title: 1063_7xIR #2

status: Public on Mar 01 2020

city: Moscow

first: Daniil

last: Nikitin

address: Miklucho-Maklaya

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

hyb_protocol: Biotinylated fragmented ssDNA was then hybridized onto the GeneChip® Human Gene 1.0 ST Array (Affymetrix) according to the manufacturer’s instructions. The hybridization was carried out at 45°C in the GeneChip® Hybridization Oven 640 (Affymetrix) for 16 h. Washing and staining of the arrays on the Gene Chip® Fluidics Station 450 (Affymetrix) were performed according to the manufacturer’s recommendation. The amplification of the antibody signal, washing and staining protocols were used to stain the arrays with streptavidin R-phycoerythrin (SAPE; Invitrogen). SAPE solution was added twice together with a biotinylated anti-streptavidin antibody (Vector Laboratories, Burlingame, CA, USA) staining step in order to amplify staining

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix). Affymetrix AGCC Software (version 2.0) (Affymetrix) was used for the extraction of intensity data

data_processing: Signal intensity sata were analyzed using the affy and Limma packages of Bioconductor (R language).

source_name: radiation-treated human glioma stem cells

label_protocol: A terminal labeling reaction (Biotin) was conducted using the WT Labeling Kit (Affymetrix)

growth_protocol: GSCs were maintained in NeuroBasal medium supplemented with the B27 component (Invitrogen Life technologies), fibroblast growth factor (FGF) and epidermal growth factor (EGF) (10 and 20 ng/mL, respectively, Biochrom GmbH, Merck KGaA, Germany)

extract_protocol: RNA isolation was performed using the Trizol (Invitrogen) method according to the manufacturer’s instructions. The samples were treated with DNAse I (Sigma-Aldrich, St. Louis, MO USA).

treatment_protocol: Hypofractionated radiation regimen consisted of seven fractions of 2 Gy of X-rays generated by a Gulmay RS225 GS014 X-ray machine (Gulmay Medical Ltd, Camberley, UK) at a current of 200 kV, a voltage of 15 mA and a dose rate of 1 Gy/min. GSC spheres were triturated one day before radiation treatment. Immediately after irradiation cells were placed back to the incubator for recovery and propagation until the next radiation treatment

tag: treatment

value: radiation-treated


title: 1063_7xIR #1

type: RNA

label: biotin

molecule: total RNA

organism: Homo sapiens


title: 1083_7xIR #2


title: 1083_7xIR #1


title: 1083 Untreated control #3

source_name: untreated human glioma stem cells

value: untreated


title: 1083 untreated control #1


title: 1063 Untreated control #1


title: 1083 Untreated ciontrol #2


title: 1083_7xIR #3


title: 1063_7xIR #3


title: 1063 Untreated control #2


title: 1063  Untreated control #3


title: 1051 Untreated control #3


title: 1095_IR_2


title: 1043_3

source_name: untreated control human glioma stem cells


title: 1051_ 7xIR #1


title: 1051_ 7xIR #3


title: 1095SP p17_1


title: 1051_ 7xIR #2


title: 1051 UNtreated control #2


title: 1051 Untreated control #1


title: 1095_IR_1


title: 1043_IR_1


title: 1043_2


title: 1095_IR_3


title: 1095SP p17_2


title: 1095SP p17_3


title: 1043_IR_3


title: RNA-TG

status: Public on Feb 21 2020

type: SRA

city: Boston

first: Shubham

last: Khetan

state: MA

address: 77 Avenue Louis Pasteur

country: USA

institute: Brigham and Women's Hospital

library_source: transcriptomic

data_processing:
The sum of the barcode counts for each oligo within replicates was median normalized, and oligos showing differential expression relative to the plasmid input were identified by modeling a negative binomial distribution with DESeq2  and applying a false discovery rate (FDR) threshold of 1%.
For sequences that displayed significant MPRA activity, a paired t-test was applied on the log-transformed RNA/plasmid ratios for each experimental replicate to test whether the reference and alternate allele had similar activity. An FDR threshold of 10% was used to identify SNPs with a significant skew in MPRA activity between alleles (allelic skew). Because the MPRA testing standard culture conditions was performed with a separate MRPA library preparation. Therefore, the DMSO-TG MPRA results were not directly compared to MPRA performed under standard culture conditions.
Genome_build: Custom; T2D_khetan_All_20180111.asi.probes.fa
Supplementary_files_format_and_content: txt

organism: Mus musculus

source_name: MIN6 mouse beta cells

growth_protocol: MIN6 were grown in DMEM (4.5 g/L glucose; Life Technologies) supplemented with 1 mM sodium pyruvate (Life Technologies), 100 μM 2-mercaptoethanol (Sigma), and 10% fetal bovine serum (Seradigm).

extract_protocol:
RNA was extracted from frozen cell pellets using the Qiagen RNeasy Midi kit. Following DNase treatment, a mixture of 3 GFP-specific biotinylated primers (Supplementary Table 1; #120, #123 and #126) were used to immunoprecipitated GFP transcripts using Streptavidin C1 Dynabeads (Life Technologies). Following another round of DNase treatment, cDNA was synthesized from GFP mRNA using SuperScript IV and purified with AMPure XP beads. Quantitative PCR using primers specific for GFP (Supplementary Table 1; #34 and #52) was used to determine the cycle at which linear amplification begins for each replicate. Replicates were diluted to approximately the same concentration based on the qPCR results, and PCR with primers #34 and #52 was used to amplify barcodes associated with the ~13.5k sequences included in the MRPA library for each replicate (9 cycles for standard culture, and 13 cycles for DMSO / 250 nM TG). A second round of PCR (6 cycles) was used to add Illumina sequencing adaptors to the DNA/RNA replicates. The resulting MPRA barcode libraries were spiked with 5% PhiX and sequenced using Illumina single-end 31 bp chemistry (with 8 bp index read), clustered at 80-90% maximum density.
Oligos were synthesized (Agilent Technologies) as 230 bp sequences containing 200 bp of genomic sequences and 15 bp of adaptor sequence on either end. Unique 20 bp barcodes were added by PCR along with additional constant sequence for subsequent incorporation into a backbone vector by Gibson assembly. The oligo library was expanded by electroporation into E. coli, and the resulting plasmid library was sequenced by Illumina 2 X 150 bp chemistry to acquire oligo-barcode pairings. The library underwent restriction digestion, and GFP with a minimal TATA promoter was inserted by Gibson assembly resulting in the 200 bp oligo sequence positioned directly upstream of the promoter and the 20 bp barcode falling in the 3’ UTR of GFP. After expansion within E. coli the final MPRA plasmid library was sequenced by Illumina 1 X 31 bp chemistry to acquire a baseline representation of each oligo-barcode pair within the library. Note: 2 separate batches of the MPRA library were prepared. The first batch was used to perform MPRA under standard culture conditions. This MPRA library was then electroporated into E. coli to obtain a second batch of the MRPA library, which was used for the DMSO-TG experiments.
Massively parallel reporter assay (MPRA)

treatment_protocol: 10 million MIN6 cells were seeded in each of seven 15 cm2 dishes. The cells were 60-70% confluent the next day. Each 15 cm2 dish was replaced with 20 ml of fresh media, and transfected with 7ug of the MPRA plasmid library using 55ul Lipofectamine 2000 (38% transfection efficiency). Six hours after transfection, media was either i) not changed (MPRA under standard culture conditions), ii) replaced with media containing 250 nM Thapsigargin dissolved in 0.025% DMSO, or iii) replaced with media containing 0.025% DMSO. Thirty hours after transfection, cells were trypsinized and collected by centrifugation. Cell pellets were frozen at -80°C. For each condition (standard culture / DMSO / 250 nM TG), MIN6 cells were transfected on five separate days to generate biological replicates.

tag: cell type


title: RNA-TG-Run2


title: 1043_IR_2


title: RNA-DMSO-Run2


title: Plasmid-Run2

library_source: genomic

molecule: genomic DNA


title: RNA-DMSO


title: 10 Untreated control #2


title: 10_7xIR #2


title: 10_7xIR #3


title: 10 Untreated control #3


title: 10 Untreated control #1


title: Plasmid


title: RNA-Baseline


title: Plasmid-Baseline


title: Bmal1-/-3_T24_rep3  [run2_VAL513A24_S24_L001]

status: Public on Feb 14 2020

city: Philadelphia

first: Utham Kashyap

last: Valekunja

state: PA

address: 3400 Civic Center Boulevard,

department: Department of Systems Pharmacology & Therapeutics, Perelman School of Medicine,

institute: University of Pennsylvania

description:
run2_VAL513A24_S24_L001
KO3_T24_rep3_FPKM

data_processing:
A TopHat-Cuffdiff pipeline was used to analyse the sequencing reads [Trapnell et al. Nat. Biotechnol. 2013].
Sequence reads were aligned to the Ensembl built mouse reference genome (GRCm38) using TopHat version 2.1.0 [Kim et al. Genome Biol.  2013].
FPKM values were computed with Cuffdiff, normalized via the median of the geometric means of fragment counts across all libraries as available in Cuffdiff package [Anders and Huber, Genome Biol. 2010].
Genome_build: GRCm38
Supplementary_files_format_and_content: FPKM

growth_protocol: Wild-type and Bmal1-/- MSF cells were grown in Dulbecco’s Modified Eagle Medium (DMEM) containing 10% (v/v) HyClone III Serum (Analab; Cat # SH30109.03), 1/100  Glutamax-I (Invitrogen; Cat # 35050-038), 1/100 Penicillin-Streptomycin (SIGMA; Cat # P4333) and 1/500 MycoZap™ (Lonza; Cat # VZA-2022) in multiple six-well plates until complete confluency (n=3, per time-point, per genotype). Wild-type and Bmal1-/-  mice liver tissues were sliced in small pieces (~500 micron) and were placed on membrane discs in multiple 24 well plates (n=3, per time-point, per genotype).

extract_protocol:
Wild-type and Bmal1-/- MSF cells and mice liver tissue time-course samples were lysed in TRI-Reagent® and Direct-zol™ RNA MiniPrep kit was used for RNA extraction following the manufacturer's instructions (Zymo Research; Cat # R2052).
mRNA contents in those samples were enriched using a NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB; Cat # E7490). The enriched mRNA samples were subjected to an Illumina TrueSeq platform compatible multiplex library preparation protocol using KAPA Stranded RNA-Seq Library Preparation Kit (Kapa Biosystems; Cat # KK8401) and libraries were prepared with TruSeq LT index adapter.

treatment_protocol: The confluent MSF cells and mice liver tissue slices were treated with 100nM (final concentration) of dexamethasone (DEX) for 15 min to synchronize the cells/tissues [Balsalobre et al. Science 2000]. MSF cells/liver tissue slices were then washed three times with PBS (37°C) and were incubated in HEPES-buffered Medium

tag: strain background

tag: genotype/variation

tag: tissue

value: mouse liver

tag: timepoint


title: Bmal1-/-3_T12_rep3  [run2_VAL513A21_S21_L001]

description:
run2_VAL513A21_S21_L001
KO3_T12_rep3_FPKM


title: Bmal1-/-2_T12_rep2  [run2_VAL513A20_S20_L001]

description:
run2_VAL513A20_S20_L001
KO2_T12_rep2_FPKM


title: Bmal1-/-2_T24_rep2  [run2_VAL513A23_S23_L001]

description:
run2_VAL513A23_S23_L001
KO2_T24_rep2_FPKM


title: Bmal1-/-1_T24_rep1  [run2_VAL513A22_S22_L001]

description:
run2_VAL513A22_S22_L001
KO1_T24_rep1_FPKM


title: Bmal1-/-3_T06_rep3  [run2_VAL513A18_S18_L001]

description:
run2_VAL513A18_S18_L001
KO3_T06_rep3_FPKM


title: Bmal1-/-2_T06_rep2  [run2_VAL513A17_S17_L001]

description:
run2_VAL513A17_S17_L001
KO2_T06_rep2_FPKM


title: Bmal1-/-1_T06_rep1  [run2_VAL513A16_S16_L001]

description:
run2_VAL513A16_S16_L001
KO1_T06_rep1_FPKM


title: Bmal1-/-1_T12_rep1  [run2_VAL513A19_S19_L001]

description:
run2_VAL513A19_S19_L001
KO1_T12_rep1_FPKM


title: Library-Oligo-Barcode

organism: synthetic construct

source_name: Library-Oligo-Barcode

tag: sample type

value: Oligo-Barcode


title: Bmal1-/-3_T00_rep3  [run2_VAL513A15_S15_L001]

description:
run2_VAL513A15_S15_L001
KO3_T00_rep3_FPKM


title: Bmal1-/-2_T00_rep2  [run2_VAL513A14_S14_L001]

description:
run2_VAL513A14_S14_L001
KO2_T00_rep2_FPKM


title: WT2_T24_rep2  [run2_VAL513A11_S11_L001]

description:
run2_VAL513A11_S11_L001
WT2_T24_rep2_FPKM

value: wild type


title: Bmal1-/-1_T00_rep1  [run2_VAL513A13_S13_L001]

description:
run2_VAL513A13_S13_L001
KO1_T00_rep1_FPKM


title: WT3_T24_rep3  [run2_VAL513A12_S12_L001]

description:
run2_VAL513A12_S12_L001
WT3_T24_rep3_FPKM


title: WT1_T24_rep1  [run2_VAL513A10_S10_L001]

description:
run2_VAL513A10_S10_L001
WT1_T24_rep1_FPKM


title: WT3_T12_rep3  [run2_VAL513A9_S9_L001]

