santa Cruz, sc-899)


title: ChIPseq_minusOHT_shBRCA1#1_RNAPIIpSer2

value: EtOH


title: Control [C189]

description:
8691758032_B_Grn.idat
Control
C189

value: intestinal mucus


title: ChIPseq_minusOHT_shSCR_RNAPIIN20


title: FL2_AN17188.4_5R04C02


title: ChIPseq_minusOHT_shSCR_RNAPIIpSer2


title: ChIPseq_plusOHT_shBRCA1#1_RNAPIIN20


title: ChIPseq_minusOHT_shBRCA1#1_RNAPIIN20


title: FL2_SD020/10.1_5R04C01


title: ChIPseq_plusOHT_inputRNAPII


title: Control [C89]

description:
8691758032_C_Grn.idat
Control
C89


title: Control [C179]

description:
8691758032_A_Grn.idat
Control
C179


title: Control [C77]

description:
8691758032_D_Grn.idat
Control
C77


title: ChIPseq_minusOHT_inputRNAPII


title: RNAseq_2_minusOHT_shBRCA1#1_rep2

description: RNAseq_2_SH-EP-NMYCER_shBRCA1_countmatrix.txt


title: ChIPseq_plusOHT_RNAPIIpSer2


title: Celiac Disease [C139]

description:
8691758046_L_Grn.idat
Celiac Disease
C139

value: CeD


title: FL2_A053/90.1_5R03C02


title: ChIPseq_minusOHT_RNAPIIpSer2


title: FL2_A066/00.1_5R03C01


title: ChIPseq_plusOHT_RNAPIIN20


title: FL2_SD003/09.1_5R05C01


title: ChIPseq_minusOHT_RNAPIIN20


title: Celiac Disease [C98]

description:
8691758046_I_Grn.idat
Celiac Disease
C98

value: positive


title: FL2_SD035/08.1_5R02C02


title: Celiac Disease [C91]

description:
8691758046_J_Grn.idat
Celiac Disease
C91

value: Male


title: Celiac Disease [C150]

description:
8691758046_K_Grn.idat
Celiac Disease
C150


title: FL2_SWED-018.1_5R02C01


title: ChIPseq_plusOHT_inputNMYC

value: SH-EP-NMYCER


title: ChIPseq_minusOHT_inputNMYC


title: FL2_A071/95.1_5R01C02

value: frontal cortex


title: ChIPseq_plusOHT_NMYC

value: NMYC (B8.4.B, Santa Cruz, sc-53993)


title: ChIPseq_minusOHT_NMYC


title: FL2_SD007/10.1_5R01C01


title: Celiac Disease [C138]

description:
8691758046_H_Grn.idat
Celiac Disease
C138


title: FL2_A136/10.1_4R06C02


title: ChIPseq_pWZL-NMYCwt_BRCA1

source_name: SH-EP

value: SH-EP

value: pWZL-NMYCwt

value: BRCA1 (Bethyl, A300-000A)


title: Celiac Disease [C142]

description:
8691758046_G_Grn.idat
Celiac Disease
C142


title: ChIPseq_pWZL-empty_BRCA1

value: pWZL-empty


title: ChIPseq_plusOHT_BRCA1


title: ChIPseq_minusOHT_BRCA1


title: Celiac Disease [C46]

description:
8691758046_F_Grn.idat
Celiac Disease
C46

value: Female


title: Celiac Disease [C206]

description:
8691758046_D_Grn.idat
Celiac Disease
C206


title: FL2_AN03098.1_4R06C01

value: M

value: schizophrenic


title: FL2_A218/93.1_4R05C02


title: FL2_AN07790.1_4R05C01


title: ChIPseq_pWZL-NMYCwt_input


title: Stat5 OE 4

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Ileal crypts isolated from VilCreER;icS5 (STAT5IEC+++) C57Bl6, male mouse at 12 weeks

data_processing:
Following removal of primers and barcodes, raw reads passing quality filtration were aligned to the mm10 mouse genome using TopHat aligment and Cufflinks assembly with annotations provided by UCSC.
Reads were filtered for expression >3 in 100% of at least one experimental condition.
ANOVA was performed to identify differentially regulated transcripts between the three Stat5 conditions, where p<0.05 and fc>1.5 was considered significant.
Genome_build: mm10
Supplementary_files_format_and_content: text file with transcript information and FPKM

organism: Mus musculus

source_name: Ileal crypts

growth_protocol: Ileal crypts were isolated from 12-week-old mice, by shaking intestinbal tissue in PBS with 10mM EDTA at 37C for 30 minutes.

extract_protocol:
Total RNA was extracted using mirVana mRNA isolation kit using the total RNA extraction protocol.  Integrity was determined by Bioanalyzer.
Single end libraries were constructed according to standard Illumina protocols.

tag: genotype

value: VilCreER;icS5 (STAT5IEC+++)

tag: background

tag: age at sac

value: 12 weeks

tag: Sex


title: Stat5 OE 3


title: Celiac Disease [C184]

description:
8691758046_B_Grn.idat
Celiac Disease
C184


title: Stat5 OE 5


title: FL2_A356/99.1_4R04C01

value: F

value: control


title: FL2_A128/95.1_4R03C02


title: Celiac Disease [C153]

description:
8691758046_C_Grn.idat
Celiac Disease
C153

value: intestinal mucus

value: CeD


title: Stat5 OE 1

value: Male


title: Stat5 OE 2


title: Celiac Disease [C34]

description:
8691758046_A_Grn.idat
Celiac Disease
C34

value: positive


title: ChIPseq_plusOHT_input

tag: cell line

value: SH-EP-NMYCER


title: FL2_SWED-010.1_4R04C02

value: frontal cortex


title: FL2_SD001/09.1_4R03C01


title: Stat5 KO 2

description: Ileal crypts isolated from VilCreER;Stat5 (STAT5IEC-/-) C57Bl6, male mouse at 12 weeks

value: VilCreER;Stat5 (STAT5IEC-/-)


title: ChIPseq_minusOHT_input

tag: treatment

value: EtOH


title: A375_Vector_xenograft [Vector3]

city: Los Angeles

first: Vasu

last: Punj

state: CA

address: Biggy Street

institute: USC

data_processing:
Illumina Casava1.7 software was used for basecalling.
Reads were trimmed for quality score and adaptor sequences were also removed. The high-quality reads (between 30-45 million) that passed quality filters were aligned to the human reference genome (GRCh38) using STAR aligner, allowing up to two mismatches in conjunction with the gene model from Ensemble 92. Reads were quantitated by counting the number of reads across exons.
A  gene was designated as "differentially expressed", if it  pass the FDR adjusted p < 0.05 in DEseq ( Anders and Huber 2010, Genome Biol., 11, R106 ) as well as in null model of hypothesis (Kani et al (2017, Mol. Cancer Ther., 16, 1645)
Genome_build: GRCh38
Supplementary_files_format_and_content: normalized read counts

growth_protocol: A375 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum, 2 mM L-glutamine, and 1% penicillin-streptomycin. Cells were maintained at 370 C with 5% CO2.

extract_protocol:
For RNA isolation Qiagen RNeasy Kit (Qiagen, Valencia, CA) was used according to the manufacturer's instructions.
Strand-specific library perpetration was carried out using a KAPA Stranded mRNA-Seq Kit, with KAPA mRNA Capture Beads (KAPA Biosystem Wilmington, MA). The samples were sequenced using a 2 x 150 Paired End (PE) configuration. RNA-Seq was performed with Genewiz (Plainfield, NJ, USA).

treatment_protocol: For subcutaneous xenografts, A375 cells stably expressing WT TFEB or TFEB mutants (5 x 10^6) were injected subcutaneously into the lower flank of 5-6 six-week-old female NOD/SCID mice. After a three-weeks of post-inoculation, mice were sacrificed, and tumors were dissected and processed for RNA isolation.

tag: host strain

value: 5-6 wk-old female NOD/SCID

tag: cell line background

tag: cell line genotype/variation

value: Vector

tag: time point

value: 3 weeks post-injection

value: A375 melanoma xenografts


title: FL2_A344/95.1_4R02C02

tag: tissue

tag: gender

value: M

tag: disease state

value: schizophrenic


title: FL2_AN04122.3_4R02C01


title: A375_Vector_xenograft [Vector1]


title: A375_Vector_xenograft [Vector2]


title: A375_Wild type TFEB_xenograft [TFEB2]

source_name: A375_Wild type TFEB_xenograft

value: Wild type TFEB


title: Stat5 Ctrl 3

description: Ileal crypts isolated from VilCreER;Stat5 (STAT5+/+) C57Bl6, male mouse at 12 weeks

value: VilCreER;Stat5 (STAT5+/+)

value: 12 weeks


title: Celiac Disease [C166]

description:
8691758046_E_Grn.idat
Celiac Disease
C166

value: intestinal mucus

value: Female


title: FL2_AN15948.1_4R01C02

value: control


title: A375_Wild type TFEB_xenograft [TFEB1]


title: A375_Inactive TFEB mutant_xenograft [S142E3]

source_name: A375_Inactive TFEB mutant_xenograft

value: Inactive TFEB mutant


title: CEP_C1.7_3R06C02

value: X

value: CHECK


title: A375_Inactive TFEB mutant_xenograft [S142E2]


title: A375_Active TFEB mutant_xenograft [S142A3]

source_name: A375_Active TFEB mutant_xenograft

value: Active TFEB mutant


title: Stat5 Ctrl 2

value: Male


title: FL2_AN03019.1_3R06C01

value: frontal cortex

value: F


title: A375_Active TFEB mutant_xenograft [S142A1]

value: 5-6 wk-old female NOD/SCID

value: 3 weeks post-injection


title: FL2_SD039/08.1_4R01C01

value: M


title: FL2_A149/94.1_3R05C02

value: schizophrenic


title: Stat5 Ctrl 1


title: SAM24335234 Embryo Peg10 KO Diff 2%O2

city: South San Francisco

first: Rohit

last: Reja

address: 1 DNA Way

institute: Genentech

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

molecule: polyA RNA

source_name: RNA from pluripotent trophoblast stem cells

extract_protocol: Total RNA was extracted using a RNeasy kit with on-column DNase digestion (Qiagen) and 0.5 ug used for library preparation with a TruSeq RNA Sample Preparation Kit v2 (Illumina). The libraries were multiplexed and then sequenced on a HiSeq2500 (Illumina) to generate 30 million paired end 75 bp reads.

