title: CD138-selected myeloma cells_88


title: CD138-selected myeloma cells_89

status: Public on Feb 10 2021

type: genomic

city: Little rock

first: CAN

last: LI

state: AR

address: 4301 W MARKHAM ST

country: USA

institute: University of Arkansas for Medical Sciences

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

scan_protocol: The Arrays were then washed using Affymetrix fluidics station 450, and scanned using the Gene Chip Scanner 3000.

data_processing:
Hybridization-based genomic profiling arrays were performed according to the manufacturer’s protocols. CEL files obtained by the CytoScan HD array platform were analyzed using the Chromosome Analysis Suite software package (Affymetrix), and the Nexus copy number software (Biodiscovery Inc., Hawthorne, CA, USA) using annotations of genome version GRCh37 (hg19). Only those achieving the manufacturer’s quality cut-off measures were included in the analysis.
Arrays from CD138-selected samples from newly diagnosed multiple myeloma patients' bone marrows.

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary myeloma cells

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from CD138+ cells isolated from MM patients’ bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Qubit fluorometer and agarose gel electrophoresis.

tag: tissue

value: Bone marrow


title: CD138-selected myeloma cells_90


title: input_NPP1_12h_Rep3

type: SRA

city: Uppsala

first: Minerva

middle: Susana

last: Trejo Arellano

state: Uppsala

address: Almas Allé 5

department: Plant Biology

country: Sweden

institute: SLU

library_source: genomic

data_processing:
Quality control was done with an in-house R script
Adapter trimmng was done with reaper (EMBL-EBI)
Clean reads from independent biological replicates were mapped to the TAIR10 genome using Bowtie v.2 (-v 2 -m 1) (Langmead et al., 2009), first replicate wise to evaluate their similarity and after pooled together.
Delineation of significant ChIP-enriched regions and differential analysis between the PCD-inducible and the mock samples were done with SICER (Zang et al., 2009) using the input as the control library with a redundancy threshold of 1, a window size of 200 bp, a gap size of 600 bp, and FDR = 0.01.
For the RNA-seq analyses, untrimmed reads were mapped to the Arabidopsis reference genome TAIR10 using STAR (v2.5.3.a, Dobin et al., 2013). Expression counts were generated using the R function summarizeOverlaps from the package HTSeq in union mode on exons from the reference transcriptome AtRTD2 (Zhang et al., 2017). Differential expression analyses were performed using the R package DESeq2 (v1.20.0, Love et al., 2014). Genes with absolute log2FoldChange >= 1 and FDR <= 0.05 were considered as differentially expressed.
Subsequent analysis were performed in R. The gene and transposable element models used were from TAIR10 gff annotation file
Genome_build: TAIR10
Supplementary_files_format_and_content: For the ChIP-seq, bed files with the enriched peaks are presented
Supplementary_files_format_and_content: For the RNA-seq, tables with the values of the differential expression analysis for genes and TEs are presented in text files

organism: Arabidopsis thaliana

source_name: input_NPP1_12h_mature leaf

growth_protocol: All seeds were surface-sterilized using 70% and 90% ethanol, stratified for 2 days at 4°C, germinated in soil and grown under short day conditions (8 hours light, 16 hours dark) for 6 weeks.

extract_protocol:
RNA was extracted from samples 12 hours after induction from three independent biological replicates using TRIzol reagent (Invitrogen), treated with Turbo DNAse (Thermo Fisher Scientific). For chromatin immunoprecipitation, leaf material at 12 hours after induction was collected in PBS (137 mM NaCl, 2.7 mM KCl, 4.3 mM Na2HPO4, 1.4 mM KH2PO4) supplemented with 0.1% Tween and cross‐linked using 1% formaldehyde for 10 min under vacuum. Cross-linking was stopped by glycine at final concentration 125 mM for 5 min under vacuum. Leaves were rinsed with water, blotted dry and frozen in liquid nitrogen. About 200 mg of liquid nitrogen-frozen leaves were used for crude nuclei extraction according to (Mozgová et al., 2015). ChIP experiments were performed were done as previously described (Mozgová et al., 2015) from three independent biological replicates.
RNA sequencing libraries were prepared using TruSeq RNA Library Preparation Kit v2 (Illumina) and 18 samples were pooled for sequencing in one lane of the Illumina HiSeq2000 platform. ChIP-seq libraries were prepared with Microplex Library Preparation kit v2 (Diagenode) with 2 ng of eluted DNA as starting material and 12 samples were pooled for sequencing in one lane of Ilumina HiSeq 2500 platform with Single reads of 50 bp length.

treatment_protocol: After 6 weeks, plants were vacuum infiltrated with 2µM 17β-estradiol or mock (ddH2O) to induce the expression of transgenes (Brand et al., 2006) and incubated for additional 12 hours under continuous light.

tag: ecotype background

value: Columbia

tag: genotype/variation

value: 6 week old leaves

tag: chip anitbody

value: none (input)

tag: biological replicate

tag: demultiplexbarcode


title: CD138-selected myeloma cells_86


title: CD138-selected myeloma cells_87


title: input_NPP1_12h_Rep2


title: CD138-selected myeloma cells_82


title: input_NPP1_12h_Rep1


title: CD138-selected myeloma cells_91


title: CD138-selected myeloma cells_83


title: jc5401 TET2 Untreated ZR75-1

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cancer Research UK, Cambridge Institute

description:
TET2 Untreated ZR75-1
zr75_1_tet2_untreated.bed.gz

data_processing:
Reads were mapped to hg38 genome using Bowtie2 version 2.2.6 (Langmead B and  Salzberg S., 2012).
Aligned reads with the mapping quality less than 5 were filtered out.
The read alignments from three replicates were combined into single library and peaks were called with MACS2 version 2.1.1.2016 (Zhang Y1 at al., 2008) using sequences from MCF7 chromatin extracts as a background input control.
The peaks yielded with MACS2 q value <= 1e-4 were selected for downstream analysis.
Meme version 4.9.1 (Timothy et al., 2009) was used to detect known and discover novel binding motifs amongst tag-enriched sequences.
For visualizing tag density and signal distribution heatmap the read coverage in a window of +/- 2.5 or 5 kb region flanking the tag midpoint was generated using the bin size of 1/100 of the window length.
Differential binding analysis (Diffbind) was performed as described previously (Brown and Stark, 2011).
Genome_build: GRCh38
Supplementary_files_format_and_content: bed/text

source_name: TET2 Untreated ZR75-1

growth_protocol: MCF7 cells were grown in DMEM supplemented with 10% FBS, 2mM L-glutamine, 50 U/ml penicillin, 50 ug/ml streptomycin. ZR75-1 cells were grown in RPMI supplemented with 10% FBS, 2mM L-glutamine and 50 U/ml penicillin and 50 ug/ml streptomycin.

extract_protocol:
Cells were crosslinked with 2mM DSG for 20 min followed by crosslinking in 1% formaldehyde for 10 min and then quenched in 100mM glycine. Nuclear enrichment was performed followed by sonication for 15 minutes (Bioruptor plus, Diagenode). Chromatin was immunoprecipitated over night using specific antibodies. Beads were washed six times in RIPA buffer and eluted from beads using SDS buffer. After RNase and proteinase K treatment, DNA was purified by phenol/chloroform extraction.
Libraries were prepared using the Thruplex kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: For the siRNA-mediated knockdown, cells were transfected with ON-TARGETplus SMARTPools (Dharmacon) targeting ER or TET2. A non-targeting siRNA pool was used as a control. For fulvestrant (ICI 182 780, "ICI") treatment, cells were treated with 100nM compound or vehicle for 3 hours.

tag: cell line

tag: cell type

value: Breast cancer

tag: treatment

value: No treatment

tag: chip antibody

value: ab94580 (Abcam)


title: jc5399 ER Untreated ZR75-1

description:
ER Untreated ZR75-1
zr75_1_er_untreated.bed.gz

source_name: ER Untreated ZR75-1

value: ab3575 (Abcam)/06-935 (Millipore)


title: input_XVE_12h_Rep3

source_name: input_XVE_12h_mature leaf


title: CD138-selected myeloma cells_81


title: CD138-selected myeloma cells_79


title: jc5384 ER Untreated MCF7

description:
ER Untreated MCF7
mcf7_er_untreated.bed.gz

source_name: ER Untreated MCF7


title: CD138-selected myeloma cells_80


title: input_XVE_12h_Rep2


title: CD138-selected myeloma cells_78


title: jc5383 TET2 Untreated MCF7

description:
TET2 Untreated MCF7
mcf7_tet2_untreated.bed.gz

source_name: TET2 Untreated MCF7


title: input_XVE_12h_Rep1


title: CD138-selected myeloma cells_77


title: H3K9me2_RPT2_12h_Rep2

source_name: H3K9me2_RPT2_12h_mature leaf


title: jc5381 ER Untreated MCF7


title: jc5402 ER Untreated ZR75-1


title: CD138-selected myeloma cells_76


title: CD138-selected myeloma cells_75


title: CD138-selected myeloma cells_74


title: H3K9me2_RPT2_12h_Rep1


title: CD138-selected myeloma cells_85


title: CD138-selected myeloma cells_73


title: jc5386 TET2 Untreated MCF7


title: H3K9me2_NPP1_12h_Rep2

source_name: H3K9me2_NPP1_12h_mature leaf


title: CD138-selected myeloma cells_84


title: CD138-selected myeloma cells_72


title: CD138-selected myeloma cells_70


title: jc5378 ER Untreated MCF7


title: CD138-selected myeloma cells_71


title: CD138-selected myeloma cells_69


title: CD138-selected myeloma cells_68


title: H3K9me2_NPP1_12h_Rep1


title: CD138-selected myeloma cells_67


title: jc5375 ER Untreated MCF7


title: CD138-selected myeloma cells_66


title: H3K9me2_XVE_12h_Rep2

source_name: H3K9me2_XVE_12h_mature leaf


title: jc5374 Input Untreated ZR75-1

description: Input Untreated ZR75-1

source_name: Input Untreated ZR75-1

value: input


title: CD138-selected myeloma cells_65


title: CD138-selected myeloma cells_63


title: H3K9me2_XVE_12h_Rep1


title: CD138-selected myeloma cells_64


title: jc5373 Input Untreated ZR75-1

description: Input Untreated ZR75-1


title: jc5380 TET2 Untreated MCF7


title: CD138-selected myeloma cells_62


title: CD138-selected myeloma cells_61


title: H3K27me3_RPT2_12h_Rep2

source_name: H3K27me3_RPT2_12h_mature leaf


title: H3K27me3_RPT2_12h_Rep1


title: jc5372 Input Untreated ZR75-1

description: Input Untreated ZR75-1


title: CD138-selected myeloma cells_59


title: jc5371 Input Untreated ZR75-1

description: Input Untreated ZR75-1


title: CD138-selected myeloma cells_60


title: H3K9me2_XVE_12h_Rep3


title: jc5377 TET2 Untreated MCF7


title: jc5366 Input Untreated MCF7

description: Input Untreated MCF7

source_name: Input Untreated MCF7


title: CD138-selected myeloma cells_58


title: H3K27me3_NPP1_12h_Rep3

source_name: H3K27me3_NPP1_12h_mature leaf


title: CD138-selected myeloma cells_56


title: jc5365 Input Untreated MCF7

description: Input Untreated MCF7


title: CD138-selected myeloma cells_57


title: H3K27me3_NPP1_12h_Rep2


title: CD138-selected myeloma cells_54


title: CD138-selected myeloma cells_53


title: CD138-selected myeloma cells_55


title: H3K27me3_NPP1_12h_Rep1


title: jc5364 Input Untreated MCF7

description: Input Untreated MCF7


title: CD138-selected myeloma cells_50


title: jc4076 siTET2 MCF7

library_source: transcriptomic

data_processing:
STAR, version 2.6.1a, was used to align reads against hg38 reference genome.
The read counting was performed using intrinsic function of STAR.
For normalized measurement of mRNA expression the read counts were converted into RPKM values.
Differential gene expression analysis was performed using DESeq2 workflow.
Genome_build: GRCh38
Supplementary_files_format_and_content: text

molecule: total RNA

source_name: Breast cancer cell line

growth_protocol: MCF7 cells were grown in DMEM supplemented with 10% FBS, 2mM L-glutamine, 50 U/ml penicillin, 50 ug/ml streptomycin.