description:
run2_VAL513A9_S9_L001
WT3_T12_rep3_FPKM


title: WT3_T06_rep3  [run2_VAL513A6_S6_L001]

description:
run2_VAL513A6_S6_L001
WT3_T06_rep3_FPKM


title: WT2_T12_rep2  [run2_VAL513A8_S8_L001]

description:
run2_VAL513A8_S8_L001
WT2_T12_rep2_FPKM


title: WT1_T12_rep1  [run2_VAL513A7_S7_L001]

description:
run2_VAL513A7_S7_L001
WT1_T12_rep1_FPKM


title: WT2_T06_rep2  [run2_VAL513A5_S5_L001]

description:
run2_VAL513A5_S5_L001
WT2_T06_rep2_FPKM


title: WT1_T06_rep1  [run2_VAL513A4_S4_L001]

description:
run2_VAL513A4_S4_L001
WT1_T06_rep1_FPKM


title: WT2_T00_rep2  [run2_VAL513A2_S2_L001]

description:
run2_VAL513A2_S2_L001
WT2_T00_rep2_FPKM


title: WT1_T00_rep1  [run2_VAL513A1_S1_L001]

description:
run2_VAL513A1_S1_L001
WT1_T00_rep1_FPKM


title: Bmal1-/-3_T24_rep3 [run1_VAL513A24_S24]

description:
run1_VAL513A24_S24_L00*
KO3_T24_rep3_FPKM


title: Bmal1-/-2_T24_rep2 [run1_VAL513A23_S23]

description:
run1_VAL513A23_S23_L00*
KO2_T24_rep2_FPKM


title: Bmal1-/-3_T12_rep3 [run1_VAL513A21_S21]

description:
run1_VAL513A21_S21_L00*
KO3_T12_rep3_FPKM


title: Bmal1-/-1_T24_rep1 [run1_VAL513A22_S22]

description:
run1_VAL513A22_S22_L00*
KO1_T24_rep1_FPKM


title: Bmal1-/-2_T12_rep2 [run1_VAL513A20_S20]

description:
run1_VAL513A20_S20_L00*
KO2_T12_rep2_FPKM


title: Bmal1-/-1_T12_rep1 [run1_VAL513A19_S19]

description:
run1_VAL513A19_S19_L00*
KO1_T12_rep1_FPKM


title: Bmal1-/-2_T06_rep2 [run1_VAL513A17_S17]

description:
run1_VAL513A17_S17_L00*
KO2_T06_rep2_FPKM


title: Bmal1-/-1_T06_rep1 [run1_VAL513A16_S16]

description:
run1_VAL513A16_S16_L00*
KO1_T06_rep1_FPKM


title: Bmal1-/-3_T06_rep3 [run1_VAL513A18_S18]

description:
run1_VAL513A18_S18_L00*
KO3_T06_rep3_FPKM


title: Bmal1-/-3_T00_rep3 [run1_VAL513A15_S15]

description:
run1_VAL513A15_S15_L00*
KO3_T00_rep3_FPKM


title: WT3_T24_rep3 [run1_VAL513A12_S12]

description:
run1_VAL513A12_S12_L00*
WT3_T24_rep3_FPKM


title: WT2_T24_rep2 [run1_VAL513A11_S11]

description:
run1_VAL513A11_S11_L00*
WT2_T24_rep2_FPKM


title: WT1_T12_rep1 [run1_VAL513A7_S7]

description:
run1_VAL513A7_S7_L00*
WT1_T12_rep1_FPKM


title: WT1_T24_rep1 [run1_VAL513A10_S10]

description:
run1_VAL513A10_S10_L00*
WT1_T24_rep1_FPKM


title: WT3_T00_rep3  [run2_VAL513A3_S3_L001]

description:
run2_VAL513A3_S3_L001
WT3_T00_rep3_FPKM


title: WT3_T06_rep3 [run1_VAL513A6_S6]

description:
run1_VAL513A6_S6_L00*
WT3_T06_rep3_FPKM


title: WT1_T06_rep1 [run1_VAL513A4_S4]

description:
run1_VAL513A4_S4_L00*
WT1_T06_rep1_FPKM


title: WT3_T00_rep3 [run1_VAL513A3_S3]

description:
run1_VAL513A3_S3_L00*
WT3_T00_rep3_FPKM


title: WT2_T00_rep2 [run1_VAL513A2_S2]

description:
run1_VAL513A2_S2_L00*
WT2_T00_rep2_FPKM


title: WT2_T06_rep2 [run1_VAL513A5_S5]

description:
run1_VAL513A5_S5_L00*
WT2_T06_rep2_FPKM


title: Bmal1-/- ex-vivo liver CT69 run2

description:
mRNA_Seq,50bpSE
VAL724A48_S48_L005

source_name: Bmal1-/- ex-vivo liver CT69

value: ex-vivo Liver

tag: age

value: adult

tag: time point


title: Bmal1-/- ex-vivo liver CT66 run3

description:
mRNA_Seq,50bpSE
VAL724A47_S47_L008

source_name: Bmal1-/- ex-vivo liver CT66


title: Bmal1-/- ex-vivo liver CT66 run2

description:
mRNA_Seq,50bpSE
VAL724A47_S47_L005


title: Bmal1-/- ex-vivo liver CT69 run1

description:
mRNA_Seq,50bpSE
VAL724A48_S48_L002


title: Bmal1-/-2_T00_rep2 [run1_VAL513A14_S14]

description:
run1_VAL513A14_S14_L00*
KO2_T00_rep2_FPKM


title: Bmal1-/- ex-vivo liver CT63 run3

description:
mRNA_Seq,50bpSE
VAL724A46_S46_L008

source_name: Bmal1-/- ex-vivo liver CT63


title: Bmal1-/-1_T00_rep1 [run1_VAL513A13_S13]

description:
run1_VAL513A13_S13_L00*
KO1_T00_rep1_FPKM


title: Bmal1-/- ex-vivo liver CT66 run1

description:
mRNA_Seq,50bpSE
VAL724A47_S47_L002


title: 1043_1


title: Bmal1-/- ex-vivo liver CT63 run2

description:
mRNA_Seq,50bpSE
VAL724A46_S46_L005


title: WT2_T12_rep2 [run1_VAL513A8_S8]

description:
run1_VAL513A8_S8_L00*
WT2_T12_rep2_FPKM


title: Bmal1-/- ex-vivo liver CT63 run1

description:
mRNA_Seq,50bpSE
VAL724A46_S46_L002


title: Bmal1-/- ex-vivo liver CT60 run3

description:
mRNA_Seq,50bpSE
VAL724A45_S45_L008

source_name: Bmal1-/- ex-vivo liver CT60


title: WT3_T12_rep3 [run1_VAL513A9_S9]

description:
run1_VAL513A9_S9_L00*
WT3_T12_rep3_FPKM


title: Bmal1-/- ex-vivo liver CT60 run2

description:
mRNA_Seq,50bpSE
VAL724A45_S45_L005


title: Bmal1-/- ex-vivo liver CT60 run1

description:
mRNA_Seq,50bpSE
VAL724A45_S45_L002


title: Bmal1-/- ex-vivo liver CT57 run2

description:
mRNA_Seq,50bpSE
VAL724A44_S44_L005

source_name: Bmal1-/- ex-vivo liver CT57


title: Bmal1-/- ex-vivo liver CT54 run3

description:
mRNA_Seq,50bpSE
VAL724A43_S43_L008

source_name: Bmal1-/- ex-vivo liver CT54


title: Bmal1-/- ex-vivo liver CT57 run1

description:
mRNA_Seq,50bpSE
VAL724A44_S44_L002


title: Bmal1-/- ex-vivo liver CT69 run3

description:
mRNA_Seq,50bpSE
VAL724A48_S48_L008


title: Bmal1-/- ex-vivo liver CT54 run1

description:
mRNA_Seq,50bpSE
VAL724A43_S43_L002


title: Bmal1-/- ex-vivo liver CT51 run3

description:
mRNA_Seq,50bpSE
VAL724A42_S42_L008

source_name: Bmal1-/- ex-vivo liver CT51


title: Bmal1-/- ex-vivo liver CT48 run2

description:
mRNA_Seq,50bpSE
VAL724A41_S41_L005

source_name: Bmal1-/- ex-vivo liver CT48


title: Bmal1-/- ex-vivo liver CT48 run3

description:
mRNA_Seq,50bpSE
VAL724A41_S41_L008


title: WT1_T00_rep1 [run1_VAL513A1_S1]