value: Embryo

value: Peg10 KO Diff 2%O2

value: Peg10 knockout (KO)

tag: cell type

value: pluripotent trophoblast stem cells


title: A375_Active TFEB mutant_xenograft [S142A2]

value: A375 melanoma xenografts


title: Stat5 KO 1

value: VilCreER;Stat5 (STAT5IEC-/-)

value: 12 weeks


title: SAM24335223 Embryo Peg10 KO TSC

value: Peg10 KO TSC


title: SAM24335215 Embryo WT TSC

value: WT TSC

value: Peg10 wildtype (WT)


title: A375_Wild type TFEB_xenograft [TFEB3]

value: Wild type TFEB


title: FL2_A186/93.2_3R05C01

value: frontal cortex


title: SAM24335219 Embryo WT differentiated TSC

value: WT differentiated TSC


title: FL2_A105/92.1_3R04C02


title: FL2_AN04969.1_3R03C02

value: control


title: A375_Inactive TFEB mutant_xenograft [S142E1]

value: 5-6 wk-old female NOD/SCID

value: Inactive TFEB mutant

value: 3 weeks post-injection


title: FL2_SWED-007.1_3R04C01

value: F

value: schizophrenic


title: SAM24335217 Embryo WT differentiated TSC

value: Embryo


title: SAM24335235 Embryo Peg10 KO Diff 2%O2

value: Peg10 KO Diff 2%O2

value: Peg10 knockout (KO)

value: pluripotent trophoblast stem cells


title: SAM24335236 Embryo WT Diff 2%O2

value: WT Diff 2%O2


title: SAM24335214 Embryo WT TSC


title: SAM24335225 Embryo Peg10.KODifferentiatedTSC


title: SAM24335227 Embryo Peg10.KODifferentiatedTSC


title: Peg10-KO-Day5-rep2

data_processing:
Library strategy: eCLIP-Seq
eCLIP data analysis pipeline from (Van Nostrand et al. 2016 Nat Methods.) was run to remove 3' barcodes and adapter sequences.  Reads were then trimmed and filtered for repetitive elements, and aligned to the mm10 reference sequence using STAR.  PCR duplicate reads were removed from the BAM files.
Peaks were called with matched Peg10 knock out samples using MACS2.
Genome_build: mm10
Supplementary_files_format_and_content: Peak files are in XLS format

source_name: Pluripotent trophoblast stem cells

extract_protocol:
Extraction of RNAs  was performed according to the eCLIP protocol (Van Nostrand et al. 2016 Nat Methods.)
Libraries were sequenced 50 bp single end on HiSeq 4000 (Illumina).

tag: background strain

value: Pluripotent trophoblast stem cells

tag: chip antibody

value: anti-PEG10 (in-house)


title: SAM24335218 Embryo WT differentiated TSC

value: Peg10 wildtype (WT)


title: Peg10-WT-Day5-rep2


title: SAM24335221 Embryo Peg10 KO TSC

value: Peg10 KO TSC


title: Peg10-WT-Day0-rep2


title: Peg10-KO-Day0-rep2


title: Peg10-KO-Day5-rep1


title: SAM24335224 Embryo Peg10 KO TSC


title: SAM24335226 Embryo Peg10.KODifferentiatedTSC


title: Peg10-WT-Day5-rep1


title: Peg10-KO-Day0-rep1


title: SAM24335222 Embryo Peg10 KO TSC


title: SAM24335216 Embryo WT TSC

value: WT TSC


title: Peg10-WT-Day0-rep1


title: FL2_AN18085.2_2R04C02

value: frontal cortex


title: FL2_A194/95.1_3R02C02

value: M


title: FL2_AN01077.1_3R03C01

value: control


title: FL2_AN12312.1_3R01C01


title: FL2_AN12203.1_2R05C01


title: FL2_SWED-024.1_3R01C02


title: FL2_SD018/10.1_2R04C01


title: FL2_SD025/08.1_3R02C01


title: FL2_SWED-019.1_2R06C01


title: FL2_SD028/10.1_2R03C02


title: FL2_AN11937.1_2R05C02


title: FL2_SWED-025.1_2R06C02


title: FL2_AN09659.2_2R03C01


title: SAM24335237 Embryo WT Diff 2%O2


title: SAM24335233 Embryo Peg10 KO Diff 2%O2


title: SAM24335213 Embryo WT TSC


title: NP Trm cells

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 Cliinc sequence core using the pipeline Illumina's RTA software (v2.5.2)
Reads aligned to mouse reference genome (mm10) using Tophat (v2.1.1) with default parameters
Raw count and RPKM were calcualted using RSeQC (v2.3.6) with mm10.refseq.bed12
We further calculated the logFC (Fold Change) by dividing FPKMnp/FPKMpa with additional restrictions on FPKM values as min(FPKMnp, FPKMpa) > 0 and max(FPKMnp, FPKMpa) > 5, and genes were sorted by logFC for GSEA analysis
Genome_build: mm10

source_name: T lymphocytes

growth_protocol: Both NP and PA resident memory CD8 T cells are sorted from total lung cells by flow cytometry.

extract_protocol:
RNAs were extracted using RNeasy Mini Kit.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Prep Kit v2.

treatment_protocol: all cells from influenza A virus PR8 infected C57BL/6 mice.

value: sorted CD8 T cells

tag: passages

tag: strain


title: FL2_A091/93.1_2R02C02


title: FL2_AN17166.1_2R02C01


title: WT-s

city: College Park

first: Jiqiang

last: Ling

state: MD

address: 2202 Microbiology Bldg., 4062 Campus Dr.

department: Cell Biology and Molecular Genetics

institute: The University of Maryland, College Park

description: WTs vs SDs comparisons.csv

data_processing:
High-throughput RNA sequencing data were preprocessed for alignment with Cutadapt(64) to remove Illumina sequencing adapters and low-quality bases (PHRED<20) from the ends of reads.
Trimmed read pairs were then aligned to the NCBI GenBank assembly GCA_000022165.1 for S. enterica serovar Typhimurium 14028 using Bowtie2, and the resulting SAM files were converted to BAM files using SAMtools.
Aligned reads were quantified to individual genes in the annotated genome using Cufflinks and differential expression analysis among samples was performed with Cuffdiff using multi-read correction and FPKM library normalization.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028

source_name: wild type

growth_protocol: Luria Broth at 37 degrees up to mid-log or stationary phase

extract_protocol:
Total RNA was prepared using the RNAprotect Bacteria Reagent and RNeasy Protect Bacteria Kit (Qiagen, Valencia, CA, USA) according to the user’s manuals.
Standard protocol by Genewiz
Strand-specific RNA library preparation with rRNA depletion

tag: genotype/variation

value: wild type

tag: growth phase

value: early-stationary


title: WT-m

description: WTm vs SDm comparisons.csv

value: mid-log


title: SAM24335220 Embryo WT differentiated TSC

value: Embryo

value: WT differentiated TSC

tag: genotype


title: replicate 3 of passage 2 MuVp2r3

city: new york

first: satoshi

last: ikegame

state: new york

address: 1468 madison avenue, Annenbergbuilding 17-24

department: microbiology

institute: Icahn school of medicine at Mount Sinai

description:
replicate 3 of passage 2
RNA from the virion

data_processing:
Albacore software used for basecalling
bwa for alignment
Genome_build: KY295909 (with some modification for technical reason; 'GCG' at the positon of 2630-2632 is replaced by 'TAATAG') for Sendai virus reference sequence, KY295913 (with some modification for tequnical reason; 'TGATGA' insertion at the position of 2768) for mumps virus reference sequence
Supplementary_files_format_and_content: processed data show the coverage of sequence

organism: Mumps orthorubulavirus

source_name: african green monkey renal cells

growth_protocol: Mixture of 8 or 6 viruses (8 in Sendai virus, 6 in mumps virus) which have a unique 15 bp insert in the virus genome were infected to Vero cells. Then passaged twice.

extract_protocol:
QIAamp viral RNA extraction kit were used to extract RNA from supernatant.
RNAs were reverse transcribed and amplified by superscript III one-step. Amplified amplicon were processed by Ligation sequencing kit of Oxford nanopore's technology.

value: Vero cells


title: SAM24335228 Embryo Peg10.KODifferentiatedTSC

value: Peg10 knockout (KO)

value: pluripotent trophoblast stem cells


title: replicate 2 of passage 2 MuVp2r2

description:
replicate 2 of passage 2
RNA from the virion


title: FL2_AN15414.1_2R01C01


title: SL-s

description: WTs vs SLs comparisons.csv

source_name: rpsL* mutant

value: rpsL* mutant


title: FL2_SWED-026.1_1R06C02

source_name: genomic DNA from frontal cortex post-mortem brain tissue

value: F

value: schizophrenic


title: replicate 1 of passage 2 MuVp2r1

description:
replicate 1 of passage 2
RNA from the virion


title: FL2_SWED-016.1_1R06C01


title: FL2_SD023/11.1_1R05C02


title: replicate 1 of passage 1 MuVp1r1

description:
replicate 1 of passage 1
RNA from the virion


title: FL2_SWED-011.1_1R05C01


title: replicate 2 of passage 1 MuVp1r2

description:
replicate 2 of passage 1
RNA from the virion


title: replicate 3 of passage 1 MuVp1r3

description:
replicate 3 of passage 1
RNA from the virion


title: ChIPseq_plusOHT_shBRCA1#2_input

source_name: SH-EP-NMYCER

tag: cell line

value: SH-EP-NMYCER

tag: shRNA

tag: antibody


title: SD-m

description: WTm vs SDm comparisons.csv

source_name: rpsD* mutant

value: rpsD* mutant


title: PA Trm cells


title: SD-s

description: WTs vs SDs comparisons.csv


title: SLC35F2 KO H9 rep2

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

country: South Korea

institute: Pusan National University

description: Total RNA

data_processing:
The read quality of RNAseq raw fastq files were checked using FastQC (v0.11.7) and the adapter sequences in reads were eliminated using cutadapt (v1.8.1).
Trimmed fastq files were aligned to GRCh38 genome using STAR aligner(v2.6.0a), then the read counts for genes were acquired using HTseq (v0.11.0) with Gencode v22 annotation GTF (https://www.gencodegenes.org/human/release_22.html).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read count values for each sample.

source_name: hESC cell line (WA09)

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Extracted total RNA were processed with Illumina TruSeq Stranded mRNA LT Sample Prep (Part #15031047 Rev. E)
The Illumina sequencer generated raw images and base calling through RTA (Real Time Anlysis) program. Base calls binary is converted into FASTQ through bcl2fastq package. The data were normalised using quantile normalisation with IlluminaGUI in R

value: hESC

value: SLC35F2 KO


title: FL2_SWED-005.1_2R01C02

value: frontal cortex

value: M


title: SL-m

description: WTm vs SLm comparisons.csv


title: input MuVp0

description:
input
RNA from the virion

value: input


title: Control H9 rep2

description: Total RNA

value: control


title: FL2_SD041/11.2_1R04C01


title: FL2_AN05617.1_1R04C02


title: SLC35F2 KO H9 rep1

description: Total RNA


title: FL2_A123/94.1_1R03C02


title: replicate 2 of passage 2 SeVp2r2

organism: Respirovirus muris


title: FL2_SD040/10.1_1R03C01


title: FL2_AN19868.2_1R01C01


title: input SeVp0

description:
input
RNA from the virion


title: replicate 2 of passage 1 SeVp1r2


title: replicate 3 of passage 2 SeVp2r3


title: FL2_AN12408.1_1R02C02


title: FL2_SWED-017.1_1R01C02


title: replicate 1 of passage 1 SeVp1r1


title: FL2_AN04660.1_1R02C01


title: replicate 3 of passage 1 SeVp1r3


title: Control H9 rep1

description: Total RNA


title: MDA-468 3

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: The microarray hybridization was performed in Affymetrix U133 Plus 2.0 microarray chips at Affymetrix F450 fluidics station using the EukGE-WS2v5_450 protocol.