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit according to the manufacturer's instructions.
Libraries were prepared using the TruSeq mRNA Stranded Sample prep kit from Illumina.

treatment_protocol: Cells were transfected with ON-TARGETplus SMARTPools (Dharmacon) targeting ER, GATA3 or TET2. A non-targeting siRNA pool was used as a control.

value: Breast cancer cell line

tag: replicate


title: CD138-selected myeloma cells_51


title: jc5363 Input Untreated MCF7

description: Input Untreated MCF7


title: CD138-selected myeloma cells_52


title: CD138-selected myeloma cells_47


title: H3K27me3_XVE_12h_Rep2

source_name: H3K27me3_XVE_12h_mature leaf


title: jc4075 siGATA3 MCF7


title: CD138-selected myeloma cells_48


title: CD138-selected myeloma cells_45


title: CD138-selected myeloma cells_49


title: R1_XEN_H3K27Ac_BS_rep1_PE

city: Jerusalem

first: Adi

last: Alajem

state: Israel

address: Givat Ram Campus

department: Biological Chemistry

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Basecalls were performed using illumina nextseq and bcl2fastq
ChIP-seq reads were aligned to the mm9 genome assembly using Bismark and bowtie
Data were aligned single ended (SE)
Single CpGs were extracted using Bismark_methylation_extractor program.
We applied HOMER to find peaks and used bedtools to intersect peaks with reads
We counted the number of methylated vs. non methylated CpGs within 200-bp bins.
for single cell analysis:
In house perl based pipeline for generating single cell matrix bed file (available upon request):
1.   Deconvolution to single cell fastq files
Read1 (45bp): N(7-10)- GAGTGATTGCTTGTGACGCCTT-N{8}- N{5}
7-10 bp == Barcode1
22bp == spacer
8bp == Barcode2
5bp== UMI
Read2 (35bp):
Align to mRNA transcripts.
2.   Single cell alignment using RSEM + Bowtie2
rsem-calculate-expression --num-threads 1 --bowtie2 --single-cell-prior --estimate-rspd FASTQ REFERENCE OUTFOLDER
3.   Matrix generator
Genome_build: mm9
Supplementary_files_format_and_content: bed

organism: Mus musculus

source_name: extraembryonic endoderm-induced differentiated cells

growth_protocol: R1 ESCs were grown on 0.1% gelatin-coated dishes and maintained in ESC medium (DMEM, 15% ESC-grade fetal calf serum, 50 μg/mL penicillin, 50 μg/mL streptomycin, 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM nonessential amino acids, 0.1 mM β-mercaptoethanol, and 1000 U/ml LIF), supplemented with 1 μM PD0325901, an inhibitor of MEK/ERK pathway, and 3 μM CHIR99021, an inhibitor of GSK3.

extract_protocol:
Cells were lysed, treated with MNAse, and histone-DNA complexes were isolated with antibody.
DNA samples were converted to blunt-ended, phosphorylated DNA using End-It™ DNA End-Repair Kit. DNA was purified using ratio of 1:1.8 sample:AMPure XP beads. An adenosine was added to the 3’ end of the DNA fragments using Klenow (3’-5’ exo-) (New England Biolabs, M0212L). DNA was purified using ratio of 1:1.8 sample:AMPure XP beads. Methylated adapters were added by ligation using DNA ligase (New England Biolabs, M2200S). DNA was purified using ratio of 1:1.2 sample:AMPure XP beads. Next the DNA was subjected to bisulfite conversion using the EZ DNA Methylation Gold kit (Zymo Research) according to the manufacturer’s instructions. The bisulfite-converted DNA samples were amplified using KAPA HiFi HotStart Uracil (KK2801) with 25 μM full-length primer mix containing Illumina library indices for multiplexing. Amplified libraries were purified using 0.7x reaction volume of AMPure XP beads and eluted in 10 mM Tris-HCl [pH 8]. Library fragments were selected and isolated using the PureLink DNA gel extraction kit (Invitrogen). The resulting libraries had an average size of 350-550 bp. Size-selected libraries were diluted to 4 nM concentration and combined for paired end, single index sequencing on the Illumina NextSeq 550 instrument, using an illumina 550 High Output v2 (75 cycles) kit. Cycle distribution was 45 cycles for Read 1, 35 cycles for Read 2, and 8 cycles for the library index read.
ChIP-Bisulfite-Seq, single cell RNA-Seq

treatment_protocol: For "2 days no 2i" the cells were grown with ESC medium without 2i. For retinoic acid-induced differentiation, cells were grown on 0.1% gelatin-coated dishes for 4 days in ESC medium (10% fetal calf serum without LIF) supplemented with 1 µM retinoic acid. For XEN differentiation,R1 cells were grown on 0.1% gelatin-coated dishes for 9 days in RPMI 1640 with 15% ESC-grade fetal calf serum, 0.1 mM β-mercaptoethanol, Penicillin/Streptomycin 100 U/mL, 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM nonessential amino acids, 10 ng/mL Activin A and 0.1 µM Retinoic acid.

value: R1 ESCs

tag: passages


title: jc4070 siNT MCF7

value: Non-targeting control siRNA


title: CD138-selected myeloma cells_46

source_name: Primary myeloma cells


title: jc4074 siESR1 MCF7


title: CD138-selected myeloma cells_42


title: CD138-selected myeloma cells_44


title: jc4061 siTET2 MCF7


title: R1_XEN_H3K27Ac_BS_rep2_PE


title: H3K27me3_XVE_12h_Rep3


title: CD138-selected myeloma cells_43


title: CD138-selected myeloma cells_41


title: R1_XEN_H3K4me1_BS_rep1_PE


title: CD138-selected myeloma cells_40


title: CD138-selected myeloma cells_38


title: Experimental inflammation

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: 10X chromium

data_processing:
fastq quality read filtering (>80% with Sanger Q>20)
cell barcode demultiplexing
Cellranger mkfastq
Cellranger count
cite-seq-count demultiplexing
Genome_build: mm10
Supplementary_files_format_and_content: filtered read counts>500 UMIs

molecule: polyA RNA

source_name: peripheral blood, joint, peritoneum, lung

extract_protocol: 10X Genomics library prep (3' V1, V2, V3) Library were sequenced using a NextSeq 500

treatment_protocol: K/BxN serum transfer arthritis: Serum from 9 to 11-week-old K/BxN mice was pooled and 150 μl were injected intraperitoneally into male WT mice aged 8 weeks on day 0 and day 2. Arthritis was confirmed clinically and using a caliper to measure thickness of wrists and ankles. Mice were scored on day 6 (clinical score > 10 on a scale from 0-12) and were euthanized on day 7. Blood from arthritic mice was obtained by cardiac puncture. Joint neutrophils were obtained by medial and lateral incision of the femorotibial joint as followed by lavage with cold PBS.  Experimental Pneumonitis:  Male WT mice aged 8 weeks were anesthetized with ketamine/xylazine, and 25 ng of IL-1β in 30 μL of phosphate-buffered saline (PBS) were administrated intranasally. After 3 hours, mice were euthanized and bronchoalveolar lavage (BAL) was performed using cold PBS.  Experimental Peritonitis: Male WT mice aged 8 weeks were injected intraperitoneally with 25 ng IL-1β in 200 μL of PBS. After 3 hours, mice were euthanized and peritoneal cells were harvested from the peritoneum with 5 mL of cold PBS.

value: Sorted CD11b+ Ly6G+ PI-negative live neutrophils

tag: strain

tag: Sex

value: male


title: jc4060 siGATA3 MCF7


title: R1_XEN_H3K4me1_BS_rep2_PE


title: jc4059 siESR1 MCF7


title: CD138-selected myeloma cells_37


title: Spleen Healthy tissues run 2

description: 10X chromium

source_name: spleen

value: spleen


title: CD138-selected myeloma cells_36


title: H3K27me3_XVE_12h_Rep1


title: Bone Marrow Healthy tissues run 2

description: 10X chromium

source_name: bone marrow

value: bone marrow


title: CD138-selected myeloma cells_33


title: CD138-selected myeloma cells_34


title: CD138-selected myeloma cells_32


title: jc4046 siTET2 MCF7


title: Blood Healthy tissues run 2

description: 10X chromium

source_name: peripheral blood

value: peripheral blood


title: CD138-selected myeloma cells_31

value: Bone marrow


title: jc4044 siESR1 MCF7


title: CD138-selected myeloma cells_39


title: CD138-selected myeloma cells_30


title: Spleen Healthy tissues run 1

description: 10X chromium


title: jc4045 siGATA3 MCF7


title: CD138-selected myeloma cells_29


title: CD138-selected myeloma cells_26


title: Blood Healthy tissues run 1

description: 10X chromium


title: CD138-selected myeloma cells_25


title: jc4040 siNT MCF7


title: CD138-selected myeloma cells_28


title: jc4031 siTET2 MCF7


title: CD138-selected myeloma cells_27


title: CD138-selected myeloma cells_35


title: CD138-selected myeloma cells_24


title: CD138-selected myeloma cells_23


title: jc4055 siNT MCF7


title: CD138-selected myeloma cells_22


title: d6_CIII_F480hi_3

city: Frankfurt

first: Tobias

last: Schmid

address: Theodor-Stern-Kai 7

department: Institute of Biochemistry I

country: Germany

institute: Goethe University Frankfurt

description: F480hi_normalized_read_counts_d6CIIIvsVEH

data_processing:
data were processed using the blue-bee pipeline (https://lexogen.bluebee.com/quantseq/)
umi2index
Trimming: bbduk v35.92
Alignment: STAR Aligner with modified ENCODE settings
UMI collapse
Gene Read Counting: HTSeq-count with kit-specic options (FWD)
differential analysis: DESeq2 Pipeline
Genome_build: Mouse (GRCm38)
Supplementary_files_format_and_content: text files containing the normalized read counts for F480lo or F480hi macrophages

source_name: peritoneal lavage

extract_protocol:
Macrophages were isolated from peritoneal lavages by FACS-sorting to obtain F4/80lo (CD45+, CD11b+, F4/80&MerTKlo, MHCIIhi) and F4/80hi (sorted for CD45+, CD11b+, F4/80&MerTKhi macrophages) macrophages. Total RNA was isolated using the RNeasy Micro Kit (Qiagen).
QuantSeq 3’ mRNA-Seq Library Prep Kit with the UMI (unique molecular identifiers) Second Strand Synthesis Module for QuantSeq (Lexogen).

treatment_protocol: Peritonitis was induced in C57BL/6 mice by i.p. injection of 5 mg/kg body weight zymosan A. Starting at day 1 after zymosan injection, mice received daily i.p. injections of the mPGES-1 inhibitor compound III (CIII) (25 mg/kg) or the respective vehicle control (1% Tween-80, 0.5% Carboxymethyl-Cellulose, 0.9% NaCl solution).

value: F4/80hi macrophages

value: C57/BL6 (female)

value: compound III


title: d6_CIII_F480hi_2


title: CD138-selected myeloma cells_21


title: jc4029 siESR1 MCF7


title: d6_CIII_F480hi_1


title: CD138-selected myeloma cells_20


title: jc4025 siNT MCF7


title: CD138-selected myeloma cells_17


title: CD138-selected myeloma cells_18


title: jc4016 siTET2 MCF7


title: d6_VEH_F480hi_3

value: control


title: d6_VEH_F480hi_2


title: jc4030 siGATA3 MCF7


title: d6_VEH_F480hi_1


title: CD138-selected myeloma cells_12


title: CD138-selected myeloma cells_13


title: CD138-selected myeloma cells_16


title: d6_CIII_F480lo_3

description: F480lo_normalized_read_counts_d6CIIIvsVEH

value: F4/80lo macrophages


title: jc4014 siESR1 MCF7


title: CD138-selected myeloma cells_15


title: CD138-selected myeloma cells_14


title: jc4001 siTET2 MCF7


title: jc4010 siNT MCF7


title: CD138-selected myeloma cells_10


title: CD138-selected myeloma cells_9


title: CD138-selected myeloma cells_11


title: d6_CIII_F480lo_2


title: d6_CIII_F480lo_1


title: CD138-selected myeloma cells_7


title: jc4000 siGATA3 MCF7


title: CD138-selected myeloma cells_19


title: CD138-selected myeloma cells_8


title: d6_VEH_F480lo_3


title: CD138-selected myeloma cells_6


title: jc3999 siESR1 MCF7


title: d6_VEH_F480lo_2


title: CD138-selected myeloma cells_4


title: CD138-selected myeloma cells_5


title: CD138-selected myeloma cells_3


title: jc3995 siNT MCF7


title: d6_VEH_F480lo_1


title: CD138-selected myeloma cells_1


title: HAP1-C-allele-#2-DMSO-Rep3

city: Oxford

first: Ping

last: Zhang

address: Roosevelt Drive

department: Ludwig Institute for Cancer Research

institute: University of Oxford

data_processing:
Sequencing reads were mapped to hg19 using the HISAT2 alignment algorithm (version 2.1.0).
The aligned Binary-sequence Alignment Format (BAM) files were used to determine the transcript counts through featureCounts (version 1.6.2)
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: a tab-delimited text file includes transcript counts for each sample

source_name: HAP1 cells

growth_protocol: Hap1 cells were cultured in IMDM (Sigma-Aldrich Co Ltd) supplemented with 10% fetal bovine serum and 1% penicillin/streptomyci.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (QIAGEN) according the manufacturer’s instructions.
Library was prepared using a standardised protocol (QuantSeq 3′ mRNA-Seq Library Prep Kit, Lexogen)  followed by sequencing using a HiSeq4000 platform (Illumina) at the Oxford Genomics Centre (Wellcome Trust Centre for Human Genetics, Oxford, UK).

