title: LDC_RNA_PT4

first: Shimeng

state: Illinois

address: 320 East Superior Street

data_processing:
Libraries were sequenced under 75bp single-end sequencing format. Adapters were trimmed using cutadapt. Trimmed reads were aligned to the hg19 reference genome using STAR default parameter. Raw count files were generated using HTSeq based on Ensembl Release 75 annotation. Differentily expressed genes were detected using DESeq2 following the cutoff FDR-adjusted P<0.05. Key differentially expressed genes among LM populations were validated through qPCR.
Genome_build: hg19
Supplementary_files_format_and_content: The processed files are HTSeq raw count files from each RNA-Seq sample.

source_name: Primary uterine leiomyoma cells

extract_protocol:
LM primary cells were isolated from fresh LM tissues and sorted using FACS. Primary cells were isolated from fresh uterine LM tissue (patient number= 4). Individual LM cell populations were isolated using CD34 and CD49b cell surface markers (LSC: CD34+/CD49b+; LIC: CD34+/CD49b-; LDC: CD34-/CD49b-) using FACS. At least 100,000 cells were collected for each population. Total RNA was extracted from using Qiagen RNeasy RNA micro kit (Qiagen, 74004).
Next-generation sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep with Sample Purification Beads (NEB, #7775).

tag: tissue preparation

value: Primary P0 cells

tag: cell population

value: CD34-/CD49b- Leiomyoma differentiated cell

value: uterine leiomyoma

tag: patient id

value: Patient 4


title: LDC_RNA_PT3

status: Public on Oct 01 2020

type: SRA

city: Chicago

last: Liu

country: USA

institute: Northwestern University

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

value: Patient 3


title: LDC_RNA_PT2

value: Patient 2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C6_ad001

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: ACA,PL,ILA

tag: Sex

value: male

tag: age

tag: strain


title: Trifluoperazine_Dose2_Rep1

first: Sonia

last: Brockway

state: IL

address: 303 E Superior St, SQBRC 7-500

department: Biochemistry and Molecular Genetics

data_processing:
Library strategy: QMAP-Seq
Individual samples were demultiplexed based on i5 and i7 index sequences by running bcl2fastq Conversion Software (Illumina).
Data was processed using QMAP-Seq bioinformatic analysis pipeline (https://github.com/mendillolab/QMAP-Seq). Briefly, sgRNA and cell line barcode sequences were extracted from Read 1 sequences as follows: [ACACCG][sgRNA:20][Interval:102][CellLineBarcode:8]. The number of reads for each cell line-sgRNA pair was counted, allowing up to one nucleotide mismatch per barcode. Cell number was interpolated from sequencing reads using sample-specific standard curves. The number of cells for a compound-treated sample was normalized to the median number of cells for the DMSO-treated samples.
Data was filtered using the following exclusion criteria. First, samples with low read counts were excluded. Second, cell line-sgRNA pairs with high variation (standard deviation of log2(cell number) > 0.7) were excluded. Third, compounds with an AUC > 550 for any cell line-sgRNA pair were excluded. Fourth, noncytotoxic cell line-compound pairs (relative cell number of sgNT with highest dose ≥ 90%) were excluded. Fifth, cell line-compound pairs without a dose-dependent reduction in cell viability (difference in relative cell number of sgNT between lowest and highest dose < 25%) were excluded.
Genome_build: N/A (sgRNA library sequencing)
Supplementary_files_format_and_content: Plain text document (.txt) files with read counts for each cell line-sgRNA pair. Individual files for each sample.
Supplementary_files_format_and_content: Comma-separated values (.csv) file with relative cell numbers (i.e., cell number (%DMSO)) for each cell line-sgRNA-compound-dose-replicate combination. Matrix table with data for all samples.

source_name: Pool of 5 breast cancer cell lines

growth_protocol: Cell line pools were cultured in RPMI-1640, 10% Tet System Approved FBS, 1% Penicillin/Streptomycin, 100 ng/mL doxycycline for 7 days prior to compound treatment.

extract_protocol:
Cell line pools were lysed with lysis buffer (10% 10x Taq DNA Polymerase Buffer, 0.45% IGEPAL CA-630, 0.45% TWEEN 20, 10% Proteinase K, 79.1% Nuclease-Free Water) containing cell spike-in standards. Cells were incubated at 60°C for 1 hour. Proteinase K from lysis buffer was inactivated at 95°C for 15 minutes.
Barcoded region was PCR amplified with a unique set of indexed primers for each sample. PCR products were pooled and purified twice. Sequencing library was diluted, combined with PhiX, denatured, and sequenced on a NovaSeq 6000 (Illumina).

treatment_protocol: Cell line pools were treated with compound or DMSO over a four-point concentration range (10-fold dilutions) in duplicate using either a standard dose range (10 nM to 10 μM) or a low dose range (1 nM to 1 μM). Dose1=lowest dose. Dose4=highest dose. Cells were treated for 72 hours.

tag: cell lines

tag: sgrnas

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2

tag: compound treatment


title: Vincristine_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C6_ad012


title: LIC_RNA_PT4

value: CD34+/CD49b- Leiomyoma intermediate cell


title: LDC_RNA_PT1

value: Patient 1


title: Crizotinib_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C6_ad006


title: STF31_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C6_ad010


title: LIC_RNA_PT3


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C6_ad007


title: LIC_RNA_PT2


title: Carfilzomib_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C6_ad008


title: Cyclophosphamide_Dose2_Rep1


title: LSC_RNA_PT4

value: CD34+/CD49b+ Leiomyoma stem cell


title: Simvastatin_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C5_ad012


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C6_ad004


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C5_ad001


title: LSC_RNA_PT2


title: LIC_RNA_PT1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C5_ad007


title: LSC_RNA_PT3


title: PT3_LDC_Input

description: Fregmented genomic DNA from PT231_LDC_IP sample

data_processing:
Libraries were sequenced under 75bp paired-end sequencing format. Adapters were trimmed using cutadapt. Sequences were aligned to the hg19 reference genome using Bowtie2. Histone style peak calling, differential binding analysis (getDifferentialPeaksReplicates.pl), and motif analysis were performed using Homer under default settings. Differentilly methylated regions (DMRs) were detected with a fold enrichment over background tag count ≥4 and poisson enrichment p-value over background tag count <0.0001. Differential DNA methylation at select regions was validated through Methylcap followed by qPCR.
Genome_build: hg19
Supplementary_files_format_and_content: The processed files are peak files from each individual MethylCap-Seq.

extract_protocol:
Primary cells were isolated from fresh uterine LM tissue (patient number = 3). Individual LM cell populations were isolated using CD34 and CD49b cell surface markers (LSC: CD34+/CD49b+; LIC: CD34+/CD49b-; LDC: CD34-/CD49b-) using FACS. At least 200,000 cells were collected for each population. Genomic DNA was extracted using DNeasy Blood and Tissue Kit (Qiagen, 69504) and fragmented to 300-500bp using Covaris M220. Methylated DNA fragments were captured using the MethylCap Kit (Diagenode, C02020010).
Next-generation sequencing libraries were prepared using the KAPA Hyper Prep Kit (KAPA Biosystems, KK8502) and KAPA Single-Indexed Adapter Kit (KAPA Biosystems, KK8710).


title: Etoposide_Dose2_Rep1


title: FiveFluorouracil_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C5_ad010


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D10_ad008


title: LSC_RNA_PT1


title: Letrozole_Dose2_Rep1


title: PD318088_Dose2_Rep1


title: Trametinib_Dose2_Rep1


title: Mebendazole_Dose2_Rep1


title: KX2391_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C4_ad001


title: PT1_LDC_Input

description: Fregmented genomic DNA from PT206_LDC_IP sample


title: PT3_LIC_Input

description: Fregmented genomic DNA from PT231_LIC_IP sample


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C5_ad006


title: WP1130_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C5_ad004


title: PT2_LIC_Input

description: Fregmented genomic DNA from PT230_LIC_IP sample


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C4_ad007


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C5_ad008


title: Doxorubicin_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C4_ad006


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C4_ad010


title: PT3_LSC_Input

description: Fregmented genomic DNA from PT231_LSC_IP sample


title: PT1_LIC_Input

description: Fregmented genomic DNA from PT206_LIC_IP sample


title: Nilotinib_Dose2_Rep1


title: Ruxolitinib_Dose2_Rep1


title: Cisplatin_Dose2_Rep1


title: PT1_LSC_Input

description: Fregmented genomic DNA from PT206_LSC_IP sample


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C4_ad008


title: PT2_LDC_Input

description: Fregmented genomic DNA from PT230_LDC_IP sample


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C3_ad007


title: SR1001_Dose2_Rep1


title: PT2_LDC_Methylation_IP

description: MethylCap DNA


title: PT3_LDC_Methylation_IP

description: MethylCap DNA


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C3_ad010


title: Zebularine_Dose2_Rep1


title: Sitagliptin_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C3_ad006


title: DMSOPlate3WellF6_Dose2_Rep1


title: Bexarotene_Dose2_Rep1


title: PT2_LSC_Input

description: Fregmented genomic DNA from PT230_LSC_IP sample


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C3_ad004


title: Tigecycline_Dose2_Rep1


title: PT1_LIC_Methylation_IP

description: MethylCap DNA


title: PT1_LDC_Methylation_IP

description: MethylCap DNA


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C3_ad002


title: PT3_LSC_Methylation_IP

description: MethylCap DNA


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C2_ad007


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C2_ad001


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C3_ad012


title: Lenvatinib_Dose2_Rep1


title: PT3_LIC_Methylation_IP

description: MethylCap DNA


title: Dacarbazine_Dose2_Rep1


title: Decitabine_Dose2_Rep1


title: PIK93_Dose2_Rep1


title: PT2_LSC_Methylation_IP

description: MethylCap DNA


title: VER155008_Dose2_Rep1


title: H3_ChIP_LDC_merge

description: Native Histone ChIP DNA

data_processing:
Libraries were sequenced under 75bp paired-end sequencing format. Adapters were trimmed using cutadapt.  Sequences were aligned to the hg19 reference genome using Burrows-Wheeler Aligner.  Individual bam files from 4 patients were merged using Samtools. H3K4me3 and H3K27Ac enrichment at progesterone receptor binding regions was visualized using NGSPlot and quantified using normalized RPKM value on merged bam files from 4 patients.
HOMER was used for peak calling. Peak calling was done using H3 as the control (input) group.
Genome_build: hg19
Supplementary_files_format_and_content: peak files

extract_protocol:
Primary cells were isolated from fresh uterine LM tissue (patient number = 4). Individual LM cell populations were isolated using CD34 and CD49b cell surface markers (LSC: CD34+/CD49b+; LIC: CD34+/CD49b-; LDC: CD34-/CD49b-) using FACS. At least 200,000 cells were collected for each population. Low cell number native ChIP-Seq for histone modification was performed following a published protocol by Peter van Galen et al. (van Galen, Peter, et al. A Multiplexed System for Quantitative Comparisons of Chromatin Landscapes. Molecular Cell 61(1):170-180.) .
Libraries were prepared following a published protocol by Peter van Galen et al. (van Galen, Peter, et al. A Multiplexed System for Quantitative Comparisons of Chromatin Landscapes. Molecular Cell 61(1):170-180.) .

tag: chip antibody

value: H3:Active Motif (39763)


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C2_ad008


title: PT1_LSC_Methylation_IP

description: MethylCap DNA


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C2_ad010


title: DMSOPlate3WellC6_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C2_ad002


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C2_ad006


title: Valdecoxib_Dose2_Rep1


title: Fingolimod_Dose2_Rep1


title: PT2_LIC_Methylation_IP

description: MethylCap DNA


title: Sorafenib_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C12_ad010


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C12_ad012


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C12_ad008


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C12_ad007


title: PLX4720_Dose2_Rep1


title: Clofarabine_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C11_ad010


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C12_ad002


title: Linsitinib_Dose2_Rep1


title: PT1_Aza

data_processing:
Libraries were sequenced under 75bp single-end sequencing format. Sequences were aligned to the hg19 reference genome using STAR. Raw count files were generated using HTSeq based on Ensembl Release 75 annotation. Differentilly expressed genes were detected using DESeq2 following the cutoff FDR-adjusted P<0.05. Key differentially expressed genes between vehicle (DMSO) and 5'-Aza were validated through qPCR.
Genome_build: hg19
Supplementary_files_format_and_content: The processed files are HTSeq raw count files from each RNA-Seq sample

growth_protocol: Primary LM cells were isolated from fresh LM tissue and cultured in DMEM/F12 1:1 (GIBCO/BRL, 11320-082) containing 10% (vol/vol) FBS in a humidified atmosphere in 5% (vol/vol) CO2 at 37 °C.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy RNA micro kit (Qiagen, 74104).
Next-generation sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep with Sample Purification Beads (NEB, #7775).

treatment_protocol: Non-passaged primary LM cells were treated with vehicle (DMSO) or 5'-Aza (100nM) for 6 days.