scan_protocol: The microarray was scanned with an Affymetix GeneChip 7 G scanner (Affymetix, Santa Clara, CA).

data_processing: The data was analyzed by the statistical core facility at Dan L. Duncan Cancer Center at Baylor College of Mediaine. CEL files were processed in Bioconductor using Quantile method.

label_protocol: Cybrids containing mitochondria derived from MCF10A, MDA-MB-468 and 143B cells with 143B p0 cells as nuclear background are named as 10A/143B, 468/143B and 143B/143B cybrids, respectively.

growth_protocol: For generating cybrids, motochondrial donor cells (MCF10A, MDA-MB-468 and 143B TK-) were enucleated by overnight actinomycin-D treatment and fused with the 143B p0 cells using 45% polyethylene glycol (MW 1450; Sigma cat P-5402) for 60 seconds. One day following fusion, cells were cultured in selection medium with bromodeoxyuridine (BrdU) but without uridine. Unfused control 143 p0 cells could not survive without uridine and mitochondria donor cells were killed by BrdU.

extract_protocol: RNA from 10A/143B and 468/143B cybrids were extracted in triplicate and 5ug of total RNA was used for first- and second-strand cDNA synthesis.

treatment_protocol: According to Affymetix protocol.


title: replicate 1 of passage 2 SeVp2r1


title: MDA-468 2


title: MCF10A 3


title: MCF10A 2


title: MCF10A 1


title: MDA-468 1


title: TCRb+YFP+CD44hi+CD27- IL17aCre-YFP (WT), replicate 6

status: Public on Mar 20 2019

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Six micrograms (6 ug) of cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix Mouse Gene 2.0 ST GeneChip array.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Signals were summarized using the Robust Multichip Algorithm (RMA) using Partek Genomics Suite software v6.6 (Partek, Inc) or by fitting a linear model implemented in the R package “limma” (Ritchie et al., 2015). The YFP+ WT and Raptor-KO fate mapped TH17 cells were summarized as one group, while the CD44intCD27+ and CD44hiCD27- fate mapped TH17 cells were summarized as a separate group.

source_name: sorted TCRb+YFP+CD44hiCD27- T-cells from draining lymph node on day 9 after MOG immunization

label_protocol: For TCRb+YFP+ WT and TCRb+YFP+ Raptor-ko fate mapped TH17 cells, ten nanograms (10 ng) of total RNA were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module. For the CD44intCD27hi and CD44+CD27- fate mapped TH17 cells, five hundred picograns (500 pg) of total RNA were converted into biotinylated cDNA using the Affymetrix WT Pico protocol (Applied Biosystems P/N 902623).

growth_protocol: Cells were freshly sorted from draining lymph nodes on day 9 after subcutaneous immunization with 200ug Myelin Oligodendrocyte Glycoprotein (AA35-55) (MOG 35-55) emulsified in 200 ul of  incomplete Freund's adjuvant supplemented with 1 mg of Mycobacterium tuberculosis strain H37Ra (Complete Freund's Adjuvant).

extract_protocol: RNA samples were prepared according to the manufacturer's instructions of Rneasy Micro kit from Qiagen

treatment_protocol: Sorted cells were lysed with lysis buffer from Rneasy Micro kit from Qiagen

value: C57BL/6 background

tag: Sex

value: female


title: NDL_Slk_wt_3

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

country: Canada

institute: Ottawa Hospital Research Institute

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Expression Console 1.4.1.46

source_name: SLK wild-type cells

label_protocol: not provided

growth_protocol: Cells were cultured in DMEM/F12 with 10% FBS, 1% Penicllin 1% Streptamycin, 1% L-glutamine and 1% Mammary epithelial growth supplement

extract_protocol: not provided

treatment_protocol: Cells were untreated

value: NeuNDL-derived cells

value: SLK wild-type


title: wildtype SC, biological rep3

city: Chicago

first: Pei

last: Zhu

state: IL

address: 1111 S Laflin Street, Apt314

department: Department of Biochemistry and Molecular Genetics

institute: university of illinois at chicago

description: Gene expression data from SCs in resting hindlimb muscles of wildtype mice

hyb_protocol: Samples were labeled using the Affymetrix GeneChip® WT PLUS Kit as per manufacturer's protocols.

scan_protocol: The GeneChip® Hybridization, Wash, and Stain Kit was used as per manufacturer’s protocols. The GeneChip® Fluidics Station 450 was used for washing and staining using fluidics script FS450_0002.

data_processing: Signal acquisition done using on the GeneChip® Scanner 3000 7G with AGCC version 4.0.0.1567.

source_name: SCs from resting hindlimb muscles

label_protocol: Affymetrix WT Plus labeling protocol

growth_protocol: Primary SCs were direactly sorted for RNA extraction without ex-vivo culture.

extract_protocol: Total RNA was extracted from SCs using Quick-RNATM MicroPrep kit (ZYMO Research, USA).

treatment_protocol: Primary SCs were direactly sorted from resting hindlimb muscles without pre-treatment before RNA extraction.

value: male

tag: age

value: adult

value: Slug+/+


title: TCRb+YFP+CD44int+CD27+ IL17aCre-YFP (WT), replicate 3

source_name: sorted TCRb+YFP+CD44intCD27+ T-cells from draining lymph node on day 9 after MOG immunization


title: NDL_Slk_wt_1


title: TCRb+YFP+CD44hi+CD27- IL17aCre-YFP (WT), replicate 4


title: TCRb+YFP+CD44hi+CD27- IL17aCre-YFP (WT), replicate 2


title: TCRb+YFP+CD44hi+CD27- IL17aCre-YFP (WT), replicate 3


title: NDL_Slk_KO_2

source_name: SLK knockout cells

value: SLK knockout


title: TCRb+YFP+CD44hi+CD27- IL17aCre-YFP (WT), replicate 5


title: NDL_Slk_KO_3


title: SlugKO SC, biological rep2

description: Gene expression data from SCs in resting hindlimb muscles of SlugKO mice

value: Slug-/-


title: SlugKO SC, biological rep3


title: NDL_Slk_KO_1


title: NDL_Slk_wt_2


title: TCRb+YFP+CD44hi+CD27- IL17aCre-YFP (WT), replicate 1


title: SlugKO SC, biological rep1


title: wildtype SC, biological rep2


title: TCRb+YFP+CD44int+CD27+ IL17aCre-YFP (WT), replicate 5


title: wildtype SC, biological rep1


title: TCRb+YFP+CD44int+CD27+ IL17aCre-YFP (WT), replicate 6


title: TCRb+YFP+CD44int+CD27+ IL17aCre-YFP (WT), replicate 2


title: eletro2

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
Fastq reads were aligned to the mm10 reference genome with Bowtie.
NHEJ as well as frameshift/in-frame mutations were quantified with CRISPResso.
Genome_build: mm10

source_name: Retina

extract_protocol:
In case of indel analysis, retinae were dissociated (papain 10 U/ml, Worthington, 10 min, 37°C) (68) and FACS-sorted (MoFlo, Beckman Coulter, Inc.).
Genomic PCR products were subjected to library preparation using the NEBNext Ultra II DNA library Kit (NEB). Briefly, common primers are added by ligation, following by limited number of PCR cycles (eight cycles) where specific barcode for each sample was added. Amplicones were purificated with AMPure beads (Beckman Coulter) and run onto Bioanalyzer 2100 (Agilent). Equimolar amounts of library were mixed, diluited and sequenced with an Illumina MiSeq system. CASAVA software (Illumina) was used for demultiplexing.

treatment_protocol: Electoporated retinae were dissected under a fluorescence dissecting microscope. GFP+ retinae were selected for further analysis based on fluorescence intensity and diffusion but also retinal integrity.

tag: sample type

value: P0 retinae

tag: treatment

value: electroporated with pCAG-SpCas9 and pCAG-sgRNA-mMUT expression vectors

value: Heterozygous P23H knock-in mice (The Jackson Laboratory, Bar Harbor, ME)


title: TCRb+YFP+CD44int+CD27+ IL17aCre-YFP (WT), replicate 4


title: TCRb+YFP+ WT, replicate 4

source_name: sorted TCRb+YFP+ T-cells from draining lymph node on day 9 after MOG immunization


title: electro1


title: TCRb+YFP+CD44int+CD27+ IL17aCre-YFP (WT), replicate 1


title: Cont

value: electroporated with pCAG-SpCas9 and pCAG-GFP expression vectors


title: TCRb+YFP+ WT, replicate 1


title: TCRb+YFP+ WT, replicate 3


title: TCRb+YFP+ IL17aCre-Raptor-flox/flox, replicate 1


title: TCRb+YFP+ IL17aCre-Raptor-flox/flox, replicate 2


title: AAV3

value: P21 retinae

value: intravitreally injected with AAV-Cas9-VQR and AAV-U6sgRNAmMUT-RHOp-GFP-t2a-rtTA PHP.B serotype


title: AAV1


title: TCRb+YFP+ WT, replicate 2


title: AAV2


title: EFZ204935A Normal ileum

city: Spring House

first: K

last: Li

state: PA

address: 1400 McKean Road

institute: Janssen R&D

hyb_protocol: Following fragmentation, 1.875ug of cDNA was hybridized for 16 hr at 45oC on GeneChip HT HG-U133+ PM 96 array plates. GeneChips were washed and stained in the Affymetrix GeneChip Array Station.

scan_protocol: GeneChips were scanned using the GeneChipHT Scanner.

data_processing: The data was normalized by RMA using ArrayStudio version 10.

source_name: ileum biopsy

label_protocol: Target was prepared from 100ng total RNA using the NuGEN Ovation V2 kit, followed by NuGEN Encore biotin labeling module, using the manufacturer’s protocol.

extract_protocol: Total RNA was isolated with Qiagen's RNeasy mini kit according to the manufacturer’s instructions.

treatment_protocol: For each subject, biopsy samples were collected during endoscopy.  Biopsies were kept frozen –80oC until RNA preparation.