treatment_protocol: Cells were treated with Nutlin3 (10uM) or DMSO (negative control) for 6 hours

tag: teatment

value: DMSO

value: replicate 3


title: HAP1-C-allele-#2-Nutlin3-Rep3


title: HAP1-C-allele-#1-Nutlin3-Rep3


title: PW052709

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

data_processing:
Read 1 and read 2 fastq files were generated on basespace.
Raw data obtained from the Illumina NovaSeq 6000 was first corrected for index swapping to avoid cross-talk between sample index sequences using the algorithm described by Griffiths et al, Nature Communications, 2018 before assigning read addresses for each sample.
12-nt cell barcodes (CBs) and 8-nt unique molecular identifiers (UMIs) were extracted from read 1. Degenerate CBs containing either 'N's or more than four consecutive 'G's were discarded. Synthesis errors, which can result in truncated 11-nt cell barcodes, were corrected.
Read 2 were trimmed to remove poly(A) tails (> dA(7)) from the 3'-ends of each read. Any resulting fragment shorter than 24 nucleotides were discarded.
Trimmed reads were then aligned to GRCh38 (GENCODE v.24) using STAR v.2.5.0 with parameters "-- sjdbOverhang 65 --twopassMode Basic --outSAMtype BAM Unsorted". Only reads with unique, strand-specific alignments to exons were kept for further analysis.
All reads with the same CB, UMI, and gene mapping were collapsed to represent a single molecule. To correct for sequencing errors in UMIs, we further collapsed UMIs that were within Hamming distance 1 of another UMI with the same barcode and gene. To correct for sequencing errors in cell barcodes, we then collapsed CBs that were within Hamming distance one of another cell barcode, had at least 20 unique IMI-gene pairs, and had at least 75% overlap of their UMI-gene pairs. A digital gene expression matrix was then generated from these corrected barcode-UMI-gene triplets.
We estimated the number of cell barcodes corresponding to beads associated with cells in our microwell system using the emptyDrops algorithm from Lun et al, Genome Biology, 2019.
We removed CBs that satisfied any of the following criteria 1) fractional alignment to the mitochondrial genome greater than 1.96 standard deviations above the mean, 2) ratio of molecules aligning to whole gene bodies (including introns) to molecules aligning exclusively to exons greater than 1.96 standard deviations above the mean, 3) average number of reads per molecule or average number of molecules per gene >2.5 standard deviations above the mean for a given sample, 4) more than 40% of UMI bases are T or where the average number of T-bases per UMI is at least 4..
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files that contain the gene expression level of each individual cell.

source_name: acute slice culture of glioma resection

growth_protocol: Tumor specimens were collected immediately after surgical removal  and kept in ice-cold artificial cerebrospinal fluid (ACSF) solution containing 210 mM sucrose, 10 mM glucose, 2.5 mM KCl, 1.25 mM NaH2PO4, 0.5 mM CaCl2, 7 mM MgCl2 and 26 mM NaHCO3 for transportation. Preparation of ex vivo tissue slices was modified from methods described previously4. Briefly, the collected tumor specimens were placed in a drop of ice-cold ACSF and sliced using a tissue chopper (McIlwain) at a thickness of 500 µm under sterile conditions. The slices were immediately transferred to the ice-cold ACSF solution in 6-well plates using a sterile plastic Pasteur pipette half filled with ice-cold ACSF solution followed by a 15 minutes recovery in ACSF to reach room temperature. Intact and well-shaped slices (approximately 5-10 mm diameter) were then placed on top of a porous membrane insert (0.4 µm, Millipore). Then the membrane inserts were placed into 6-well plates containing 1.5 mL maintenance medium consisting of F12/DMEM (Gibco) supplemented with N-2 Supplement (Gibco) and 1% penicillin/streptomycin (Sigma). To ensure proper diffusion into the slice, culture medium was placed under the membrane insert without bubbles. A drop of 10 µl of culture medium was added directly on top of each slice to prevent the slice surface from drying. The slices were first rested for 6 hrs with the maintenance medium in a humidified incubator at 37℃ and 5% CO2. Then, the medium was replaced with pre-warmed medium containing drugs with desired concentration (Table S1) or corresponding volume of vehicle (DMSO). Slices were then cultured with the treatment medium in a humidified incubator at 37℃ and 5% CO2 for 18 hrs before being collected for dissociation.

extract_protocol:
dissociation protocol: Collected tissue samples or tissue slices were dissociated using the Adult Brain Dissociation kit (Miltenyi Biotec) on gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec) according to the manufacturer’s instructions.
mRNA molecues were captured using bead-bound oligo dT(30).
Captured mRNA molecues were reverse transcriped to obtain cDNA which is then amplified by PCR reactions. The cDNA PCR reaction product was then purified with AMPure XP beads. The purified cDNA PCR product was used as the input for Nextera XT reactions to generate sequencing library.

tag: age

tag: gender

value: F

tag: location

value: right frontal

tag: diagnosis

value: Glioblastoma, WHO Grade IV, recurrent

value: 2.5 uM etoposide


title: PW052706


title: PW053710

value: 0.2 uM panobinostat


title: HAP1-C-allele-#1-DMSO-Rep3


title: PW052705

value: vehicle (DMSO)


title: PW052703


title: HAP1-A-allele-DMSO-Rep3


title: IFCChIP-3000-H3K4me1-E142i-rep2

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen, RIMLS

description: ChIP targeting H3K4me1 modification

data_processing:
Initial data processing and base calling was performed using the Illumina Analysis Pipeline.
Reads were mapped to the mm9 (GRCh37) genome using bowtie2 2.0.2 with parameters --very-sensitive --end-to-end. Duplicate and unmapped reads were removed.  Only uniquely mapping reads (with mapq >=15) were kept.
Bigwigs were generated using bam2bw (https://bitbucket.org/simonvh/bam2bw.git) v1.25 with parameters -c –e 180.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files are directly compatible with the UCSC genome browser.

source_name: Embryonic Stem Cells (ESCs)

growth_protocol: ESCs (129/Ola background) were maintained in Dulbecco’s Modified Eagle Medium (DMEM) containing 15% fetal bovine serum, 5µM beta mercaptoethanol (BME) (Sigma) and Leukemia inhibitory factor (LIF; 1000U/ml) (Millipore), referred to as serum ESCs, or in serum-free N2B27 (or Ndiff) supplemented with PD0325901 (1 µM), CH99021 (3 µM) and LIF (1000U/ml), referred to as 2i ESCs.

extract_protocol:
Cell crosslinking, sonication and ChIP was performed as described in the methods section.
Libraries were prepared using Kapa Hyper Prep library construction kit according to manufacturer protocol. Size selection (~300 bp median final size) was performed using Ampure XP beads.

treatment_protocol: Cells were conditioned to the media for more than 14 days before harvesting.

value: Embryonic Stem Cells

tag: cell type name

tag: strain background

tag: measurement

value: ChIP-seq

value: Cultured in 2i medium


title: IFCChIP-3000-H3K27ac-E142i-rep1

description: ChIP targeting H3K27ac modification


title: IFCChIP-3000-H3K27ac-E14ser-rep1

description: ChIP targeting H3K27ac modification

value: Cultured in FCS medium


title: IFCChIP-3000-H3K4me1-E14ser-rep2

description: ChIP targeting H3K4me1 modification


title: HAP1-A-allele-Nutlin3-Rep3


title: PW051702


title: PW051708


title: HAP1-C-allele-#2-Nutlin3-Rep2

value: replicate 2


title: CD138-selected myeloma cells_2

tag: tissue

value: Bone marrow


title: HNES1-PXGL_4

city: Exeter

first: Daniel

last: Spindlow

state: Devon

address: Stocker Road

department: Living Systems Institute

institute: University of Exeter

data_processing:
cellranger mkfastq
cellranger count
Genome_build: hg38
Supplementary_files_format_and_content: raw reads count text format

source_name: HNES1 naïve stem cells

extract_protocol:
10X Single Cell GEX v3,  single live cell sorted by flow cytometry
10X Single Cell GEX v3

tag: protocol

value: PXGL

value: Human naive pluripotent stem cells (HNES1)


title: HNES1-PXGL_3

tag: cell type


title: HNES1-PXGL_2


title: HAP1-C-allele-#2-DMSO-Rep2


title: HNES1-PXGL_1


title: IFCChIP-3000-H3K4me1-E142i-rep1

value: 129/Ola background

tag: cell line

tag: antibody

value: ChIP targeting H3K4me1 modification

tag: treatment


title: HNES1-D1-N2B27-D3-4

source_name: stem cell derivative

value: one day in PDA83 then three days in N2B27


title: HNES1-D1-N2B27-D3_3


title: HAP1-C-allele-#1-DMSO-Rep2

value: DMSO

tag: replicate


title: HNES1-D1-N2B27-D3_2


title: IFCChIP-3000-H3K27ac-E14ser-rep2

value: ChIP targeting H3K27ac modification


title: HNES1-D1-N2B27-D3_1


title: HNES1-D3_1

value: three days in PDA83


title: IFCChIP-3000-H3K27ac-E142i-rep2


title: HNES1-D3_3


title: HNES1-D3_4


title: IFCChIP-3000-H3K4me3-E142i-rep1

value: ChIP targeting H3K4me3 modification


title: HAP1-A-allele-DMSO-Rep2


title: HNES1-D3_2


title: IFCChIP-3000-H3K4me1-E14ser-rep1


title: HAP1-C-allele-#1-Nutlin3-Rep2


title: HNES1-D5-P18_4

value: five days  in PDA83


title: IFCChIP-3000-H3K4me3-E142i-rep2


title: HAP1-C-allele-#2-Nutlin3-Rep1

value: replicate 1


title: HNES1-D5-P18_2


title: IFCChIP-3000-H3K27me3

value: Embryonic Stem Cells

value: ChIP targeting H3K27me3 modification


title: HNES1-D5-P18_3


title: HAP1-C-allele-#2-DMSO-Rep1


title: HNES1-D5-P18_1


title: HNES1-D1_4

value: one day in PDA83


title: HAP1-A-allele-Nutlin3-Rep2


title: IFCChIP-1000-H3K27me3-xsonic

value: Cultured in FCS medium


title: HNES1-D1_2


title: IFCChIP-3000-H3K27me3-xsonic


title: HAP1-C-allele-#1-Nutlin3-Rep1


title: HNES1-D1_1


title: HNES1-D1_3


title: teloHAEC_CRISPRa_MS2_safe_002_replicate4

city: Montreal

first: Florian

last: Wuennemann

address: 5000 Rue Bélanger

country: Canada

institute: Montreal Heart Institute

description: Safe-harbor control sgRNA for experiment 2 and 3

data_processing:
Fastq files were quality controlled using FASTQC and multiqc.
Transcript abundances were quantified from paired-end fastq files using kallisto (v. 0.46.0) against ENSEMBL reference transcripts (release 94) followed by tximport to estimate gene-level counts.
Gene level counts that were used in DESeq2 for differential expression analysis are provided.
Genome_build: Ensemble release 94
Supplementary_files_format_and_content: teloHAEC_CRISPR.RNAseq.counts.tsv.gz contains gene-level estimated counts for all samples from tximport.

source_name: teloHAEC

growth_protocol: TeloHAEC stably expressing either Cas9 or dCas9-VP64 (CRISPRa) were cultured in vascular cell basal medium (ATCC PCS-100-030).

extract_protocol:
RNA was extracted using the RNeasy plus mini kit from Qiagen.
RNA-seq experiments were carried out by the Centre d’Expertise et de Services Genome Quebec (GC) using rRNA-depleted TruSeq stranded (HMR) libraries (Illumina) on an Illumina Hiseq 4000 instrument (paired-ends, 100-bp reads) and by The Center for applied Genomics (TCAG, Toronto) using rRNA-deletion library prep on an Illumina NovaSeq-SP flow cell.

treatment_protocol: TeloHAEC stably expressing either Cas9 or dCas9-VP64 (CRISPRa) were infected with lentiviruses containing safe-harbor sgRNA as control or sgRNA targeting candidate coronary artery disease loci in the genome, at a multiplicity of 0.3. Cells were cultured for 5 (CRISPRa) or 7 days (Cas) respectively. Cas9 experiments were treated with TNFɑ (10ng/ul])  for four hours to induce a pro-inflammatory response.

value: teloHAEC

tag: cas9 variant

value: CRISPRa

tag: sgrna

value: TCAG

value: safe


title: teloHAEC_CRISPRa_MS2_safe_002_replicate3


title: HAP1-A-allele-Nutlin3-Rep1

tag: teatment


title: mH3_KO

city: Los Angeles

first: Cunyu

last: Wang

state: CA

address: 10833 Le Conte Ave

department: School of Dentistry

institute: university of California, Los Angeles

data_processing:
The reads were aligned to the hg19/mm9 build of the mouse genome using bowtie.
The sam files were converted into bam files, and then sorted using samtools.
Peak calling was perfromed using MACS2 following the instructions.
Genome_build: hg19/mm9
Supplementary_files_format_and_content: peaks

source_name: bone marrow-derived MSCs

growth_protocol: Both human MSCs and mBMSCs were maintained in DMEM supplemented with 15% FBS and 1% penicillin/streptomycin, repsectively.