description:
run1_VAL513A1_S1_L00*
WT1_T00_rep1_FPKM


title: Bmal1-/- ex-vivo liver CT54 run2

description:
mRNA_Seq,50bpSE
VAL724A43_S43_L005


title: Bmal1-/- ex-vivo liver CT51 run2

description:
mRNA_Seq,50bpSE
VAL724A42_S42_L005


title: Bmal1-/- ex-vivo liver CT42 run2

description:
mRNA_Seq,50bpSE
VAL724A39_S39_L005

source_name: Bmal1-/- ex-vivo liver CT42


title: Bmal1-/- ex-vivo liver CT45 run2

description:
mRNA_Seq,50bpSE
VAL724A40_S40_L005

source_name: Bmal1-/- ex-vivo liver CT45


title: Bmal1-/- ex-vivo liver CT57 run3

description:
mRNA_Seq,50bpSE
VAL724A44_S44_L008


title: Bmal1-/- ex-vivo liver CT42 run3

description:
mRNA_Seq,50bpSE
VAL724A39_S39_L008


title: Bmal1-/- ex-vivo liver CT45 run3

description:
mRNA_Seq,50bpSE
VAL724A40_S40_L008


title: Bmal1-/- ex-vivo liver CT48 run1

description:
mRNA_Seq,50bpSE
VAL724A41_S41_L002


title: Bmal1-/- ex-vivo liver CT45 run1

description:
mRNA_Seq,50bpSE
VAL724A40_S40_L002


title: Bmal1-/- ex-vivo liver CT42 run1

description:
mRNA_Seq,50bpSE
VAL724A39_S39_L002


title: Bmal1-/- ex-vivo liver CT39 run1

description:
mRNA_Seq,50bpSE
VAL724A38_S38_L002

source_name: Bmal1-/- ex-vivo liver CT39


title: Bmal1-/- ex-vivo liver CT36 run2

description:
mRNA_Seq,50bpSE
VAL724A37_S37_L005

source_name: Bmal1-/- ex-vivo liver CT36


title: Bmal1-/- ex-vivo liver CT39 run2

description:
mRNA_Seq,50bpSE
VAL724A38_S38_L005


title: Bmal1-/- ex-vivo liver CT39 run3

description:
mRNA_Seq,50bpSE
VAL724A38_S38_L008


title: Bmal1-/- ex-vivo liver CT33 run3

description:
mRNA_Seq,50bpSE
VAL724A36_S36_L008

source_name: Bmal1-/- ex-vivo liver CT33


title: Bmal1-/- ex-vivo liver CT36 run3

description:
mRNA_Seq,50bpSE
VAL724A37_S37_L008


title: Bmal1-/- ex-vivo liver CT51 run1

description:
mRNA_Seq,50bpSE
VAL724A42_S42_L002


title: Bmal1-/- ex-vivo liver CT30 run3

description:
mRNA_Seq,50bpSE
VAL724A35_S35_L008

source_name: Bmal1-/- ex-vivo liver CT30


title: Bmal1-/- ex-vivo liver CT33 run2

description:
mRNA_Seq,50bpSE
VAL724A36_S36_L005


title: Bmal1-/- ex-vivo liver CT36 run1

description:
mRNA_Seq,50bpSE
VAL724A37_S37_L002


title: Bmal1-/- ex-vivo liver CT30 run1

description:
mRNA_Seq,50bpSE
VAL724A35_S35_L002


title: Bmal1-/- ex-vivo liver CT30 run2

description:
mRNA_Seq,50bpSE
VAL724A35_S35_L005


title: Bmal1-/- ex-vivo liver CT27 run2

description:
mRNA_Seq,50bpSE
VAL724A34_S34_L005

source_name: Bmal1-/- ex-vivo liver CT27


title: Bmal1-/- ex-vivo liver CT27 run3

description:
mRNA_Seq,50bpSE
VAL724A34_S34_L008


title: Bmal1-/- ex-vivo liver CT33 run1

description:
mRNA_Seq,50bpSE
VAL724A36_S36_L002


title: Bmal1-/- ex-vivo liver CT24 run2

description:
mRNA_Seq,50bpSE
VAL724A33_S33_L005

source_name: Bmal1-/- ex-vivo liver CT24


title: Bmal1-/- ex-vivo liver CT27 run1

description:
mRNA_Seq,50bpSE
VAL724A34_S34_L002


title: Bmal1-/- ex-vivo liver CT21 run3

description:
mRNA_Seq,50bpSE
VAL724A32_S32_L008

source_name: Bmal1-/- ex-vivo liver CT21


title: Bmal1-/- ex-vivo liver CT24 run3

description:
mRNA_Seq,50bpSE
VAL724A33_S33_L008


title: Bmal1-/- ex-vivo liver CT24 run1

description:
mRNA_Seq,50bpSE
VAL724A33_S33_L002


title: Bmal1-/- ex-vivo liver CT21 run2

description:
mRNA_Seq,50bpSE
VAL724A32_S32_L005


title: Bmal1-/- ex-vivo liver CT15 run3

description:
mRNA_Seq,50bpSE
VAL724A30_S30_L008

source_name: Bmal1-/- ex-vivo liver CT15


title: Bmal1-/- ex-vivo liver CT18 run2

description:
mRNA_Seq,50bpSE
VAL724A31_S31_L005

source_name: Bmal1-/- ex-vivo liver CT18


title: Bmal1-/- ex-vivo liver CT18 run1

description:
mRNA_Seq,50bpSE
VAL724A31_S31_L002


title: Bmal1-/- ex-vivo liver CT15 run2

description:
mRNA_Seq,50bpSE
VAL724A30_S30_L005


title: Bmal1-/- ex-vivo liver CT12 run3

description:
mRNA_Seq,50bpSE
VAL724A29_S29_L008

source_name: Bmal1-/- ex-vivo liver CT12


title: Bmal1-/- ex-vivo liver CT18 run3

description:
mRNA_Seq,50bpSE
VAL724A31_S31_L008


title: Bmal1-/- ex-vivo liver CT12 run2

description:
mRNA_Seq,50bpSE
VAL724A29_S29_L005


title: Bmal1-/- ex-vivo liver CT12 run1

description:
mRNA_Seq,50bpSE
VAL724A29_S29_L002


title: Bmal1-/- ex-vivo liver CT09 run1

description:
mRNA_Seq,50bpSE
VAL724A28_S28_L002

source_name: Bmal1-/- ex-vivo liver CT09


title: Bmal1-/- ex-vivo liver CT09 run3

description:
mRNA_Seq,50bpSE
VAL724A28_S28_L008


title: Bmal1-/- ex-vivo liver CT09 run2

description:
mRNA_Seq,50bpSE
VAL724A28_S28_L005


title: Bmal1-/- ex-vivo liver CT06 run1

description:
mRNA_Seq,50bpSE
VAL724A27_S27_L002

source_name: Bmal1-/- ex-vivo liver CT06


title: Bmal1-/- ex-vivo liver CT06 run3

description:
mRNA_Seq,50bpSE
VAL724A27_S27_L008


title: Bmal1-/- ex-vivo liver CT00 run3

description:
mRNA_Seq,50bpSE
VAL724A25_S25_L008

source_name: Bmal1-/- ex-vivo liver CT00


title: Bmal1-/- ex-vivo liver CT06 run2

description:
mRNA_Seq,50bpSE
VAL724A27_S27_L005


title: Bmal1-/- ex-vivo liver CT03 run3

description:
mRNA_Seq,50bpSE
VAL724A26_S26_L008

source_name: Bmal1-/- ex-vivo liver CT03


title: Bmal1-/- ex-vivo liver CT00 run1

description:
mRNA_Seq,50bpSE
VAL724A25_S25_L002


title: WT ex-vivo liver CT69 run3

description:
mRNA_Seq,50bpSE
VAL724A24_S24_L007

source_name: WT ex-vivo liver CT69


title: Bmal1-/- ex-vivo liver CT03 run1

description:
mRNA_Seq,50bpSE
VAL724A26_S26_L002


title: Bmal1-/- ex-vivo liver CT03 run2

description:
mRNA_Seq,50bpSE
VAL724A26_S26_L005


title: WT ex-vivo liver CT69 run2

description:
mRNA_Seq,50bpSE
VAL724A24_S24_L004


title: Bmal1-/- ex-vivo liver CT00 run2

description:
mRNA_Seq,50bpSE
VAL724A25_S25_L005


title: WT ex-vivo liver CT69 run1

description:
mRNA_Seq,50bpSE
VAL724A24_S24_L001


title: WT ex-vivo liver CT66 run3

description:
mRNA_Seq,50bpSE
VAL724A23_S23_L007

source_name: WT ex-vivo liver CT66


title: 10_7xIR #1

source_name: radiation-treated human glioma stem cells


title: Bmal1-/- ex-vivo liver CT15 run1

description:
mRNA_Seq,50bpSE
VAL724A30_S30_L002


title: Bmal1-/- ex-vivo liver CT21 run1

description:
mRNA_Seq,50bpSE
VAL724A32_S32_L002


title: WT ex-vivo liver CT66 run1

description:
mRNA_Seq,50bpSE
VAL724A23_S23_L001


title: WT ex-vivo liver CT63 run3

description:
mRNA_Seq,50bpSE
VAL724A22_S22_L007

source_name: WT ex-vivo liver CT63


title: WT ex-vivo liver CT63 run2

description:
mRNA_Seq,50bpSE
VAL724A22_S22_L004


title: WT ex-vivo liver CT63 run1

description:
mRNA_Seq,50bpSE
VAL724A22_S22_L001


title: WT ex-vivo liver CT60 run3

description:
mRNA_Seq,50bpSE
VAL724A21_S21_L007

source_name: WT ex-vivo liver CT60


title: WT ex-vivo liver CT57 run3

description:
mRNA_Seq,50bpSE
VAL724A20_S20_L007

source_name: WT ex-vivo liver CT57


title: WT ex-vivo liver CT57 run2

description:
mRNA_Seq,50bpSE
VAL724A20_S20_L004


title: WT ex-vivo liver CT60 run1

description:
mRNA_Seq,50bpSE
VAL724A21_S21_L001


title: WT ex-vivo liver CT54 run3

description:
mRNA_Seq,50bpSE
VAL724A19_S19_L007

source_name: WT ex-vivo liver CT54


title: WT ex-vivo liver CT57 run1

description:
mRNA_Seq,50bpSE
VAL724A20_S20_L001


title: WT ex-vivo liver CT66 run2

description:
mRNA_Seq,50bpSE
VAL724A23_S23_L004


title: WT ex-vivo liver CT54 run1

description:
mRNA_Seq,50bpSE
VAL724A19_S19_L001


title: WT ex-vivo liver CT48 run2

description:
mRNA_Seq,50bpSE
VAL724A17_S17_L004

source_name: WT ex-vivo liver CT48


title: WT ex-vivo liver CT45 run1

description:
mRNA_Seq,50bpSE
VAL724A16_S16_L001

source_name: WT ex-vivo liver CT45


title: WT ex-vivo liver CT48 run1

description:
mRNA_Seq,50bpSE
VAL724A17_S17_L001


title: WT ex-vivo liver CT45 run3

description:
mRNA_Seq,50bpSE
VAL724A16_S16_L007


title: WT ex-vivo liver CT48 run3

description:
mRNA_Seq,50bpSE
VAL724A17_S17_L007


title: WT ex-vivo liver CT42 run1

description:
mRNA_Seq,50bpSE
VAL724A15_S15_L001

source_name: WT ex-vivo liver CT42


title: WT ex-vivo liver CT39 run2

description:
mRNA_Seq,50bpSE
VAL724A14_S14_L004

source_name: WT ex-vivo liver CT39


title: WT ex-vivo liver CT51 run3

description:
mRNA_Seq,50bpSE
VAL724A18_S18_L007

source_name: WT ex-vivo liver CT51


title: WT ex-vivo liver CT51 run1

description:
mRNA_Seq,50bpSE
VAL724A18_S18_L001


title: WT ex-vivo liver CT51 run2

description:
mRNA_Seq,50bpSE
VAL724A18_S18_L004


title: WT ex-vivo liver CT60 run2

description:
mRNA_Seq,50bpSE
VAL724A21_S21_L004


title: WT ex-vivo liver CT39 run1

description:
mRNA_Seq,50bpSE
VAL724A14_S14_L001


title: WT ex-vivo liver CT36 run3

description:
mRNA_Seq,50bpSE
VAL724A13_S13_L007

source_name: WT ex-vivo liver CT36


title: WT ex-vivo liver CT39 run3

description:
mRNA_Seq,50bpSE
VAL724A14_S14_L007


title: WT ex-vivo liver CT42 run2

description:
mRNA_Seq,50bpSE
VAL724A15_S15_L004


title: WT ex-vivo liver CT54 run2

description:
mRNA_Seq,50bpSE
VAL724A19_S19_L004


title: WT ex-vivo liver CT36 run2

description:
mRNA_Seq,50bpSE
VAL724A13_S13_L004


title: WT ex-vivo liver CT36 run1

description:
mRNA_Seq,50bpSE
VAL724A13_S13_L001


title: WT ex-vivo liver CT33 run3

description:
mRNA_Seq,50bpSE
VAL724A12_S12_L007

source_name: WT ex-vivo liver CT33


title: WT ex-vivo liver CT30 run2

description:
mRNA_Seq,50bpSE
VAL724A11_S11_L004

source_name: WT ex-vivo liver CT30


title: WT ex-vivo liver CT30 run1

description:
mRNA_Seq,50bpSE
VAL724A11_S11_L001


title: WT ex-vivo liver CT33 run2

description:
mRNA_Seq,50bpSE
VAL724A12_S12_L004


title: WT ex-vivo liver CT27 run3

description:
mRNA_Seq,50bpSE
VAL724A10_S10_L007

source_name: WT ex-vivo liver CT27


title: WT ex-vivo liver CT33 run1

description:
mRNA_Seq,50bpSE
VAL724A12_S12_L001


title: WT ex-vivo liver CT27 run2

description:
mRNA_Seq,50bpSE
VAL724A10_S10_L004


title: WT ex-vivo liver CT30 run3

description:
mRNA_Seq,50bpSE
VAL724A11_S11_L007


title: WT ex-vivo liver CT45 run2

description:
mRNA_Seq,50bpSE
VAL724A16_S16_L004


title: WT ex-vivo liver CT42 run3

description:
mRNA_Seq,50bpSE
VAL724A15_S15_L007


title: WT ex-vivo liver CT24 run3

description:
mRNA_Seq,50bpSE
VAL724A9_S9_L007

source_name: WT ex-vivo liver CT24


title: WT ex-vivo liver CT27 run1

description:
mRNA_Seq,50bpSE
VAL724A10_S10_L001


title: WT ex-vivo liver CT21 run3

description:
mRNA_Seq,50bpSE
VAL724A8_S8_L007

source_name: WT ex-vivo liver CT21


title: WT ex-vivo liver CT18 run3

description:
mRNA_Seq,50bpSE
VAL724A7_S7_L007

source_name: WT ex-vivo liver CT18


title: WT ex-vivo liver CT21 run1

description:
mRNA_Seq,50bpSE
VAL724A8_S8_L001


title: WT ex-vivo liver CT21 run2

description:
mRNA_Seq,50bpSE
VAL724A8_S8_L004


title: WT ex-vivo liver CT18 run2

description:
mRNA_Seq,50bpSE
VAL724A7_S7_L004


title: WT ex-vivo liver CT18 run1

description:
mRNA_Seq,50bpSE
VAL724A7_S7_L001


title: WT ex-vivo liver CT15 run3

description:
mRNA_Seq,50bpSE
VAL724A6_S6_L007

source_name: WT ex-vivo liver CT15


title: WT ex-vivo liver CT15 run2

description:
mRNA_Seq,50bpSE
VAL724A6_S6_L004


title: WT ex-vivo liver CT12 run1

description:
mRNA_Seq,50bpSE
VAL724A5_S5_L001

source_name: WT ex-vivo liver CT12


title: WT ex-vivo liver CT09 run3

description:
mRNA_Seq,50bpSE
VAL724A4_S4_L007

source_name: WT ex-vivo liver CT09


title: WT ex-vivo liver CT12 run3

description:
mRNA_Seq,50bpSE
VAL724A5_S5_L007


title: WT ex-vivo liver CT12 run2

description:
mRNA_Seq,50bpSE
VAL724A5_S5_L004


title: WT ex-vivo liver CT15 run1

description:
mRNA_Seq,50bpSE
VAL724A6_S6_L001


title: WT ex-vivo liver CT09 run2

description:
mRNA_Seq,50bpSE
VAL724A4_S4_L004


title: WT ex-vivo liver CT09 run1

description:
mRNA_Seq,50bpSE
VAL724A4_S4_L001


title: WT ex-vivo liver CT06 run3

description:
mRNA_Seq,50bpSE
VAL724A3_S3_L007

source_name: WT ex-vivo liver CT06


title: WT ex-vivo liver CT00 run2

description:
mRNA_Seq,50bpSE
VAL724A1_S1_L004

source_name: WT ex-vivo liver CT00


title: WT ex-vivo liver CT00 run1

description:
mRNA_Seq,50bpSE
VAL724A1_S1_L001


title: WT ex-vivo liver CT24 run2

description:
mRNA_Seq,50bpSE
VAL724A9_S9_L004


title: WT ex-vivo liver CT24 run1

description:
mRNA_Seq,50bpSE
VAL724A9_S9_L001


title: Sample_16_N5B

status: Public on Jan 07 2020

city: Cardiff

first: Caleb

last: Webber

address: Hadyn Ellis Building, Maindy road

department: School of Medicine

country: United Kingdom

institute: Cardiff University

data_processing:
Paired end Fastq files for the human samples each had read 1( R1) of length 26 bp and Read 2 (R2) 98 bp
Sequencing reads were aligned against the GRCh38_premrna build for SN and cortex samples using 10x Cell Ranger v2.1
Digital gene expression matrices (with gene expression counts) for detected cell associated barcodes and unique molecular identifiers (UMIs) were generated by Cell Ranger software (v2.1 for SN  and cortex samples)
Digital gene expression matrices were analyzed for cell type clustering and identification for all SN and cortex samples using Seurat (v2.3.4)
Genome_build: GRCh38_premrna
Supplementary_files_format_and_content: digital gene expression matrix (sparse format): matrix market format, rows = genes/transcripts, columns = barcodes/cells ; barcodes list: names of barcodes/cells for corresponding DGE matrix file;genes list: names of transcripts/genes for corresponding DGE matrix file for each cortex and SN sample

molecule: polyA RNA

source_name: Brain

extract_protocol:
Briefly, 3mm2 pieces of fresh-frozen brain tissue were placed in homogenization buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris Buffer pH 8.0, 1 mM DTT, 1X protease inhibitor, 0.4 U ul-1 RNaseIN, 0.2 U ul-1 Superasin, 0.1% v/v Triton X-100) for 10 minutes prior to mechanical disruption with a dounce homogenizer.  Homogenate was filtered through a 35 mM cell strainer before concentrating nuclei by centrifugation 400 g 5 minutes.  Nuclei were resuspended in FACS buffer (1 XPBS, 1 RNase-Free BSA, 0.2 U μl−1 of RNasin Plus RNase inhibitor, 10 ng ml-1 Hoechst 33342) prior to FACS to obtain a population of nuclei free cellular debris.Nuclei were washed once in PBS and resuspended in 0.04% BSA in PBS for loading on the 10x Chromium 3’ chip.
Cell capturing  and library preparation was carried as per kit instructions (Chromium Single Cell Kit [v2 chemistry])

value: Brain

tag: tissue region

value: Substantia nigra

tag: gender

value: Female

tag: batch

value: Day 2

tag: post-mortem-interval(hours)


title: H3-HA_TBP-AA_T0 (rep1)

status: Public on Jan 09 2020

city: Geneva

first: Julien

last: Soudet

address: 30 quai Ansermet

department: BICEL

country: Switzerland

institute: Université de Genève

description: single-end 100bp

data_processing:
Sequence data was aligned to SacCer3 via bowtie2 with default settings. To visualize occupancy on the genome browser, Homer’s makeTagDirectory and makeUCSCfile codes were used to generate bigWig files, which were each normalized to 10 million. The cross correlation of Watson and Crick reads was used to infer the average fragment length, and reads were extended by this value.
Genome_build: saccer3
Supplementary_files_format_and_content: bigwig files of H3, H3-HA densities and ratios of H3-HA over H3