tag: tissue

value: ileum

tag: diagnosis

value: Normal (non-IBD)

tag: subject

value: Normal

tag: visit

tag: i-wk8 response

tag: gi involvement

tag: ileum ses-cd score


title: EFZ188703A Normal ileum


title: EFZ181631A Normal ileum


title: EFZ188395A Normal ileum


title: EFZ216356A Normal ileum


title: EFZ203383A Normal ileum


title: EFZ176281A Normal ileum


title: EFZ172297A Normal ileum


title: EFZ174673A Normal ileum


title: EFZ207317A Normal ileum


title: EFZ181312A Normal ileum


title: EFZ174605A Normal ileum


title: EFZ197138A Normal ileum


title: EFZ181273A Normal ileum


title: EFZ184192A Normal ileum


title: EFZ181564A Normal ileum


title: EFZ173508A Normal ileum


title: EFZ194887A Normal ileum


title: EFZ205063A Normal ileum


title: EFZ166972A Normal ileum


title: CNTO1275CRD3002-20345 M-WK44 ileum

value: Crohn's disease (CD)

value: Ust

value: Y

value: Ileum and colon


title: CNTO1275CRD3002-20350 M-WK44 ileum

value: Ileum only


title: EFZ171541A Normal ileum


title: EFZ208692A Normal ileum


title: EFZ159583A Normal ileum


title: CNTO1275CRD3002-20894 M-WK44 ileum

value: N


title: EFZ170759A Normal ileum


title: EFZ209642A Normal ileum


title: CNTO1275CRD3002-20170 M-WK44 ileum

value: Colon only


title: EFZ168281A Normal ileum


title: CNTO1275CRD3002-20004 M-WK44 ileum


title: CNTO1275CRD3002-20459 M-WK44 ileum


title: CNTO1275CRD3002-20632 M-WK44 ileum


title: CNTO1275CRD3002-20648 M-WK44 ileum


title: CNTO1275CRD3002-20106 M-WK44 ileum


title: CNTO1275CRD3002-20141 M-WK44 ileum


title: CNTO1275CRD3002-20058 M-WK44 ileum


title: CNTO1275CRD3002-20133 M-WK44 ileum


title: CNTO1275CRD3002-20087 M-WK44 ileum


title: CNTO1275CRD3002-20531 M-WK44 ileum


title: CNTO1275CRD3002-20542 M-WK44 ileum


title: CNTO1275CRD3002-20623 M-WK44 ileum


title: CNTO1275CRD3002-20584 M-WK44 ileum


title: CNTO1275CRD3002-20306 M-WK44 ileum


title: CNTO1275CRD3002-20257 M-WK44 ileum


title: CNTO1275CRD3002-21026 M-WK44 ileum


title: CNTO1275CRD3002-20969 M-WK44 ileum


title: CNTO1275CRD3002-20279 M-WK44 ileum


title: CNTO1275CRD3002-20838 M-WK44 ileum


title: CNTO1275CRD3002-20769 M-WK44 ileum


title: CNTO1275CRD3002-20685 M-WK44 ileum


title: CNTO1275CRD3002-20166 M-WK44 ileum


title: CNTO1275CRD3002-20215 M-WK44 ileum


title: CNTO1275CRD3002-20219 M-WK44 ileum


title: CNTO1275CRD3002-20045 M-WK44 ileum


title: CNTO1275CRD3002-20886 M-WK44 ileum


title: CNTO1275CRD3002-20836 M-WK44 ileum


title: CNTO1275CRD3002-20971 M-WK44 ileum


title: CNTO1275CRD3002-20929 M-WK44 ileum


title: CNTO1275CRD3002-21010 M-WK44 ileum


title: CNTO1275CRD3002-21032 M-WK44 ileum


title: CNTO1275CRD3002-20021 M-WK44 ileum


title: CNTO1275CRD3002-20843 M-WK44 ileum


title: CNTO1275CRD3002-20151 M-WK44 ileum


title: CNTO1275CRD3002-20851 M-WK44 ileum


title: CNTO1275CRD3002-20962 M-WK44 ileum


title: CNTO1275CRD3002-20667 M-WK44 ileum


title: CNTO1275CRD3002-20927 M-WK44 ileum


title: CNTO1275CRD3002-20209 M-WK44 ileum


title: CNTO1275CRD3002-20182 M-WK44 ileum

value: Pbo


title: CNTO1275CRD3002-21017 M-WK44 ileum


title: CNTO1275CRD3002-20980 M-WK44 ileum


title: CNTO1275CRD3002-20009 M-WK44 ileum


title: CNTO1275CRD3002-20548 M-WK44 ileum


title: CNTO1275CRD3002-20879 M-WK44 ileum


title: CNTO1275CRD3002-20458 M-WK44 ileum


title: CNTO1275CRD3002-20286 M-WK44 ileum


title: CNTO1275CRD3002-20270 M-WK44 ileum


title: CNTO1275CRD3002-20563 M-WK44 ileum


title: CNTO1275CRD3002-20821 M-WK44 ileum


title: CNTO1275CRD3002-20908 M-WK44 ileum


title: CNTO1275CRD3002-20038 M-WK44 ileum


title: CNTO1275CRD3002-20514 M-WK44 ileum


title: CNTO1275CRD3002-20728 M-WK44 ileum


title: CNTO1275CRD3002-20003 M-WK44 ileum


title: CNTO1275CRD3002-20301 M-WK44 ileum


title: CNTO1275CRD3002-20783 M-WK44 ileum


title: CNTO1275CRD3002-20504 M-WK44 ileum


title: CNTO1275CRD3002-21035 M-WK44 ileum


title: CNTO1275CRD3002-21011 M-WK44 ileum


title: CNTO1275CRD3002-20295 M-WK44 ileum


title: CNTO1275CRD3002-20244 M-WK44 ileum


title: CNTO1275CRD3002-20805 M-WK44 ileum


title: CNTO1275CRD3002-20922 M-WK44 ileum


title: CNTO1275CRD3002-20155 M-WK44 ileum


title: CNTO1275CRD3002-20405 M-WK44 ileum


title: CNTO1275CRD3002-20781 M-WK44 ileum


title: CNTO1275CRD3002-20565 M-WK44 ileum


title: CNTO1275CRD3002-20395 M-WK44 ileum


title: CNTO1275CRD3002-20978 M-WK44 ileum


title: CNTO1275CRD3002-20449 M-WK44 ileum


title: CNTO1275CRD3002-20513 M-WK44 ileum


title: CNTO1275CRD3002-20196 M-WK44 ileum


title: CNTO1275CRD3002-20616 M-WK44 ileum


title: CNTO1275CRD3002-20959 M-WK44 ileum


title: CNTO1275CRD3002-20072 M-WK44 ileum


title: CNTO1275CRD3002-20176 M-WK44 ileum


title: CNTO1275CRD3002-20732 M-WK44 ileum


title: CNTO1275CRD3002-20529 M-WK44 ileum


title: CNTO1275CRD3002-20291 M-WK44 ileum


title: CNTO1275CRD3002-21043 M-WK44 ileum


title: CNTO1275CRD3002-20231 M-WK44 ileum


title: CNTO1275CRD3002-20791 M-WK44 ileum


title: CNTO1275CRD3002-20821 I-WK8 ileum


title: CNTO1275CRD3002-20886 I-WK8 ileum


title: CNTO1275CRD3002-20971 I-WK8 ileum


title: CNTO1275CRD3002-20929 I-WK8 ileum


title: CNTO1275CRD3002-20215 I-WK8 ileum


title: CNTO1275CRD3002-21010 I-WK8 ileum


title: CNTO1275CRD3002-20928 I-WK8 ileum


title: CNTO1275CRD3002-20350 I-WK8 ileum


title: CNTO1275CRD3002-20836 I-WK8 ileum


title: CNTO1275CRD3002-20894 I-WK8 ileum


title: CNTO1275CRD3002-20623 I-WK8 ileum


title: CNTO1275CRD3002-20257 I-WK8 ileum


title: CNTO1275CRD3002-20170 I-WK8 ileum


title: CNTO1275CRD3002-20641 I-WK8 ileum


title: CNTO1275CRD3002-20648 I-WK8 ileum


title: CNTO1275CRD3002-20584 I-WK8 ileum


title: CNTO1275CRD3002-20219 I-WK8 ileum


title: CNTO1275CRD3002-20058 I-WK8 ileum


title: CNTO1275CRD3002-20234 I-WK8 ileum


title: CNTO1275CRD3002-20043 I-WK8 ileum


title: CNTO1275CRD3002-20798 I-WK8 ileum


title: CNTO1275CRD3002-20969 I-WK8 ileum


title: CNTO1275CRD3002-20713 I-WK8 ileum


title: CNTO1275CRD3002-20166 I-WK8 ileum


title: CNTO1275CRD3002-20004 I-WK8 ileum


title: CNTO1275CRD3002-20632 I-WK8 ileum


title: CNTO1275CRD3002-20779 I-WK8 ileum


title: CNTO1275CRD3002-21026 I-WK8 ileum


title: CNTO1275CRD3002-20838 I-WK8 ileum


title: CNTO1275CRD3002-20141 I-WK8 ileum


title: CNTO1275CRD3002-20087 I-WK8 ileum


title: CNTO1275CRD3002-20133 I-WK8 ileum


title: CNTO1275CRD3002-20513 I-WK8 ileum


title: CNTO1275CRD3002-20438 I-WK8 ileum


title: CNTO1275CRD3002-21032 I-WK8 ileum


title: CNTO1275CRD3002-20673 I-WK8 ileum


title: CNTO1275CRD3002-20187 M-WK44 ileum


title: CNTO1275CRD3002-20769 I-WK8 ileum


title: CNTO1275CRD3002-20295 I-WK8 ileum


title: CNTO1275CRD3002-20279 I-WK8 ileum


title: CNTO1275CRD3002-20685 I-WK8 ileum


title: CNTO1275CRD3002-20098 I-WK8 ileum


title: CNTO1275CRD3002-20404 I-WK8 ileum


title: CNTO1275CRD3002-20021 I-WK8 ileum


title: CNTO1275CRD3002-20667 I-WK8 ileum


title: CNTO1275CRD3002-20198 I-WK8 ileum


title: CNTO1275CRD3002-21011 I-WK8 ileum


title: CNTO1275CRD3002-20459 I-WK8 ileum


title: CNTO1275CRD3002-20106 I-WK8 ileum


title: CNTO1275CRD3002-20975 I-WK8 ileum


title: CNTO1275CRD3002-20531 I-WK8 ileum


title: CNTO1275CRD3002-20878 I-WK8 ileum


title: CNTO1275CRD3002-20927 I-WK8 ileum


title: CNTO1275CRD3002-21017 I-WK8 ileum


title: CNTO1275CRD3002-20237 I-WK8 ileum


title: CNTO1275CRD3002-20548 I-WK8 ileum


title: CNTO1275CRD3002-20980 I-WK8 ileum


title: CNTO1275CRD3002-20017 I-WK8 ileum


title: CNTO1275CRD3002-20908 I-WK8 ileum


title: CNTO1275CRD3002-20458 I-WK8 ileum


title: CNTO1275CRD3002-20851 I-WK8 ileum


title: CNTO1275CRD3002-21019 I-WK8 ileum

value: Discontinued


title: CNTO1275CRD3002-20761 I-WK8 ileum


title: CNTO1275CRD3002-20529 I-WK8 ileum


title: CNTO1275CRD3002-20182 I-WK8 ileum


title: CNTO1275CRD3002-20514 I-WK8 ileum


title: CNTO1275CRD3002-20203 I-WK8 ileum


title: CNTO1275CRD3002-20209 I-WK8 ileum


title: CNTO1275CRD3002-20051 I-WK8 ileum


title: CNTO1275CRD3002-20065 I-WK8 ileum


title: CNTO1275CRD3002-20559 I-WK8 ileum


title: CNTO1275CRD3002-20962 I-WK8 ileum


title: CNTO1275CRD3002-20656 I-WK8 ileum


title: CNTO1275CRD3002-20329 I-WK8 ileum


title: CNTO1275CRD3002-20653 I-WK8 ileum


title: CNTO1275CRD3002-20270 I-WK8 ileum


title: CNTO1275CRD3002-20556 I-WK8 ileum


title: CNTO1275CRD3002-20554 I-WK8 ileum


title: CNTO1275CRD3002-20082 I-WK8 ileum


title: CNTO1275CRD3002-20541 I-WK8 ileum


title: CNTO1275CRD3002-20173 I-WK8 ileum


title: CNTO1275CRD3002-20037 I-WK8 ileum


title: CNTO1275CRD3002-20171 I-WK8 ileum


title: CNTO1275CRD3002-21028 I-WK8 ileum


title: CNTO1275CRD3002-20109 I-WK8 ileum


title: CNTO1275CRD3002-20301 I-WK8 ileum


title: CNTO1275CRD3002-20783 I-WK8 ileum