extract_protocol:
ChIP assays were performed using a ChIP assay kit (Upstate Biotechnology, Cat No: 17-295) per the manufacturer's instructions. Briefly, cells were double crosslinked with 10 mM DTBP for 10 min at room temperature, followed by incubation in 1% formaldehyde for 15 min in a 37 °C water bath. Nuclei were extracted and sonication was perfromed to generate 200–500 bp genomic DNA fragments. Chromatin complexes were immunoprecipitated with the related antibodies and Dynabeads Protein A/G. The precipitated DNA was purified using DNA clean and concentrator (Zymo Research).
Libraries were prepared using KAPA Hyper Prep Kit (Kapa Biosystems, Cat No:  KK8502)

treatment_protocol: The MSCs were subjected to osteogenic induction (OI) for 4 hours.

value: bone marrow-derived MSCs (mBMSCs)

tag: genotype/variation

value: Prx1Cre; Kdm4bf/f mice (KO)


title: teloHAEC_Cas9_sgRNA_02249_replicate1

description: sgRNA targeting CAD locus


title: HAP1-A-allele-DMSO-Rep1


title: teloHAEC_Cas9_sgRNA_02249_replicate2

description: sgRNA targeting CAD locus


title: mH3_WT

value: Prx1Cre; Kdm4bw/w mice (WT)


title: teloHAEC_CRISPRa_sgRNA_25344_replicate2

description: sgRNA targeting CAD locus


title: teloHAEC_CRISPRa_sgRNA_25344_replicate1

description: sgRNA targeting CAD locus


title: teloHAEC_Cas9_safe_001_replicate2

description: Safe-harbor control sgRNA for experiment 5


title: HexPos-3000-H3K4me3

description: ChIP targeting H3K4me3 modification

value: Embryonic Stem Cells (ESCs)

value: Hex-GFP

value: Cultured in 2i medium

tag: chip antibody


title: Bone Marrow Healthy tissues run 1

description: 10X chromium

value: Sorted CD11b+ Ly6G+ PI-negative live neutrophils

tag: strain

tag: Sex

value: male

value: bone marrow


title: PW051704

tag: age

tag: gender

value: F

tag: location

value: right frontal

tag: diagnosis

value: Glioblastoma, WHO Grade IV, recurrent

value: 0.2 uM panobinostat


title: PW053707


title: teloHAEC_Cas9_safe_001_replicate1

value: teloHAEC


title: teloHAEC_CRISPRa_sgRNA_06147_replicate2

description: sgRNA targeting CAD locus

value: CRISPRa


title: IFCChIP-3000-H3K9me3-xsonic

tag: strain background

value: 129/Ola background

value: Embryonic Stem Cells

value: ChIP targeting H3K9me3 modification

value: Cultured in FCS medium


title: HexNeg-3000-H3K4me3

description: ChIP targeting H3K4me3 modification

tag: cell type


title: teloHAEC_CRISPRa_sgRNA_06147_replicate1

description: sgRNA targeting CAD locus

tag: cell line

value: TCAG


title: HAP1-C-allele-#1-DMSO-Rep1

value: DMSO

value: replicate 1


title: HSPC donor3 - fEVs

city: Rotterdam

first: Jeroen

last: van de Peppel

address: 's Gravendijkwal 230

institute: ErasmusMC

description: HSPC donor3 were 24h treated with SCF, Flt3L and fEVs

data_processing:
Paired end sequencing was performed on an Illumina NovaSeq 6000 using 100 cycles for each mate.
Fastq files were constructed using bcl2fastq (v2.20.0.422).
SMARTer + polyT adapters were removed using fqtrim (v0.9.7)
Pseudo counts were measured on the trimmed Fastq files using salmon (v1.3.0) using flags gcBias seqBias.
Database used for the analysis ensembl GRCh38.rel98
Data was analysed with DESeq2 package retrieved from bioconductor
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample

source_name: hematopoietic stem and progenitor cell

growth_protocol: Adult human bone marrow aspirates (40-70 years old) were obtained from the sternum of patients undergoing cardiac surgery after given informed consent and approval of the medical ethics review board. Collection of fetal tissues for research purposes was approved by the medical ethical review board of the Academic Medical Centre (AMC). The fetal human bone marrow samples were obtained from the HIS facility of the AMC, Amsterdam. All material has been collected from donors from whom a written informed consent for the use of the material for research purposes. Low-density mononuclear cells (MNC) were separated by Ficoll gradient centrifugation and cultured in Dulbecco’s modified Eagle’s medium, GlutaMAXtm and low glucose (Thermo Fisher Scientific, USA) supplemented with 10% fetal bovine serum (FBS, Bodinco, The Netherlands) and 1% penicillin-streptomycin (Sigma Aldrich, Germany), referred in this article as BMSC medium. Non adherent cells were removed by replacing the medium after 48 hours of incubation. Cells were either frozen or expanded up to passage 5, in order to harvest sufficient amounts of EVs. Adult and Fetal BMSC-derived EVs were isolated from BMSCs supernatant, after confluent layers of cells cultured in T175 flasks were exposed for 24 hours to serum-free BMSC medium.

extract_protocol:
Total RNA was isolated using NucleoSpin RNA XS kit (Macherey-Nagel, Germany) according to the manufacturer’s instructions. RNA concentration and size distribution profile were analyzed on an Agilent Bioanalyzer RNA 6000 Pico chip (Thermo Fisher Scientific, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Freshly isolated UCB-CD34+ cells were immediately frozen or cultured for 24 hours with 50ng/mL recombinant human SCF and 50ng/mL FMS-like tyrosine kinase 3 ligand  in the absence or presence of aEVs or fEVs. The vesicles were isolated from 20 mL conditioned medium by low speed centrifugation (1500 rpm, 5 minutes; 4500 rpm, 10 minutes) followed by ultracentrifugation (20,000g, 30 minutes; 100,000g, 1 hour at 4°C) of the supernatant using the SW32Ti rotor (Beckman Coulter, Fullerton, CA, USA).

value: hematopoietic stem and progenitor cell

tag: donor

value: fetal EVs


title: HSPC donor2 - fEVs

description: HSPC donor2 were 24h treated with SCF, Flt3L and fEVs

tag: treatment


title: HSPC donor2 - aEVs

description: HSPC donor2 were 24h treated with SCF, Flt3L and aEVs

value: adult EVs


title: HSPC donor2 - Control

description: HSPC donor2 were 24h treated with SCF and Flt3L

value: control


title: Macrophages, without stimulation + porous Ti disc, donor 9

type: RNA

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Gene expression data from human unstimulated macrophages cultured for 6 days on porous titanium discs

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of human Hugene-1_0-type from Affymetrix. A Custom CDF Version 18 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotin

source_name: Buffy coat, donor 9

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Macrophages were cultured in Macrophage Serum Free Medium at a concentration of 2x10^6 cells/ml, supplemented with 1ng/ml M-CSF, 10^-8M Dexamethasone for 6 days

extract_protocol: RNA was extracted using E.Z.N.A. total RNA Kit I according to manufacturer´s instructions.

treatment_protocol: Macrophages were cultured on cell culture plastic or on porous titanium discs. Additionally they were stimulated at day 0 either with IL-4 (10ng/ml) or with IFNgamma (100ng/ml) or left untreated as control.

tag: tissue

value: PBMC derived monocytes

tag: donornr

value: NO

tag: titanium

value: Ti


title: MERVLNeg-3000-H3K4me3

description: ChIP targeting H3K4me3 modification

value: (129S6/SvEvTac x C57BL/6NCrl)F1

value: Embryonic Stem Cells (ESCs)

value: MERVL-GFP

value: Cultured in 2i medium


title: HSPC donor1 - fEVs

description: HSPC donor1 were 24h treated with SCF, Flt3L and fEVs


title: Macrophages, without stimulation, donor 9

description: Gene expression data from human unstimulated macrophages cultured for 6 days on cell culture plastic

value: ctrl


title: IFCChIP-500-H3K4me3-xsonic

description: ChIP targeting H3K4me3 modification


title: HSPC donor1 - Control

description: HSPC donor1 were 24h treated with SCF and Flt3L


title: HSPC donor1 - aEVs

description: HSPC donor1 were 24h treated with SCF, Flt3L and aEVs


title: Macrophages, IL4 stimulation, donor 9

description: Gene expression data from human macrophages stimulated with IL-4 and cultured for 6 days on cell culture plastic


title: Macrophages, IL4 stimulation + porous Ti disc, donor 9

description: Gene expression data from human macrophages stimulated with IL-4 and cultured for 6 days on porous titanium discs


title: Macrophages, IFNgamma stimulation, donor 9

description: Gene expression data from human macrophages stimulated with IFNgamma and cultured for 6 days on cell culture plastic

value: IFN


title: jc7460 MCF7 GATA3 vehicle mutant GATA3

description:
GATA3  vehicle GATA3 mutant MCF7
gata3_mut_veh.bed.gz

value: Breast cancer

value: Vehicle

value: mutant


title: Zscan4cPos-3000-H3K4me3

description: ChIP targeting H3K4me3 modification


title: HSPC donor3 - aEVs

description: HSPC donor3 were 24h treated with SCF, Flt3L and aEVs


title: IFCChIP-500-H3K4me3-rep2

description: ChIP targeting H3K4me3 modification

value: Cultured in FCS medium


title: Zscan4cNeg-3000-H3K4me3

description: ChIP targeting H3K4me3 modification


title: jc7459 MCF7 GATA3 vehicle mutant GATA3


title: IFCChIP-500-H3K4me3-rep1

description: ChIP targeting H3K4me3 modification


title: Macrophages, without stimulation + porous Ti disc, donor 13

source_name: Buffy coat, donor 13


title: HSPC donor3 - Control

description: HSPC donor3 were 24h treated with SCF and Flt3L

value: hematopoietic stem and progenitor cell


title: Macrophages, without stimulation, donor 13


title: jc7458 MCF7 GATA3 vehicle mutant GATA3


title: MERVLPos-3000-H3K4me3

description: ChIP targeting H3K4me3 modification


title: jc7453 MCF7 GATA3 vehicle wild type GATA3

description:
GATA3 vehicle MCF7
gata3_wt_veh.bed.gz

value: wild type


title: jc7452 MCF7 GATA3 vehicle wild type GATA3

description:
GATA3 vehicle MCF7
gata3_wt_veh.bed.gz


title: PW053711

value: F

value: right frontal

value: Glioblastoma, WHO Grade IV, recurrent

value: vehicle (DMSO)


title: IFCChIP-3000-H3K4me3-xsonic-rep3

description: ChIP targeting H3K4me3 modification


title: jc7448 MCF7 TET2 vehicle mutant GATA3

description:
TET2 vehicle GATA3 mutant MCF7
tet2_mut_veh.bed.gz


title: IFCChIP-3000-H3K4me3-xsonic-rep2

description: ChIP targeting H3K4me3 modification


title: IFCChIP-3000-H3K4me3-xsonic-rep1

description: ChIP targeting H3K4me3 modification


title: Macrophages, IL4 stimulation + porous Ti disc, donor 13

value: PBMC derived monocytes

value: Ti


title: jc7446 MCF7 TET2 vehicle mutant GATA3


title: jc7441 MCF7 TET2 vehicle wild type GATA3

description:
TET2 vehicle MCF7
tet2_wt_veh.bed.gz


title: jc4015 siGATA3 MCF7

source_name: Breast cancer cell line

value: Breast cancer cell line

tag: replicate


title: jc7454 MCF7 GATA3 vehicle wild type GATA3

description:
GATA3 vehicle MCF7
gata3_wt_veh.bed.gz

tag: genotype/variation


title: jc7442 MCF7 TET2 vehicle wild type GATA3

description:
TET2 vehicle MCF7
tet2_wt_veh.bed.gz

tag: chip antibody


title: Macrophages, IL4 stimulation, donor 13


title: IFCChIP-3000-H3K4me3-rep1

description: ChIP targeting H3K4me3 modification

value: Embryonic Stem Cells (ESCs)


title: Macrophages, IFNgamma stimulation + porous Ti disc, donor 13

description: Gene expression data from human macrophages stimulated with IFNgamma and cultured for 6 days on porous titanium discs


title: jc7429 MCF7 ER vehicle wild type GATA3

description:
ER vehicle MCF7
er_wt_veh.bed.gz


title: jc7440 MCF7 TET2 vehicle wild type GATA3

description:
TET2 vehicle MCF7
tet2_wt_veh.bed.gz


title: IFCChIP-3000-H3K4me3-rep3

description: ChIP targeting H3K4me3 modification


title: Macrophages, without stimulation, donor 11

source_name: Buffy coat, donor 11

value: NO


title: IFCChIP-3000-H3K4me1-xsonic-rep2

description: ChIP targeting H3K4me1 modification


title: jc7436 MCF7 ER vehicle mutant GATA3

description:
ER vehicle GATA3 mutant MCF7
er_mut_veh.bed.gz


title: Macrophages, IL4 stimulation + porous Ti disc, donor 11


title: IFCChIP-3000-H3K4me3-rep2

description: ChIP targeting H3K4me3 modification


title: jc7435 MCF7 ER vehicle mutant GATA3


title: Macrophages, IFNgamma stimulation, donor 11

value: ctrl


title: jc7422 MCF7 Input vehicle mutant GATA3

description: Input vehicle GATA3 mutant MCF7


title: jc7434 MCF7 ER vehicle mutant GATA3


title: jc7430 MCF7 ER vehicle wild type GATA3

description:
ER vehicle MCF7
er_wt_veh.bed.gz


title: Macrophages, without stimulation + porous Ti disc, donor 11


title: IFCChIP-3000-H3K4me1-rep2

description: ChIP targeting H3K4me1 modification


title: IFCChIP-3000-H3K4me1-xsonic-rep3

description: ChIP targeting H3K4me1 modification


title: jc7447 MCF7 TET2 vehicle mutant GATA3


title: jc7428 MCF7 ER vehicle wild type GATA3

description:
ER vehicle MCF7
er_wt_veh.bed.gz


title: Macrophages, IL4 stimulation, donor 11


title: Align-3

city: Suita

first: Jong-Kook

last: LEE

address: 2-2 Yamada-oka

department: Cardiovascular Regenerative Medicine

country: Japan

institute: Osaka University Graduate School of Medicine

description:
gene_RPKM_edgeR_test_A2.xlsx
gene_RPKM_edgeR_test_C2.xlsx
gene_norm_TCC.xlsx