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C11_ad007


title: Gefitinib_Dose2_Rep1


title: PT3_Aza


title: H3K4me3_ChIP_LIC_merge

description: Native Histone ChIP DNA

value: H3K4me3:Millipore (07-473)


title: H3K4me3_ChIP_LSC_merge

description: Native Histone ChIP DNA


title: H3_ChIP_LSC_merge

description: Native Histone ChIP DNA


title: H3_ChIP_LIC_merge

description: Native Histone ChIP DNA


title: H3K4me3_ChIP_LDC_merge

description: Native Histone ChIP DNA


title: H3K27Ac_ChIP_LSC_merge

description: Native Histone ChIP DNA

value: H3K27Ac: Active Motif (39133)


title: H3K27Ac_ChIP_LDC_merge

description: Native Histone ChIP DNA


title: PT2_Aza


title: PT3_Veh


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C10_ad012


title: Niclosamide_Dose2_Rep1


title: Fluvastatin_Dose2_Rep1


title: Cabozantinib_Dose2_Rep1


title: H3K27Ac_ChIP_LIC_merge

description: Native Histone ChIP DNA


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C11_ad012


title: CHIR99021_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C10_ad010


title: PT1_Veh


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C11_ad001


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C11_ad002


title: MK0752_Dose2_Rep1


title: Ki8751_Dose2_Rep1


title: Fulvestrant_Dose2_Rep1


title: PN_unstim_S7: PN MGT1mV/PNGT2mCh control unsorted

city: Berlin

first: Gaetano

last: Gargiulo

address: Robert-Rössle-Straße 10

department: Molecular Oncology

country: Germany

institute: Max Delbrüch Center

data_processing:
hisat2 v2.1.0
samtools (v1.9) view -F 4 -bh
SeqMonk v1.42
Genome_build: hg38

source_name: brain, transformed human neuronal progenitor cels from subventricuar zone

extract_protocol:
The total RNA was extracted by lysing the cell pellets in AL buffer (Qiagen), supplemented with Proteinase K (Invitrogen) and DNAse I (Thermo Scientific), subsequently purified with AMPure beads and eluted in EB buffer (Qiagen).
RNA-seq libraries where constructed from 1μg of RNA following the standard Illumina TruSeq Stranded Total RNA protocol

treatment_protocol: The MES-hGICs-MGT#1 were propagated in RHB-A complete medium (20 ng/ml EGF, 20 ng/ml bFGF, 1 μg/ml heparin, 5% penicillin and streptomycin, 20 ng/ml PDGF-AA) at 37°C in a 5% CO2, 3% O2 and 95% humidity incubator. C20hMG cells were propagaed RHB-A medium supplemented with 1% FBS, 1%P/S and 1µM Dexamethason under the same maintenance conditions.

tag: tissue

value: PN-hGICs-MGT#1, mVenus unsorted

tag: culture conditions

value: Monoculture

tag: growth medium

value: RHB-A


title: PN_TNFa_S8: PN MGT1mV/PNGT2mCh TNFa unsorted

value: brain, transformed human neuronal progenitor cels from subventricuar zone


title: Parthenolide_Dose2_Rep1


title: C20MG_C20M2_S14: C20hMG naïve (12.2.19)

source_name: brain, immortalized primary human microglia

value: C20hMG Medium (RHB-A + 1% FBS + 1%P/S + 1µM Dexa)


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C10_ad007


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C1_ad012


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C10_ad006


title: Dabrafenib_Dose2_Rep1


title: DMSOPlate3WellF3_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C10_ad002


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C1_ad010


title: C20MG_C20M2_S13: C20hMG naïve (21.1.19)

value: brain, immortalized primary human microglia


title: Blebbistatin_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C1_ad001


title: MES_TNFa_S2: MES MGT1mV/PNGT2mCh TNFa unsorted

value: MES-hGICs-MGT#1, mVenus unsorted


title: MES_unstim_S1: MES MGT1mV/PNGT2mCh control unsorted


title: C20MG_RHBA1_S15: C20 RHB-A medium 1 (08.04.19)


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C1_ad002


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C1_ad004


title: Abiraterone_Dose2_Rep1


title: Erlotinib_Dose2_Rep1


title: PT2_Veh

value: Primary P0 cells

value: Patient 2

value: uterine leiomyoma


title: Alisertib_Dose2_Rep1

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2


title: DMSOPlate3WellC3_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C1_ad006

value: ACA,PL,ILA

value: male


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C10_ad008


title: C20MG_RHBA2_S15: C20 RHB-A medium 2 (08.04.19)


title: Anastrozole_Dose2_Rep1


title: C20MG_MEgt2_S10: C20 cocult B2 (15.03.19)

value: Co-culture with MES-hGICs-MGT#1-high


title: C20MG_MEgt3_S11: C20 cocult B1 (15.03.19)


title: Exemestane_Dose2_Rep1


title: MEhigh_c20MG3_S8: MES cocult C (15.03.19)

value: MES-hGICs-MGT#1, mVenus-high

value: Co-culture with C20hMG


title: NVPAUY922_Dose2_Rep1


title: C20MG_MEgt1_S9: C20hMG from coculture with MES MGT1mV/PNGT2mCh (22.02.19)


title: C20MG_C20M1_S12: C20hMG naïve (IJ)


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B9_ad010


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B9_ad012


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B9_ad007


title: Nelarabine_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B9_ad001


title: Regorafenib_Dose2_Rep1


title: Cimetidine_Dose2_Rep1


title: MEhigh_c20MG1_S6: MES MGT1mV/PNGT2mCh cocult C20hMG mVenus high (22.02.19)


title: MEhigh_c20MG2_S7: MES cocult B (15.03.19)


title: MEhigh_TNFa1_S4: MES MGT1mV/PNGT2mCh TNFa mVenus high (22.02.19)

value: RHB-A + 10 ng/ml TNFa


title: MEhigh_TNFa2_S5: MES MGT1mV/PNGT2mCh TNFa mVenus high (7.5.18)


title: Mitoxantrone_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C1_ad008


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B9_ad002


title: MEgt_CTRL3_S3: MES MGT1mV/PNGT2mCh Ctrl C (15.03.19)


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B8_ad001


title: Cediranib_Dose2_Rep1


title: MEgt_CTRL2_S2: MES MGT1mV/PNGT2mCh Ctrl B (15.03.19)


title: PHA793887_Dose2_Rep1


title: Thalidomide_Dose2_Rep1


title: MEgt_CTRL1_S1: MES MGT1mV/PNGT2mCh control unsorted (22.02.19)


title: RITA_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B8_ad012


title: Temozolomide_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B8_ad010


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B8_ad006


title: Dexamethasone_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B8_ad004


title: 2 MGT1 mVenus high (in vitro)

data_processing:
Data was mapped using bowtie2 v2.3.5
Aligned files were sorted using samtools v1.9
BigWigFiles were generated using bedtools v2.27.1 genomeCov and wigToBigWig v4
Genome_build: hg38
Supplementary_files_format_and_content: BigWigFiles were generated using bedtools v2.27.1 genomeCov and wigToBigWig v4

growth_protocol: For the in vitro samples, MES-hGICs-MGT#1 were propagated in RHB-A complete medium at 37 °C in a 5% CO2, 3% O2 and 95% humidity incubator. For the in vivo samples, MES-hGICs-MGT#1 were passaged through NSG mice for 7-9 weeks prior to sacrificing (humane endpoint) and tumor cell extraction.

extract_protocol:
ATAC-seq was performed on 20-50,000 (in vivo experiment) or 50-100,000 (in vitro experiment) cells following the standard Illumina Nextera DNA Library Prep tagmentation protocol. Transposition was stopped by addition of Proteinase K and lysing the cell pellets in AL buffer (Qiagen) at 56C for 10min. Tagmented DNA was subsequently purified using AMPure beads.
The optimal number of PCR cycles for amplification of tagmented DNA was determined per each sample using 2 μl of template followed by qPCR amplification using heat activated Kappa Hifi polymerase and EvaGreen 1x. Final ATAC-seq library construction was performed in 50 μl qPCR volume and 8-12 μl of template DNA. Illumina compatible primers were previously described elsewhere (Buenrostro et al. 2013).

treatment_protocol: No treatment

tag: sample type

value: In vitro


title: Tacrolimus_Dose2_Rep1


title: 1 MGT1 mVenus high (in vitro)


title: 1 MGT1 mVenus low (in vitro)

value: MES-hGICs-MGT#1, mVenus--low


title: Tivozanib_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B9_ad008


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B8_ad008


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B7_ad002


title: 147 MGT1 mVenus high

value: In vivo


title: 149 MGT1 mVenus low

value: MES-hGICs-MGT#1, mVenus-low


title: 147 MGT1 mVenus low


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B8_ad007


title: BrefeldinA_Dose1_Rep2


title: 149 MGT1 mVenus high


title: Brivanib_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B7_ad010


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B7_ad008


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B7_ad006


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B8_ad002


title: Everolimus_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B7_ad004


title: Dasatinib_Dose1_Rep2


title: Sildenafil_Dose1_Rep2


title: 2 MGT1 mVenus low (in vitro)


title: Bendamustine_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B6_ad012


title: DC-alone-8hour

city: Jena

first: Bastian

last: Seelbinder

address: Adolf-Reichwein-Straße 23

department: Systems Biology and Bioinformatics

institute: Hans-Knoell-Institute Jena

data_processing:
Quality and adapter trimming were performed using Trimmomatic version 0.36, including windows size trimming (size 10, Q25), 3’ ad 5’ quality clipping (Q5) and sequences with less than 30 bp were removed.
Read mapping was performed using HiSat2 with default parameters.
Gene abundance estimation (counting) was performed using featureCounts with default parameters.
Genome_build: GRCH38 89; Human herpesvirus 5 strain TB40E clone TB40-BAC4
Supplementary_files_format_and_content: Gene abundance matrix was created by featureCounts based on the combined annotation of both organisms.

source_name: dendritic cells

growth_protocol: CellGro GMP serum-free DC medium for up to 12h

extract_protocol:
Total RNA has been extracted and purified using the RiboPure RNA purification kit. Fragments were sequenced using Sequencing by synthesis (Illumina NextSeq 500).
RNA libraries were prepared for single-end sequencing using standard Illumina protocols.