title: CNTO1275CRD3002-20781 I-WK8 ileum


title: CNTO1275CRD3002-20953 M-WK44 ileum


title: CNTO1275CRD3002-20187 I-WK8 ileum


title: CNTO1275CRD3002-20304 I-WK8 ileum


title: CNTO1275CRD3002-20998 I-WK8 ileum


title: CNTO1275CRD3002-20009 I-WK8 ileum


title: CNTO1275CRD3002-20449 I-WK8 ileum


title: CNTO1275CRD3002-20805 I-WK8 ileum


title: CNTO1275CRD3002-20922 I-WK8 ileum


title: CNTO1275CRD3002-20405 I-WK8 ileum


title: CNTO1275CRD3002-20258 I-WK8 ileum


title: CNTO1275CRD3002-21043 I-WK8 ileum


title: CNTO1275CRD3002-20791 I-WK8 ileum


title: CNTO1275CRD3002-20244 I-WK8 ileum


title: CNTO1275CRD3002-20273 I-WK8 ileum


title: CNTO1275CRD3002-20231 I-WK8 ileum


title: CNTO1275CRD3002-20504 I-WK8 ileum


title: CNTO1275CRD3002-20038 I-WK8 ileum


title: CNTO1275CRD3002-20959 I-WK8 ileum


title: CNTO1275CRD3002-20358 I-WK8 ileum


title: CNTO1275CRD3002-20732 I-WK8 ileum


title: CNTO1275CRD3002-20395 I-WK8 ileum


title: CNTO1275CRD3002-20176 I-WK8 ileum


title: CNTO1275CRD3002-20728 I-WK8 ileum


title: CNTO1275CRD3002-21035 I-WK8 ileum


title: CNTO1275CRD3002-20953 I-WK8 ileum


title: CNTO1275CRD3002-20196 I-WK8 ileum


title: CNTO1275CRD3002-20381 I-WK8 ileum


title: CNTO1275CRD3002-20978 I-WK8 ileum


title: CNTO1275CRD3002-20290 I-WK8 ileum


title: CNTO1275CRD3002-20865 I-WK8 ileum


title: CNTO1275CRD3002-20637 I-WK8 ileum


title: CNTO1275CRD3002-20090 I-WK8 ileum


title: CNTO1275CRD3002-20678 I-WK8 ileum


title: CNTO1275CRD3002-20970 I-WK8 ileum


title: CNTO1275CRD3002-20346 I-WK8 ileum


title: CNTO1275CRD3002-20291 I-WK8 ileum


title: CNTO1275CRD3002-20367 I-WK8 ileum


title: CNTO1275CRD3002-20547 I-WK8 ileum


title: CNTO1275CRD3002-20239 I-WK8 ileum


title: CNTO1275CRD3002-21010 I-WK0 ileum


title: CNTO1275CRD3002-20929 I-WK0 ileum


title: CNTO1275CRD3002-20072 I-WK8 ileum


title: CNTO1275CRD3002-20821 I-WK0 ileum


title: CNTO1275CRD3002-20441 I-WK8 ileum


title: CNTO1275CRD3002-20928 I-WK0 ileum


title: CNTO1275CRD3002-20350 I-WK0 ileum


title: CNTO1275CRD3002-20170 I-WK0 ileum


title: CNTO1275CRD3002-20577 I-WK8 ileum


title: CNTO1275CRD3002-20757 I-WK8 ileum


title: CNTO1275CRD3002-20484 I-WK8 ileum


title: CNTO1275CRD3002-20604 I-WK8 ileum


title: CNTO1275CRD3002-20295 I-WK0 ileum


title: CNTO1275CRD3002-20836 I-WK0 ileum


title: CNTO1275CRD3002-20838 I-WK0 ileum


title: CNTO1275CRD3002-20879 I-WK8 ileum


title: CNTO1275CRD3002-20257 I-WK0 ileum


title: CNTO1275CRD3002-20584 I-WK0 ileum


title: CNTO1275CRD3002-20971 I-WK0 ileum


title: CNTO1275CRD3002-21032 I-WK0 ileum


title: CNTO1275CRD3002-20459 I-WK0 ileum


title: CNTO1275CRD3002-20438 I-WK0 ileum


title: CNTO1275CRD3002-20648 I-WK0 ileum


title: CNTO1275CRD3002-20345 I-WK0 ileum


title: CNTO1275CRD3002-20043 I-WK0 ileum


title: CNTO1275CRD3002-20279 I-WK0 ileum


title: CNTO1275CRD3002-20621 I-WK0 ileum


title: CNTO1275CRD3002-20219 I-WK0 ileum


title: CNTO1275CRD3002-20969 I-WK0 ileum


title: CNTO1275CRD3002-20623 I-WK0 ileum


title: CNTO1275CRD3002-20215 I-WK0 ileum


title: CNTO1275CRD3002-20104 I-WK0 ileum


title: CNTO1275CRD3002-20141 I-WK0 ileum


title: CNTO1275CRD3002-20058 I-WK0 ileum


title: CNTO1275CRD3002-20004 I-WK0 ileum


title: CNTO1275CRD3002-20713 I-WK0 ileum


title: CNTO1275CRD3002-20106 I-WK0 ileum


title: CNTO1275CRD3002-20779 I-WK0 ileum


title: CNTO1275CRD3002-20351 I-WK0 ileum


title: CNTO1275CRD3002-20851 I-WK0 ileum


title: CNTO1275CRD3002-20542 I-WK0 ileum


title: CNTO1275CRD3002-20798 I-WK0 ileum


title: CNTO1275CRD3002-20166 I-WK0 ileum


title: CNTO1275CRD3002-20894 I-WK0 ileum


title: CNTO1275CRD3002-20769 I-WK0 ileum


title: CNTO1275CRD3002-20673 I-WK0 ileum


title: CNTO1275CRD3002-20975 I-WK0 ileum


title: CNTO1275CRD3002-20843 I-WK0 ileum


title: CNTO1275CRD3002-20685 I-WK0 ileum


title: CNTO1275CRD3002-20393 I-WK0 ileum


title: CNTO1275CRD3002-20667 I-WK0 ileum


title: CNTO1275CRD3002-20198 I-WK0 ileum


title: CNTO1275CRD3002-20404 I-WK0 ileum


title: CNTO1275CRD3002-20151 I-WK0 ileum


title: CNTO1275CRD3002-20863 I-WK0 ileum


title: CNTO1275CRD3002-20675 I-WK0 ileum


title: CNTO1275CRD3002-21011 I-WK0 ileum


title: CNTO1275CRD3002-20980 I-WK0 ileum


title: CNTO1275CRD3002-20927 I-WK0 ileum


title: CNTO1275CRD3002-20174 I-WK0 ileum


title: CNTO1275CRD3002-20681 I-WK0 ileum


title: CNTO1275CRD3002-20878 I-WK0 ileum


title: CNTO1275CRD3002-20529 I-WK0 ileum


title: CNTO1275CRD3002-20660 I-WK0 ileum


title: CNTO1275CRD3002-20962 I-WK0 ileum


title: CNTO1275CRD3002-20270 I-WK0 ileum


title: CNTO1275CRD3002-20182 I-WK0 ileum


title: CNTO1275CRD3002-20237 I-WK0 ileum


title: CNTO1275CRD3002-20879 I-WK0 ileum


title: CNTO1275CRD3002-21017 I-WK0 ileum


title: CNTO1275CRD3002-20514 I-WK0 ileum


title: CNTO1275CRD3002-20814 I-WK0 ileum


title: CNTO1275CRD3002-20908 I-WK0 ileum


title: CNTO1275CRD3002-20848 I-WK0 ileum


title: CNTO1275CRD3002-21019 I-WK0 ileum


title: CNTO1275CRD3002-20559 I-WK0 ileum


title: CNTO1275CRD3002-20653 I-WK0 ileum


title: CNTO1275CRD3002-20761 I-WK0 ileum


title: CNTO1275CRD3002-20286 I-WK0 ileum


title: CNTO1275CRD3002-20051 I-WK0 ileum


title: CNTO1275CRD3002-20082 I-WK0 ileum


title: CNTO1275CRD3002-20245 I-WK0 ileum


title: CNTO1275CRD3002-20556 I-WK0 ileum


title: CNTO1275CRD3002-20173 I-WK0 ileum


title: CNTO1275CRD3002-20171 I-WK0 ileum


title: CNTO1275CRD3002-20109 I-WK0 ileum


title: CNTO1275CRD3002-20142 I-WK0 ileum


title: CNTO1275CRD3002-20986 I-WK0 ileum


title: CNTO1275CRD3002-20329 I-WK0 ileum


title: CNTO1275CRD3002-20304 I-WK0 ileum


title: CNTO1275CRD3002-20781 I-WK0 ileum


title: CNTO1275CRD3002-20728 I-WK0 ileum


title: CNTO1275CRD3002-20065 I-WK0 ileum


title: CNTO1275CRD3002-20647 I-WK0 ileum


title: CNTO1275CRD3002-20481 I-WK0 ileum


title: CNTO1275CRD3002-20554 I-WK0 ileum


title: CNTO1275CRD3002-20922 I-WK0 ileum


title: CNTO1275CRD3002-20565 I-WK0 ileum


title: CNTO1275CRD3002-20679 I-WK0 ileum


title: CNTO1275CRD3002-20405 I-WK0 ileum


title: CNTO1275CRD3002-20805 I-WK0 ileum


title: CNTO1275CRD3002-20656 I-WK0 ileum


title: CNTO1275CRD3002-20783 I-WK0 ileum


title: CNTO1275CRD3002-20009 I-WK0 ileum


title: CNTO1275CRD3002-20301 I-WK0 ileum


title: CNTO1275CRD3002-20003 I-WK0 ileum


title: CNTO1275CRD3002-20187 I-WK0 ileum


title: CNTO1275CRD3002-20358 I-WK0 ileum


title: CNTO1275CRD3002-20395 I-WK0 ileum


title: CNTO1275CRD3002-20472 I-WK0 ileum


title: CNTO1275CRD3002-21035 I-WK0 ileum


title: CNTO1275CRD3002-20231 I-WK0 ileum


title: CNTO1275CRD3002-20978 I-WK0 ileum


title: CNTO1275CRD3002-20432 I-WK0 ileum


title: CNTO1275CRD3002-20504 I-WK0 ileum


title: CNTO1275CRD3002-20616 I-WK0 ileum


title: CNTO1275CRD3002-20953 I-WK0 ileum


title: CNTO1275CRD3002-20732 I-WK0 ileum


title: CNTO1275CRD3002-20791 I-WK0 ileum


title: CNTO1275CRD3002-20637 I-WK0 ileum


title: CNTO1275CRD3002-20239 I-WK0 ileum


title: CNTO1275CRD3002-20678 I-WK0 ileum


title: CNTO1275CRD3002-20604 I-WK0 ileum


title: CNTO1275CRD3002-20196 I-WK0 ileum


title: CNTO1275CRD3002-20072 I-WK0 ileum


title: CNTO1275CRD3002-20291 I-WK0 ileum


title: CNTO1275CRD3002-20244 I-WK0 ileum


title: CNTO1275CRD3002-20757 I-WK0 ileum


title: CNTO1275CRD3002-20290 I-WK0 ileum


title: CNTO1275CRD3002-21043 I-WK0 ileum


title: CNTO1275CRD3002-20176 I-WK0 ileum


title: CNTO1275CRD3002-20336 I-WK0 ileum


title: CNTO1275CRD3002-20408 I-WK0 ileum


title: CNTO1275CRD3002-20865 I-WK0 ileum


title: CNTO1275CRD3002-20090 I-WK0 ileum


title: CNTO1275CRD3002-20429 I-WK0 ileum


title: 48H pRRM12 C

city: Boca Raton

first: Massimo

last: Caputi

state: Florida

address: 777 Glades Road

department: Biomedical Science

institute: Florida Atlantic University

data_processing:
Reads quality control was carried out utilizing FastQC
Reads were aligned to the GRCh38 assembly of the human genome utilizing the HiSat2 tool running in a Galaxy environment
Aligned reads were assembled into transcripts utilizing the ENSMBL reference human transcript assembly and counted utilizing the CuffDiff2 tool running in a Galaxy environment
The following comparisons were carried out: 15H pSP6 vs 15H pSRSF1, 15H pSP6 vs 15H pRRM12, 48H pSP6 vs 48H pSRSF1, 48H pSP6 vs 48H pRRM12. Gene differentially expressed were prioritized on the base of their Log2 change in expression and the p value associated with the expression fold change.
Splicing analysis was carried out utilizing the Callisto pseudo-aligner and the IsoformSwitchAnalyzeR tool.
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file include FPKM values for each Sample and log2 value for each comparison. R data frame files contain quantification of alternative isoform switching events.