data_processing:
Illumina package bcl2fastq software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using TopHat (v2.1.1)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: human induced pluripotent stem cell

growth_protocol: 201B7 human iPS cells were differentiated to cardiomyocyte by using PSC Cardiomyocyte Differentiation Kit

extract_protocol:
TruSeq Stranded mRNA Library Prep Kit (Cat#RS-122-2103) 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: hiPS-CMs were dissociated into single cells and replated onto the flat, random, align patterns for one week

value: iPS-derived Cardiomyocytes

value: post differentiated day30

value: cultured on the aligned nanofiber bottom for one week


title: Macrophages, IFNgamma stimulation + porous Ti disc, donor 11

value: IFN


title: jc7424 MCF7 Input vehicle mutant GATA3

description: Input vehicle GATA3 mutant MCF7

value: Breast cancer

value: Vehicle

value: mutant


title: jc7423 MCF7 Input vehicle mutant GATA3

description: Input vehicle GATA3 mutant MCF7


title: Align-2


title: Macrophages, IFNgamma stimulation, donor 13


title: Macrophages, IFNgamma stimulation + porous Ti disc, donor 9


title: IFCChIP-3000-H3K4me1-xsonic-rep1

description: ChIP targeting H3K4me1 modification

value: Cultured in FCS medium


title: jc7418 MCF7 Input vehicle wild type GATA3

description: Input vehicle MCF7

value: wild type


title: Macrophages, without stimulation, donor 10

source_name: Buffy coat, donor 10


title: IFCChIP-3000-H3K36me3-xsonic

description: ChIP targeting H3K36me3 modification


title: IFCChIP-3000-H3K4me1-rep1

description: ChIP targeting H3K4me1 modification


title: Macrophages, without stimulation + porous Ti disc, donor 10


title: jc7417 MCF7 Input vehicle wild type GATA3

description: Input vehicle MCF7


title: Random-3

description:
gene_RPKM_edgeR_test_C2.xlsx
gene_RPKM_edgeR_test_B.xlsx
gene_norm_TCC.xlsx

value: cultured on the randomized nanofiber bottom for one week


title: Align-1


title: Random-2


title: jc7416 MCF7 Input vehicle wild type GATA3

description: Input vehicle MCF7


title: Random-1


title: Flat-3

description:
gene_RPKM_edgeR_test_A2.xlsx
gene_RPKM_edgeR_test_B.xlsx
gene_norm_TCC.xlsx

value: cultured on Flat bottom for one week


title: Macrophages, IL4 stimulation, donor 10

value: PBMC derived monocytes


title: Flat-2


title: Flat-1


title: IFCChIP-3000-H3K36me3-rep1

description: ChIP targeting H3K36me3 modification


title: IFCChIP-3000-H3K27ac-xsonic-rep3

description: ChIP targeting H3K27ac modification


title: Macrophages, IL4 stimulation + porous Ti disc, donor 10

value: Ti


title: IFCChIP-3000-H3K27ac-xsonic-rep2

description: ChIP targeting H3K27ac modification


title: Macrophages, IFNgamma stimulation, donor 10


title: IFCChIP-3000-H3K36me3-rep2

description: ChIP targeting H3K36me3 modification


title: IFCChIP-3000-H3K27ac-rep2

description: ChIP targeting H3K27ac modification


title: IFCChIP-3000-H3K27ac-rep1

description: ChIP targeting H3K27ac modification


title: IFCChIP-1000-H3K4me3-rep3

description: ChIP targeting H3K4me3 modification


title: IFCChIP-1000-H3K4me3-rep2

description: ChIP targeting H3K4me3 modification


title: Macrophages, IFNgamma stimulation + porous Ti disc, donor 10


title: IFCChIP-1000-H3K4me3-rep1

description: ChIP targeting H3K4me3 modification


title: Macrophages, without stimulation + porous Ti disc, donor 8

description: Gene expression data from human unstimulated macrophages cultured for 6 days on porous titanium discs

source_name: Buffy coat, donor 8


title: Macrophages, IFNgamma stimulation + porous Ti disc, donor 8


title: Macrophages, IFNgamma stimulation, donor 8


title: Macrophages, without stimulation, donor 8


title: Macrophages, IL4 stimulation + porous Ti disc, donor 8


title: IFCChIP-1000-H3K4me1-xsonic

description: ChIP targeting H3K4me1 modification


title: Pentatherapy-2

city: bethesda

first: james

middle: w

last: hodge

state: md

address: 10/8b13, 9000 rockville pike

department: LTIB

institute: NCI

description: Day 28 post tumor transplant

scan_protocol: This was a nanostring analysis run by our contractor in Frederick.

data_processing: These data were analyzed via Nsolver Analysis Software Version 4.0.70

source_name: MC32a Tumor

growth_protocol: All cell lines were passaged for less than 6 months, free of Mycoplasma and cultured at 37°C/5% CO2.

extract_protocol: RNAzol

treatment_protocol: For the Ad-CEA + N-803 combination, 8-16-week-old female C57BL/6 CEA-Tg mice were implanted on the right flank with MC38-CEA tumor cells (3x105 cells/mouse subcutaneous (s.c.)). MC38-CEA-bearing mice were treated with Ad-CEA (107 viral particles, s.c.) on days 7, 14, and 21 and N-803 (1g, s.c.) on days 10 and 17. For the depletion experiment, -CD8 antibody (2.43, 100 g, (i.p.); BioXcell, Lebanon, NH) and -NK1.1 antibody (PK136, BioXCell, Lebanon, NH) were injected on days 3, 4, 5, 12, 19, and 26 post-tumor inoculation. For the kinetic studies, naïve female C57BL/6 CEA-transgenic (Tg) were injected concurrently with Ad-CEA and N-803.  For the pentatherapy combination, 8-16-week-old C57BL/6 CEA-Tg mice were implanted with MC38-CEA (3x105 cells/mouse, s.c.) or LL2-CEA (5x105 cells/mouse, intravenous (i.v.)). The tumor-bearing mice were injected with GITR agonist (500 g, i.p.) on day 5 post-tumor inoculation; Ad-CEA (107 viral particles, s.c.) on days 7, 14, and 21; OX40 agonist (100 g, i.p.) on days 7, 14, and 21; N-803 (1g, s.c.) on days 14 and 21; and IDOi, which was incorporated in the food, was given starting day 7.

tag: agent

value: Pentatherapy


title: IFCChIP-100-H3K4me3-rep2

description: ChIP targeting H3K4me3 modification

value: Embryonic Stem Cells (ESCs)


title: IFCChIP-1000-H3K27ac-xsonic

description: ChIP targeting H3K27ac modification


title: Macrophages, IL4 stimulation, donor 8


title: Pentatherapy-1

description: Day 28 post tumor transplant


title: IFCChIP-1000-H3K36me3-xsonic

description: ChIP targeting H3K36me3 modification


title: IFCChIP-100-H3K4me3-rep1

description: ChIP targeting H3K4me3 modification


title: IDO-2

description: Day 28 post tumor transplant

value: IDO


title: IFCChIP-1000-H3K4me3-xsonic

description: ChIP targeting H3K4me3 modification


title: IFCChIP-3000-H3K27ac-xsonic-rep1

description: ChIP targeting H3K27ac modification


title: IDO-1

description: Day 28 post tumor transplant


title: Macrophages, without stimulation + porous Ti disc, donor 7

source_name: Buffy coat, donor 7

value: NO


title: Macrophages, IL4 stimulation + porous Ti disc, donor 7


title: IDO-3

description: Day 28 post tumor transplant


title: Macrophages, without stimulation, donor 7

value: ctrl


title: Macrophages, IFNgamma stimulation + porous Ti disc, donor 7


title: Macrophages, IL4 stimulation, donor 7


title: GITR-1

description: Day 28 post tumor transplant

value: GITR


title: MDA-MB-231 cells - Flag PAK5_rep1

city: Shenyang

first: Yang

last: Li

state: Liaoning

address: No. 77, Puhe Road, Shenyang North New Area

department: Department of Cell Biology, Key Laboratory of Cell Biology, National Health Commission of the PRC, and Key Laboratory of Medical Cell Biology, Ministry of Education of the PRC

country: China

institute: China Medical University

data_processing:
After sequencing, the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads.
The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left. miRDeep2 software was used to predict the novel miRNAs with these trimmed reads.
Then, the trimmed reads were aligned to merged pre-miRNA databases (known pre-miRNA from miRBase v21 plus the newly predicted pre-miRNAs) using Novoalign software (v2.07.11) with at most one mismatch. Reads (counts < 2) were discarded when calculating the miRNA expression.
In order to characterize the isomiR variability, sequences that matched the miRNA precursors in the mature miRNAs region ±4 nt (no more than 1 mismatch) were accepted as mature miRNA isomiRs, which were grouped according to the 5-prime (5p) or 3-prime (3p) arm of the precursor hairpin. The numbers of mapped tags that were defined as the raw expression levels of that miRNA.
To correct for the difference in tag counts between samples, the tag counts were scaled to TPM (the copy number of transcripts per million) based on the total number of tag aligned. Choosing a different isomiR sequence for measuring miRNA expression can affect the ability to detect differential miRNA expression.
Genome_build: miRbase
Supplementary_files_format_and_content: miRNA_Expression

source_name: breast cancer MDA-MB-231 cells

growth_protocol: The human breast cancer cell lines MDA-MB-231 were obtained from Shanghai cell bank of CAS-Chinese Academy of Sciences. MDA-MB-231 cells were cultured in Leibovitz's L-15 Medium containing 10% FBS (fetal bovine serum). Cells were routinely maintained in a humidified chamber at 37°C and 5% CO2.

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Total RNA was extracted from breast cancer cells using the TRIzol reagent (Invitrogen/Life Technologies) following the manufacturer’s protocol. Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps: 1) 3'-adaptor ligation; 2) 5'-adaptor ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of ~135-155 bp PCR amplified fragments (corresponding to ~15-35 nt small RNAs). The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 50 cycles on Illumina NextSeq per the manufacturer's instructions.

treatment_protocol: Flag PAK5 and Falg vector lentivirus were obtained from Shanghai Genechem Co., Ltd. Virus supernatant was incubated on target cells for 24 hours, following the manufacturer’s instructions. Infected cells were selected in puromycin, as optimized for cell line.

value: breast cancer cells

value: Flag-tagged PAK5 (Flag-PAK5) was stably expressed in mammary adenocarcinoma MDA-MB-231 cells


title: MDA-MB-231 cells - Flag_rep3

value: Flag vector was stably expressed in mammary adenocarcinoma MDA-MB-231 cells


title: MDA-MB-231 cells - Flag_rep1


title: MDA-MB-231 cells - Flag_rep2


title: MDA-MB-231 cells - Flag PAK5_rep2


title: MDA-MB-231 cells - Flag PAK5_rep3


title: GITR-2

description: Day 28 post tumor transplant


title: GITR-3

description: Day 28 post tumor transplant


title: Macrophages, IL4 stimulation, donor 6

source_name: Buffy coat, donor 6


title: Macrophages, without stimulation, donor 6


title: No treatment-3-re-run

description: Day 28 post tumor transplant

value: No treatment-3-re-run


title: os40-3

description: Day 28 post tumor transplant


title: Macrophages, IFNgamma stimulation, donor 7

value: IFN


title: Macrophages, IFNgamma stimulation, donor 6


title: n803-3

description: Day 28 post tumor transplant


title: ox40-1

description: Day 28 post tumor transplant


title: Macrophages, IFNgamma stimulation + porous Ti disc, donor 6


title: WT_GL_3

city: DALLAS

first: David

middle: Reid

last: Corey

state: TX

address: 6001 Forest Park Road

department: Pharmacology

institute: UT-Southwestern Medical Center at Dallas

data_processing:
Illumina Casava1.7 software used for basecalling.
Briefly, raw sequencing reads were adapter-trimmed and then mapped to hg38/Gencode v27 transcriptome using STAR-2.5.3a. Gene quantification and differential analysis were carried with Salmon (0.11.0) and DeSeq2. CLIPper and in-house scripts were used for eCLIP-seq peak calling and normalization.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include gene counts for each sample

growth_protocol: McCoy’s 5a Medium (GIBCO # 16600) + 10% FBS was used as the growth media for all the cell lines studies.