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown overnight at 30°C  to a density at OD600 nm of 0.5–0.7 in Casamino acid medium supplemented with 2% raffinose and 0.1% glucose and lacking adenine, tryptophan and/or uracil for plasmid selection.

extract_protocol:
A detailed protocol for ChIP can be found at http://www.mimo.unige.ch/STRUBIN_LABb.htm. ChIP-Seq was performed using chromatin prepared from about 2 × 109 yeast cells (10-fold more than for conventional ChIP). Immunoprecipitation was with 20 μl anti-HA antibodies (16B12, Covance) or 10 μl anti-H3 antibodies (1791, Abcam).
After de-crosslinking and DNA purification, samples were treated with RNaseA (20 mg/mL, Sigma) for 1 hour at 37⁰C in 1x NEB buffer 2 followed by a 45 minute Calf Intestinal Phosphatase (NEB) treatment. DNA was extracted with phenol:chloroform:isoamyl alcohol and ethanol precipitated with GlycoBlue. DNA ends were polished with END-it (Epicentre) at room temperature for 1 hour. AMPure XP beads (Beckman-Coultier) were used to perform a double size selection, first adding 0.5x beads to deplete longer fragments from the supernatant which was then applied to 1.3x more beads to size select upwards of 100bp. A-tailing was performed on the beads with Klenow exo- polymerase (Epicentre). Clean-up was performed with the addition of 1.8x ABR buffer (15% PEG, 2.5 M NaCl) to the beads, which were then washed with 70% ethanol. DNA ligation (FastLink, Epicentre) to NEXTFlex (Bioo Scientific) multiplexed adapters was performed on the beads. Clean-up was performed as above with the exception of an additional ethanol wash and elution of the DNA from the beads with 39 mL water. Test 18 and 20 cycle PCR reactions were performed with 10 mL each, with a view to reduce the number of amplification cycles. The remainder of the ligated material was PCR amplified under optimum conditions. Amplified material was cleaned-up with AMPure beads as above. StrataClone was used to check the quality of the libraries. Samples were mixed in equimolar amounts (determined by KAPA Library Quantitation) and submitted to the UMass Deep Sequencing Core for HiSeq 100SR with multiplex indexing.

treatment_protocol: Cells were  arrested in G1 by treatment with 600 ng/mL alpha-factor (Primm srl, Italy) for 3 hr. Expression of H3HA was induced at T0 (min) by directly adding galactose to a final concentration of 2% . Where indicated, rapamycin (LC laboratories) was added at the same time to a final concentration of 4 ug/ml to induce nuclear depletion of TBP-FRB.  Glucose (0.5% final) was added to the control cultures (without rapamycin) to limit the induction of H3HA.

tag: genetic background

value: HHY154 genetic background

tag: genotype

tag: cell cycle phase


title: H3-HA_TBP-AA_T30 (rep1)

description: single-end 100bp


title: H3_TBP-AA_T0 (rep1)

description: single-end 100bp


title: H3_Control_T30 (rep1)

description: single-end 100bp


title: H3-HA_Control_T0 (rep1)

description: single-end 100bp


title: H3_TBP-AA_T30 (rep1)

description: single-end 100bp


title: WT ex-vivo liver CT03 run2

description:
mRNA_Seq,50bpSE
VAL724A2_S2_L004

source_name: WT ex-vivo liver CT03


title: WT ex-vivo liver CT00 run3

description:
mRNA_Seq,50bpSE
VAL724A1_S1_L007


title: WT ex-vivo liver CT03 run1

description:
mRNA_Seq,50bpSE
VAL724A2_S2_L001


title: CTCF ChIP - WT

status: Public on Jan 06 2020

city: Amsterdam

first: Angela

last: Sedeno Cacciatore

state: Noord-Holland

address: Plesmanlaan 121

department: Gene regulation

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Reads were trimmed using TrimGalore (Martin, 2011).
Reads were mapped to hg19 using Bowtie2.1.0 (Langmead and Salzberg, 2012) with default settings.
Peak calling was performed using MACS2 (Feng et al., 2012) with default options.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak

source_name: WT

growth_protocol: HAP1 cells (Carette et al., 2011) were cultured in IMDM (Invitrogen) supplemented with 10% FCS (Clontech), 1% Penicillin-Streptomycin (Invitrogen) and 0.5% Ultraglutamin (Lonza).

extract_protocol:
Cells were fixed in 1% formaldehyde; 50mM Hepes-KOH; 100mM NaCl; 1 mM EDTA; 0,5 mM EGTA. Cell lysis was performed in LB1 buffer with final pH 7,5 (50 mM Hepes-KOH; 140mM NaCl; 1mM EDTA, 10% Glycerol, 0.5% NP-40; 0,25% Triton X-100; Proteinase inhibitor) for 20 minutes at 4°C. Subsequently, nuclei were lysed using LB2, pH 8,0 (10mM Tris-HCl; 200 mM NaCl; 1mM EDTA; 0,5mM EGTA; Proteinase inhibitor) for 10 minutes at 4°C. Pellets were resuspended in LB3 pH8,0 (10mM Tris-HCl; 100mM NaCl; 1 mM EDTA; 0,5 mM EGTA; 0.1% Na-Deoxycholate; 0.5% N-lauroylsarcosine; Proteinase inhibitor). Cross-linked chromatin was sheared (400-800 bp) using a Covaris S2 with Tube and Caps (Covaris, 520048), using the following settings: duty cycle: 10%, intensity: 4, cycles per burst: 200 time 40 seconds with 20 cycles. Chromatin precipitation was performed overnight using antibody-bound (CTCF 5 μl, SMC1 10 μl  per IP) proteinA coupled DynaBeads (Invitrogen). Elution and decrosslinking was performed overnight at 65°C in EB pH 8,0 (50mM Tris-HCl; 10mM EDTA; 1% SDS). Samples were treated with Proteinase K and RNAseA for 2 hours. DNA was isolated using phenol extraction and ethanol precipitation.
Library preparation was done using a KAPA Library preparation kit using the manufacturer’s protocol.

treatment_protocol: gRNA targeting exon 1 of CTCF were designed and annealed into pX330 (primer: 5’- CGATTTTGAGGAAGAACAGC-3’). To modify the targeted locus we co-transfected a 120 basepair repair oligo containing the desired mutation and a silent mutation (repair oligo: 5’ – CCAAAAAGAGCAAACTGCGTTATACAGAGGAGGGCAAAGATGTAGATGTGTCTGTCGCCGATGCTGAAGAAGAACAGCAGGAGGGTCTGCTATCAGAGGTTAATGCAGAGAAAGTGGTTG-3’). pBabePuro was co-transfected in a 10:1 ratio to the pX330. Transfected clones were selected using 2 µg/µl puromycin for 2 days. gDNA of clones was isolated and send for Sanger sequencing to check for the desired mutation.

tag: cell line

value: Wild-Type

tag: replicate

tag: chip antibody

value: CTCF (Cell Signaling 3418S)


title: SCC1 ChIP - CTCF Y226A, F228A

source_name: CTCF Y226A, F228A

value: CTCF Y226A, F228A

value: SCC1 (Abcam ab992)


title: WT ex-vivo liver CT06 run2

description:
mRNA_Seq,50bpSE
VAL724A3_S3_L004

tag: strain background


title: WT ex-vivo liver CT03 run3

description:
mRNA_Seq,50bpSE
VAL724A2_S2_L007


title: CK-EL38-C

status: Public on Nov 25 2019

city: Beijing

first: Run-Ze

last: Sun

address: No.20 Nanxincun, Xiangshan, Haidian District

department: Institute of Botany

country: China

institute: Chinese Academy of Sciences

data_processing:
Bowtie2 v2.2.5 was used to map clean reads to reference, allowing no more than two nucleotides mismatched.
Level of gene expression was calculated using the FPKM (expected fragments per kilobase of transcript per million fragments mapped) method.
Genome_build: Vitis vinifera  (PN40024) genome V2 download from Grape Genome Database (CRIBI)
Supplementary_files_format_and_content: excel file (.xlsx) include FPKM values for each sample

organism: Vitis vinifera

source_name: grape berries

growth_protocol: The own-rooted vines in this vineyard were planted in 2000, arranged in north–south rows with 2.5 m × 1 m vine spacing and equipped with a furrow irrigated system, spur-pruned (15 nodes per linear metre) and trained to a modified Vertical-Shoot-Positioned (M-VSP) trellis system. Nutrition and pest managements were carried out according to industry standards for this cultivar and the region as described previously.

extract_protocol:
A sub-sample of 50 berries were randomly selected from each biological replicate for RNA extraction. Total RNAs for RNA-seq analysis were isolated from frozen deseeded berries using a Plant Total RNA Extraction Kit (Sigma, St. Louis, MO, USA), and further purified by DNase I (Promega, Madison, WI, USA) digestion. RNA integrity and concentration were analyzed using the Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE, USA) and the Aglient 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).
cDNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For cluster bagging treatment, an individual cluster was placed into a two-layer kraft paper bags (36 × 36 cm), yellow exterior layer with the black interior layer coated with wax), with a bent straw to keep ventilation inside the bag. Each treatment was arranged in a completely randomized experimental design with three biological replicates. In each biological replicate, treatments were applied to 15 vines randomly selected from both south and north sites of the vineyard.

tag: cultivar

value: Cabernet Sauvignon

value: berries

tag: developmental stage

tag: treatment

value: CK


title: WT ex-vivo liver CT06 run1

description:
mRNA_Seq,50bpSE
VAL724A3_S3_L001

tag: tissue


title: SCC1 ChIP - WT


title: CK-EL36-B


title: H3-HA_Control_T30 (rep1)

description: single-end 100bp


title: CK-EL37-A


title: CK-EL37-B


title: CK-EL36-C


title: CK-EL37-C


title: CK-EL38-A


title: CK-EL38-B


title: H3_Control_T0 (rep1)

description: single-end 100bp


title: CTCF ChIP - CTCF Y226A, F228A


title: CK-EL36-A


title: SB_80_MBON-γ1pedc>α/β_MB112C_nlsGFP _F_Hand_348-cells

status: Public on Nov 05 2019

city: Ashburn

first: Yoshinori

last: Aso

state: Virginia

address: 19700 Helix Drive

institute: Janelia Research Campus, Howard Hughes Medical Institute

data_processing:
The libraries were pooled and sequenced on an Illumina NextSeq 550 with 75 base pair reads.
Sequencing adapters were trimmed from the reads with Cutadapt v2.1.0 (Martin, 2011) prior to alignment with STAR v2.7.5c (Dobin et al., 2013) to the Drosophila r6.34 genome assembly on Flybase (Thurmond et al., 2019).
The resulting transcript alignments were passed to RSEM v1.3.0 (B. Li & Dewey, 2011) to generate gene expression counts.
Genome_build: Drosophila melanogaster r6.34 genome assembly on Flybase (Thurmond et al., 2019).
Supplementary_files_format_and_content: single Microsoft Excel file that includes TPM values for each sample and splicing isoform

organism: Drosophila melanogaster

growth_protocol: Drosophila adults were collected daily as they eclosed, and aged 3-5 days prior to dissection.