source_name: HEK293_48H pRRM12

extract_protocol:
Total RNA was extracted either 15 hrs or 48 hrs post-transfection for each of the three biological replica. The total RNA was DNased and depleted of ribosomal RNA.
cDNA libraries were generated utilizing the TrueSeq RNA library prep kit (Illumina).
Libraries were sequenced utilizing a Illumina Illumina HiSeq 2500 sequencer at a depth of  40 million paired ends reads with 100 nt read length.

treatment_protocol: Transfection protocol: HEK293 cells were transfected utilizing Lipofectamine2000 (Invitrogene) following standard protocols and one of three expression vectors. The SRSF1 expression vector (p-CMV-SRSF1-Sport6), Sthe RSF1 RRM1 and 2 expression vector (p-CMV-RRM12-Sport6) or the control vector (p-CMV-Sport6)

tag: genotype/variation

value: Transient transfection p-CMV-RRM12-Sport6 48Hrs


title: 48H pSP6 C

source_name: HEK293_48H pSP6

value: Transient transfection p-CMV-Sport6 48Hrs


title: 48H pSRSF1 C

source_name: HEK293_48H pSRSF1

value: Transient transfection p-CMV-SRSF1-Sport6 48Hrs


title: CNTO1275CRD3002-20547 I-WK0 ileum


title: 48H pRRM12 B


title: 48H pSP6 B


title: HEK293_mutant3_input

city: Sherbrooke

first: Karine

last: Choquet

state: Québec

address: 3201 rue Jean-Mignault

department: Biochemistry and Functional Genomics

institute: Université de Sherbrooke

data_processing:
Read trimming was performed with Trimmomatic v0.35
Alignment was performed with STAR v2.3.0e (RNA-seq and small RNA-seq) or bowtie2 v.2.2.9 (ChIP-seq)
Reads were counted with featureCounts v1.5.0
Normalization and differential expression analysis (RNAseq and small RNAseq) were performed with DESeq2
ChIP-seq read counts were normalized to the median of total read counts and Pol III occupancy scores were calculated as the log2(IPread_count/Inputread_count)
Genome_build: hg19
Supplementary_files_format_and_content: For each dataset, raw and normalized counts per sample are provided in one file (tsv, csv or txt)

source_name: HEK293 cell line

growth_protocol: HEK293 and MO3.13 cells were grown in DMEM supplemented with 10% FBS and 1% pen-strep

extract_protocol: Illumina TruSeq

treatment_protocol: CRISPR-Cas9 editing was used to introduce POLR3A mutations or BC200 KO

value: mutant

tag: chip antibody


title: CNTO1275CRD3002-20484 I-WK0 ileum


title: 48H pRRM12 A


title: CNTO1275CRD3002-20367 I-WK0 ileum


title: CNTO1275CRD3002-20829 I-WK0 ileum


title: CNTO1275CRD3002-20959 I-WK0 ileum


title: 48H pSP6 A


title: CNTO1275CRD3002-20631 I-WK0 ileum


title: HEK293_mutant2_input


title: HEK293_control3_input

value: control


title: HEK293_control2_input


title: HEK293_mutant3_ChIPseq

description:
HEK293.ChIP.Pol3_known.normCounts.csv
HEK293.Pol3_known.scores.csv


title: CNTO1275CRD3002-20441 I-WK0 ileum

value: ileum


title: 15H pSRSF1 C

source_name: HEK293_15H pSRSF1

value: Transient transfection p-CMV-SRSF1-Sport6 15 Hrs


title: 15H pRRM12 C

source_name: HEK293_15H pRRM12

value: Transient transfection p-CMV-RRM12-Sport6 15 Hrs


title: HEK293_mutant2_ChIPseq


title: 48H pSRSF1 A


title: CNTO1275CRD3002-20577 I-WK0 ileum

value: Crohn's disease (CD)


title: CNTO1275CRD3002-20963 I-WK0 ileum


title: 48H pSRSF1 B


title: CNTO1275CRD3002-20149 I-WK0 ileum


title: 15H pSP6 C

source_name: HEK293_15H pSP6

value: Transient transfection p-CMV-Sport6 15 Hrs


title: CENP-A LAP G2 input

city: Santa Cruz

first: Karen

middle: Hayden

last: Miga

address: 501 Engineering 2 Building, 1156 High Street,

department: Biomolecular Engineering Department

institute: UC Santa Cruz

data_processing:
Paired-end reads were merged (using PEAR) and mapped (using Bwa-Mem, standard parameters). Enrichment peaks for ChIP experiments were determined using SICER algorithm (v1.0.3), using relevant input reads as background. Stringent parameters previously optimized for human CENP-A (Lacoste et al., 2014) were used: threshold for redundancy allowed for chip reads: 1, threshold for redundancy allowed for control reads: 1, window size: 200 bps, fragment size: 150 bps, shift in window length is 150, effective genome size as a fraction of the reference genome of hg38: 0.74, gap size: 400 bps, e-value for identification of candidate islands that exhibit clustering: 1000, and false discovery rate controlling significance: 0.00001. In parallel, MACs peak calling was performed (macs14), and wiggle tracks were created to represent read depth of each dataset independently.
A rigorous evaluation of ectopic CENP-A peaks (peaks predicted outside of centromeric regions) was performed using k-mer enrichment.  Each ectopic peak was reformatted into 50-bp sliding windows (in both orientations, with slide of 1bp).  The normalized frequency of each 50-mer candidate windows were evaluated in each ChIP-seq dataset relative to a normalized observed frequency in the corresponding background dataset.  Scores were determined as the log transformed normalized value of the ratio between ChIP-seq and background, and those with a score greater than or equal to 2 were included in our study as a high-confident enrichment set. There were 12,550 G1 ectopic CENP-A peaks that are >5-fold over background and 1,260 peaks at G2.
Merge paired-end reads using PEAR (Zhang et al., 2014) https://sco.h-its.org/exelixis/web/software/pear/doc.html
Map merged paired reads using Bwa-Mem (Li, 2013; Li and Durbin, 2010) https://github.com/lh3/bwa
Peak calling using MACS (macs14) (Zhang et al., 2008) http://liulab.dfci.harvard.edu/MACS/
Peak calling using SICER (v1.0.3) (Zang et al., 2009) https://home.gwu.edu/~wpeng/Software.htm
Genome_build: hg38
Supplementary_files_format_and_content: UCSC genome tools

source_name: HeLa cells

growth_protocol: Cells were synchronized as previously described (Nechemia-Arbely et al., 2017). Briefly, suspension HeLa cells were treated with 2 mM thymidine in complete medium or 19 h, pelleted and washed twice in PBS, and released in complete medium containing 24 μM deoxycytidine for 9 h followed by addition of thymidine to a final concentration of 2 mM for 16 h, after which cells were released again into complete medium containing 24 μM deoxycytidine. For G2, cells were harvested 7 hours after release from the second thymidine block. For G1, thymidine was added for a third time, 7 hours after the release and cells were harvested 11 hours after that (a total of 18 hours after the release from the second thymidine block).

extract_protocol:
TAP- or LAP -tagged chromatin were purified in two steps. In the first step native TAP-tagged chromatin was immunoprecipitated by incubating the bulk soluble mononucleosome pool with rabbit IgG (Sigma-Aldrich) coupled to Dynabeads M-270 Epoxy (Thermo Fisher Scientific, 14301). Alternatively, CENP-ALAP chromatin was immunoprecipitated using mouse anti-GFP antibody (clones 19C8 and 19F7, Monoclonal Antibody Core Facility at Memorial Sloan-Kettering Cancer Center, New York) (Heiman et al., 2008) coupled to Dynabeads M-270 Epoxy. Chromatin extracts were incubated with antibody bound beads for 16 h at 4 ÅãC. Bound complexes were washed once in buffer A (20 mM HEPES at pH 7.7, 20 mM KCl, 0.4 mM EDTA and 0.4 mM DTT), once in buffer A with 300 mM KCl and finally twice in buffer A with 300 mM KCl, 1 mM DTT and 0.1% Tween 20. In the second step, TAP-chromatin complexes were incubated 16 h in final wash buffer with 50μl recombinant TEV protease, resulting in cleavage of the TAP tag and elution of the chromatin complexes from the beads. Alternatively, CENP-ALAP chromatin was eluted from the beads by cleaving the LAP tag using PreScission protease (4 h, 4ÅãC). For CENP-ATAP co-IP experiments, bound complexes were washed and proteins associating with CENP-ATAP were denatured by boiling in sample buffer, run on SDS-PAGE and blotted for CAF1 subunits and MCM2.
ChIP libraries were prepared following Illumina protocols with minor modifications (Illumina, San Diego, CA). To reduce biases induced by PCR amplification of a repetitive region, libraries were prepared from 80-100 ng of input or ChIP DNA. The DNA was end-repaired and A-tailed and Illumina Truseq adaptors were ligated. Libraries were run on a 2% agarose gel. Since the chromatin was digested to mononucleosomes, following adaptors ligation the libraries size was 250-280 bp. The libraries were size selected for 200-375 bp. The libraries were then PCR-amplified using only 5-6 PCR cycles since the starting DNA amount was high. Resulting libraries were sequenced using 100 bp, paired-end sequencing on a HiSeq 2000 instrument per manufacturer’s instructions with some modifications (Illumina, San Diego, CA).