extract_protocol:
For RNA_seq samples, RNA was harvested using Trizol reagent. Illumina Whole Transcriptome RNA Sample Prep Kit (strand specific) was used with 50 ng-1 ug of total RNA for the construction of library. For the eCLIP-seq, cell cytoplasmic fraction was obtained wtih hypotonic buffer from 10 million cell and used for immunprecipitation or size-matched input samples.
RNA libraries were prepared for sequencing using standard Illumina protocols or eCLIP-seq protocol (Van Nostrand, et. al, Nature Methods, 2016, 13, 508-514)

value: human colon cancer cell line HCT-116

tag: passages

tag: antibody used

tag: genotype

value: wild type, siGL2


title: Macrophages, IL4 stimulation + porous Ti disc, donor 6


title: WT_GL_2


title: n803-2

description: Day 28 post tumor transplant


title: WT_GL_1


title: Macrophages, without stimulation + porous Ti disc, donor 6


title: Macrophages, without stimulation + porous Ti disc, donor 5

source_name: Buffy coat, donor 5


title: WT_6C_3

value: wild type, siTNRC6C


title: WT_6C_2


title: ad-CEA-2

description: Day 28 post tumor transplant

value: ad-CEA


title: ad-CEA-3

description: Day 28 post tumor transplant


title: AB_6C_3

value: TNRC6A-/-, TNRC6B-/-, siTNRC6C


title: WT_6C_1


title: AB_6C_1


title: AB_6C_2


title: AB_GL_3

value: TNRC6A-/-, TNRC6B-/-, siGL2


title: n803-1

description: Day 28 post tumor transplant


title: Macrophages, IL4 stimulation, donor 5

value: PBMC derived monocytes


title: AB_GL_2


title: No treatment-2

description: Day 28 post tumor transplant

value: No treatment


title: No treatment-3

description: Day 28 post tumor transplant


title: MRC-065NF MURAL

first: Thomas

middle: Constantine

last: Nardelli

state: Quebec

address: 3655 Prom. Sir-William-Osler

department: Pharmacology and Therapeutics

institute: McGill University

description: SG11514161_257236311939_S001_GE1_1105_Oct12_2_2.txt

hyb_protocol: After 17 h of hybridization at 65 degees celsius, the microarray slides were washed as per the recommendations for the Agilent hybridization kit.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (SureScan G2600D) using one color scan setting for 8x60k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software Version 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12). Scale normalization 75.0 percentile .

source_name: Mural Granulosa

label_protocol: Sample input was 100 ng of total RNA to generate fluorescent cRNA using the Agilent's low input Quick Amp labeling kit and 600 ng of Cy3 labeled cDNA was used for the single-color microarray.

extract_protocol: Total RNA was extracted using theRNeasy Plus minikit (Qiagen)

value: Mural Granulosa


title: No treatment-1

description: Day 28 post tumor transplant


title: MRC-145C MURAL

description: SG11514161_257236311939_S001_GE1_1105_Oct12_1_2.txt


title: MRC-008NF MURAL

description: SG11514161_257236311939_S001_GE1_1105_Oct12_2_1.txt


title: MRC-082C MURAL

description: SG11514161_257236311939_S001_GE1_1105_Oct12_2_4.txt


title: MRC-129C MURAL

description: SG11514161_257236311939_S001_GE1_1105_Oct12_2_3.txt


title: MRC-087C MURAL

description: SG11514161_257236311939_S001_GE1_1105_Oct12_1_3.txt


title: Macrophages, IFNgamma stimulation, donor 5

description: Gene expression data from human macrophages stimulated with IFNgamma and cultured for 6 days on cell culture plastic


title: Macrophages, IFNgamma stimulation + porous Ti disc, donor 5

value: Ti


title: Macrophages, without stimulation, donor 5

description: Gene expression data from human unstimulated macrophages cultured for 6 days on cell culture plastic

value: NO

value: ctrl


title: MRC-114NF MURAL

description: SG11514161_257236311939_S001_GE1_1105_Oct12_1_1.txt


title: ad-CEA-1

description: Day 28 post tumor transplant


title: AB_GL_1


title: MRC-167C MURAL

description: SG11514161_257236311938_S001_GE1_1105_Oct12_2_4.txt


title: AB_2

value: TNRC6A-/-, TNRC6B-/-


title: MRC-115NF MURAL

description: SG11514161_257236311938_S001_GE1_1105_Oct12_2_3.txt


title: AB_3


title: Macrophages, IL4 stimulation + porous Ti disc, donor 5

description: Gene expression data from human macrophages stimulated with IL-4 and cultured for 6 days on porous titanium discs


title: MRC-122NF MURAL

description: SG11514161_257236311938_S001_GE1_1105_Oct12_2_2.txt


title: AB_1


title: ox40-2

description: Day 28 post tumor transplant


title: MRC-049NF MURAL

description: SG11514161_257236311938_S001_GE1_1105_Oct12_1_4.txt


title: B_2


title: B_1


title: MRC-053NF MURAL

description: SG11514161_257236311938_S001_GE1_1105_Oct12_1_2.txt


title: MRC-149C MURAL

description: SG11514161_257236311938_S001_GE1_1105_Oct12_2_1.txt


title: MRC-029C MURAL

description: SG11514161_257236311938_S001_GE1_1105_Oct12_1_3.txt


title: B_3


title: A_3


title: MRC-086NF MURAL

description: SG11514161_257236311937_S001_GE1_1105_Oct12_2_2.txt


title: A_2


title: WT_3

value: wild type


title: MRC-039NF MURAL

description: SG11514161_257236311937_S001_GE1_1105_Oct12_1_4.txt


title: WT_2


title: MRC-051NF MURAL

description: SG11514161_257236311937_S001_GE1_1105_Oct12_2_3.txt


title: WT_1


title: MRC-055NF CUMULUS

description: SG11514161_257236311889_S001_GE1_1105_Oct12_2_4.txt

source_name: Cumulus Granulosa

value: Cumulus Granulosa


title: MRC-115C MURAL

description: SG11514161_257236311937_S001_GE1_1105_Oct12_1_1.txt


title: Nuc-WT-P29

value: human colon cancer cell

value: HCT 116

tag: eclip antibody


title: HPV16 positive cervical squamous cell carcinoma 7

city: Taiyuan

first: Haixia

last: Luo

address: 382 Wuyi Road

institute: The Second Hospital of Shanxi Medical University

description: Gene expression data from cervical squamous cell carcinoma

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix Human  Clariom® D Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The tissue that was harvested indivdually from the cervix were stored at iquid itrogen temperatures at once with protected by Rnasin inhibitor.

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

treatment_protocol: After grinded under the ice, cervix tissue were collected for further total RNA extraction.


title: Nuc-WT-P28


title: MRC-082C CUMULUS

description: SG11514161_257236311889_S001_GE1_1105_Oct12_2_3.txt


title: MRC-079C MURAL

description: SG11514161_257236311937_S001_GE1_1105_Oct12_2_1.txt


title: A_1

value: human colon cancer cell line HCT-116


title: HPV16 positive cervical squamous cell carcinoma 6


title: MRC-113C MURAL

description: SG11514161_257236311937_S001_GE1_1105_Oct12_1_2.txt


title: MRC-115C CUMULUS

description: SG11514161_257236311889_S001_GE1_1105_Oct12_2_2.txt


title: Nuc-A123-P14


title: Nuc-A123-P12


title: MRC-086NF CUMULUS

description: SG11514161_257236311889_S001_GE1_1105_Oct12_2_1.txt


title: Nuc-WT-P27


title: OVCAR8_AZD1775_2

city: Wuhan

first: Rouou

last: Xiao

state: hubei province

address: Donghu road

institute: Zhongnan hospital

data_processing:
Sequenced reads were mapped to human reference genome (hg38) using STAR (2.5.2a) with default parameters.
Aligned reads were summarized into gene counts using the featureCounts (v1.5.0) command of the Subread package with default parameters in conjunction with the human gencode annotation file (hg38 release 85).
Genome_build: hg38
tab-delimited text file containing raw read counts for all samples
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene frkm and counts for every gene and every sample

source_name: OVCAR8 cells

growth_protocol: OVCAR8 cells were cultured in regular growth medium (RPMI-1640 medium + 10% FBS + 1%P/S)

extract_protocol:
The TruSeq stranded RNA sample prep kit was used for library generation according to Illumina's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For samples 1-2, OVCAR8 cells were treated with DMSO for 48 h. For samples 3-4, OVCAR8 cells treated with 400 nM AZD1775 for 48 h. For samples 5-6, OVCAR8 cells were stable knockdown using lentiviral delivery of XBP1 shRNA for 48 h and selected with 2 μg/ml puromycin for 7 days. For samples 7-8, selected OVCAR8 sh-XBP1 cells were treated with 400 nM AZD1775 for 48 h.

value: ovary


title: HPV16 positive cervical squamous cell carcinoma 5


title: HPV16 positive HSIL 5

description: Gene expression data from HSIL

source_name: HPV16 positive HSIL

value: HPV16 positive HSIL


title: MRC-145C CUMULUS

description: SG11514161_257236311889_S001_GE1_1105_Oct12_1_2.txt


title: Nuc-A12-P11


title: HPV16 positive cervical squamous cell carcinoma 3


title: HPV16 positive HSIL 4

description: Gene expression data from HSIL


title: HPV16 positive cervical squamous cell carcinoma 4


title: OVCAR8_AZD1775_1

value: OVCAR8 cells treated with 400 nM AZD1775


title: Nuc-A12-P10


title: MRC-129C CUMULUS

description: SG11514161_257236311889_S001_GE1_1105_Oct12_1_1.txt


title: HPV16 positive cervical squamous cell carcinoma 1


title: OVCAR8_DMSO_2

value: OVCAR8 cells treated with DMSO


title: HPV16 positive cervical squamous cell carcinoma 2


title: normal cervical epithelium 7

description: Gene expression data from normal cervical epithelium

source_name: normal cervical epithelium

value: normal cervical epithelium


title: Nuc-A12-P9


title: OVCAR8_DMSO_1


title: MRC-065NF CUMULUS

description: SG11514161_257236311888_S001_GE1_1105_Oct12_2_2.txt


title: MRC-115NF CUMULUS

description: SG11514161_257236311888_S001_GE1_1105_Oct12_2_3.txt


title: HPV16 positive HSIL 1

description: Gene expression data from HSIL


title: MRC-167C CUMULUS

description: SG11514161_257236311888_S001_GE1_1105_Oct12_2_4.txt


title: Nuc-A2-P10


title: Nuc-A123-P11


title: Nuc-A2-P9


title: MRC-149C CUMULUS

description: SG11514161_257236311888_S001_GE1_1105_Oct12_2_1.txt


title: MRC-051NF CUMULUS

description: SG11514161_257236311888_S001_GE1_1105_Oct12_1_4.txt


title: HPV16 positive HSIL 3

description: Gene expression data from HSIL


title: normal cervical epithelium 6


title: Nuc-A2-P8


title: Nuc-A1-P8


title: normal cervical epithelium 3


title: HPV16 positive HSIL 6

description: Gene expression data from HSIL


title: MRC-141C CUMULUS

description: SG11514161_257236311888_S001_GE1_1105_Oct12_1_3.txt


title: HPV16 positive HSIL 2

description: Gene expression data from HSIL


title: normal cervical epithelium 5


title: Nuc-A1-P7


title: normal cervical epithelium 4


title: A498_S3

city: Lund

first: Ines

last: Ambite

address: Klinikgatan 28

department: Laboratory Medicine

institute: Lund University

description: Gene expression data from A498 cells

hyb_protocol: 6ug of fragmented and labelled cRNA was hybridized onto Human Genome U219 array strips (Affymetrix) for 16 hours at 45 °C, washed, stained (Applied Biosystems, ThermoFisher Scientific).

scan_protocol: Scanning was done using the GeneAtlas system (Affymetrix).

data_processing: The data was normalized using Robust Multi Average (RMA) implemented in the Partek® Genomics Suite™.

source_name: A498 kidney cells

label_protocol: 100 ng of total RNA was amplified, labeled and fragmented using the GeneChip 3´IVT PLUS Kit (ThermoFisher Scientific). Biotinylated cRNA was prepared according to the standard Affymetrix's protocol.

growth_protocol: E. coli strains were grown on tryptic soy agar (16 h, 37˚C). The human epithelial cell line A498 (ATCC HTB44, human kidney carcinoma) was cultured in RPMI-1640 supplemented with 1 mM sodium pyruvate, 1 mM non-essential amino acids and 10% fetal calf serum. Bacteria activation of the cells was studied on confluent cell layers in 6-well tissue culture plates (Nunc). A498 cells on confluent cell layers in 6-well tissue culture plates, were infected with 10^5 CFU/ml of bacteria in serum-free media for 4 hours.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and on-column DNase digestion, according to the manufacturer's instructions.

treatment_protocol: Cell culture medium was aspirated and replaced with fresh serum-free RPMI. E. coli strains were diluted in PBS and added to the cells at a concentration of 10^5 CFU/ml for 4 hours. The control sample was treated with a similar volume of PBS.