extract_protocol:
For each sample, 60-100 brains were dissected in freshly prepared, ice cold Adult Hemolymph Solution (AHS; 108 mM NaCl, 5 mM KCl, 2 mM CaCl2, 8.2 mM MgCl2, 4 mM NaHCO3, 1 mM NaH2PO4, 5 mM HEPES, 6 mM Trehalose, 10 mM Sucrose), and the major tracheal branches removed. The brains were transferred to an 1.5 ml Eppendorf tube containing 500 microliters 1 mg/ml Liberase DH (Roche, prepared according to the manufacturer’s recommendation) in AHS, and digested for 1 h at room temperature. The Liberase solution was removed and the brains washed three times with ice cold AHS. The final wash was removed completely and 400 microliters of AHS+2% Fetal Bovine Serum (FBS, Sigma) were added. The brain samples were gently triturated with a series of fire-polished, FBS-coated Pasteur pipettes of descending pore sizes until the tissue was homogenized, after which the tube was allowed to stand for 2-3 min so that the larger debris could settle.  For hand sorting, the cell suspension was transferred to a Sylgard-lined Glass Bottom Dish (Willco Wells), leaving the debris at the bottom of the Eppendorf tube, and distributed evenly in a rectangular area in the center of the plate with the pipet tip. The cells were allowed to settle for 10-30 min prior to picking. Fluorescent cells were picked with a mouth aspirator consisting of a 0.8 mm Nalgene Syringe Filter (Thermo), a short stretch of tubing, a plastic needle holder, and a pulled Kwik-Fil Borosilicate Glass capillary (Fisher). Cells picked off the primary plate were transferred to a Sylgard-lined 35 mm Mat Tek Glass Bottom Microwell Dishes (Mat Tek) filled with 170 microliters AHS+2%FBS, allowed to settle, and then re-picked. Three washes were performed in this way before the purified cells were picked and transferred into 50 microliters buffer XB from the PicoPure RNA Isolation Kit (Life Technologies), lysed for 5 m at 42 ˚C, and stored at -80 ˚C.  For FACS sorting, the cell suspension was passed through a Falcon 5 ml round-bottom tube fitted with a 35 micrometer cell strainer cap (Fisher), and sorted on a Becton Dickson FACSAria II cell sorter, gated for single cells with a fluorescence intensity exceeding that of a non-fluorescent control. Positive events were sorted directly into 50 microliters PicoPure XB buffer, the sample lysed for 5 m at 42 ˚C, and stored at -80 ˚C.
Total RNA was extracted from 100-500 pooled cells using the PicoPure kit (Life Technologies) according to the manufacturer’s recommendation, including the on-column DNAse step. The extracted RNA was converted to cDNA and amplified with the Ovation RNA-Seq System V2 (NuGEN), and the yield quantified by NanoDrop (Thermo). The cDNA was fragmented and the sequencing adaptors ligated onto the fragments using the Ovation Rapid Library System (NuGEN). Library quality and concentration was determined with the Kapa Illumina Library Quantification Kit (KK4854, Kapa Biosystems),

tag: genetic driver

tag: reporter

value: nlsGFP

tag: Sex

tag: sorting

value: Hand

tag: number of sorted cells

value: 348 cells


title: 15_12_3_MBON-α1_MB310C_unc84-GFP_F_Hand_184-cells

value: 184 cells


title: SB_81_MBON-γ1pedc>α/β_MB112C_nlsGFP _F_Hand_352-cells

value: 352 cells


title: 14_10_3_MBON-α3_G239_nlsGFP _F_Hand_251-cells

value: 251 cells


title: 14_10_6_MBON-β1>α_MB433B_nlstdTomato_F_Hand_279-cells

value: nlstdTomato

value: 279 cells


title: SB_79_MBON-γ1pedc>α/β_MB112C_nlsGFP _F_Hand_350-cells

value: Female

value: 350 cells


title: 15_12_4_PAM-γ4<γ1γ2_MB312C_nlstdTomato_F_Hand_378-cells

source_name: PAM-γ4<γ1γ2 and  PAM-γ4 dopaminergic neurons

value: 378 cells


title: 14_10_5_PAM-α1_MB043C_nlstdTomato_F_Hand_1048-cells

source_name: PAM-α1 dopaminergic neurons

value: 1048 cells


title: 14_10_4_PMA-β1, PAM-β2_MB213B_nlstdTomato_F_Hand_1048-cells

source_name: PMA-β1, PAM-β2 dopaminergic neurons


title: 15_10_8_PAM-γ5_MB315C_nlstdTomato_F_Hand_266-cells

source_name: PAM-γ5 dopaminergic neurons

value: 266 cells


title: 16_9_8_PAM-β′2a_MB109B_nlstdTomato_F_Hand_274-cells

source_name: PAM-β′2a dopaminergic neurons

value: 274 cells


title: 15_10_5_PPL1-α′2α2_MB058B_nlstdTomato_F_Hand_284-cells

source_name: PPL1-α′2α2 dopaminergic neurons

value: 284 cells


title: 16_9_7_PPL1-α′2α2_MB058B_nlstdTomato_F_Hand_284-cells


title: 15_10_6_PAM-γ3_MB441B_nlstdTomato_F_Hand_280-cells

source_name: PAM-γ3 dopaminergic neurons

value: 280 cells


title: AdjacentNormalStroma_patient8 [Stroma_8N]

status: Public on Feb 03 2020

first: Rongfang

last: Shen

address: No. 17 South Panjiayuan, Chaoyang District

department: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

hyb_protocol: 0.72 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 30ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 30ul of 2x Agilent GE hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Hmn GE 8×60K V2 Microarrays (G4851B) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute twice at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately.

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

data_processing: Background correction with normexp method and normalization with quantile method in  R package limma were applied to process raw data.Probes indicated by the ControlType column and expression less than one arrays above background were filtered.

source_name: Adjacent normal tissue, more than 5 cm away from tumor

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the LowInput QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Fresh tissues were cleaned with normal saline solution and frozen at 80°C within 30 min after  surgical resection before RNA preparation.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen, MD, USA). The RNA was quantified using an ND-1000 UV-VIS Spectrophotometer (NanoDrop Technologies, DE, USA), and its integrity was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). An RNA with integrity number (RIN) greater than 7.0 was used in this study.

treatment_protocol: Stroma compartment of cancer and adjacent normal samples were obtained by microdissection. All colorectal tissue tissues were embedded in OCT (Thermo Fisher) and cut into slices in freezing microtome, each slice with a diameter of 10 μm, then laying freezing tissue slices in hematoxylin for 25 seconds. Next, stroma tissues were isolated with a needle under microscope and collected with Eppendorf tubes.

tag: subject status

value: rectal cancer

tag: gender

value: male

tag: age

tag: tissue type

value: adjacent normal tissue

tag: family history

value: no

tag: blood vessel invasion

tag: nerve invasion

tag: adjuvant chemotherapy

value: yes

tag: chemotherapy regimens

value: XELOX

tag: adjuvant radiotherapy


title: 20_12_2_MB-DPM_SS01240_nlstdTomato__Hand_123-cells

source_name: MB-DPM

value: Hand

value: 123 cells


title: 21_1_1_MBON-α′3_MB027B_nlstdTomato_F_FACS_315-cells

value: nlstdTomato

value: FACS

value: 315 cells


title: 21_1_3_MBON-α′3_MB027B_nlstdTomato_F_FACS_285-cells

value: Female

value: 285 cells


title: 21_1_6_MBON-γ5β′2a_SS01308_nlstdTomato_F_FACS_297-cells

value: 297 cells


title: 20_12_1_MB-DPM_SS01240_nlstdTomato__Hand_130-cells

value: 130 cells


title: 15_12_6_PPL1-γ1pedc_SS01248_nlstdTomato_F_Hand_396-cells

source_name: PPL1-γ1pedc dopaminergic neurons

value: 396 cells


title: AdjacentNormalStroma_patient4 [Stroma_4N]

value: female


title: 19_4_2_PMA-β1, PAM-β2_MB213B_nlstdTomato_F_Hand_381-cells

value: 381 cells


title: AdjacentNormalStroma_patient6 [Stroma_6N]

value: colon cancer


title: 19_4_4_PAM-α1_MB043C_nlstdTomato_F_Hand_385-cells

value: 385 cells


title: 15_10_7_PPL1-α3_SS01399_mCD8::GFP_F_Hand_252-cells

source_name: PPL1-α3 dopaminergic neurons

value: 252 cells


title: 15_12_5_PAM-β′2a_MB109B_nlstdTomato_F_Hand_442-cells

value: 442 cells


title: 19_9_6_PAM-γ3_MB441B_nlstdTomato_F_FACS_570-cells

value: 570 cells


title: 19_9_4_PAM-γ4<γ1γ2_MB312C_nlstdTomato_F_FACS_629-cells

value: 629 cells


title: 19_9_5_PAM-γ3_MB441B_nlstdTomato_F_FACS_600-cells

value: 600 cells


title: 19_4_3_PAM-β′2a_MB109B_nlstdTomato_F_Hand_405-cells

value: nlstdTomato

value: Hand

value: 405 cells


title: 19_4_5_PPL1-α3_SS01399_mCD8::GFP_F_FACS_462-cells

value: Female

value: FACS

value: 462 cells


title: 19_9_3_PAM-γ4<γ1γ2_MB312C_nlstdTomato_F_FACS_703-cells

value: 703 cells


title: 19_4_8_PPL1-γ2 α′1_MB296B_unc84-GFP_F_Hand_279-cells

source_name: PPL1-γ2 α′1 dopaminergic neurons

value: 279 cells


title: 19_4_7_PPL1-γ2 α′1_MB296B_unc84-GFP_F_Hand_285-cells

value: 285 cells


title: 21_1_5_MBON-γ5β′2a_SS01308_nlstdTomato_F_FACS_183-cells

value: 183 cells


title: 19_4_1_PAM-γ5_MB315C_nlstdTomato_F_Hand_390-cells

value: 390 cells


title: 21_1_4_MBON-γ5β′2a_SS01308_nlstdTomato_F_FACS_174-cells

value: 174 cells


title: 20_1_6_KC-α/β_MB008C_nlstdTomato_F_FACS_2500-cells

source_name: KC-α/β

value: 2500 cells


title: 19_5_1_PPL1-γ2 α′1_MB296B_unc84-GFP_F_FACS_289-cells

value: 289 cells


title: 19_9_2_PAM-γ5_MB315C_nlstdTomato_F_Hand_766-cells

value: 766 cells


title: 20_1_5_KC-α/β_MB008C_nlstdTomato_F_FACS_2500-cells


title: 19_9_1_PAM-γ5_MB315C_nlstdTomato_F_Hand_722-cells

value: 722 cells


title: 20_1_4_KC-α/β_MB008C_nlstdTomato_F_FACS_2500-cells


title: 21_1_2_MBON-α′3_MB027B_nlstdTomato_F_FACS_308-cells

value: 308 cells


title: 19_4_6_PPL1-γ1pedc_SS01248_mCD8::GFP_F_Hand_358-cells

value: 358 cells


title: 20_11_5_KC-α′/β′_MB005C_nlstdTomato_F_FACS_1000-cells

source_name: KC-α′/β′

value: nlstdTomato

value: 1000 cells


title: 20_11_4_KC-α′/β′_MB005C_nlstdTomato_F_FACS_1000-cells

value: Female


title: 20_1_3_KC-γ_MB623C_nlstdTomato_F_FACS_2500-cells

source_name: KC-γ

value: FACS


title: 20_11_3_KC-α′/β′_MB005C_nlstdTomato_F_FACS_1000-cells


title: 20_11_2_KC-α′/β′_MB005C_nlstdTomato_F_FACS_1000-cells


title: 20_1_1_KC-γ_MB623C_nlstdTomato_F_FACS_2500-cells


title: YoshiWGB_5_MB-APL_NP2631-GH146-flp_mCD8::GFP__Hand_36-cells

source_name: MB-APL

value: Hand

value: 36 cells


title: YoshiWGB_4_MB-APL_NP2631-GH146-flp_mCD8::GFP__Hand_25-cells

value: 25 cells


title: YoshiWGB_3_MB-APL_NP2631-GH146-flp_mCD8::GFP__Hand_28-cells

value: 28 cells


title: YoshiWGB_2_MB-APL_NP2631-GH146-flp_mCD8::GFP__Hand_20-cells

value: 20 cells


title: YoshiWGB_1_MB-APL_NP2631-GH146-flp_mCD8::GFP__Hnad_28-cells

value: Hnad


title: T4/T5 48h APF

city: Los Angeles

first: Yerbol

middle: Z.

last: Kurmangaliyev

state: CA

address: 675 Charles E. Young Drive South

institute: University of California, Los Angeles

data_processing:
Raw Illumina base call files (*.bcl files) were converted into fastq files using bcl2fastq (--use-bases-mask=Y26n*,I8n*,Y100n*)
Fastq files were processed using Cell Ranger (2.2.0) pipeline using default parameters.
Reference transcriptome package for Cell Ranger was generated using Drosophila melanogaster genome sequence and gene annotations from FlyBase (release 6.22).
Single-cell data analysis was performed using Seurat package (2.3.4). Cluster assignments are listed in clust48.txt and clust24.txt files.
Genome_build: FlyBase 6.22
Supplementary_files_format_and_content: cellranger count output files (MEX format); cluster assignments (tsv format)

source_name: Optic Lobe

extract_protocol:
FACS-sorted single-cell suspension was captured using 10X Chromium platform
Single-cell RNA-Seq libraries were generated using Chromium Single Cell Reagent Kit V2 according to the manufacturer's protocol, with 12 cycles of PCR for cDNA amplification.
Single-cell RNA-Seq

tag: cell type

value: T4/T5 neurons

value: 48h APF


title: T4/T5 24h APF

value: 24h APF


title: TotalRNA_Control_rep3

status: Public on Oct 09 2019

city: Glasgow

first: Sarah

middle: Louise

last: Gillen

address: Beatson Institute, Garscube Estate, Switchback Road, Bearsden

institute: Beatson Institute for Cancer Research

data_processing:
cutadapt (v1.16) to remove adapter sequence
deduplication of UMIs with cd-hit-dup
alignment to rRNA fasta file with bowtie (v1.1.2)
alignment to transcriptome with bowtie (v1.1.2)
get counts of RPF start positions with python script
RPF counts at each nt normalised for mRNA abundance (TPM of Total RNA)
Genome_build: hg19
Supplementary_files_format_and_content: csv file of ribosome occupancy at each codon (P-site alignment to first nt of codon) for the most abundant transcript per gene (as identified from the RNA-seq).  Ribosome Protected Fragments (RPFs) filtered for 28-30nt in length and in-frame. P-site offset has been applied and the columns for the 5'UTR, CDS and 3'UTR contain comma separated values per nt for number of RPF P-sites aligning at each position. These have been normalised for mRNA abundance (TPM) and are the mean of three are the mean of three biological replicates
Total RNA samples
cutadapt to remove adapter sequence
deduplication of UMIs with cd-hit-dup
alignment to genome with tophat2 (v2.1.1)
HTseq (v0.9.1) used for counts
Genome_build: hg19
Supplementary_files_format_and_content: Translational_Efficiency.csv contains translational efficiency measures for the ribosome profiling.  RPF reads 28-30nt in length located +45nt into the CDS and -15nt from the stop codon (to remove any bias due to cycloheximide usage) were divided by the Total RNA levels to account for abundance (TPM) to calculate translational efficiency.