value: Epithelial carcinoma

tag: cell cycle


title: CENP-A TAP G2 input

tag: cell line


title: CENP-A TAP G1 input


title: CNTO1275CRD3002-20346 I-WK0 ileum

value: Ileum and colon


title: 15H pSP6 B


title: 15H pRRM12 A


title: 15H pSRSF1 A


title: 15H pSP6 A


title: BrdU_S7_IP.REP

value: BrdU


title: BrdU_S4_IP.REP


title: BrdU_S4_INPUT.REP


title: BrdU_S7_INPUT.REP


title: BrdU_S1_INPUT.REP


title: BrdU_S1_IP.REP


title: RNA_P33_D0

city: Boston

first: Joann

middle: Diray

last: Arce

state: MA

address: 300 Longwood Ave

department: Infectious Disease

institute: Boston Childrens Hospital- Harvard Medical School

data_processing:
Base-calling and de-multiplexing were done using built-in software on the Illumina HiSeq 2500
fastq file quality control was performed using FastQC v.0.11.5 and MulitQC v.0.8.dev0
fastq files were aligned to the human genome using STAR v.2.5
read count tables were generated from bam fles using htseq-count v.0.6.1p1
globin transcripts were removed from libraries ("ENSG00000206172","ENSG00000188536", "ENSG00000244734","ENSG00000223609")
Genome_build: Ensembl GRCh38.86
Supplementary_files_format_and_content: tab delimited files containing uniquely mapped reads per gene for each sample

source_name: whole blood

extract_protocol:
Blood was stored in RNAlater (Ambion), RNA was extracted using a RiboPure Blood kit (ThermoFisher) and polyA RNA was purified using a NEBNEXT Poly(A) mRNA magnetic isolation kit (NEB)
cDNA libraries were constructed for sequencing using a KAPA Stranded Total RNA Kit (Kapa Biosystems)

tag: day of life

value: M

tag: subject id


title: RNA_P35_D3

tag: Sex

value: F


title: RNA_P35_D0


title: RNA_P34_D0


title: RNA_P34_D3


title: RNA_P33_D1


title: CENPA-TAP_S4.REP

value: CENP-A


title: RNA_P32_D0


title: RNA_P31_D3


title: RNA_P31_D0


title: CENPA_async_INPUT.TAP

value: Asynchronous


title: RNA_P30_D1


title: CENPA_async.LAP


title: CENPA_S_G2.LAP


title: H3_async.TAP


title: CENP-A_async_INPUT.LAP


title: CENPA_S_G2.TAP


title: RNA_P32_D7


title: REP1-K3AKO-SF

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

data_processing:
RNASeq raw data quality control by FastQC
RNASeq raw data clean performed by cutadapt
RNASeq data mapping to hg19 reference genome by tophat2 with at most 2 mismatch for each reads. Cuflinks was used for differential expression gene analysis,gene expression value with more than 2 fold change was defined differential expression genes.
Genome_build: hg19
Supplementary_files_format_and_content: txt format file for RNASeq gene expression level in each sample.

source_name: HCT116_KDM3A KO

extract_protocol:
For RNASeq 5ug total RNA was used, and mRNA purification was performed using oligo-dT magnic beads(NEBNext PolyA mRAN magnetic isolation module # E7490). mRNA was fragmented and reverse transcript into 200-400bp dscDNA for library construction(NEB # E7525 # E6111).
Vazyme ND604 kit was used for RNASeq  library construction. Brifely, about 10-100ng dscDNA was used as initiation for end repair and prepared for adaptor ligation. After adaptor ligation, PCR amplification with 8-13 cycles for each library and gel selection was used for library size selection and purification.

value: KDM3A knockout

tag: culture condition

value: addition of FBS into the no-serum culture after cell-starved for for 24 h


title: CNTO1275CRD3002-20068 I-WK0 ileum

value: Pbo

value: N

value: Ileum only


title: RNA_P29_D0


title: RNA_P29_D7


title: REP2-K3AKO-M

value: mock; normal state


title: CENPA_G1.TAP


title: RNA_P28_D3


title: REP1-K3AKO-S

value: starvation; no-serum


title: RNA_P28_D0


title: RNA_P26_D3


title: REP1-K3AKO-M


title: RNA_P27_D1


title: RNA_P30_D0


title: RNA_P27_D0


title: REP2-WT-SF

value: wild type


title: RNA_P26_D0


title: REP1-WT-SF


title: REP2-K3AKO-SF


title: RNA_P25_D1


title: RNA_P25_D0


title: REP2-WT-S


title: RNA_P24_D3


title: REP1-WT-S


title: CENPA_async.TAP


title: REP2-K3AKO-S


title: REP2-WT-M


title: RNA_P24_D0


title: REP2-INPUT-Sonication-K3AKO-M

data_processing:
ChIPSeq raw data quality control by FastQC
ChIPSeq raw data clean performed by cutadapt
Raw reads were aligned using Bowtie2 (version 2.1.0) to build version hg19 of the human genome retaining only uniquely mapped reads. Redundant reads were removed using SAMtools.
MACS2 (version 2.1.1) was used to call peaks
The genomic location of the peaks and their distance to the TSS of annotated genes were using the annotatePeaks.pl of HOMER
Genome_build: hg19
Supplementary_files_format_and_content: bigwig format file for ChIPSeq enriched level in each sample

extract_protocol:
Lysates were clarified from sonicated and enzyme digestion nuclei and histone-DNA complexes were isolated with antibody.
Vazyme ND604 kit was used for ChIPSeq  library construction. Brifely, about 10-100ng dsDNA was used as initiation for end repair and prepared for adaptor ligation. After adaptor ligation, PCR amplification with 8-13 cycles for each library and gel selection was used for library size selection and purification.

tag: cell type


title: REP1-WT-M


title: RNA_P23_D0


title: REP1-INPUT-Sonication-K3AKO-M


title: RNA_P23_D7


title: RNA_P22_D7


title: REP2-INPUT-MNase-K3AKO-M


title: RNA_P22_D0


title: REP1-INPUT-MNase-K3AKO-M


title: REP2-INPUT-Sonication-WT-M

source_name: INPUT-Sonication-WT-M


title: REP1-INPUT-Sonication-WT-M


title: RNA_P21_D0


title: RNA_P21_D3


title: REP2-INPUT-MNase-WT-M

source_name: INPUT-MNase-WT-M


title: RNA_P19_D3


title: REP1-INPUT-MNase-WT-M


title: REP2-H3K27me3-ChIPSeq-WT-SF

value: SF; addition of FBS into the no-serum culture after cell-starved for for 24 h


title: RNA_P19_D0


title: RNA_P17_D7


title: RNA_P16_D7


title: REP1-H3K27me3-ChIPSeq-WT-SF


title: RNA_P17_D0


title: REP2-H3K27me3-ChIPSeq-WT-S


title: RNA_P16_D0


title: REP1-H3K27me3-ChIPSeq-WT-S


title: RNA_P15_D1


title: REP2-H3K27me3-ChIPSeq-WT-M


title: RNA_P15_D0


title: RNA_P14_D3


title: REP1-H3K27me3-ChIPSeq-WT-M


title: RNA_P14_D0


title: RNA_P13_D1


title: REP2-H3K4me3-ChIPSeq-WT-S

value: H3K4me3(Millipore, 2739249)


title: REP1-H3K4me3-ChIPSeq-WT-S


title: RNA_P12_D1


title: REP2-H3K4me3-ChIPSeq-WT-M


title: RNA_P12_D0


title: REP1-H3K4me3-ChIPSeq-WT-M


title: RNA_P13_D0


title: RNA_P11_D1


title: REP2-H3K9me2-ChIPSeq-K3AKO- SF

source_name: H3K9me2-ChIPSeq-K3AKO- SF


title: RNA_P11_D0


title: REP2-H3K9me2-ChIPSeq-K3AKO-S


title: REP1-H3K9me2-ChIPSeq-K3AKO- SF


title: RNA_P10_D0


title: RNA_P09_D3


title: REP1-H3K9me2-ChIPSeq-K3AKO-S


title: RNA_P10_D7


title: REP2-H3K4me3-ChIPSeq-WT-SF


title: REP2-H3K9me2-ChIPSeq-K3AKO-M


title: REP1-H3K4me3-ChIPSeq-WT-SF


title: REP1-H3K9me2-ChIPSeq-K3AKO-M


title: HEK293_mutant2-3_smRNAseq

description:
HEK293.smRNAseq.rawCounts.2.txt
HEK293.smRNAseq.norm.2.txt

extract_protocol:
Small RNA (< 200 nt) enriched with Qiagen miRNeasy
KAPA stranded RNA-seq library preparation

value: mutant


title: REP1-H3K9me2-ChIPSeq-WT- SF

source_name: H3K9me2-ChIPSeq-WT- SF


title: HEK293_mutant3_smRNAseq

description:
HEK293.smRNAseq.rawCounts.1.txt
HEK293.smRNAseq.norm.1.txt


title: HEK293_mutant2-2_smRNAseq


title: RNA_P09_D0


title: REP2-H3K9me2-ChIPSeq-WT-S


title: REP2-H3K9me2-ChIPSeq-WT-M


title: REP1-H3K9me2-ChIPSeq-WT-S


title: HEK293_control3-3_smRNAseq

value: control


title: HEK293_mutant1_smRNAseq


title: HEK293_mutant2-1_smRNAseq

description:
HEK293.smRNAseq.rawCounts.1.txt
HEK293.smRNAseq.norm.1.txt
HEK293.smRNAseq.rawCounts.2.txt
HEK293.smRNAseq.norm.2.txt


title: HEK293_control3-2_smRNAseq


title: REP1-H3K9me2-ChIPSeq-WT-M


title: REP2-PolII-ChIPSeq-WT-SF

source_name: PolII-ChIPSeq-WT-SF

value: RNA Polymersase II CTD repeat YSPTSPS(abcam, ab817)