tag: infected with

value: E. coli 536 PAI I deletion mutant


title: A498_S1

description: Gene expression data from A498 cells

value: none (control)


title: A498_S2

description: Gene expression data from A498 cells

value: Ecoli 536


title: MRC-053NF CUMULUS

description: SG11514161_257236311888_S001_GE1_1105_Oct12_1_2.txt


title: normal cervical epithelium 2


title: Nuc-A1-P6


title: Cyto-WT-P28


title: Cyto-WT-P29


title: MRC-029C CUMULUS

description: SG11514161_257236311887_S001_GE1_1105_Oct12_2_4.txt


title: MRC-114NF CUMULUS

description: SG11514161_257236311887_S001_GE1_1105_Oct12_2_3.txt


title: MRC-079C CUMULUS

description: SG11514161_257236311887_S001_GE1_1105_Oct12_1_4.txt


title: MRC-008NF CUMULUS

description: SG11514161_257236311887_S001_GE1_1105_Oct12_2_2.txt


title: MRC-168C CUMULUS

description: SG11514161_257236311887_S001_GE1_1105_Oct12_1_3.txt


title: Cyto-A123-P14


title: Cyto-A123-P12


title: Cyto-A123-P11


title: Cyto-WT-P27


title: MRC-113C CUMULUS

description: SG11514161_257236311887_S001_GE1_1105_Oct12_1_2.txt


title: normal cervical epithelium 1


title: WTA V (Hyb_B)

city: Foster City

first: Luhua

middle: Hedberg

address: 746 Pinta Ln

institute: Stanford University

description:
replicate 1, repeated sample
SAMPLE 8

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Scanning was done using an iScan array scanner.

data_processing: The data were normalised using average normalisation with IlluminaGUI in R

source_name: IL-2 cultured splenic NK cells

label_protocol: Biotinylated cRNA were prepared with the Total Prep Amplification kit for Illumina arrays

growth_protocol: Murine splenic NK cells were stimulated with IL-2 (1000U/mL) for 8 days.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser (double check).

value: spleen

value: NK cells

tag: strain

value: wildtype

tag: Sex

value: Female

tag: age

value: 8 weeks


title: Cyto-A12-P11

tag: cell type

tag: cell line


title: Cyto-A12-P10


title: MRC-129C [BDE-153 MURAL]

description: SG11514161_257236311939_S001_GE1_1105_Oct12_2_3.txt

source_name: mural granulosa cells

tag: exposure

value: LOW


title: WTC V

description:
replicate 3
SAMPLE 5

tag: tissue


title: WTB V

description:
replicate 2
SAMPLE 4


title: MRC-008NF [BDE-153 MURAL]

description: SG11514161_257236311939_S001_GE1_1105_Oct12_2_1.txt


title: Cyto-A2-P10

value: human colon cancer cell


title: KOA V (Hyb_B)

description:
replicate 1, repeated sample
SAMPLE 6

value: AhR-/-


title: KOA V

description:
replicate 1
SAMPLE 1


title: KOB V

description:
replicate 2
SAMPLE 2


title: Cyto-A12-P9

value: HCT 116


title: MRC-115NF [BDE-153 MURAL]

description: SG11514161_257236311938_S001_GE1_1105_Oct12_2_3.txt

value: HIGH


title: KOC V

description:
replicate 3
SAMPLE 7


title: WTA V

description:
replicate 1
SAMPLE 3


title: Cyto-A2-P9


title: MRC-114NF [BDE-153 MURAL]

description: SG11514161_257236311939_S001_GE1_1105_Oct12_1_1.txt


title: MRC-167C [BDE-153 MURAL]

description: SG11514161_257236311938_S001_GE1_1105_Oct12_2_4.txt


title: Cyto-A2-P8


title: MRC-039NF CUMULUS

description: SG11514161_257236311887_S001_GE1_1105_Oct12_1_1.txt

value: Cumulus Granulosa


title: Intestine_polyp_S1_exp3

description: Gene expression data from C57BL/6J mice intestine experiment 3

hyb_protocol: 6ug of fragmented and labelled cRNA was hybridized onto Mouse Genome 430 PM array strips (Affymetrix) for 16 hours at 45 °C, washed, stained (Applied Biosystems, ThermoFisher Scientific).

data_processing: Transcriptomic data was normalized using Robust Multi Average implemented in the Transcriptome Analysis Console software (v.4.0.1.36, Applied Biosystems, ThermoFisher Scientific).

source_name: Mice APC min/+ cancer experiment 3

growth_protocol: C57BL/6J-APCmin/J mice develop spontaneous intestinal adenoma formation, mice were used at either the age of 11 weeks, or 20 weeks. C57BL/6J WT mice were used as healthy controls and for toxicity assessment.

extract_protocol: At sacrifice, intestines were aseptically harvested for mRNA extraction and and analysis. Total RNA was extracted (RNeasy Mini kit, Qiagen) according to the manufacturer's instructions.

treatment_protocol: The treatment group received E. coli 536 WT supernatants (200 µl, 10 µg/kg) or recombinant Lon Protease (250 µg/ml) by oral gavage or per-orally, twice daily for 14 days. Sham treated animals received PBS. For toxicity testing in C57BL/6J WT mice (8 weeks old) were exposed to recombinant Lon protease (rLon) per-orally twice daily for 14 days. Controls received PBS.

tag: mouse strain

value: intestine

tag: experiment

tag: treatment

value: rLon


title: MRC-049NF [BDE-153 MURAL]

description: SG11514161_257236311938_S001_GE1_1105_Oct12_1_4.txt


title: Intestine_polyp_S3_exp3

value: PBS


title: Intestine_polyp_S10_exp2

description: Gene expression data from C57BL/6J-APCmin/J intestinal polyps experiment 2

source_name: Mice APC min/+ cancer experiment 2


title: Cyto-A1-P8


title: Intestine_polyp_S4_exp3


title: MRC-053NF [BDE-153 MURAL]

description: SG11514161_257236311938_S001_GE1_1105_Oct12_1_2.txt


title: Cyto-A1-P7


title: MRC-039NF [BDE-153 MURAL]

description: SG11514161_257236311937_S001_GE1_1105_Oct12_1_4.txt


title: Cyto-A1-P6


title: ChIPseq_pS2_EtOH_DMSO_rep2

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

data_processing:
Base calling perfomed using Illumina's FASTQ Generation software v1.0.0
ChIPseq reads were aligned with Bowtie1 to hg19 and to mm10 for the spike-in
Input of different conditions was merged
human reads were normalized to the number of spike-in reads
metagenes were established with ngs.plot.r v2.63
read distribution was determined with betdools intersect v2.26.0, either over specified regions or over the whole genome in 100-nt-bins
Genome_build: hg19, mm10
Supplementary_files_format_and_content: begraph files were generated with bedtools genomecov

source_name: osteosarcoma cell line

growth_protocol: U2OS cells expressing doxycycline-inducible MYC

extract_protocol:
crosslink (5 min), harvest, spike-in with 10 % NIH-3T3, lysis of cells, fragment with covaris
libraries were prepared for sequencing using standard NEB protocols

treatment_protocol: Treated with/without doxycycline for 24 hrs and with or without BI8626 for 4 hrs

value: U-2 OS

value: osteosarcoma cell line

value: Ethanol and DMSO

tag: chip antibody

value: anti-Pol II pS2 (ab5095)


title: ChIPseq_INPUT_rep2

value: merge of all conditions


title: ChIPseq_pS2_EtOH_BI8626_rep2

value: Ethanol and BI8626


title: Intestine_polyp_S12_exp2


title: MRC-115C [BDE-153 MURAL]

description: SG11514161_257236311937_S001_GE1_1105_Oct12_1_1.txt


title: MRC-113C [BDE-153 MURAL]

description: SG11514161_257236311937_S001_GE1_1105_Oct12_1_2.txt


title: MRC-129C [BDE-153 CUMULUS]

description: SG11514161_257236311889_S001_GE1_1105_Oct12_1_1.txt

source_name: cumulus granulosa cells


title: Intestine_polyp_S11_exp2


title: MRC-115C [BDE-153 CUMULUS]

description: SG11514161_257236311889_S001_GE1_1105_Oct12_2_2.txt


title: MRC-103NF CUMULUS

description: SG11514161_257236311889_S001_GE1_1105_Oct12_1_3.txt


title: MRC-167C [BDE-153 CUMULUS]

description: SG11514161_257236311888_S001_GE1_1105_Oct12_2_4.txt


title: Intestine_polyp_S2_exp3


title: ChIPseq_pS2_Dox_BI8626_rep2

value: Doxycyclin and BI8626


title: MRC-115NF [BDE-153 CUMULUS]

description: SG11514161_257236311888_S001_GE1_1105_Oct12_2_3.txt


title: ChIPseq_MYC_EtOH_DMSO_rep2

value: anti-MYC (ab32072)


title: ChIPseq_MYC_EtOH_BI8626_rep2


title: MRC-053NF [BDE-153 CUMULUS]

description: SG11514161_257236311888_S001_GE1_1105_Oct12_1_2.txt

value: LOW


title: Intestine_polyp_S8_exp2


title: Intestine_polyp_S7_exp2


title: MRC-114NF [BDE-153 CUMULUS]

description: SG11514161_257236311887_S001_GE1_1105_Oct12_2_3.txt


title: ChIPseq_MYC_Dox_DMSO_rep2

value: Doxycyclin and DMSO


title: ChIPseq_pS2_Dox_DMSO_rep2


title: Intestine_polyp_S5_exp2


title: Intestine_polyp_S9_exp2


title: MRC-008NF [BDE-153 CUMULUS]

description: SG11514161_257236311887_S001_GE1_1105_Oct12_2_2.txt


title: ChIPseq_CTR9_EtOH_DMSO_rep2


title: MRC-113C [BDE-153 CUMULUS]

description: SG11514161_257236311887_S001_GE1_1105_Oct12_1_2.txt


title: Intestine_polyp_S6_exp2


title: ChIPseq_MYC_Dox_BI8626_rep2


title: ChIPseq_CTR9_EtOH_BI8626_rep2


title: Intestine_polyp_S3_exp2


title: MRC-082C [BDE-47 MURAL]

description: SG11514161_257236311939_S001_GE1_1105_Oct12_2_4.txt


title: ChIPseq_CTR9_Dox_DMSO_rep2


title: ChIPseq_CTR9_Dox_BI8626_rep2


title: MRC-129C [BDE-47 MURAL]

description: SG11514161_257236311939_S001_GE1_1105_Oct12_2_3.txt


title: Intestine_polyp_S2_exp2


title: ChIPseq_A10_EtOH_DMSO_rep2

value: anti-Pol II (sc-17798)


title: MRC-008NF [BDE-47 MURAL]

description: SG11514161_257236311939_S001_GE1_1105_Oct12_2_1.txt


title: MRC-087C [BDE-47 MURAL]

description: SG11514161_257236311939_S001_GE1_1105_Oct12_1_3.txt


title: Intestine_polyp_S4_exp2

description: Gene expression data from C57BL/6J-APCmin/J intestinal polyps experiment 2


title: Intestine_polyp_S7_exp1

description: Gene expression data from C57BL/6J-APCmin/J intestinal polyps experiment 1

source_name: Mice APC min/+ cancer experiment 1


title: MRC-145C [BDE-47 MURAL]

description: SG11514161_257236311939_S001_GE1_1105_Oct12_1_2.txt


title: Intestine_polyp_S10_exp1


title: ChIPseq_A10_EtOH_BI8626_rep2


title: MRC-114NF [BDE-47 MURAL]

description: SG11514161_257236311939_S001_GE1_1105_Oct12_1_1.txt


title: Intestine_polyp_S9_exp1


title: ChIPseq_A10_Dox_BI8626_rep2


title: Intestine_polyp_S5_exp1


title: Intestine_polyp_S8_exp1


title: ChIPseq_A10_Dox_DMSO_rep2


title: MRC-149C [BDE-47 MURAL]

description: SG11514161_257236311938_S001_GE1_1105_Oct12_2_1.txt


title: Intestine_polyp_S1_exp2


title: ChIPseq_MYCER_pS2_30min_OHT_rep2

data_processing:
Base calling perfomed using Illumina's FASTQ Generation software v1.0.0
ChIPseq reads were aligned with Bowtie2 to hg19 and to mm10 for the spike-in
human reads were normalized to the number of spike-in reads
metagenes were established with ngs.plot.r v2.41.2
Genome_build: hg19, mm10
Supplementary_files_format_and_content: begraph files were generated with bedtools (v2.26.0) genomecov

growth_protocol: cells were grwon in DMEM for 24 h

extract_protocol:
crosslink (5 min), harvest, 10% of NIH 3T3 spike in, lysis of cells, fragment with covaris
libraries were prepared for sequencing using standard NEB protocols

treatment_protocol: treat with EtOH, or 4-OHT (200 nM) for 10 min or 30 min

value: 30' 4-OHT treament

value: Anti RNA Pol2 phospho Ser2 (rabbit, abcam, ab5095)


title: MRC-049NF [BDE-47 MURAL]