value: dendritic cells

tag: strain or line

value: DC

tag: sampling time point (hours)

tag: temperature

value: 37 degrees C

tag: atmosphere

tag: media

value: CellGro GMP serum-free DC medium

tag: parameter

value: rin/rna integrity number:9.5

value: concentration (ng/ul):48

value: volume (microliter):60


title: Topotecan_Dose1_Rep2

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2


title: DC-alone-4hour

tag: cell type

value: rin/rna integrity number:9.6

value: concentration (ng/ul):50


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B7_ad012

tag: brain region

value: ACA,PL,ILA

tag: Sex

value: male

tag: age


title: DC-alone-6h

data_processing:
Quality and adapter trimming were performed using Trimmomatic version 0.36, including windows size trimming (size 15, Q25), 3’ ad 5’ quality clipping (Q3) and sequences with less than 30 bp were removed.
Read mapping was performed using HiSat2 with default parameters and -k 2.
Gene abunstance estimation (counting) was performed using featureCounts with default parameters.
Genome_build: GRCH38 89; Af293 s03-m05-r05
Supplementary_files_format_and_content: Gene abundance matrix was created by featureCounts based on the combined annotation of both organisms.

tag: strainorline

value: 37 degreeC

value: 5percent  CO3

value: rin/rna integrity number:8.9

value: concentration (ng/microliter):86.02

value: volume (microliter):69


title: DC-alone-2h

value: dendritic cells

value: rin/rna integrity number:9.2

value: concentration (ng/microliter):91.17

value: volume (microliter):61


title: PYR41_Dose1_Rep2

tag: cell lines

tag: sgrnas

tag: compound treatment


title: Donor4_01_DC_alone

data_processing:
Quality and adapter trimming were performed using Trimmomatic version 0.36, including windows size trimming (size 10, Q25), 3’ ad 5’ quality clipping (Q5) and sequences with less than 30 bp were removed.
Read mapping was performed using HiSat2 with default parameters.
Gene abunstance estimation (counting) was performed using featureCounts with default parameters.
Genome_build: GRCH38 89; Af293 s03-m05-r09; Human herpesvirus 5 strain TB40E clone TB40-BAC4
Supplementary_files_format_and_content: Gene abundance matrix was created by featureCounts based on the combined annotation of all 3 organisms.

growth_protocol: CellGro GMP serum-free DC medium for up to 9h

extract_protocol:
Total RNA has been extracted and purified using the RiboPure RNA purification kit. Fragments were sequenced using Sequencing by synthesis (Illumina NextSeq 500).
RNA libraries were prepared for strand-specific sequencing using standard Illumina protocols.

value: DC

tag: number of fungal organisms (moi)

tag: samplingtimepoint (hours)

tag: compound

value: CellGro GMP serum-free DC medium

tag: rin/rna integrity number

tag: concentration (ng/ul)

tag: volume (ul)

tag: kit

value: RiboPure RNA purification kit

value: adapter ligation; strand specific


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B6_ad010

tag: strain


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B6_ad001


title: Donor3_01_DC_alone

tag: temperature

tag: atmosphere

tag: media


title: Ornidazole_Dose1_Rep2

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2


title: DC-alone-12hour

tag: cell type

tag: strain or line

tag: sampling time point (hours)

value: 37 degrees C

tag: parameter

value: rin/rna integrity number:9.3

value: concentration (ng/ul):32

value: volume (microliter):60


title: Saracatinib_Dose1_Rep2

tag: cell lines

tag: sgrnas


title: Donor2_01_DC_alone

tag: strainorline

tag: number of fungal organisms (moi)


title: Chlorambucil_Dose1_Rep2

tag: compound treatment


title: Pazopanib_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B6_ad007

tag: brain region

value: ACA,PL,ILA

tag: Sex

value: male

tag: age


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B5_ad012


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B6_ad006


title: Rigosertib_Dose1_Rep2


title: Gemcitabine_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B6_ad004


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B5_ad001


title: DC-alone-4h

value: 37 degreeC

value: 5percent  CO3

value: rin/rna integrity number:8.5

value: concentration (ng/microliter):67.36

value: volume (microliter):65


title: Ciclopirox_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B5_ad007


title: T12-06767

city: Nijmegen

first: Theo

middle: S

last: Plantinga

address: Geert Grooteplein Zuid 10

department: Department of Pathology

country: Netherlands

institute: Radboud University Medical Center

description:
T12-06767
overall comparison.fpkm_tracking
Papillary thyroid cancer TERT wild-type subgroup.fpkm_tracking

data_processing:
Mapping of reads by running TopHat (part of RNA sequencing Tuxedo tool on the GenePattern server of Broad Institute (www.genepattern.broadinstitute.org))
Assessment of differential expression by running Cuffdiff (part of RNA sequencing Tuxedo tool on the GenePattern server of Broad Institute (www.genepattern.broadinstitute.org))
Genome_build: hg19
Supplementary_files_format_and_content: FPKM_tracking
Supplementary_files_format_and_content: overall comparison.fpkm_tracking: Output of cuffdiff for the comparison of all digoxin-treated thyroid cancer cases with all matched control thyroid cancer cases not treated with digoxin
Supplementary_files_format_and_content: Follicular thyroid cancer oncocytic variant TERT mutant subgroup.fpkm_tracking: Output of cuffdiff for the comparison of digoxin-treated thyroid cancer cases with matched control thyroid cancer cases not treated with digoxin within the subgroup of TERT mutant follicular thyroid cancer - oncocytic variant cases
Supplementary_files_format_and_content: Follicular thyroid cancer oncocytic variant TERT wild-type.fpkm_tracking: Output of cuffdiff for the comparison of digoxin-treated thyroid cancer cases with matched control thyroid cancer cases not treated with digoxin within the subgroup of TERT wild-type follicular thyroid cancer - oncocytic variant cases
Supplementary_files_format_and_content: Follicular thyroid cancer TERT mutant subgroup.fpkm_tracking: Output of cuffdiff for the comparison of digoxin-treated thyroid cancer cases with matched control thyroid cancer cases not treated with digoxin within the subgroup of TERT mutant follicular thyroid cancer cases
Supplementary_files_format_and_content: Follicular thyroid cancer TERT wild-type subgroup.fpkm_tracking: Output of cuffdiff for the comparison of digoxin-treated thyroid cancer cases with matched control thyroid cancer cases not treated with digoxin within the subgroup of TERT wild-type follicular thyroid cancer cases
Supplementary_files_format_and_content: Follicular variant papillary thyroid cancer TERT mutant subgroup.fpkm_tracking: Output of cuffdiff for the comparison of digoxin-treated thyroid cancer cases with matched control thyroid cancer cases not treated with digoxin within the subgroup of TERT mutant follicular variant papillary thyroid cancer cases
Supplementary_files_format_and_content: Papillary thyroid cancer TERT mutant subgroup.fpkm_tracking: Output of cuffdiff for the comparison of digoxin-treated thyroid cancer cases with matched control thyroid cancer cases not treated with digoxin within the subgroup of TERT mutant papillary thyroid cancer cases
Supplementary_files_format_and_content: Papillary thyroid cancer TERT wild-type subgroup.fpkm_tracking: Output of cuffdiff for the comparison of digoxin-treated thyroid cancer cases with matched control thyroid cancer cases not treated with digoxin within the subgroup of TERT wild-type papillary thyroid cancer cases

source_name: Non-medullary thyroid carcinoma tissue

growth_protocol: Not applicable, human primary tissue is starting material

extract_protocol:
RNA was extracted with RNA-Bee 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 Bioanalyzer.
According to the manufacturers' protocol of the NuGEN SoLo hybridization and library construction kit

tag: gender

value: Female

tag: genotype/variation

value: TERT wild-type

tag: tumor histology

value: Papillary thyroid cancer

tag: agent


title: KU55933_Dose1_Rep2


title: T08-19226

description:
T08-19226
overall comparison.fpkm_tracking
Papillary thyroid cancer TERT wild-type subgroup.fpkm_tracking

value: Digoxin


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B5_ad006

tag: strain


title: Lovastatin_Dose1_Rep2


title: RG108_Dose1_Rep2


title: T11-10890

description:
T11-10890
overall comparison.fpkm_tracking
Follicular thyroid cancer oncocytic variant TERT wild-type.fpkm_tracking

value: Male

value: Follicular thyroid cancer - oncocytic variant


title: Donor1_01_DC_alone

tag: cell type

value: dendritic cells

value: DC

tag: samplingtimepoint (hours)

tag: temperature

tag: atmosphere

tag: media

value: CellGro GMP serum-free DC medium

tag: rin/rna integrity number

tag: concentration (ng/ul)

tag: volume (ul)

tag: kit

value: RiboPure RNA purification kit

value: adapter ligation; strand specific


title: T14-21491

description:
T14-21491
overall comparison.fpkm_tracking
Papillary thyroid cancer TERT wild-type subgroup.fpkm_tracking


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B5_ad004

tag: brain region

value: ACA,PL,ILA

value: male


title: T08-06913

description:
T08-06913
overall comparison.fpkm_tracking
Follicular thyroid cancer oncocytic variant TERT wild-type.fpkm_tracking


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B6_ad008

tag: Sex


title: T15-12493

description:
T15-12493
overall comparison.fpkm_tracking
Follicular thyroid cancer oncocytic variant TERT wild-type.fpkm_tracking

tag: age


title: DMSOPlate2WellF10_Dose1_Rep2

tag: cell lines

tag: sgrnas

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2

tag: compound treatment


title: Paclitaxel_Dose1_Rep2


title: T12-26690

description:
T12-26690
overall comparison.fpkm_tracking
Papillary thyroid cancer TERT wild-type subgroup.fpkm_tracking

tag: gender

tag: genotype/variation

tag: tumor histology

tag: agent


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B4_ad010

tag: strain


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B4_ad008


title: T11-10463

description:
T11-10463
overall comparison.fpkm_tracking
Follicular thyroid cancer TERT mutant subgroup.fpkm_tracking

value: TERT mutant

value: Follicular thyroid cancer


title: T04-20394

description:
T04-20394
overall comparison.fpkm_tracking
Follicular thyroid cancer oncocytic variant TERT mutant subgroup.fpkm_tracking


title: T10-20041

description:
T10-20041
overall comparison.fpkm_tracking
Follicular thyroid cancer TERT mutant subgroup.fpkm_tracking


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B4_ad006


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B5_ad008


title: DMSOPlate2WellC10_Dose1_Rep2


title: T13-07291

description:
T13-07291
overall comparison.fpkm_tracking
Follicular thyroid cancer TERT wild-type subgroup.fpkm_tracking


title: DimethylFumarate_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B5_ad002


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B4_ad002


title: T10-09975

description:
T10-09975
overall comparison.fpkm_tracking
Follicular thyroid cancer TERT mutant subgroup.fpkm_tracking


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B4_ad004


title: Nitroxoline_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B3_ad007


title: Lapatinib_Dose1_Rep2


title: T13-07693

description:
T13-07693
overall comparison.fpkm_tracking
Follicular thyroid cancer oncocytic variant TERT mutant subgroup.fpkm_tracking


title: T12-11032

description:
T12-11032
overall comparison.fpkm_tracking
Follicular thyroid cancer oncocytic variant TERT wild-type.fpkm_tracking


title: Selumetinib_Dose1_Rep2


title: Crizotinib_Dose1_Rep2


title: Trifluoperazine_Dose1_Rep2


title: BardoxoloneMethyl_Dose1_Rep2


title: T05-45259

description:
T05-45259
overall comparison.fpkm_tracking
Papillary thyroid cancer TERT mutant subgroup.fpkm_tracking


title: T06-13960

description:
T06-13960
overall comparison.fpkm_tracking
Follicular thyroid cancer TERT wild-type subgroup.fpkm_tracking