source_name: HEK293 cells

growth_protocol: HEK293 cells grown in DMEM with 10% FBS and 2mM L-glutamine

extract_protocol:
Cells were lysed with 400ul lysis buffer (20mM Tris-Cl pH 7.4, 150mM NaCl, 5mM MgCl2, 1mM DTT and 100ug/ml CHX, 25U/ml Turbo DNase, 1% Triton X100), 50ul lysate taken for total RNA and the rest digested with RNase I and ran on a sucrose cushion to produce the RPF sample
All samples were rRNA depleted using Illumina RiboZero Gold; libraries for Ribo-Seq were prepared with Nextflex small RNA-seq; libraries for RNA-Seq were prepared with Nextflex rapid directional qRNA-seq

tag: sirna treatment

value: Control siRNA

tag: cell line


title: RPF_Control_rep3

data_processing:
Library strategy: Ribo-Seq
cutadapt (v1.16) to remove adapter sequence
deduplication of UMIs with cd-hit-dup
alignment to rRNA fasta file with bowtie (v1.1.2)
alignment to transcriptome with bowtie (v1.1.2)
get counts of RPF start positions with python script
RPF counts at each nt normalised for mRNA abundance (TPM of Total RNA)
Genome_build: hg19
Supplementary_files_format_and_content: csv file of ribosome occupancy at each codon (P-site alignment to first nt of codon) for the most abundant transcript per gene (as identified from the RNA-seq).  Ribosome Protected Fragments (RPFs) filtered for 28-30nt in length and in-frame. P-site offset has been applied and the columns for the 5'UTR, CDS and 3'UTR contain comma separated values per nt for number of RPF P-sites aligning at each position. These have been normalised for mRNA abundance (TPM) and are the mean of three are the mean of three biological replicates
Total RNA samples
cutadapt to remove adapter sequence
deduplication of UMIs with cd-hit-dup
alignment to genome with tophat2 (v2.1.1)
HTseq (v0.9.1) used for counts
Genome_build: hg19
Supplementary_files_format_and_content: Translational_Efficiency.csv contains translational efficiency measures for the ribosome profiling.  RPF reads 28-30nt in length located +45nt into the CDS and -15nt from the stop codon (to remove any bias due to cycloheximide usage) were divided by the Total RNA levels to account for abundance (TPM) to calculate translational efficiency.


title: RPF_Control_rep1


title: TotalRNA_Control_rep1


title: RPF_Control_rep2


title: 20_1_2_KC-γ_MB623C_nlstdTomato_F_FACS_2500-cells

tag: genetic driver

tag: reporter

value: 2500 cells


title: TotalRNA_Control_rep2


title: GP_228

status: Public on May 26 2019

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

country: France

institute: ICO (Integrated Center of Oncology Nantes)

description: Triple-negative breast cancer tumours

hyb_protocol: Double-stranded complementary DNA (cDNA) and labeled complementary RNA (cRNA) were synthesized from the total RNA and hybridized to the Affymetrix Human U133 Plus 2 gene chips (Affymetrix, Santa Clara, CA).

scan_protocol: The chips were further processed and scanned according to the manufacturer’s protocol using the GeneChip Scanner 3000 7G.

data_processing: The arrays were normzalized using the MAS 5.0 Affymetrix software (Expression Console - Affymetrix).

label: Biotin

source_name: Breast tumor biospsie

label_protocol: According to manufacturer protocol

extract_protocol: Total RNA was prepared using the RNeasy® Mini kit (Qiagen, Valencia, CA). The integrity of the RNA was assessed for each sample using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: ihc

value: TNBC

tag: er

tag: pr

tag: pathological type

value: ductal


title: GP_224

description: Triple-negative breast cancer tumours


title: GP_223

description: Triple-negative breast cancer tumours


title: GP_230

description: Triple-negative breast cancer tumours


title: GP_220

description: Triple-negative breast cancer tumours


title: GP_237

description: Triple-negative breast cancer tumours


title: GP_232

description: Triple-negative breast cancer tumours


title: GP_225

description: Triple-negative breast cancer tumours


title: GP_236

description: Triple-negative breast cancer tumours


title: GP_219

description: Triple-negative breast cancer tumours


title: GP_222

description: Triple-negative breast cancer tumours

value: lobular


title: GP_233

description: Triple-negative breast cancer tumours


title: GP_227

description: Triple-negative breast cancer tumours


title: GP_229

description: Triple-negative breast cancer tumours


title: GP_216

description: Triple-negative breast cancer tumours


title: GP_221

description: Triple-negative breast cancer tumours


title: GP_234

description: Triple-negative breast cancer tumours


title: GP_231

description: Triple-negative breast cancer tumours


title: GP_217

description: Triple-negative breast cancer tumours


title: GP_226

description: Triple-negative breast cancer tumours


title: GP_211

description: Triple-negative breast cancer tumours


title: GP_218

description: Triple-negative breast cancer tumours


title: GP_238

description: Triple-negative breast cancer tumours


title: GP_235

description: Triple-negative breast cancer tumours


title: GP_215

description: Triple-negative breast cancer tumours


title: GP_210

description: Triple-negative breast cancer tumours


title: GP_213

description: Triple-negative breast cancer tumours


title: GP_214

description: Triple-negative breast cancer tumours


title: GP_209

description: Triple-negative breast cancer tumours


title: GP_212

description: Triple-negative breast cancer tumours


title: GP_208

description: Triple-negative breast cancer tumours


title: GP_203

description: Triple-negative breast cancer tumours


title: GP_204

description: Triple-negative breast cancer tumours


title: GP_202

description: Triple-negative breast cancer tumours


title: GP_201

description: Triple-negative breast cancer tumours


title: GP_206

description: Triple-negative breast cancer tumours


title: GP_207

description: Triple-negative breast cancer tumours


title: GP_200

description: Triple-negative breast cancer tumours


title: GP_199

description: Triple-negative breast cancer tumours


title: GP_198

description: Triple-negative breast cancer tumours


title: GP_196

description: Triple-negative breast cancer tumours


title: GP_205

description: Triple-negative breast cancer tumours


title: GP_197

description: Triple-negative breast cancer tumours


title: GP_190

description: Triple-negative breast cancer tumours


title: GP_189

description: Triple-negative breast cancer tumours

value: other


title: GP_191

description: Triple-negative breast cancer tumours


title: GP_192

description: Triple-negative breast cancer tumours


title: GP_183

description: Triple-negative breast cancer tumours


title: GP_186

description: Triple-negative breast cancer tumours


title: GP_194

description: Triple-negative breast cancer tumours


title: GP_185

description: Triple-negative breast cancer tumours


title: GP_184

description: Triple-negative breast cancer tumours


title: GP_195

description: Triple-negative breast cancer tumours


title: GP_188

description: Triple-negative breast cancer tumours


title: GP_182

description: Triple-negative breast cancer tumours


title: GP_187

description: Triple-negative breast cancer tumours


title: GP_180

description: Triple-negative breast cancer tumours


title: GP_193

description: Triple-negative breast cancer tumours


title: GP_179

description: Triple-negative breast cancer tumours


title: GP_181

description: Triple-negative breast cancer tumours


title: GP_176

description: Triple-negative breast cancer tumours


title: GP_175

description: Triple-negative breast cancer tumours


title: GP_178

description: Triple-negative breast cancer tumours


title: GP_173

description: Triple-negative breast cancer tumours


title: GP_169

description: Triple-negative breast cancer tumours


title: GP_171

description: Triple-negative breast cancer tumours


title: GP_165

description: Triple-negative breast cancer tumours


title: GP_164

description: Triple-negative breast cancer tumours


title: GP_166

description: Triple-negative breast cancer tumours


title: GP_159

description: Triple-negative breast cancer tumours


title: GP_161

description: Triple-negative breast cancer tumours


title: GP_170

description: Triple-negative breast cancer tumours


title: GP_172

description: Triple-negative breast cancer tumours


title: GP_160

description: Triple-negative breast cancer tumours


title: GP_174

description: Triple-negative breast cancer tumours


title: GP_167

description: Triple-negative breast cancer tumours


title: GP_168

description: Triple-negative breast cancer tumours


title: GP_163

description: Triple-negative breast cancer tumours


title: GP_150

description: Triple-negative breast cancer tumours


title: GP_162

description: Triple-negative breast cancer tumours


title: GP_152

description: Triple-negative breast cancer tumours


title: GP_158

description: Triple-negative breast cancer tumours


title: GP_154

description: Triple-negative breast cancer tumours


title: GP_148

description: Triple-negative breast cancer tumours


title: GP_177

description: Triple-negative breast cancer tumours


title: GP_157

description: Triple-negative breast cancer tumours


title: GP_153

description: Triple-negative breast cancer tumours


title: GP_149

description: Triple-negative breast cancer tumours


title: GP_147

description: Triple-negative breast cancer tumours


title: GP_155

description: Triple-negative breast cancer tumours


title: GP_144

description: Triple-negative breast cancer tumours


title: GP_145

description: Triple-negative breast cancer tumours


title: GP_156

description: Triple-negative breast cancer tumours


title: GP_151

description: Triple-negative breast cancer tumours


title: GP_136

description: Triple-negative breast cancer tumours


title: GP_138

description: Triple-negative breast cancer tumours


title: GP_137

description: Triple-negative breast cancer tumours


title: GP_140

description: Triple-negative breast cancer tumours


title: GP_142

description: Triple-negative breast cancer tumours


title: GP_135

description: Triple-negative breast cancer tumours


title: GP_143

description: Triple-negative breast cancer tumours


title: GP_122

description: Triple-negative breast cancer tumours


title: GP_131

description: Triple-negative breast cancer tumours


title: GP_130

description: Triple-negative breast cancer tumours


title: GP_146

description: Triple-negative breast cancer tumours


title: GP_141

description: Triple-negative breast cancer tumours


title: GP_133

description: Triple-negative breast cancer tumours


title: GP_123

description: Triple-negative breast cancer tumours


title: GP_125

description: Triple-negative breast cancer tumours


title: GP_118

description: Triple-negative breast cancer tumours


title: GP_121

description: Triple-negative breast cancer tumours


title: GP_119

description: Triple-negative breast cancer tumours


title: GP_126

description: Triple-negative breast cancer tumours


title: GP_132

description: Triple-negative breast cancer tumours


title: GP_129

description: Triple-negative breast cancer tumours


title: GP_120

description: Triple-negative breast cancer tumours


title: GP_127

description: Triple-negative breast cancer tumours


title: GP_124

description: Triple-negative breast cancer tumours


title: GP_134

description: Triple-negative breast cancer tumours


title: GP_128

description: Triple-negative breast cancer tumours


title: GP_115

description: Triple-negative breast cancer tumours


title: HEK 293 cells, ribosome profiling, siDDX3, Replicate 2

status: Public on Mar 25 2019

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description:
Ribosome Profiling
DE_summary_table.csv

data_processing:
Library strategy: Ribo-seq
Ribo-seq fastq files were stripped of the adapter sequences using cutadapt. UMI sequences were removed and reads were collapsed to fasta format. Reads shorter than 20 nt were removed. Reads were first aligned against rRNA (accession number U13369.1), and to a collection of snoRNAs, tRNAs and miRNA (retrieved using the UCSC table browser) using bowtie2 in the ‘local’ alignment mode.
Reads were mapped to the hg38 version of the genome (without scaffolds) using STAR 2.6.0a supplied with the GENCODE 25 .gtf file. The following parameter were used:
--alignEndsType EndToEnd (Ribo-seq and PAR-CLIP) --outFilterMismatchNmax 2 --outFilterMismatchNoverLmax 0.04 (Ribo-seq) --outFilterMismatchNmax 3 (PAR-CLIP and RNA-seq) --outFilterMultimapNmax 20 --outSAMmultNmax 1 --outMultimapperOrder Random (All)
De-novo splice junction discovery was disabled for all datasets.
Peak calling for PAR-CLIP reads was performed with PARalyzer v1.5 in the “EXTEND_BY_READ” mode using the following parameters:
BANDWIDTH=3 CONVERSION=T>C MINIMUM_READ_COUNT_PER_GROUP=5 MINIMUM_READ_COUNT_PER_CLUSTER=5 MINIMUM_READ_COUNT_FOR_KDE=5 MINIMUM_CLUSTER_SIZE=8 MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER=1 MINIMUM_CONVERSION_COUNT_FOR_CLUSTER=1 MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION=5 MINIMUM_READ_LENGTH=13 MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES=0
Peaks with more than 10 reads were retained for subsequent analysis.
Genome_build: hg38
Supplementary_files_format_and_content: comma-separated text or BigWig tracks

source_name: HEK 293 FlpIn Trex

growth_protocol: HEK 293 FlpIn TRex cells (Invitrogen R78007) were cultured in DMEM supplemented with 10% Fetal Bovine Serum (FBS). Stable cell lines expressing inducible flag-HA-DDX3 were generated as described (Spitzer et al., PMID: 24011039)

extract_protocol:
smallRNA sequencing library
For  RNA-sequencing, Cells were resuspended in Trizol (Invitrogen) and, following Chloroform-mediate phase separation, RNA extracted from the aqueous phase using the RNeasy kit (Qiagen). Ribosome profiling (Calviello et al., PMID: 26657557) and PAR-CLIP (Maatz et al., PMID: 28369676) were performed as described.
See column "library construction protocol" in the SAMPLES section.