title: HEK293_control3-1_smRNAseq


title: REP2-H3K9me2-ChIPSeq-WT- SF


title: HEK293_control2_smRNAseq


title: REP2-PolII-ChIPSeq-WT-M

source_name: PolII-ChIPSeq-WT-M


title: REP2-PolII-ChIPSeq-WT-S

source_name: PolII-ChIPSeq-WT-S


title: REP1-PolII-ChIPSeq-WT-SF


title: REP1-PolII-ChIPSeq-WT-S


title: HEK293_mutant3_RNAseq

description:
HEK293.Ensembl.ensGene.exon.s2.raw.tsv.gz
HEK293.Ensembl.ensGene.exon.s2.norm.tsv.gz

extract_protocol:
Total RNA extracted with Qiagen miRNeasy
Illumina TruSeq rRNA-depleted stranded library preparation


title: HEK293_control1_smRNAseq


title: 15H pSRSF1 B

value: Transient transfection p-CMV-SRSF1-Sport6 15 Hrs


title: HEK293_control3_RNAseq


title: REP2-H3K27ac-ChIPSeq-K3AKO-SF

value: H3K27ac(abcam, ab4729)


title: HEK293_mutant2_RNAseq


title: HEK293_control2_RNAseq


title: REP1-H3K27ac-ChIPSeq-K3AKO-SF


title: REP2-H3K27ac-ChIPSeq-K3AKO-S


title: HEK293_mutant1_RNAseq


title: 15H pRRM12 B

value: Transient transfection p-CMV-RRM12-Sport6 15 Hrs


title: REP1-PolII-ChIPSeq-WT-M


title: REP1-H3K27ac-ChIPSeq-K3AKO-S


title: HEK293_control1_RNAseq


title: VEGF-F1_2

city: Daejeon

first: Yoonjung

last: Choi

address: 291 Daehak-ro, Yuseong-gu

institute: KAIST

data_processing:
Prepared libraries were sequenced on a HiSeq2500 with single-end method (100-bp reads).
The sequenced reads were aligned to the human genome (version: Hg19) using the STAR aligner (v.2.4.0)
The number of mapped reads was further analyzed using HOMER and DESeq
Genome_build: Hg19
Supplementary_files_format_and_content: RNA-seq : tab-delimited text files include RPKM values for each Sample

source_name: HUVEC

growth_protocol: Human umbilical vein endothelial cells (HUVECs, Cat#CC-2519, Lonza) were cultured in EBM-2 (Cat#CC-3156, Lonza) supplemented with EGM-2 (Cat#CC-3162, Lonza) and 100 µg/ml penicillin/streptomycin on gelatin (Cat#G1890, Sigma-Aldrich; 0.1% in DDW) pre-coated plates. The cells were grown at 37°C and 5% CO2.

extract_protocol:
mRNA-seq libraries were made using NEXTflexTM Rapid RNA-Seq kit (cat. 5138) from isolated mRNA.
mRNA-seq libraries were made using NEXTflexTM Rapid RNA-Seq kit (cat. 5138) from isolated mRNA.

treatment_protocol: HUVEC cells were treated with VEGF (2.5 nM) or ginsenosides (F1 and Rh1, 10 μM) for one hour. Otherwise, the cells were pre-treated with VEGF (2.5 nM) for an hour and sequentially treated with ginsenoisdes (F1 and Rh1, 10 μM) for another hour.

value: Human Umbilical Vein Endothelial Cells

tag: treatment

value: VEGF (2.5 nM) + ginsenoisdes (F1 10 μM)


title: REP2-H3K27ac-ChIPSeq-K3AKO-M

value: KDM3A knockout


title: VEGF-Rh1_2

value: VEGF (2.5 nM)  + ginsenoisdes (Rh1 10 μM)


title: REP1-H3K27ac-ChIPSeq-K3AKO-M


title: Rh1_2

value: ginsenoisdes (Rh1 10 μM)


title: REP2-H3K27ac-ChIPSeq-WT-SF


title: VEGF_2

value: VEGF (2.5 nM)


title: HEK293_control3_ChIPseq


title: Ctrl_2


title: REP1-H3K27ac-ChIPSeq-WT-SF


title: F1_2

value: ginsenoisdes (F1 10 μM)


title: REP1-H3K27ac-ChIPSeq-WT-S

value: starvation; no-serum


title: VEGF-Rh1_1


title: VEGF-F1_1


title: VEGF_1


title: REP2-H3K27ac-ChIPSeq-WT-M

value: wild type

value: mock; normal state


title: REP2-TEAD1-ChIPSeq-K3AKO-SF

value: SF; addition of FBS into the no-serum culture after cell-starved for for 24 h

value: TEAD1(Cell Signaling Technology.12292S)


title: Rh1_1


title: REP1-H3K27ac-ChIPSeq-WT-M


title: REP2-TEAD1-ChIPSeq-K3AKO-S


title: F1_1


title: REP1-TEAD1-ChIPSeq-K3AKO-SF


title: RNA_H30_D7

tag: tissue

value: whole blood

value: M


title: REP2-TEAD1-ChIPSeq-K3AKO-M


title: RNA_H29_D1


title: REP1-TEAD1-ChIPSeq-K3AKO-M


title: RNA_H29_D0


title: REP2-TEAD1-ChIPSeq-WT-S


title: REP2-H3K27ac-ChIPSeq-WT-S


title: RNA_H27_D0

value: F


title: RNA_H27_D1


title: REP2-TEAD1-ChIPSeq-WT-M


title: REP1-TEAD1-ChIPSeq-WT-SF


title: REP1-TEAD1-ChIPSeq-WT-S


title: RNA_H25_D0


title: RNA_H24_D7


title: RNA_H24_D0


title: RNA_H25_D3


title: RNA_H23_D1


title: RNA_H23_D0


title: RNA_H21_D7


title: RNA_H20_D1


title: RNA_H22_D0


title: RNA_H30_D0


title: REP1-TEAD1-ChIPSeq-K3AKO-S


title: RNA_H21_D0


title: RNA_H20_D0


title: REP2-TEAD1-ChIPSeq-WT-SF


title: RNA_H19_D0


title: REP1-TEAD1-ChIPSeq-WT-M


title: RNA_H18_D0


title: RNA_H16_D3


title: RNA_H19_D7


title: RNA_H17_D0


title: RNA_H16_D0


title: RNA_H22_D1


title: RNA_H12_D3


title: RNA_H12_D0


title: RNA_H14_D0


title: RNA_H15_D3


title: RNA_H13_D3


title: RNA_H11_D7


title: RNA_H10_D3


title: RNA_H11_D0


title: RNA_H06_D3


title: RNA_H10_D0


title: RNA_H09_D0


title: RNA_H18_D1


title: RNA_H06_D0


title: RNA_H05_D7


title: RNA_H05_D0


title: RNA_H17_D7


title: RNA_H14_D7


title: linearRELL1

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

description: linearRELL1 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.

data_processing:
Library strategy: SHAPE-MaP
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Mapped to  target RNA sequence by ShapeMapper software (v2.1.3) and circSHAPEmapper (--target RNA.fa --out folder --nproc 16 --verbose --serial --min-depth 50 –modified –untreated --denatured)
Reads from SHAPE-MaP libraries were processed with default settings in ShapeMapper software version v2.1.3. Pre-processed reads were then mapped to target sequences by Bowtie2 (v2.1.0) (-p 24 --local --sensitive-local --mp 3,1 --rdg 5,1 --rfg 5,1 --dpad 30 --maxins 800 --ignore-quals --no-unal). Mutation rates (MutR) were calculated at each position by summing the number of mismatches and indels (deletions and insertions) and dividing by the number of all mapped reads to the position. SHAPE reactivities were calculated by [(ModifiedMutR – UntreatedMutR)/DenaturedMutR] and further normalized by a model-free box-plot approach (Deigan et al., 2009).
Genome_build: hg19 for human samples (For circSHAPE-Map, circCAMSAP1, circCCNB1, circEPHB4, circEZH2, circFCHO2, circFGFR1_1, circPOLR2A, circPVT1, circRELL1, circSDHAF2, circTBCD, circUIMC1, circARID1B, circCNN2, circDHX34, circFKBP8, circKIAA0368, circMBOAT2, circPIP5K1C, circPPP1CB, circPROSC, circPTK2, circSLC22A23, circSNHG4, circTMEM181, circVAPB, circASAP1, circASXL1, circDYNC1H1, circFGFR1_2, circLDLRAD3, circPHF21A, circRTN4, circSMARCA5; For linearSHAPE-Map, linearCAMSAP1, linearCCNB1, linearEPHB4, linearEZH2, linearFCHO2, linearFGFR1_1, linearPOLR2A, linearPVT1, linearRELL1, linearSDHAF2, linearTBCD, linearUIMC1).
Supplementary_files_format_and_content: TXT files include the read depths, standard errors and SHAPE reactivity of each base. Column "Norm_profile" is the SHAPE reactivity.

source_name: PA1 cells

growth_protocol: PA-1 (human ovarian adenocarcinoma cell) were cultured with MEMα medium supplemented with 10% FBS.

extract_protocol:
For SHAPE-MaP, isolated RNAs were treated with DNase I (Ambion, DNA-freeTM kit) to remove possible DNA contamination. About 50-100 μg of RNAs were obtained under each treatment, and were then used for SHAPE-MaP reverse transcription by adding 1 μL (200 U/μL) of SuperScript II (Invitrogen), 6 mM Mn2+ and gene-specific primers for linear or circular RNAs (5S rRNA was used as a spike-in control). Mn2+ was removed using G-25 micro-spin columns (GE Healthcare) after SHAPE-MaP reverse transcription. Second-strand synthesis was performed with Q5 hot start high-fidelity DNA polymerase and nested PCR was performed to further improve DNA yield.
SHAPE-MaP libraries were prepared from 1 ng of DNAs for linear (linearSHAPE-MaP) or circular (circSHAPE-MaP) RNAs, and size-selected with AmpureXP beads (Agencourt) with a 1:1 (bead to sample) ratio to obtain library DNA products spanning 100-400 bp in length. Final libraries were quantified using Agilent Bioanalyzer 2100 and QuBit high-sensitivity dsDNA assay. Deep sequencing was performed by Illumina NextSeq 500 at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: For SHAPE-MaP, PA1 cells were incubated with 900 uL of fresh cell culture medium and 100 μL of 10x SHAPE Chemical in DMSO with the final concentration of NAI at 100 mM for 10 minutes at 37°C.

value: ovarian adenocarcinoma cell line PA1

tag: type

value: cDNA

value: DC samples denatured by formamide at 95℃; DMSO samples only DMSO; NAI samples modified by NAI in DMSO.


title: linearUIMC1

description: linearUIMC1 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: RNA_H15_D0


title: linearTBCD

description: linearTBCD of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: linearSDHAF2

description: linearSDHAF2 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: RNA_H04_D0


title: RNA_H13_D0


title: RNA_H02_D7


title: linearPVT1

description: linearPVT1 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: RNA_H09_D3


title: RNA_H01_D0


title: RNA_H02_D0


title: RNA_H01_D1


title: linearPOLR2A

description: linearPOLR2A of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.