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B5_ad010


title: T05-08892

description:
T05-08892
overall comparison.fpkm_tracking
Follicular variant papillary thyroid cancer TERT mutant subgroup.fpkm_tracking

value: Follicular-variant papillary thyroid cancer


title: T05-30787

description:
T05-30787
overall comparison.fpkm_tracking
Follicular variant papillary thyroid cancer TERT mutant subgroup.fpkm_tracking

value: Female


title: Tivantinib_Dose1_Rep2


title: STF31_Dose1_Rep2


title: RacRotigotine_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B3_ad004


title: Vincristine_Dose1_Rep2


title: WP1130_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B2_ad010


title: T05-07468

description:
T05-07468
overall comparison.fpkm_tracking
Follicular thyroid cancer oncocytic variant TERT wild-type.fpkm_tracking

value: TERT wild-type


title: THP1 6h  in growth medium replicat 1

city: Paris

first: Olivier

last: Espeli

address: 11 place Marcelin Berthelot

department: CIRB

country: France

institute: College de France

description:
hg19
B120U6

data_processing:
Reads alignment was performed using Bowtie 2 (Langmead &  Salzberg, 2012) and significant fold changes accessed with the DE-seq pipeline (Anders & Huber, 2010).
Genome_build: hg19  and NC_011993.1
Supplementary_files_format_and_content: Custom interface id, gene name, NCBI ID https://www.ncbi.nlm.nih.gov/nuccore/NC_011993.1, RPKM Condition 1, RPKM condition 2, Fold change (condition 2/condition 1), Deseq  P value
Genome_build: hg19
Supplementary_files_format_and_content: gene_id (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25), gene type, gene name, RPKM Condition 1, RPKM condition 2, Fold change (condition 2/condition 1), Deseq  P value

source_name: THP1 macrophages

growth_protocol: Macrophages were  infected and imaged as previously described (Demarre et al., 2017). Infections were performed at MOI 30 (measured by CFU), resulting in the observation of 3 LF82 bacteria per macrophage on average at 1 h P.I..

extract_protocol:
Total RNA were extracted from THP1 macrophages infected by WT LF82 at 1 h and 6h P.I. Control experiments were performed with macrophages alone and bacteria alone cultivated for 1 h and 6 h in DMEM medium at 37°C and 5% CO2 without agitation. RNA extraction was performed as described before (Demarre et al, 2019).
Experiments were performed from biological duplicate. Human rRNAs were depleted using the Ribo-Zero kit, then strand-specific libraries were constructed using the TruSeq Stranded Total RNA kit (Illumina).
Paired-end sequencing (2 x 100 nt) was performed on a HiSeq 2500 sequencer.

tag: sample name

tag: cell type

value: THP1 macrophages


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B3_ad006


title: T09-006550

description:
T09-006550
overall comparison.fpkm_tracking
Papillary thyroid cancer TERT mutant subgroup.fpkm_tracking

value: Papillary thyroid cancer


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B3_ad008


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B2_ad012


title: Cyclophosphamide_Dose1_Rep2


title: Carfilzomib_Dose1_Rep2


title: T14-16951

description:
T14-16951
overall comparison.fpkm_tracking
Papillary thyroid cancer TERT mutant subgroup.fpkm_tracking


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B2_ad001


title: T08-33030

description:
T08-33030
overall comparison.fpkm_tracking
Papillary thyroid cancer TERT mutant subgroup.fpkm_tracking

value: Male

value: Digoxin


title: THP1 6h  in growth medium replicat 2

description:
hg19
B120U13


title: Letrozole_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B2_ad006


title: EPC3-hTERT 2% alcohol

city: Philadelphia

first: Michael

last: Gonzalez

state: Pennsylvania

address: 3535 Market St

department: Translational Medicine and Human Genetics

institute: University of Pennsylvania

data_processing:
Sequencing reads were aligned to mm10 reference using STAR
Resulting BAM files were read into R and GenomicAlignments and summarizeOverlaps libraries were used to generate count matrices
The DESeq2 library was used for secondary analysis and differential gene expression between experimental groups
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file of gene counts per sample

source_name: esophageal epitheium

growth_protocol: Telomerase immortalized non-transformed human esophageal epithelial cells (EPC1-hTERT, EPC2-hTERT and EPC3-hTERT) were routinely cultured in Keratinocyte serum-free media supplemented with Bovine pituitary extract (BPE) and Epidermal growth factor EGF (1ng/ml). Cells were cultured to 70-80% confluence in a humidified CO2 incubator

extract_protocol:
Cells were lyzed in RLT buffer and RNA was isolated using Qiagen's Rneasy Minin kit. RNA was stored in -80 until further processing.
Next-generation sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA library preparation kit, using high quality RNA (RIN >= 8.7) and 200ng of input. Libraries were assessed for quality using the PerkinElmer Labchip GX and qPCR using the Kapa Library Quantification Kit and the Life Technologies Viia7 Real-time PCR instrument. Libraries were diluted to 2nM and sequenced in a paired-end (2 x 100bp), dual-indexed format on the Illumina HiSeq2500 using the High Output v4 chemistry.

treatment_protocol: Cells were seeded in 6-well plates and subconfluent cells were exposed to alcohol (ethanol, 0% or 2%) diluted in complete culture media for 8 hours. Plates were sealed with parafilm to avoid evaporation. Control plates were subjected to same set-up.

tag: tissue

value: esophageal epitheium

tag: cell line

tag: genetic modification

value: Telomerase immortalized (h-TERT)


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B2_ad008


title: EPC3-hTERT 1% alcohol


title: EPC3-hTERT 0% alcohol


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B3_ad002


title: T11-15042

description:
T11-15042
overall comparison.fpkm_tracking
Papillary thyroid cancer TERT mutant subgroup.fpkm_tracking


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B2_ad004


title: EPC2-hTERT 2% alcohol


title: THP1 1h  in growth medium replicat 2

description:
hg19
B120U11


title: T05-03067

description:
T05-03067
overall comparison.fpkm_tracking
Papillary thyroid cancer TERT mutant subgroup.fpkm_tracking


title: FiveFluorouracil_Dose1_Rep2


title: Simvastatin_Dose1_Rep2


title: THP1 1h  in growth medium replicat 1

description:
hg19
B120U4


title: Trametinib_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B2_ad002


title: Etoposide_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B12_ad012


title: T03-09059

description:
T03-09059
overall comparison.fpkm_tracking
Papillary thyroid cancer TERT mutant subgroup.fpkm_tracking


title: EPC2-hTERT 0% alcohol


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B12_ad010


title: EPC1-hTERT 2% alcohol


title: Mebendazole_Dose1_Rep2


title: PD318088_Dose1_Rep2


title: Sitagliptin_Dose1_Rep2


title: Nilotinib_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B12_ad007


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B11_ad012


title: ZFP90_promoter_bait_SW480

city: Shanghai

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

country: China

institute: Renji Hospital

data_processing:
Library strategy: 4C-seq
The fastq were parsed based on the bait-specific primer sequence and mapped to the reduced hg19 genome using bowtie2 with the default parameters
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph with RPM

source_name: SW480 cells

growth_protocol: The human HCT116 and SW480 colorectal cancer cell were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.

extract_protocol:
DNA was extracted by phenol-chloroform and ethanol precipitated with glycogen as a carrier
4C-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The 4C-seq protocol was performed following a protocol(PMID:23411633)

value: human colorectal cancer cells

tag: passage


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B11_ad008

tag: brain region


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B12_ad006

tag: Sex


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B12_ad002

tag: age


title: Doxorubicin_Dose1_Rep2

tag: cell lines


title: EPC1-hTERT 0% alcohol


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B11_ad007


title: KX2391_Dose1_Rep2

tag: sgrnas


title: 16172: ABAF490

first: Jonathan

last: Schug

address: 12-156 Smilow Ctr Trans Research

department: School of Medicine

data_processing:
Illumina basecalling with bcl2fastq, various versions
Read alignment and expression calculation; using RUM (Grant et al. Bioinformatics  doi: 10.1093/bioinformatics/btr427)
Conversion from reads to trimmed normalized CPMs.  Briefly CPMs for genes between 25 to 75% quantiles were used to compute a normalization factor which was then applied to all CPMs.
Manual and semi-automated cell type calling. Marker genes and differentially expressed genes used to rate cell type and purity which was subsequently curated.
Genome_build: hg19
Supplementary_files_format_and_content: TSV files with raw rea counts or normalized CPMs.  Donor annotation and called cell types included as well.

molecule: polyA RNA

extract_protocol: Fluidigm C1 single-cell RNA-Seq using 96-well chip

value: pancreas

tag: celltype

value: pancreatic islets

tag: agecategory

value: adult

tag: healthcategory

value: control

tag: combinedcategory

value: Adult

value: dropped


title: Ruxolitinib_Dose1_Rep2

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2

tag: compound treatment


title: EPC2-hTERT 1% alcohol


title: rs9929219_RL_region_bait_SW480


title: SR1001_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B11_ad006

value: ACA,PL,ILA

value: male

tag: strain


title: rs9929219_RL_region_bait_HCT116

source_name: HCT116 cells


title: Zebularine_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B12_ad001


title: rs9929218_RR_region_bait_SW480


title: EPC1-hTERT 1% alcohol


title: Cisplatin_Dose1_Rep2


title: DMSOPlate2WellF6_Dose1_Rep2


title: rs9929218_RR_region_bait_HCT116


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B12_ad008


title: ZFP90_promoter_bait_HCT116


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B11_ad002


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B10_ad008


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B10_ad012


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B10_ad007


title: Tigecycline_Dose1_Rep2


title: DMSOPlate2WellC6_Dose1_Rep2


title: ZFP90-antibody-treatment

data_processing:
The FASTQ files were aligned to hg19 using Bowtie2. Enriched regions were determined by the MACS1.4 program
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph

growth_protocol: The human HCT116 colorectal cancer cell were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.

extract_protocol:
DNA were extracted by Phenol chloroform
chip-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CRC cells were cross-linked with 1% formaldehyde, isolated with SDS lysis buffer. Subsequently, the chromatin was sonicated and immunoprecipitated with ZFP90 antibody (SIGMA, Missouri, U.S.) and IgG (CST, Massachusetts, U.S.).