treatment_protocol: Cells were subjected to RNA interference as indicated.

tag: RNAi treatment

value: DDX3 siRNA pool

tag: rna isolation

value: Ribosome Profiling

tag: adapter sequence

value: TGGAATTCTCGGGTGCCA


title: HEK 293 cells, ribosome profiling, ctrl, Replicate 2

description:
Ribosome Profiling
DE_summary_table.csv

value: ctrl siRNA pool


title: HEK 293 cells, ribosome profiling, siDDX3, Replicate 1

description:
Ribosome Profiling
DE_summary_table.csv


title: GP_114

description: Triple-negative breast cancer tumours


title: GP_117

description: Triple-negative breast cancer tumours


title: GP_116

description: Triple-negative breast cancer tumours


title: HEK 293 cells, DDX3-K230E PAR-CLIP, Replicate 1

description:
PAR-CLIP
PARAlyzer_clusters.csv

data_processing:
Ribo-seq fastq files were stripped of the adapter sequences using cutadapt. UMI sequences were removed and reads were collapsed to fasta format. Reads shorter than 20 nt were removed. Reads were first aligned against rRNA (accession number U13369.1), and to a collection of snoRNAs, tRNAs and miRNA (retrieved using the UCSC table browser) using bowtie2 in the ‘local’ alignment mode.
Reads were mapped to the hg38 version of the genome (without scaffolds) using STAR 2.6.0a supplied with the GENCODE 25 .gtf file. The following parameter were used:
--alignEndsType EndToEnd (Ribo-seq and PAR-CLIP) --outFilterMismatchNmax 2 --outFilterMismatchNoverLmax 0.04 (Ribo-seq) --outFilterMismatchNmax 3 (PAR-CLIP and RNA-seq) --outFilterMultimapNmax 20 --outSAMmultNmax 1 --outMultimapperOrder Random (All)
De-novo splice junction discovery was disabled for all datasets.
Peak calling for PAR-CLIP reads was performed with PARalyzer v1.5 in the “EXTEND_BY_READ” mode using the following parameters:
BANDWIDTH=3 CONVERSION=T>C MINIMUM_READ_COUNT_PER_GROUP=5 MINIMUM_READ_COUNT_PER_CLUSTER=5 MINIMUM_READ_COUNT_FOR_KDE=5 MINIMUM_CLUSTER_SIZE=8 MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER=1 MINIMUM_CONVERSION_COUNT_FOR_CLUSTER=1 MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION=5 MINIMUM_READ_LENGTH=13 MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES=0
Peaks with more than 10 reads were retained for subsequent analysis.
Genome_build: hg38
Supplementary_files_format_and_content: comma-separated text or BigWig tracks

source_name: HEK 293 FlpIn Trex flagHA-DDX3

value: Untreated

value: PAR-CLIP


title: HEK 293 cells, stranded polyA RNA-seq, ctrl, Replicate 2

description:
Stranded RNA-seq
DE_summary_table.csv

extract_protocol:
TruSeq Stranded mRNA Library Prep Kit
For  RNA-sequencing, Cells were resuspended in Trizol (Invitrogen) and, following Chloroform-mediate phase separation, RNA extracted from the aqueous phase using the RNeasy kit (Qiagen). Ribosome profiling (Calviello et al., PMID: 26657557) and PAR-CLIP (Maatz et al., PMID: 28369676) were performed as described.
See column "library construction protocol" in the SAMPLES section.

value: total RNA

value: GATCGGAAGAGCACACGT


title: HEK 293 cells, stranded polyA RNA-seq, siDDX3, Replicate 2

description:
Stranded RNA-seq
DE_summary_table.csv


title: HEK 293 cells, stranded polyA RNA-seq, siDDX3, Replicate 1

description:
Stranded RNA-seq
DE_summary_table.csv


title: HEK 293 cells, stranded polyA RNA-seq, ctrl, Replicate 1

description:
Stranded RNA-seq
DE_summary_table.csv


title: HEK 293 cells, ribosome profiling, ctrl, Replicate 1

description:
Ribosome Profiling
DE_summary_table.csv


title: HEK 293 cells, DDX3-K230E PAR-CLIP, Replicate 2

description:
PAR-CLIP
PARAlyzer_clusters.csv


title: GP_112

description: Triple-negative breast cancer tumours


title: Ctr_rep1

status: Public on Dec 04 2018

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

institute: University of Lausanne

data_processing:
The libraries were sequenced on NextSeq500 with 85 bp paired end
The data was mapped agains Ensembl release 90 using STAR (v.2.5.1b).
Counts per gene were derived using featureCounts (v1.5.1)
Genome_build: BDGP6
Supplementary_files_format_and_content: counts per gene as tab separated file (tsv), read depth normalised bigwig tracks (bw)

source_name: S2R+ cells

growth_protocol: S2R+ cells are maintained in Schenider Medium at room temperature

extract_protocol:
Cells were pelleted and RNA was isolated with Trizol using standart protocol
Librariesfor sequencing were prepared according to the NEBNext® Ultra™ Directional RNA Library Prep Kit protocol.

treatment_protocol: 3 dsRNA treatments (6 days total)

tag: treatment

value: 10 ug of dsRNA against LacZ

tag: replicate

tag: passages


title: GP_113

description: Triple-negative breast cancer tumours

tag: adjuvant chemotherapy


title: GP_111

description: Triple-negative breast cancer tumours


title: GP_110

description: Triple-negative breast cancer tumours


title: Shiftwork Sham, biological rep 4

status: Public on Apr 23 2019

city: Guelph

first: Dr. Tami

middle: A.

last: Martino

state: Ontario

address: 50 Stone Road E

department: Centre for Cardiovascular Investigations, Department of Biomedical Science

country: Canada

institute: University of Guelph

hyb_protocol: Following fragmentation, cRNA were hydridized on Affymetrix GeneChip Mouse Gene 2.0 ST arrays, according to manufacturer's instructions. GeneChips were washed and stained on the Gene Atlas platform.

scan_protocol: GeneChips were scanned on the GeneAtlas platform.

data_processing: The data were analyzed with GeneSpring GX software v. 14.9 using default Affymetrix settings.

source_name: Shiftwork Sham Heart

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA.

growth_protocol: The mice were collected at 8 weeks of age (24-hours post-MI surgery) at 6 hours after lights on.

extract_protocol: Total RNA was extracted using the TRIzol method according to manufacturer's instructions.

treatment_protocol: The hearts were collected and snap frozen in liquid nitrogen and stored at -80C.

tag: strain

tag: tissue

value: myocardium


title: Shiftwork Sham, biological rep 5


title: GP_109

description: Triple-negative breast cancer tumours


title: Shiftwork Sham, biological rep 2


title: GP_108

description: Triple-negative breast cancer tumours


title: Shiftwork Sham, biological rep 3


title: Ctr_rep2


title: Ctr_rep3


title: FIL_3_rep_2

status: Public on Nov 20 2018

city: Clayton

first: Traude

last: Beilharz

state: VIC

address: Wellington Rd

department: Biomedicine Discovery Institute

country: Australia

institute: Monash University

description:
Illumina index 5
Control Treatment 30min

data_processing:
Processing is automated using the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools), and proceeds as follows:
Reads are stipped of trailing poly(A) sequence.
Reads are aligned using bowtie2 (v2.2.5 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Multi-mapping reads are assigned to one location at random.
Alignments are extended where the stripped poly(A) sequence matches As present in the genome. A poly(A) tail is called present if there are at least four untemplated As remaining in the stripped sequence.
Reads aligning to genes are counted. As 3'UTR annotations are not always accurate, reads up to 200 bases down-strand of a gene are counted towards that gene. Total reads per gene, reads with a poly(A) tail per gene, and average poly(A) tail length are tabulated.
Genome_build: C albicans SC5314 assembly 21 plus AF167163 downloaded from NCBI
Supplementary_files_format_and_content: read_count.csv contains counts of reads aligning to each gene in each sample.   tail_count.csv contains count of reads with a poly(A) tail aligning to each gene in each sample. This is used when detecting differential tail length as the more reads there are, the higher the accuracy of the average in tail.csv.   tail.csv contains the average poly(A) tail length observed in reads with a poly(A) tail for each gene in each sample.   These files are sufficient for differential expression and differential tail length analysis.

organism: Candida albicans

source_name: Candida in Spider media (DMSO)

growth_protocol: Candida albicans (DSY1050) was grown in either rich media (YPD) or in filimentation media (SPIDER). The drug MDIVI-1  was added after 2 hours and monitored over a time course of treatment.

extract_protocol:
Total Candida RNA was extracted by the hot phenol method.  One microgram of total RNA was used for library preparation by the PAT-seq method (Harrison et al., 2015).
Library construction was by the PAT-seq approach (Harrison et al 2015)
9pM of libraries per lane using Illumina c-bot. Illumina protocol 15006165 Rev J, July 2012
1 x 150bp sequencing using Illumina protocol 15035788 Rev A, Oct 2012

treatment_protocol: 100 μΜ MDIVI-1 was added after 2h of growth in Spider media. Sampels were taken after 15min, 30min, 45min, 1h, 2h, 3h, and 4h,

tag: background strain

tag: genotype/variation

value: drug pump mutant

tag: agent

value: DMSO

tag: time point


title: FIL_6_rep_2

description:
Illumina index 8
control Treatment 2 hour

value: 2 hour


title: INHIB_5_rep_2

description:
Illumina index 21
Test Treatment 1 hour

source_name: Candida in Spider media (MDIVI-1)

value: 1 hour


title: INHIB_6_rep_2

description:
Illumina index 18
Test Treatment 2 hour


title: FIL_4_rep_2

description:
Illumina index 6
Control Treatment 45min


title: INHIB_3_rep_2

description:
Illumina index 15
Test Treatment 30min


title: INHIB_4_rep_2

description:
Illumina index 17
Test Treatment 45min


title: FIL_5_rep_2

description:
Illumina index 7
Control Treatment 1 hour


title: INHIB_2_rep_2

description:
Illumina index 12
Test Treatment 15min


title: INHIB_1_rep_2

description:
Illumina index 11
Filimenation 2 hours

value: Filimenation 2 hours


title: FIL_2_rep_2

description:
Illumina index 4
Control Treatment 15min


title: Normal MI, biological rep 3

status: Public on Nov 30 2018

source_name: Normal MI Heart


title: Sham, biological rep 1

source_name: Sham Heart


title: Sham, biological rep 3


title: Normal MI, biological rep 2


title: Normal MI, biological rep 1


title: Shiftwork MI, biological rep 3

source_name: Shiftwork MI Heart


title: INHIB_4_rep_1

description:
Illumina index 34
Test Treatment 45min


title: INHIB_6_rep_1

description:
Illumina index 36
Test Treatment 2 hour


title: Sham, biological rep 5


title: INHIB_5_rep_1

description:
Illumina index 35
Test Treatment 1 hour


title: YPD_R1_rep_2

description:
Illumina index 1
Log phase cells

source_name: Candida in Rich media

value: Log phase cells


title: YPD_R2_rep_2

description:
Illumina index 2
Log phase cells


title: Shiftwork MI, biological rep 2


title: INHIB_2_rep_1

description:
Illumina index 32
Test Treatment 15min


title: INHIB_3_rep_1

description:
Illumina index 33
Test Treatment 30min


title: Sham, biological rep 4


title: Shiftwork MI, biological rep 1


title: YPD_R2_rep_1

description:
Illumina index 30
Log phase cells

tag: growth phase


title: FIL_6_rep_1

description:
Illumina index 27
control Treatment 2 hour


title: FIL_3_rep_1

description:
Illumina index 24
Control Treatment 30min


title: FIL_2_rep_1

description:
Illumina index 23
Control Treatment 15min


title: YPD_R1_rep_1

description:
Illumina index21
Log phase cells


title: Patient_6_Epicardial

status: Public on Jan 10 2018

city: Provo

first: David

middle: Wayne

last: Sant

state: UT

address: 1712 South East Bay Blvd, Building 5 Suite 300

department: Biomedical Informatics

institute: Noorda College of Osteopathic Medic

data_processing:
Basecalls performed using CASAVA version 1.4
Bases were quality trimmed to q20 and adaptors were removed using Trim_Galore!
RNA-seq reads were aligned to the GRCh38 transcriptome using STAR
RNA-seq counts were generated during alignment using STAR
Genome_build: GRCh38
Supplementary_files_format_and_content: Count files were generated using STAR

source_name: Epicardial Adipose Tissue

extract_protocol:
MACS Dissociator followed by Qiagen RNEasy
TruSeq RNA Prep kit v2