description: SG11514161_257236311938_S001_GE1_1105_Oct12_1_4.txt


title: ChIPseq_MYCER_INPUT_rep2

value: input


title: Intestine_polyp_S6_exp1

value: intestine


title: ChIPseq_MYCER_pS2_10min_OHT_rep2

value: 10' 4-OHT treament


title: MRC-051NF [BDE-47 MURAL]

description: SG11514161_257236311937_S001_GE1_1105_Oct12_2_3.txt

value: HIGH


title: Intestine_polyp_S1_exp1

value: rLon


title: Intestine_polyp_S3_exp1


title: Intestine_polyp_S4_exp1


title: MRC-113C [BDE-47 MURAL]

description: SG11514161_257236311937_S001_GE1_1105_Oct12_1_2.txt


title: MRC-029C [BDE-47 MURAL]

description: SG11514161_257236311938_S001_GE1_1105_Oct12_1_3.txt


title: Intestine_polyp_S2_exp1


title: ChIPseq_MYCER_CTR9_0min_OHT_rep2

value: osteosarcoma cell line

value: EtOH treatment

value: CTR9 (rabbit, bethyl laboratories, A301-395)


title: MRC-082C [BDE-47 CUMULUS]

description: SG11514161_257236311889_S001_GE1_1105_Oct12_2_3.txt

source_name: CUMULUS


title: MRC-103NF [BDE-47 CUMULUS]

description: SG11514161_257236311889_S001_GE1_1105_Oct12_1_3.txt


title: MRC-145C [BDE-47 CUMULUS]

description: SG11514161_257236311889_S001_GE1_1105_Oct12_1_2.txt


title: ChIPseq_MYCER_INPUT_rep1


title: ChIPseq_MYCER_MYC_30min_OHT_rep1

value: c-Myc (Y69)(rabbit, abcam, ab32072)


title: MRC-129C [BDE-47 CUMULUS]

description: SG11514161_257236311889_S001_GE1_1105_Oct12_1_1.txt


title: ChIPseq_MYCER_pS2_0min_OHT_rep2


title: Bladder_tumor_S4_exp3

description: Gene expression data from MB49-induced murine bladder cancer experiment 3

source_name: Mice bladder cancer experiment 3

growth_protocol: Bladder cancer was induced in C57BL/6J female mice by intravesical instillation of MB49 cells. On day 0, bladders were emptied and preconditioned by intravesical instillation of 100 μl poly-L-lysine solution (0.1 mg/ml) for 30 minutes followed by instillation of MB49 mouse bladder carcinoma cells (2 × 10^5 in 100 μl PBS).

extract_protocol: At sacrifice, bladders were aseptically harvested for mRNA extraction and and analysis. Total RNA was extracted (RNeasy Mini kit, Qiagen) according to the manufacturer's instructions.

treatment_protocol: The treatment group received Lon protease (250 µg/ml) or E. coli 536 or PAI I536 bacterial supernatant (approximately 1 hour) by intravesical instillation on days 3, 5, 7, 9 and 11. Sham treated animals received PBS and healthy mice bladders were used as control. Bladder samples were collected after 12 days and 27 days (follow-up). For long-term experiments, mice were treated for 12 days with Lon protease (250 µg/ml) followed by twice weekly until day 35. For toxicity testing in C57BL/6J WT female mice, recombiant Lon protein (250 µg/ml) was instilled intravesically on days 3, 5, 7, 9 and 11 and bladders were collected for RNA isolation after 12 days. Controls received PBS.

tag: gender

value: female

value: bladder


title: Bladder_tumor_S6_exp3


title: Bladder_tumor_S5_exp3


title: Bladder_tumor_S3_exp3

value: PBS


title: Bladder_tumor_S1_exp3


title: ChIPseq_MYCER_MYC_10min_OHT_rep1


title: Bladder_tumor_S2_exp3


title: Bladder_tumor_S7_exp2

description: Gene expression data from MB49-induced murine bladder cancer experiment 2

source_name: Mice bladder cancer experiment 2


title: Bladder_tumor_S7_exp3


title: MRC-039NF [BDE-47 MURAL]

description: SG11514161_257236311937_S001_GE1_1105_Oct12_1_4.txt


title: ChIPseq_MYCER_CTR9_30min_OHT_rep2


title: Bladder_tumor_S6_exp2


title: ChIPseq_MYCER_MYC_0min_OHT_rep1


title: MRC-149C [BDE-47 CUMULUS]

description: SG11514161_257236311888_S001_GE1_1105_Oct12_2_1.txt

value: LOW


title: ChIPseq_MYCER_CTR9_10min_OHT_rep2


title: MRC-051NF [BDE-47 CUMULUS]

description: SG11514161_257236311888_S001_GE1_1105_Oct12_1_4.txt


title: ChIPseq_MYCER_CTR9_30min_OHT_rep1


title: MRC-114NF [BDE-47 CUMULUS]

description: SG11514161_257236311887_S001_GE1_1105_Oct12_2_3.txt


title: ChIPseq_MYCER_CTR9_0min_OHT_rep1


title: ChIPseq_MYCER_CTR9_10min_OHT_rep1


title: Bladder_tumor_S5_exp2


title: MRC-008NF [BDE-47 CUMULUS]

description: SG11514161_257236311887_S001_GE1_1105_Oct12_2_2.txt


title: ChIPseq_MYCER_pS2_30min_OHT_rep1


title: MRC-113C [BDE-47 CUMULUS]

description: SG11514161_257236311887_S001_GE1_1105_Oct12_1_2.txt


title: ChIPseq_MYCER_pS2_10min_OHT_rep1


title: MRC-039NF [BDE-47 CUMULUS]

description: SG11514161_257236311887_S001_GE1_1105_Oct12_1_1.txt


title: ChIPseq_MYCER_pS2_0min_OHT_rep1


title: Bladder_tumor_S4_exp2


title: MRC-082C [10-PBDE_MURAL]

description: SG11514161_257236311939_S001_GE1_1105_Oct12_2_4.txt


title: Bladder_tumor_S2_exp2


title: Bladder_tumor_S1_exp2


title: BLISS_MYC_AID_A6

data_processing:
Base calling perfomed using Illumina's FASTQ Generation software v1.0.0
reads were demultiplexed according to sample-barcode with UMI-tools v1.0.1
barcodes used as following: A1: CATCACGC, A2: GTCGTTCC, A3: TGATGATC, A4: ACGACATC, A5: CATCATCC, A6: ACGACCGC
reads were aligned with Bowtie2 v2.3.4.1 to hg19
reads were filtered with bedtools intersect v2.26.0
bedgraph-files were normalized within each replicate to the condition with the lowest amount of AsiSI-induced breaks (BLISS8), or readnormalized between replicates ("BLISS Etoposide")
reads were counted for specific regions using the R package exomeCopy v1.18.0
density plots were generated using the R package metagene2 v3.10
Genome_build: hg19
Supplementary_files_format_and_content: begraph files were generated with bedtools genomecov

growth_protocol: U2OS cells expressing doxycycline-inducible MYC or K562 cells carrying endogenously AID-tagged MYC

extract_protocol:
blunting of DSB, adapter ligation, DNA purification and fragmentation, in vitro transcription, fragmentation
libraries were prepared for sequencing using a modified NEBNext Small RNA library preperation protocol

treatment_protocol: Treated with/without doxycycline for 24 hrs, with or without Etoposide for 3 hrs and with or without IAA for 3.5h

value: erythroleukemic cell line

value: 3.5h IAA and Etoposide


title: BLISS_MYC_AID_A5

value: Etoposide


title: MRC-029C [BDE-47 CUMULUS]

description: SG11514161_257236311887_S001_GE1_1105_Oct12_2_4.txt


title: MRC-008NF [10-PBDE_MURAL]

description: SG11514161_257236311939_S001_GE1_1105_Oct12_2_1.txt


title: Bladder_tumor_S3_exp1

description: Gene expression data from MB49-induced murine bladder cancer experiment 1

source_name: Mice bladder cancer experiment 1


title: MRC-087C [10-PBDE_MURAL]

description: SG11514161_257236311939_S001_GE1_1105_Oct12_1_3.txt

source_name: Mural Granulosa


title: RNA complexed with SprY-MS2 – sample 2

city: Rennes

first: Vincent

last: Cattoir

address: 2 rue Henri Le Guilloux

country: France

institute: CHU de Rennes

data_processing:
The reads were mapped against the genomic sequence of S. aureus HG003 strain (Genbank accession no. CP000253) and counted using the CLC Genomics Workbench software v8.1 (Qiagen).
The expression of genes in different RNA-seq samples was compared using the R package DESeq2 R package.
Genome_build: S. aureus HG003 strain (Genbank accession no. CP000253.1).
Supplementary_files_format_and_content: *.txt: Tab-delimited text files generated using the CLC Genomics Workbench software v8.1 (Qiagen).

organism: Staphylococcus aureus

source_name: Bacteria

growth_protocol: Bacterial cells of Staphylococcus aureus HG003 strain were cultured at 37°C to early- and the late-exponential-growth phases in BHI broth.

extract_protocol:
Total RNA was extracted using phenol/chloroform method with followed ethanol precipitation.
The strand-specific library preparation was performed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® and the samples were sequenced using the Illumina MiSeq instrument.

treatment_protocol: Affinity purification of target RNAs bound to MS2-tagged sRNAs expressed in vivo.

tag: ms2 tag


title: RNA complexed with SprY-MS2 – sample 3


title: Bladder_tumor_S2_exp1


title: BLISS_MYC_AID_A2

value: 3.5h IAA


title: MRC-145C [10-PBDE_MURAL]

description: SG11514161_257236311939_S001_GE1_1105_Oct12_1_2.txt


title: MRC-149C [10-PBDE_MURAL]

description: SG11514161_257236311938_S001_GE1_1105_Oct12_2_1.txt


title: BLISS_MYC_AID_A1

value: DMSO


title: BLISS8_W11_Etoposide_A4

value: U-2 OS

value: Doxycylin and Etoposide


title: Bladder_tumor_S1_exp1


title: RNA complexed with SprY-MS2 – sample 1


title: MRC-049NF [10-PBDE_MURAL]

description: SG11514161_257236311938_S001_GE1_1105_Oct12_1_4.txt

value: HIGH


title: Bladder_tumor_S8_exp3

description: Gene expression data from MB49-induced murine bladder cancer experiment 3


title: Bladder_tumor_S3_exp2

description: Gene expression data from MB49-induced murine bladder cancer experiment 2

value: rLon


title: BLISS8_W11_Etoposide_A3

value: osteosarcoma cell line

value: Doxycylin


title: MRC-053NF [10-PBDE_MURAL]

description: SG11514161_257236311938_S001_GE1_1105_Oct12_1_2.txt


title: BLISS8_W11_Etoposide_A2


title: MRC-051NF [10-PBDE_MURAL]

description: SG11514161_257236311937_S001_GE1_1105_Oct12_2_3.txt


title: RNA complexed with MS2 - sample 1 (control)


title: BLISS8_W11_Etoposide_A1

value: Ethanol


title: MRC-039NF [10-PBDE_MURAL]

description: SG11514161_257236311937_S001_GE1_1105_Oct12_1_4.txt


title: BLISS8_shCTR9_A5

value: Etoposide, stable expression of CTR9-targeting shRNA


title: MRC-113C [10-PBDE_MURAL]

description: SG11514161_257236311937_S001_GE1_1105_Oct12_1_2.txt


title: BLISS8_shCTR9_A4

value: Doxycyclin, stable expression of non-targeting shRNA


title: MRC-103NF [10-PBDE_CUMULUS]

description: SG11514161_257236311889_S001_GE1_1105_Oct12_1_3.txt

source_name: Cumulus Granulosa


title: BLISS8_shCTR9_A3

value: Ethanol, stable expression of non-targeting shRNA


title: MRC-082C [10-PBDE_CUMULUS]

description: SG11514161_257236311889_S001_GE1_1105_Oct12_2_3.txt


title: Bladder_tumor_S4_exp1

value: female

value: bladder

value: PBS


title: BLISS8_shCTR9_A2

value: Doxycyclin, stable expression of CTR9-targeting shRNA


title: MRC-145C [10-PBDE_CUMULUS]

description: SG11514161_257236311889_S001_GE1_1105_Oct12_1_2.txt

value: LOW


title: Macrophages, M2Cocktail stimulation + polished Ti disc, donor 1

description: Gene expression data from human macrophages stimulated with M2Cocktail and cultured for 6 days on polished titanium discs

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of human Hugene-1_0-type from Affymetrix. A Custom CDF Version 19 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: Buffy coat, donor 1

treatment_protocol: Macrophages were cultured on cell culture plastic or on polished titanium discs. Additionally they were stimulated at day 0 either with IL-4 (10ng/ml) or with IFNgamma (100ng/ml) or with M2Cocktail(10ng/ml M-CSF + 3ng/ml IL-4 + 10ng/ml IL-10 + 10ng/ml TGFbeta) or left untreated as control.

value: PBMC derived monocytes

tag: donornr

value: Cocktail

tag: titanium

value: TI


title: Macrophages, M2Cocktail stimulation, donor 1

description: Gene expression data from human macrophages stimulated with M2Cocktail and cultured for 6 days on cell culture plastic

value: ctrl