title: Dacarbazine_Dose1_Rep2


title: ZFP90-KO _2_RNA-seq

data_processing:
Sequence reads were mapped to the human genome (hg19) using TopHat v2.0.11 with the default options with a TopHat transcript index built from Ensembl_GRCh37.
Count files of the aligned sequencing reads were generated by the htseq-count script from the Python package HTSeq with union mode, using the GTF annotation file
Genome_build: hg19
Supplementary_files_format_and_content: count file

extract_protocol:
total RNA of HCT116 cells with different treatment was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To create ZFP90-Knockout alleles in HCT116, sgRNA were designed to target exon 3 of ZFP90

tag: genotype/variation

value: ZFP90 KO


title: Input

tag: cell type


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B1_ad012

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column


title: ZFP90-KO _3_RNA-seq


title: VER155008_Dose1_Rep2

data_processing:
Library strategy: QMAP-Seq
Individual samples were demultiplexed based on i5 and i7 index sequences by running bcl2fastq Conversion Software (Illumina).
Data was processed using QMAP-Seq bioinformatic analysis pipeline (https://github.com/mendillolab/QMAP-Seq). Briefly, sgRNA and cell line barcode sequences were extracted from Read 1 sequences as follows: [ACACCG][sgRNA:20][Interval:102][CellLineBarcode:8]. The number of reads for each cell line-sgRNA pair was counted, allowing up to one nucleotide mismatch per barcode. Cell number was interpolated from sequencing reads using sample-specific standard curves. The number of cells for a compound-treated sample was normalized to the median number of cells for the DMSO-treated samples.
Data was filtered using the following exclusion criteria. First, samples with low read counts were excluded. Second, cell line-sgRNA pairs with high variation (standard deviation of log2(cell number) > 0.7) were excluded. Third, compounds with an AUC > 550 for any cell line-sgRNA pair were excluded. Fourth, noncytotoxic cell line-compound pairs (relative cell number of sgNT with highest dose ≥ 90%) were excluded. Fifth, cell line-compound pairs without a dose-dependent reduction in cell viability (difference in relative cell number of sgNT between lowest and highest dose < 25%) were excluded.
Genome_build: N/A (sgRNA library sequencing)
Supplementary_files_format_and_content: Plain text document (.txt) files with read counts for each cell line-sgRNA pair. Individual files for each sample.
Supplementary_files_format_and_content: Comma-separated values (.csv) file with relative cell numbers (i.e., cell number (%DMSO)) for each cell line-sgRNA-compound-dose-replicate combination. Matrix table with data for all samples.


title: IgG-antibody-treatment


title: Decitabine_Dose1_Rep2


title: Control_3_RNA-seq


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B1_ad007


title: Control_2_RNA-seq


title: Bexarotene_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B1_ad010


title: 16157: ABAF490

tag: tissue


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B1_ad004


title: Sorafenib_Dose1_Rep2


title: Valdecoxib_Dose1_Rep2


title: 16156: ABAF490


title: Control_1_RNA-seq

tag: cell line


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B11_ad010


title: Fingolimod_Dose1_Rep2


title: Lenvatinib_Dose1_Rep2


title: PLX4720_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B1_ad002


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B10_ad002


title: ZFP90-KO _1_RNA-seq


title: PIK93_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B1_ad008


title: Clofarabine_Dose1_Rep2


title: young control (N1829-1) and old control (N1829-3) young 24h LPS  (N1829-2) and old 24h LPS(N1829-4)

city: Hannover

first: Christina

last: Brandenberger

address: Carl-Neuberg-Str. 1

department: Institute of Functional and Applied Anatomy

institute: Hannover Medical School

data_processing:
The proprietary 10x Genomics CellRanger pipeline (v3.1.0) was used to perform the following steps. The BCL files were converted to FASTQ files with cellranger mkfastq using the respective sample sheet with utilized 10X barcodes of the ‘master-samples’. mkfastq wraps Illumina's bcl2fastq and provides a number of convenient features in addition to the features of bcl2fastq. HTO data could be separated this way from expression data and end up in the ‘Undetermined’ fastq file fraction. Fastq data derived from the two replicates and 10x lanes (expression, and HTO) was separated based on individual barcodes, sequenced with index read 1. Based on the fastq files the gene expression and feature barcoding data was processed using cellranger counts with default parameters except for the setting of expected cells (--expect-cells 10000). For this step the Feature Reference was build according to the specification of TotalSeq™-A antibodies. Cellranger was used to align read data to the reference genome provided by 10X Genomics (Mouse reference dataset 3.0.0; mm10) using the aligner STAR, counting aligned reads per gene, and calculating clustering and summary statistics for the ‘master-samples’. This step considers the feature barcoding to count HTO tags.
The ‘master-samples’ were demultiplexed to get the ‘sub-samples’ by use of Seurat (v3.1.5) in R (v3.6.3) with a method based on the vignette “Demultiplexing with hashtag oligos (HTOs)” of Satjja Lab (https://satijalab.org/seurat/v3.1/hashing_vignette.html). Briefly described, the HTO data were log-normalized and clustered to end up in optimized separation of ‘sub-sample’ data based on HTO signals, finally receiving individual lists of cell barcodes of the distinct ‘sub-samples’.
Data analysis and visualization of master samples generated with cellranger was done with 10x Genomics Loupe Browser 4.0.0. Cell types were allocated to the different clusters of the ‘master-samples’ by using the gene/feature expression tool and searching and identifying cell types by known markers. To do so, genes previously identified in the atlas of the aging mouse lung mapped by single cell transcriptomics were used. The gene expression tool was also applied to visualize expression of genes related to cell cycle arrest in the different cell populations. Cells identified as AE2 were further separated and assigned to the four experimental groups, using the filters tool based on the HTO data. Within the AE2 and the four experimental groups a significant feature comparison analysis was done to find highly expressed genes in each cluster relative to the other clusters of interest und to generate a heat map of the most prominent genes expressed in each cluster. Furthermore a direct comparison of LPS treated vs control was done in AE2 of young and old mice and a comparison of old vs young in controls and LPS treated AE2 isolates.
Genome_build: Mouse reference dataset 3.0.0; mm10
Supplementary_files_format_and_content: Matrix (csv) file containing cell barcodes, genes and normalized read counts, representing demultiplexed 'sub-sample' data.

source_name: AE2 cells

growth_protocol: AE2 were isolated from young and old control or ALI mice 24 h after experimental start. The lungs were first lavaged 2 times with 0.7 mL PBS and then filled via intra-tracheal instillation with 1.5 mL dispase (5000U, Corning, #3544235) and 200 microliter low melting agarose. Lungs were excised from the thorax and further incubated in dispase for 45 min. The airways filled with agarose were then removed, the lungs were minced and incubated with 0.5% DNAse. A cell suspension was generated and collected cells were then filtered and washed prior to tabeling with EpCAM and HTO antibodies.

extract_protocol:
The harvested lung cell suspension was incubated with biotinylated EpCAM antibody (BioLegend #118203) for 30 min on ice, followed by washing steps and 30 min incubation with oligo barcoded PE streptavidin TotalSeq™-A antibodies (BioLegend #405251, 405253, 405255, 405257) as described in the supplier’s manual. For each experimental group (young control, young 24 h LPS, old control, old 24 h LPS) a different oligo barcoded antibody was used. The cells were then sorted for EpCAM positive cells. DAPI was used to detect and exclude dead cells. The harvested cells were counted and the four experimental groups were pooled in equal number for scRNA-seq analysis. The pooled samples were loaded on one 10x Genomics lane. One of such pooled cell sample generated in the course the cell hashing approach is referred to as one ‘master-sample’ in the following description. The whole experiment was performed twice in the form of an independent biological replica experiment. Accordingly, in this experiment, two ‘master-samples’ do exist (N1828 and N1829), representing the two replicates and including four experimental groups each.
Library preparation for scRNA-seq analysis was performed according to the Chromium Single Cell 3ʹ Reagent Kit v3 User Guide (Manual Part Number CG000183 Rev A; 10x Genomics). According to the protocol a given 1.6-fold excess of cells was loaded to the 10x controller in order to reach a target number of 10000 cells per ‘master sample’. Fragment length distribution of generated libraries was monitored using ‘Bioanalyzer High Sensitivity DNA Assay’ (5067-4626; Agilent Technologies). Quantification of libraries was performed by use of the ‘Qubit® dsDNA HS Assay Kit’ (Q32854; ThermoFisher Scientific).

treatment_protocol: Young and old mice treated with saline or 2.5 mg/kg BW LPS were sacrificed 24 h later.

value: EpCAM positive lung cells

tag: treatment

tag: genotype

value: mixed sample (non-demultiplexed)


title: young control (N1828-1) and old control (N1828-3) young 24h LPS  (N1828-2) and old 24h LPS(N1828-4)


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A9_ad012

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B1_ad006

tag: Sex


title: Linsitinib_Dose1_Rep2

extract_protocol:
Cell line pools were lysed with lysis buffer (10% 10x Taq DNA Polymerase Buffer, 0.45% IGEPAL CA-630, 0.45% TWEEN 20, 10% Proteinase K, 79.1% Nuclease-Free Water) containing cell spike-in standards. Cells were incubated at 60°C for 1 hour. Proteinase K from lysis buffer was inactivated at 95°C for 15 minutes.
Barcoded region was PCR amplified with a unique set of indexed primers for each sample. PCR products were pooled and purified twice. Sequencing library was diluted, combined with PhiX, denatured, and sequenced on a NovaSeq 6000 (Illumina).


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A9_ad001

tag: age


title: CHIR99021_Dose1_Rep2

tag: cell lines


title: RNA-seq_WT_rep2

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

data_processing:
fastq files were aligned to GRCm38/mm10 reference  genome using Kallisto
Genes with zero read count in more than three conditions were filtered out.
differential expression analysis was run using DESeq 2 package and data normalized
Differential genes were found between the two conditions at a BH  corrected P-value < 0.05.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text file with normalized counts

source_name: CD8 T cells

growth_protocol: At D8 p.i. with Cl13, CD8 T cells were isolated from spleens of infected recipients

extract_protocol:
RNA were isolated using the QIAGEN RNeasy Micro Kit with 2 x 104  cell per sample
cDNA libraries were generated using SMARTSeq V4 Ultra Low kit. Libraries were  quantified by qPCR using a KAPA Library Quant Kit (KAPA Biosystems).

treatment_protocol: VEX+GFP+ cells are  sorted using FACS with >95% purity

value: CD8 T cells

tag: background strain

value: wild-type

value: LCMV Clone13 infection


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A9_ad010


title: Ki8751_Dose1_Rep2

tag: sgrnas


title: RNA-seq_WT_rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A9_ad006


title: RNA-seq_Fli1KO_rep5


title: RNA-seq_Fli1KO_rep4


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A9_ad004


title: Gefitinib_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A9_ad002


title: RNA-seq_Fli1KO_rep3


title: RNA-seq_Fli1KO_rep2


title: RNA-seq_WT_rep3


title: 16149: ABAF490

tag: celltype

tag: agecategory

value: acinar


title: Niclosamide_Dose1_Rep2


title: RNA-seq_Fli1KO_rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A8_ad002


title: Cabozantinib_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A8_ad007


title: MK0752_Dose1_Rep2


title: CnR_Igg_rep1

data_processing:
Reads were aligned to mm10 reference genome using Bowtie2 v2.3.4.1 with options suggested  by Henikoff (Skene et al., 2018).
Picard tools v1.96 was used to remove presumed PCR duplicates using  the MarkDuplicates command. Bam files containing uniquely mapped reads were created using Samtools  v1.1. For downstream analysis, biological replicates (3 per condition) were merged at this step. Bedtools  v2.28.0 was used to generate fragment BED files with size 40bp-500bp. Blacklist regions, random  chromosomes, and mitochondria were removed
Read per million (RPM) normalized bigwig files were created using bedGraphToBigWig (UCSC) and were  used to visualize binding signals. Peaks were called using MACS v2.1 using the broadPeak setting with  p-value cutoff of 1e-8, -f BEDPE and IgG as controls
Genes proximal to peaks were annotated against the  mm10 genome using annotatePeaks.pl from HOMER v4. Fli1 binding motifs were identified using  findMotifsGenome.pl from HOMER v4
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text file with normalized counts

extract_protocol:
CUT&RUN experiments were performed as previously described(Skene et al., 2018) with modifications
CUT&RUN DNA library was prepared as previously descried(Liu et al., 2018) with slight modifications.  Briefly, all DNA precipitated from pA-MN digestion was used for library preparation using NEBNext Ultra II  DNA Library Prep Kit (NEB).

treatment_protocol: The antibodies used were: Fli1, ab15289, used at 1:50 (abcam) and guinea pig anti-rabbit IgG, used at  1:100, ABIN101961 (antibodies-online).

value: Igg control

tag: antibody

value: Fli1 (Abcam ab15289)

tag: protocol

value: Cut and Run Chipseq


title: CnR_Igg_rep2

value: guinea pig anti-rabbit IgG, ABIN101961


title: CnR_Igg_rep3


title: Fulvestrant_Dose1_Rep2

tag: compound treatment


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A8_ad006

tag: strain


title: DMSOPlate2WellF3_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A8_ad010


title: Fluvastatin_Dose1_Rep2


title: Parthenolide_Dose1_Rep2


title: CnR_Fli1_rep3

tag: cell type


title: Dabrafenib_Dose1_Rep2


title: CnR_Fli1_rep1


title: Erlotinib_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A8_ad001


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A9_ad008


title: DMSOPlate2WellC3_Dose1_Rep2


title: ATAC-seq_WT_rep2

description:
WT_rep2
R_2_S3

data_processing:
fastq files were aligned to GRCm38/mm10 reference  genome using bowtie2
Samtools/bedtools were used to process and filter mitochondrial reads and to remove duplicates.Peak calling was performed using MACS v2 (FDR q-value 0.01).
differential expression analysis was run using DESeq 2 package and data normalized
Differentially  accessible regions were identified following DESeq2 normalization using an FDR cut-off < 0.05
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bed files with peak coordinates, combUnionReadsWithLabels.txt contains peaks accessibility counts.

extract_protocol:
Sorted cells (2.5 x 104) were washed  twice in cold PBS and resuspended in 50μl of cold lysis buffer (10nM Tris-HCl, pH 7.4, 10mM NaCl, 3mM  MgCl2, 0.1% Tween). Lysates were centrifuge (750xg, 10min, 4oC) and nuclei were resuspended in 50μl of  transposition reaction mix (TD buffer [25μl], Tn5 Transposase [2.5μl], nuclease-free water [22.5μl];  (Illumina)) and incubated for 30min at 37oC.
Transposed DNA fragments were purified using a Qiagen  Reaction MiniElute Kit, barcoded with NEXTERA dual indexes (Illumina) and amplified by PCR for 11  cycles using NEBNext High Fidelity 2x PCR Master Mix (New England Biolabs).

value: LCMV Clone 13 infection


title: ATAC-seq_WT_rep1

description:
WT_rep1
R_1_S2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A7_ad001


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A7_ad012


title: Abiraterone_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A8_ad004


title: Anastrozole_Dose1_Rep2


title: CnR_Fli1_rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A7_ad007


title: Blebbistatin_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A7_ad006


title: ATAC-seq_Fli1KO_rep4

description:
Fli1KO_rep4
360_2_S7


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A7_ad004


title: ATAC-seq_Fli1KO_rep3

description:
Fli1KO_rep3
360_1_S6


title: ATAC-seq_Fli1KO_rep2

description:
Fli1KO_rep2
290_2_S5


title: Alisertib_Dose1_Rep2


title: Exemestane_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A8_ad012


title: NVPAUY922_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A7_ad008


title: Nelarabine_Dose1_Rep2


title: Smc1-HA 24 hpm HiChIP mboi

city: Hefei

first: xiaoyuan

last: song

address: Huangshan Road

institute: University of Science & Technology of China

data_processing:
Raw HiC and HiChIP data were processed through the HiC-Pro (2.9.0) pipeline (PMID: 26619908) to generate .hic files and call loops with cLoops (0.9). Raw HiC and HiChIP data also processed through the HiCExplorer tools 2.1.4 (PMID:29335486) for A/B compartments and chromatin domains analysis.
hic files were generated using HiC-Pro (2.9.0) script: hicpro2juicebox.sh
TADs were found with HiCExplorer (2.1.4) tool 'hicFindTADs'  with '-delta 0.3' for Cell 1.5 hpm, 3 hpm, 24 hpm and MAC 1.5 hpm, 3 hpm, 24 hpm; with '-delta 0.2' for Smc1 (mboi) 3 hpm and 24 hpm; with '-delta 0.15' for Smc1 (mboi) 1.5 hpm
PCA analysis was performed with HiCExplorer (2.1.4) tool 'hicPCA'
Loop calling was performed with cLoops (0.9)
Genome_build: TetrahymenaMicro2016, TetrahymenaMacro2014
Supplementary_files_format_and_content: hic files contain the HiC contact matrix at different resolution.  Txt files contain the chromatin domains found by HiCExplorer (2.1.4).

organism: Tetrahymena thermophila

source_name: Tetrahymena thermophila cells

growth_protocol: Tetrahymena thermophila strains B2086, Cu428, B2086 with Smc1-HA (gift from Dr. Josef Loidl) and Cu428 with Rec8-GFP (gift from Dr. Josef Loidl) were used for Hi-C and HiChIP experiments. Cells were cultured at 30°C in 1x SPP medium (10g Protease peptone, 2g Dextrose, 1g Yeast extract, 0.03g Sequestrene (Fe-EDTA), add water to final 1 liter and autoclave prior to use). For conjugation, cells were first starved in 10mM Tris-HCl Ph7.4 to a final density of approximately 2.5x105 cells/ml for 24 hours at 30°C without shaking. Then we mixed equal numbers of cells representing the two different mating types and incubated at 30°C for 1.5 hours, 3 hours or 24 hours without disturbing, until collecting the cells for the subsequent experiments.

extract_protocol:
We crosslinked conjugated Tetrahymena theromphila cells at 1.5 hpm, 3 hpm and 24 hpm (hpm: hours post-mixing) with 1% formaldehyde for 10 minutes at room temperature. For Hi-C, we followed in-situ Hi-C protocol, the Tetrahymena cells were lysed. Then the lysed cells, isolated MIC or MAC were digested by MboI or HindIII overnight at 37℃. DNA fragment ends were filled and labeled with dCTP, dGTP, dTTP and biotin-dATP. Proximity ligation was performed at room temperature for 4 hours. Then the DNA were de-crosslinked at 65°C overnight with Proteinase K and DNA were purified. For HiChIP, the Tetrahymena cells were lysed. Then the lysed cells, isolated MIC or MAC were digested by MboI or HindIII overnight at 37℃. DNA fragment ends were filled and labeled with dCTP, dGTP, dTTP and biotin-dATP. Proximity ligation was performed at room temperature for 4 hours. Following the in situ ligation, we fragmented the ligated chromatin with sonication. Then the crosslinked protein/DNA was immunoprecipitated using antibodies to HA (rabbit, Cell Signaling Technology C29F4 or Abcam ab9110) and GFP (Abcam ab290) and then purified by Protein A+G immunomagnetic beads. The amount of MboI or HindIII enzyme, antibody, and beads are determined by the number of cells in each sample. After immunoprecipitation, DNA was eluted from the beads by incubating at 65°C for 4 hours with Proteinase K and purified.
Both Hi-C and HiChIP DNA were sonicated and binding to M280 beads, then end-repair, dA-tailing and adapter ligation on beads. After PCR amplification and DNA purification, the libraries were sequenced on HiSeq X Ten using 150bp paired-end reads.
Hi-C and HiChIP

value: B2086:Smc1-HA and Cu428:Rec8-GFP

tag: developmental stages

value: 24 hours post-mixing

tag: hi-c digest enzyme

value: MboI

tag: hichip antibody

value: Anti-HA tag antibody ChIP Grade, abcam, ab9110


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A7_ad002

value: ACA,PL,ILA

value: male


title: Regorafenib_Dose1_Rep2

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2


title: 16128: ABAF490

tag: tissue

value: pancreas

value: pancreatic islets

value: adult

tag: healthcategory

value: control

tag: combinedcategory

value: Adult

value: dropped


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A6_ad007

tag: brain region

tag: Sex

tag: age


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A6_ad010


title: Smc1-HA 24 hpm HiChIP hindiii

value: HindIII

value: HA-Tag (C29F4) Rabbit mAb, Cell Signaling Technology


title: Smc1-HA 3 hpm HiChIP mboi

value: 3 hours post-mixing


title: Mitoxantrone_Dose1_Rep2

tag: cell lines

tag: sgrnas


title: Cimetidine_Dose1_Rep2


title: RITA_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A6_ad006


title: Smc1-HA 3 hpm HiChIP hindiii


title: ATAC-seq_Fli1KO_rep1

description:
Fli1KO_rep1
290_1_S4

tag: background strain

value: CD8 T cells

tag: genotype

tag: treatment

value: LCMV Clone 13 infection


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A6_ad004


title: Cediranib_Dose1_Rep2

tag: compound treatment


title: Rec8-GFP 24 hpm HiChIP

tag: strain

value: B2086:Smc1-HA and Cu428:Rec8-GFP

value: 24 hours post-mixing

value: Anti-GFP antibody ChIP Grade, abcam, ab290


title: CEMBA190205_5A_1_CEMBA190205_5A_2_B1_ad001

value: ACA,PL,ILA


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A6_ad001

value: male


title: 16123: ABAF490

tag: celltype

tag: agecategory

value: beta


title: PHA793887_Dose1_Rep2

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A6_ad008


title: 16121: ABAF490

value: pancreas

value: pancreatic islets


title: MIC 24 hpm Hi-C

tag: developmental stages

tag: hi-c digest enzyme


title: Rec8-GFP 3 hpm HiChIP

tag: hichip antibody


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A5_ad007


title: Dexamethasone_Dose1_Rep2


title: Tacrolimus_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A5_ad012


title: Thalidomide_Dose1_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A5_ad006


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A5_ad010


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A5_ad001


title: Temozolomide_Dose1_Rep2


title: MIC 1.5 hpm Hi-C

value: 1.5 hours post-mixing


title: Smc1-HA 1.5 hpm HiChIP mboi

value: MboI

value: Anti-HA tag antibody ChIP Grade, abcam, ab9110


title: Bendamustine_Dose1_Rep2


title: Rec8-GFP 1.5 hpm HiChIP

value: HindIII


title: MAC 24 hpm Hi-C


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A5_ad002


title: Smc1-HA 1.5 hpm HiChIP hindiii

value: HA-Tag (C29F4) Rabbit mAb, Cell Signaling Technology


title: BrefeldinA_Dose1_Rep1


title: MAC 3 hpm Hi-C

value: 3 hours post-mixing


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A5_ad008


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A4_ad012


title: Cell 3 hpm Hi-C


title: MAC 1.5 hpm Hi-C


title: Dasatinib_Dose1_Rep1


title: Brivanib_Dose1_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A4_ad010


title: Cell 24 hpm Hi-C


title: Tivozanib_Dose1_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A4_ad007


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A4_ad001


title: Sildenafil_Dose1_Rep1


title: MIC 3 hpm Hi-C


title: Cell 1.5 hpm Hi-C


title: Everolimus_Dose1_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A4_ad002


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A3_ad012


title: Saracatinib_Dose1_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A3_ad001


title: PYR41_Dose1_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A3_ad010


title: Ornidazole_Dose1_Rep1


title: Chlorambucil_Dose1_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A3_ad007


title: Rigosertib_Dose1_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A3_ad006


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A4_ad004


title: Pazopanib_Dose1_Rep1


title: Gemcitabine_Dose1_Rep1


title: Topotecan_Dose1_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A3_ad008


title: Lovastatin_Dose1_Rep1


title: wt_pooled_8e

city: Freiburg

first: Valérie

last: Hilgers

address: Stübeweg 51

institute: MPI of Immunobiology and Epigenetics

description:
elav-fne-rbp9_wt.early.APA_targets.tsv
elav-fne_wt.early.APA_targets.tsv
elav-rbp9_wt.early.APA_targets.tsv
elav_wt.early.APA_targets.tsv
fne-rbp9_wt.early.APA_targets.tsv
fne_wt.early.APA_targets.tsv
rbp9_wt.early.APA_targets.tsv
Segments_split.early.gff

data_processing:
RNA-seq data were analyzed using the RNA-seq module from snakePipes (Bhardwaj V, Manke T. Bioinformatics. 2019) with default parameters.
ELAV iCLIP sequencing reads were processed using iCount (Curk et al. 2019). iCount was used from raw sequence processing to iCLIP peak identification and quantification.
Genome_build: dm6

organism: Drosophila melanogaster

source_name: embryos (14-16h)

extract_protocol:
stranded mRNA
Phenol-chloroform RNA purification

tag: mutant

value: wild-type

tag: developmental stage


title: RG108_Dose1_Rep1


title: 5% HPL2_3

type: RNA

city: Sevilla

first: Luis

last: Lopez Navas

state: Sevilla

address: c/ Americo Vespucio, 15, Ed. S-2

department: Preclinical Research

country: Spain

institute: Red Andaluza de diseño y traslación de Terapias Avanzadas

description: Fibroblasts cultured for 8 passages with 5% HPL2 as culture supplement

hyb_protocol: Hybridization was performed with independent Human Clarion-S Microarrays (Affymetrix) following Affymetrix protocol.

scan_protocol: Microarrays were scanned with Affymetrix GeneChip Scanner 7G

data_processing: Data were analyzed with Affymetrix ® GeneChip® Command Console® 2.0 software.  Relevant Software parameters were the following: Anova Method: eBayes; DAGB threshold < 0.05; Pos/Neg AUC threshold: 0.7; Exploratory Grouping Analysis (all parameters): Default; Signal Space Transformation - Robust Microarray Analysis (SST-RMA) was used as the normalization method.

label: biotin

source_name: Skin biopsy

label_protocol: cDNA was synthetized and labelled with biotin following the instructions of the manufacturer (Affymetrix, WT PLUS)

growth_protocol: 5 % in-house HPL2 solution,  Gentamycin (final concentration 20µg/mL), glutamax (final concentration 2mM), NEAA (final concentration 0,1mM), Heparin (final concentration 2U/mL)

extract_protocol: RNA was extracted with RNeasy® Mini kit (Qiagen) following the instructions of the manufacturer.

tag: cell culture supplement

value: 5percent HPL2


title: 15% HPL2_2

description: Fibroblasts cultured for 8 passages with 15% HPL2 as culture supplement

growth_protocol: 15 % in-house HPL2 solution,  Gentamycin (final concentration 20µg/mL), glutamax (final concentration 2mM), NEAA (final concentration 0,1mM), Heparin (final concentration 2U/mL)

value: 15percent HPL2


title: wt_pooled_8c

tag: Sex


title: 15% HPL2_3


title: 10% FBS_2

description: Fibroblasts cultured for 8 passages with 10% FBS as culture supplement

growth_protocol: 10% FBS,  Gentamycin (final concentration 20µg/mL), glutamax (final concentration 2mM), NEAA (final concentration 0,1mM), Heparin (final concentration 2U/mL)

value: 10percent FBS


title: 5% HPL2_1


title: 10% FBS_3


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A2_ad012

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

tag: brain region

tag: age


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A2_ad007


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A3_ad004


title: Ciclopirox_Dose1_Rep1

growth_protocol: Cell line pools were cultured in RPMI-1640, 10% Tet System Approved FBS, 1% Penicillin/Streptomycin, 100 ng/mL doxycycline for 7 days prior to compound treatment.

tag: cell lines

tag: sgrnas


title: 10% FBS_1


title: 15% HPL2_1


title: KU55933_Dose1_Rep1


title: wt_pooled_18-22h_8d

description:
elav-fne_wt.late.APA_targets.tsv
elav_wt.late.APA_targets.tsv
fne_wt.late.APA_targets.tsv
Segments_split.late.gff

source_name: embryos (18-22h)


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A2_ad001


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A2_ad006


title: wt_pooled_18-22h_8e


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A2_ad004


title: Nitroxoline_Dose1_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A2_ad010


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A2_ad002


title: DMSOPlate1WellF10_Dose1_Rep1


title: wt_pooled_8d


title: Paclitaxel_Dose1_Rep1


title: wt_pooled_18-22h_8c


title: 16090: ABAF490

tag: tissue

value: adult

tag: healthcategory

value: control

tag: combinedcategory

value: Adult

value: dropped


title: DimethylFumarate_Dose1_Rep1

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2

tag: compound treatment


title: rbp9_pooled_7b

description:
rbp9_wt.early.APA_targets.tsv
Segments_split.early.gff

value: rbp9 mutant

value: male


title: DMSOPlate1WellC10_Dose1_Rep1


title: Lapatinib_Dose1_Rep1


title: rbp9_pooled_7c


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A12_ad012

value: ACA,PL,ILA

tag: strain


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A12_ad010


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A12_ad008


title: Tivantinib_Dose1_Rep1


title: rbp9_pooled_7a


title: fne-rbp9_pooled_5d

description:
fne-rbp9_wt.early.APA_targets.tsv
Segments_split.early.gff

value: fne-rbp9 mutant


title: fne-rbp9_pooled_5c


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A2_ad008


title: BardoxoloneMethyl_Dose1_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A12_ad007


title: wt_pooled_18-22h_8a


title: RacRotigotine_Dose1_Rep1


title: Vincristine_Dose1_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A12_ad004


title: fne_pooled_6c

description:
fne_wt.early.APA_targets.tsv
Segments_split.early.gff

value: fne mutant


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A12_ad002


title: fne_pooled_6b


title: Crizotinib_Dose1_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A12_ad001


title: Trifluoperazine_Dose1_Rep1


title: fne_pooled_18-22h_6e

description:
fne_wt.late.APA_targets.tsv
Segments_split.late.gff


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A11_ad012


title: Carfilzomib_Dose1_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A12_ad006


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A11_ad008


title: fne_pooled_18-22h_6c


title: Cyclophosphamide_Dose1_Rep1


title: fne_pooled_18-22h_6b


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A11_ad010


title: WP1130_Dose1_Rep1


title: fne_pooled_6d


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A11_ad007


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A11_ad006


title: STF31_Dose1_Rep1


title: elav-rbp9_pooled_4b

description:
elav-rbp9_wt.early.APA_targets.tsv
Segments_split.early.gff

value: elav-rbp9 mutant


title: FiveFluorouracil_Dose1_Rep1


title: fne_pooled_18-22h_6a


title: elav-rbp9_pooled_4e


title: 5% HPL2_2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A11_ad002


title: elav_pooled_2d

description:
elav_wt.early.APA_targets.tsv
Segments_split.early.gff

value: elav mutant


title: elav-rbp9_pooled_4c


title: Simvastatin_Dose1_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A11_ad001


title: elav_pooled_2c


title: fne-rbp9_pooled_5b


title: Letrozole_Dose1_Rep1


title: Etoposide_Dose1_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A11_ad004


title: Mebendazole_Dose1_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A10_ad012


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A10_ad010


title: elav_pooled_18-22h_2e

description:
elav_wt.late.APA_targets.tsv
Segments_split.late.gff


title: PD318088_Dose1_Rep1


title: Trametinib_Dose1_Rep1


title: elav_pooled_18-22h_2d


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A10_ad007


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A10_ad006


title: KX2391_Dose1_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A10_ad004


title: elav-fne-rbp9_pooled_1c

description:
elav-fne-rbp9_wt.early.APA_targets.tsv
Segments_split.early.gff

value: elav-fne-rbp9 mutant


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A10_ad002


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A10_ad001


title: elav-fne-rbp9_pooled_1a


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A1_ad001


title: elav-fne_pooled_3e

description:
elav-fne_wt.early.APA_targets.tsv
Segments_split.early.gff

value: elav-fne mutant


title: Cisplatin_Dose1_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A1_ad007


title: elav-fne_pooled_3c


title: Sitagliptin_Dose1_Rep1


title: Nilotinib_Dose1_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A1_ad006


title: Selumetinib_Dose1_Rep1


title: elav-fne_pooled_18-22h_3e

description:
elav-fne_wt.late.APA_targets.tsv
Segments_split.late.gff


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A1_ad002


title: elav-fne_pooled_3b


title: Zebularine_Dose1_Rep1


title: Doxorubicin_Dose1_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A1_ad004


title: SR1001_Dose1_Rep1


title: DMSOPlate1WellF6_Dose1_Rep1


title: elav_pooled_2b


title: elav-fne_pooled_18-22h_3c


title: Bexarotene_Dose1_Rep1


title: elav-fne-rbp9_pooled_1b


title: elav-fne_pooled_18-22h_3d


title: PyVT-Nr4a1-KO3

city: xiamen

first: yang

last: pengbo

address: xiangan

institute: xiamen university

data_processing:
Basecalls performed using Illumina Casava 1.8
Sequence reads were mapped to the GRCm38 (mm10) using hisat2 with default parameters.
featureCounts was used to estimate transcript abundance using default parameters.
Genome_build: GRCm38
Supplementary_files_format_and_content: The pymt_WT_vs_KO_raw_count file contains the raw counts output by combinding the raw counts from each sample and combining them into one file.

source_name: PyVT mouse mammary tumor cells

extract_protocol:
mRNA was isolated and purified by using RNeasy Plus Mini Kit (Qiagen). A total amount of 3 µg RNA per sample was used as input material for the construction of sequencing libraries.
RNA-seq libraries were prepared using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) and sequenced on illumina novaseq 6000  System with 150 base paired-end read.

value: FVB/NJ

tag: genotype


title: elav-fne_pooled_18-22h_3b


title: PyVT-Nr4a1-KO2


title: Ruxolitinib_Dose1_Rep1


title: Decitabine_Dose1_Rep1


title: Adult_tail_2

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description:
Whole cell RNA from tissue
Ribo_meth_seq_results.xlsx

data_processing:
Library strategy: RiboMeth-seq
Barcode separation using python script
Adaptor trimming using Cutadapt v. 2.0
Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1
Counting read ends and calculating RiboMeth-seq scores using python scripts
The output FASTA files from small RNA-seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially, SNORDs were identified by running the merged FASTA file through snoScan (Schattner et al. 2005) against zebrafish early- and late-rRNA reference sequences (Locati et al. 2017).
Genome_build: early and late zebrafish rRNA (locati et al). The reference sequences are available in the FASTA file on the series record.
Supplementary_files_format_and_content: MS Excel file contains 5' and 3' read count and calculated RiboMeth-seq score at all positions in the rRNA sequence.

organism: Danio rerio

source_name: adult tail (trunk)

extract_protocol:
Tissues were homogenized and whole cell RNA was extracted using Qiazol (Qiagen) according to the manufacturer.
RiboMeth-seq: 5-10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20-40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2',3' cyclic phosphate and 5' phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H. Profiling of ribose methylations in RNA by high-throughput sequencing. Angewandte Chemie. 2015;54(2):451-5 for detailed description

value: adult tail (trunk)

tag: rna fraction

value: size fractionated (20-40 nt) whole cell RNA


title: elav-fne_pooled_18-22h_3a


title: Tigecycline_Dose1_Rep1

source_name: Pool of 5 breast cancer cell lines


title: PyVT-Nr4a1-WT3

value: wild type


title: DMSOPlate1WellC6_Dose1_Rep1


title: Dacarbazine_Dose1_Rep1


title: PyVT-Nr4a1-WT2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_A1_ad008

source_name: C57BL/6J Male P56 Mouse Brain


title: PyVT-Nr4a1-KO1


title: PyVT-Nr4a1-WT1


title: Lenvatinib_Dose1_Rep1


title: wt_rep2

description: RNA-seq.wildtype.tpm.tsv

source_name: adult fly heads

value: wild-type

value: adult


title: PM_3

source_name: protruding-mouth stage

value: protruding-mouth stage


title: PM_2


title: Sorafenib_Dose1_Rep1

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2


title: PIK93_Dose1_Rep1


title: wt_rep1

description: RNA-seq.wildtype.tpm.tsv


title: 12_somite_2

source_name: 12-somite stage

value: 12-somite stage


title: 12_somite_3


title: elav_iClip_rep1

description:
elav_iclip.NNNGGTTNN_cDNA_peaks.bedgraph
elav_iclip.NNNGGTTNN_cDNA_peaks.intronic.bedgraph

data_processing:
Library strategy: iclip-seq
RNA-seq data were analyzed using the RNA-seq module from snakePipes (Bhardwaj V, Manke T. Bioinformatics. 2019) with default parameters.
ELAV iCLIP sequencing reads were processed using iCount (Curk et al. 2019). iCount was used from raw sequence processing to iCLIP peak identification and quantification.
Genome_build: dm6

molecule: nuclear RNA

extract_protocol:
stranded total RNA
Phenol-chloroform RNA purification

value: male and female

tag: clip barcode

value: NNNGGTTNN


title: Valdecoxib_Dose1_Rep1


title: Fingolimod_Dose1_Rep1


title: PM_1


title: 12_somite_1


title: SK8-37

city: Wuxi

first: Xuewei

last: Pan

address: 1800, Lihu Avenue

institute: Jiangnan University

data_processing:
Use software FastQC (v0.10.1) to control of raw data's quality
Use Cutadapt (version 1.9.1) to filtering low-quality data, removing contamination and joint sequence
Use bowtie2(v2.1.9) software to compare with reference sequence
Software (V 0.6.1) Htseq was used to calculate gene expression, the software used FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) method to calculate gene expression.
Differentially expressed genes between samples JNB5-1 and SK8-37 were screened based on differentially expressed genes. KEGG_B_Class function enrichment analysis were performed for significant difference genes
Genome_build: S. marcescens WW4 (NC_020211.1)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample, and gz files include raw data for each sample.

organism: Serratia marcescens

source_name: Bacteria

growth_protocol: Bacterial cultures were routinely incubated in LB medium at 30℃

extract_protocol:
The collected cells were treated with RNAprep pure Kit (TIANGEN) to extract total bacterial RNA and delivered to GENEWIZ in dry ice for transcriptome resequencing analysis
The total RNA extracted from the bacterial were subjected to rRNA removing to obtain mRNA. The mRNA was used as templates for DNA synthesis. Illumina Hiseq platform was used for the cDNA libraries sequencing

treatment_protocol: S. marcescens JNB5-1 and SK8-37 cells were grown in LB medium for 10 h before harvesting

value: mutant


title: Adult_tail_1


title: VER155008_Dose1_Rep1


title: PLX4720_Dose1_Rep1


title: Clofarabine_Dose1_Rep1


title: 32_cell_3

source_name: 32-cell stage

value: 32-cell stage


title: JNB5-1 (SK8-37 comparison)


title: Linsitinib_Dose1_Rep1


title: Donor4_06_DC_plus_CMV_0h_plus_Afu_4h30min

data_processing:
Quality and adapter trimming were performed using Trimmomatic version 0.36, including windows size trimming (size 10, Q25), 3’ ad 5’ quality clipping (Q5) and sequences with less than 30 bp were removed.
Read mapping was performed using HiSat2 with default parameters.
Gene abunstance estimation (counting) was performed using featureCounts with default parameters.
Genome_build: GRCH38 89; Af293 s03-m05-r09; Human herpesvirus 5 strain TB40E clone TB40-BAC4
Supplementary_files_format_and_content: Gene abundance matrix was created by featureCounts based on the combined annotation of all 3 organisms.

organism:
Homo sapiens
Human betaherpesvirus 5
Aspergillus fumigatus

source_name: dendritic cells

extract_protocol:
Total RNA has been extracted and purified using the RiboPure RNA purification kit. Fragments were sequenced using Sequencing by synthesis (Illumina NextSeq 500).
RNA libraries were prepared for strand-specific sequencing using standard Illumina protocols.

tag: cell type

value: dendritic cells

tag: strainorline

value: DC; A. fumigatus ATCC 46645; Human herpesvirus 5 strain TB40/E clone TB40-BAC4

tag: number of fungal organisms (moi)

tag: samplingtimepoint (hours)

tag: temperature

tag: atmosphere

tag: compound

tag: media

value: CellGro GMP serum-free DC medium

tag: rin/rna integrity number

tag: concentration (ng/ul)

tag: volume (ul)

tag: kit

value: RiboPure RNA purification kit

value: adapter ligation; strand specific


title: 32_cell_2

tag: tissue


title: Donor4_05_DC_plus_CMV_0h_plus_Afu_0h

value: A. fumigatus ATCC 46645; Human herpesvirus 5 strain TB40/E clone TB40-BAC4


title: Unf_egg_3

source_name: unfertilized egg

value: unfertilized egg

value: size fractionated (20-40 nt) whole cell RNA


title: CHIR99021_Dose1_Rep1

tag: cell lines

tag: sgrnas

tag: compound treatment


title: elav_pooled_18-22h_2b

tag: mutant

value: elav mutant

tag: developmental stage

tag: Sex

value: male


title: Ki8751_Dose1_Rep1


title: Unf_egg_1

tag: rna fraction


title: Donor3_07_DC_plus_Afu_0h_plus_CMV_2h

tag: cell type

tag: strainorline

tag: number of fungal organisms (moi)

tag: samplingtimepoint (hours)


title: elav_iClip_rep2

description:
elav_iclip.NNNTGGCNN_cDNA_peaks.bedgraph
elav_iclip.NNNTGGCNN_cDNA_peaks.intronic.bedgraph

value: wild-type

value: adult

tag: clip barcode

value: NNNTGGCNN


title: Donor3_06_DC_plus_CMV_0h_plus_Afu_4h30min

tag: temperature

tag: atmosphere

tag: compound

tag: media

tag: rin/rna integrity number


title: Fluvastatin_Dose1_Rep1

tag: cell lines

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2


title: Donor3_05_DC_plus_CMV_0h_plus_Afu_0h

tag: concentration (ng/ul)

tag: volume (ul)

tag: kit


title: Gefitinib_Dose1_Rep1

tag: sgrnas

tag: compound treatment


title: Niclosamide_Dose1_Rep1


title: 32_cell_1

tag: tissue

tag: rna fraction


title: Donor2_07_DC_plus_Afu_0h_plus_CMV_2h

tag: cell type

tag: strainorline


title: NCH1681_DAC_rep1

city: Heidelberg

first: Jongwhi

last: Park

address: INF 460

institute: Heidelberg university hospital

data_processing:
fastq files were aligned to human reference genome hg19 using the STAR aligner
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was normalized and differentially expressed genes were analyzed using DESeq2 package
Genome_build: human reference genome hg19
Supplementary_files_format_and_content: excel file include log2(FC) and P-adj values for each sample

source_name: glioma cells

growth_protocol: All cells were cultured in 5 % CO2 humidified incubator at 37 °C

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol
RNA-seq libraries were created with TruSeq Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: Cells were treated with 500 nM DAC for 7 days prior to total RNA isolation

tag: cell line

value: glioma cells

tag: treatment

value: DAC


title: Donor2_06_DC_plus_CMV_0h_plus_Afu_4h30min

tag: number of fungal organisms (moi)

tag: samplingtimepoint (hours)

tag: temperature


title: Cabozantinib_Dose1_Rep1

first: Sonia

last: Brockway

address: 303 E Superior St, SQBRC 7-500


title: Fulvestrant_Dose1_Rep1


title: Donor2_05_DC_plus_CMV_0h_plus_Afu_0h

tag: atmosphere

tag: compound

tag: media


title: NCH1681_DAC_rep2


title: MK0752_Dose1_Rep1

tag: cell lines


title: Donor1_07_DC_plus_Afu_0h_plus_CMV_2h

tag: rin/rna integrity number

tag: concentration (ng/ul)

tag: volume (ul)


title: Unf_egg_2


title: Parthenolide_Dose1_Rep1

tag: sgrnas

tag: compound treatment


title: High PCB 3

city: Costa Mesa

first: Alvine

middle: C

last: Mehinto

address: 3535 Harbor Blvd, Suite 110

institute: Southern California Coastal Water Research Project

description: Gene expression, high PCB

hyb_protocol: Microarray hybridizations were conducted on an Agilent custom-designed 8 x 15K microarray.

scan_protocol: Raw microarray data were collected using an Agilent DNA microarray scanner and processed using Agilent Feature Extraction (FE) software v11.5.1.

data_processing: After evaluation of quality control, raw data were imported into GeneSpring v13 where they were quantile normalized and log2 transformed. Hepatic transcriptome analyses were conducted using a one-way analysis of variance (ANOVA) with a threshold of significance set at p < 0.05.  No FDR (false discovery rate) correction was applied in order to include as many genes as possible for pathway analyses. Hierarchical clustering analyses were conducted using the genes significantly different (p < 0.05; fold change > ±1.2) among treatments.

organism: Pleuronichthys verticalis

source_name: Liver, high PCB treatment group, Intraperitoneally injected with a mixture of PCBs (PCB49, 52, 66, 87, 99, 101, 105, 118, 138, 149, 153, 170, 180) at a dose of 10 µg/g body mass

label_protocol: Conversion of RNA to labelled cRNA was performed using Agilent’s Low Input Quick Amp Labeling kit and Agilent’s Gene Expression Hybridization kit according to the manufacturer’s instructions

extract_protocol: Total RNA was isolated using Trizol Plus RNA Purification kit (Life Technologies) according to the manufacturer’s instructions. RNA was quantified on a NanoDrop ND-8000 spectrophotometer (NanoDrop Technologies) and RNA integrity was determined using a TapeStation (Agilent). The average RNA integrity number equivalent (RINe) was 8.9 with individual RINe ranging between 7.1 and 9.2.

treatment_protocol: Hornyhead turbot (n = 7 – 9) were exposed to 0.5 µg/g body weight (bw) PBDEs, 5 µg/g bw PBDEs, 1 µg/g bw PCBs or 10 µg/g bw PCBs via a single intraperitoneal (IP) injection. The IP injections were performed at a volume of 2 ml oil/kg body. IP control fish received an injection of peanut oil only, while seawater (SW) control fish were not injected. After 96 hours, fish were sacrificed with a lethal dose of tricaine methanesulfonate (MS 222), and body weight and standard length were recorded. Fish livers were excised, a small piece was flash frozen in liquid nitrogen and stored at -80ᵒC for gene expression analyses

tag: Sex

value: Male

tag: tissue

value: Liver


title: High PCB 40

description: Gene expression, high PCB

value: Female


title: High PCB 32

description: Gene expression, high PCB


title: High PCB 41

description: Gene expression, high PCB