tag: cell type

value: Epicardial Adipose Tissue

tag: passage

value: Fresh Frozen

tag: gender

value: Female

tag: disease state

value: Diabetic


title: INHIB_1_rep_1

description:
Illumina index 31
Filimenation 2 hours

value: Filimenation

value: 2 hours


title: FIL_1_rep_2

description:
Illumina index 3
Filimenation 2 hours


title: FIL_1_rep_1

description:
Illumina index 22
Filimenation 2 hours


title: Patient_8_Epicardial

value: Male


title: FIL_5_rep_1

description:
Illumina index 26
Control Treatment 1 hour


title: Patient_3_Epicardial

value: Nondiabetic


title: FIL_4_rep_1

description:
Illumina index 25
Control Treatment 45min


title: Patient_2_Epicardial


title: Patient_1_Epicardial


title: Pax5_ChIP_proB  [Pax5-ChIP-Seq-Tet-On]

status: Public on Feb 20 2018

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

data_processing:
base calling: HiSeq Analysis Software
alignment: bowtie2 (2.3.2)
duplicated reads and low mapping quality read removal: samtools 1.3.1
peak calling and depth coverage generation (bedGraph): macs2 2.1.0
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph format

growth_protocol: To isolate c-Kit+ progenitor cells, Ebf1-/- fetal liver cells were stained with biotinylated c-Kit antibody (BD Biosciences) and purified by streptavidin beads-mediated magnetic-activated cell sorting (MACS, Miltenyi Biotec). OP9 feeder cells were used to maintain the progenitors in OptiMEM medium supplemented with 4% FCS, 1% PSG, 50µM β-mercaptoethanol, 10ng/mL SCF, 10ng/mL Flt3L, and 5ng/mL IL-7.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes. Then they were washed with PBS and lysed for sonication. Chromatin was precipitated with a specific antibody (anti-Pax5, Santa Cruz, sc-1974X, 4µg/sample) and protein A or G-coupled sepharose beads. After elution from the beads, chromatin was decrosslinked and purified using MinElute PCR Purification Kit (Qiagen) according to the manufacturer's instructions.
Libraries were prepared via the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® library preparation protocol according to manufacturer's instructions

treatment_protocol: Ebf1-/- B cell progenitors were transduced with a Tet-on Pax5 inducible expression retroviral construct. The transduced cells were treated with 1ug/ml doxycycline to initate Pax5 expression. Cells were harvested 6 hours after treatment for analysis. Ebf1-/- RERTCre B cell progenitors were transduced with a Cre-based inducible EBF1 expression retroviral construct. The transduced cells were treated with 2μM 4-hydroxy-tamoxifen (4-OHT) to initiate EBF1 expression. After 5days, CD19+ pro-B cells were sorted for analysis.

value: Ebf1-deficient B cell progenitors

tag: stage post dox treatment

value: 6 hrs

tag: antibody


title: Patient_8_Subcutaneous

source_name: Subcutaneous Adipose Tissue

value: Subcutaneous Adipose Tissue


title: Patient_4_Subcutaneous


title: Patient_7_Subcutaneous


title: Patient_7_Epicardial


title: Patient_3_Subcutaneous


title: Patient_5_Epicardial


title: Patient_4_Epicardial


title: Patient_1_Subcutaneous


title: Patient_2_Subcutaneous


title: Patient_6_Subcutaneous


title: Patient_5_Subcutaneous


title: Subject 3080235-M, Normal Pregnancy

status: Public on Aug 24 2017

first: Alvin

middle: T.

last: Kho

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

hyb_protocol: Hybridization was processed according to the protocol for the Affymetrix GeneChip® Hybridization Control Kit.

scan_protocol: Scanning is carried out on an Affymetrix GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions.

data_processing: All 157 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output in base 2 logarithmic scale.

source_name: PAXgene whole blood, Normal Pregnancy

label_protocol: Biotinylated-cRNA was prepared according to Affymetrix manufacturers protocol.

growth_protocol: Not applicable.

extract_protocol: Total RNA was isolated from whole blood using the PAXgene Blood RNA Kit (Qiagen®) according to manufacturers protocol. The Ambion Globin Clear kit (Ambion®) was used to remove alpha and beta globin mRNA from the sample to increase the sensitivity of gene expression assays through improving the detection rate of expressed genes. The RNA was quantified using the Nanodrop 8000 and checked for high integrity before preparation of cDNA. The integrity of RNA samples was assessed using the Agilent 2100 Bioanalyzer.  Sample purity was confirmed using the NanoDrop spectrophotometer and RNA Integrity Number (RIN ≥ 8).

treatment_protocol: Not applicable.

tag: Sex

tag: ethnicity

value: White

value: Normal


title: Subject 5034421-M, Normal Pregnancy

value: Black or African American


title: Subject 6073211-M, Normal Pregnancy


title: Subject 3026263-M, Normal Pregnancy


title: Subject 3018175-M, Normal Pregnancy


title: Subject 9095285-M, Normal Pregnancy


title: Subject 7054702-M, Preeclampsia Pregnancy

source_name: PAXgene whole blood, Preeclampsia Pregnancy

value: Preeclampsia


title: Subject 4012442-M, Normal Pregnancy


title: Subject 8012930-M, Normal Pregnancy


title: Subject 7045717-M, Normal Pregnancy


title: Subject 2055393-M, Normal Pregnancy


title: Subject 6074068-M, Preeclampsia Pregnancy

value: Other


title: Subject 2083037-M, Preeclampsia Pregnancy


title: Subject 5028464-M, Normal Pregnancy


title: Subject 7013951-M, Normal Pregnancy


title: Subject 8084201-M, Normal Pregnancy


title: Subject 3040056-M, Normal Pregnancy


title: Subject 2040546-M, Preeclampsia Pregnancy


title: Subject 7081029-M, Normal Pregnancy


title: GP_139

description: Triple-negative breast cancer tumours

tag: ihc

value: TNBC

tag: er

tag: pr

tag: pathological type

value: ductal


title: Subject 3017557-M, Preeclampsia Pregnancy


title: Subject 6074164-M, Preeclampsia Pregnancy


title: Subject 4078284-M, Preeclampsia Pregnancy


title: Subject 2002666-M, Preeclampsia Pregnancy


title: Subject 3025195-M, Normal Pregnancy


title: Subject 1050601-M, Normal Pregnancy


title: Subject 3039734-M, Normal Pregnancy


title: Subject 3025682-M, Preeclampsia Pregnancy


title: Subject 1089419-M, Normal Pregnancy


title: Subject 3079044-M, Normal Pregnancy


title: Subject 2098737-M, Normal Pregnancy


title: Subject 4043229-M, Normal Pregnancy


title: Subject 5079413-M, Normal Pregnancy


title: Subject 6079515-M, Preeclampsia Pregnancy


title: Subject 7029676-M, Preeclampsia Pregnancy


title: Subject 3025567-M, Preeclampsia Pregnancy


title: Subject 1091914-M, Normal Pregnancy


title: Subject 6068170-M, Preeclampsia Pregnancy


title: Subject 6032198-M, Normal Pregnancy


title: Subject 7068972-M, Normal Pregnancy


title: Subject 6017807-M, Normal Pregnancy


title: Subject 6057555-M, Normal Pregnancy


title: Subject 4084871-M, Normal Pregnancy


title: Subject 8011100-M, Preeclampsia Pregnancy


title: Subject 6061774-M, Normal Pregnancy


title: Subject 4058470-M, Normal Pregnancy


title: Subject 9052839-M, Normal Pregnancy


title: Subject 4072444-M, Preeclampsia Pregnancy


title: Subject 7044864-M, Normal Pregnancy


title: Subject 5018713-M, Normal Pregnancy


title: Subject 1084308-M, Preeclampsia Pregnancy


title: Subject 7008408-M, Normal Pregnancy


title: Subject 6083937-M, Preeclampsia Pregnancy


title: Subject 4015811-M, Normal Pregnancy


title: Subject 4020549-M, Normal Pregnancy


title: Subject 9030732-M, Normal Pregnancy


title: Subject 3066295-M, Normal Pregnancy


title: Subject 3049942-M, Normal Pregnancy


title: Subject 4041299-M, Normal Pregnancy


title: Subject 2032617-M, Normal Pregnancy


title: Subject 4084584-M, Preeclampsia Pregnancy


title: Subject 6037614-M, Normal Pregnancy


title: Subject 7066921-M, Preeclampsia Pregnancy


title: Subject 2012577-M, Normal Pregnancy


title: Subject 5027791-M, Normal Pregnancy


title: Subject 1086430-M, Preeclampsia Pregnancy


title: Subject 5014485-M, Normal Pregnancy


title: Subject 9027966-M, Preeclampsia Pregnancy


title: Subject 3012659-M, Preeclampsia Pregnancy


title: Subject 4043864-M, Normal Pregnancy


title: Subject 8046764-M, Preeclampsia Pregnancy


title: Subject 5019090-M, Normal Pregnancy


title: Subject 2076690-M, Normal Pregnancy


title: Subject 7029286-M, Normal Pregnancy


title: Subject 9008893-M, Normal Pregnancy


title: Subject 3017519-M, Normal Pregnancy


title: Subject 8097362-M, Normal Pregnancy


title: Subject 7041367-M, Normal Pregnancy


title: Subject 5061842-M, Preeclampsia Pregnancy


title: Subject 3035464-M, Preeclampsia Pregnancy


title: Subject 6053558-M, Normal Pregnancy


title: Subject 8050628-M, Normal Pregnancy


title: Subject 7073579-M, Normal Pregnancy


title: Subject 8007807-M, Normal Pregnancy


title: Subject 1075381-M, Normal Pregnancy


title: Subject 9034020-M, Normal Pregnancy


title: Subject 4018695-M, Normal Pregnancy


title: Subject 4026626-M, Normal Pregnancy


title: Subject 6023219-M, Preeclampsia Pregnancy


title: Subject 2010858-M, Normal Pregnancy


title: Subject 3040387-M, Normal Pregnancy


title: Subject 9026397-M, Preeclampsia Pregnancy


title: Subject 3024271-M, Normal Pregnancy


title: Subject 7000235-M, Normal Pregnancy


title: Subject 7026812-M, Preeclampsia Pregnancy


title: Subject 6030914-M, Normal Pregnancy


title: Subject 8057476-M, Normal Pregnancy


title: Subject 4031608-M, Normal Pregnancy


title: Subject 3089596-M, Normal Pregnancy


title: Subject 3067074-M, Normal Pregnancy


title: Subject 9050155-M, Normal Pregnancy


title: Subject 6098802-M, Normal Pregnancy


title: Subject 3083249-M, Preeclampsia Pregnancy


title: Subject 2006605-M, Normal Pregnancy


title: Subject 2033556-M, Preeclampsia Pregnancy


title: Subject 5087337-M, Normal Pregnancy


title: Subject 3030282-M, Normal Pregnancy


title: Subject 3050398-M, Preeclampsia Pregnancy


title: Subject 3095818-M, Normal Pregnancy


title: Subject 1090275-M, Normal Pregnancy


title: Subject 6095056-M, Normal Pregnancy


title: Subject 7086373-M, Normal Pregnancy


title: Subject 6063221-M, Normal Pregnancy


title: Subject 7053108-M, Normal Pregnancy


title: Subject 5037279-M, Preeclampsia Pregnancy


title: Subject 6072206-M, Normal Pregnancy

value: Asian


title: Subject 4083145-M, Normal Pregnancy

value: Female


title: Subject 5023045-M, Normal Pregnancy


title: Subject 6009822-M, Normal Pregnancy


title: Subject 6082469-M, Preeclampsia Pregnancy


title: Subject 7027740-M, Preeclampsia Pregnancy

value: American Indian or Alaska


title: Subject 7013727-M, Preeclampsia Pregnancy


title: Subject 9009710-M, Preeclampsia Pregnancy


title: Subject 5031074-M, Normal Pregnancy


title: Subject 5010120-M, Normal Pregnancy


title: Subject 2069323-M, Normal Pregnancy


title: Subject 3051856-M, Normal Pregnancy


title: Subject 8023284-M, Normal Pregnancy


title: Subject 8056467-M, Preeclampsia Pregnancy


title: Subject 5035754-M, Preeclampsia Pregnancy


title: Subject 8009468-M, Preeclampsia Pregnancy


title: Subject 8021460-M, Normal Pregnancy


title: Subject 5075311-M, Preeclampsia Pregnancy


title: Subject 1039695-M, Normal Pregnancy


title: Subject 8054547-M, Normal Pregnancy


title: Subject 9078067-M, Normal Pregnancy


title: Subject 9005775-M, Normal Pregnancy


title: Subject 6051478-M, Normal Pregnancy


title: Subject 3070934-M, Normal Pregnancy


title: Subject 3092584-M, Normal Pregnancy


title: Subject 5097746-M, Normal Pregnancy


title: Subject 8071607-M, Normal Pregnancy


title: Subject 1020307-M, Preeclampsia Pregnancy


title: Subject 5005274-M, Preeclampsia Pregnancy


title: Subject 7016148-M, Preeclampsia Pregnancy


title: Subject 7061969-M, Normal Pregnancy


title: Subject 3044380-M, Normal Pregnancy


title: Subject 9096035-M, Normal Pregnancy


title: Subject 4035971-M, Normal Pregnancy


title: Subject 2052394-M, Preeclampsia Pregnancy


title: Subject 4086732-M, Preeclampsia Pregnancy


title: Subject 7054360-M, Normal Pregnancy


title: Subject 5038816-M, Normal Pregnancy


title: Subject 7050617-M, Normal Pregnancy


title: Subject 6053887-M, Preeclampsia Pregnancy


title: Subject 3017519-M, microRNA, Normal Pregnancy

hyb_protocol: Not applicable.

scan_protocol: Not applicable.

data_processing:
Raw output values in triplets for each sample: Ct on base 2 exponent, Cq confidence Cq_Conf, amplification score Amp_Score. Triplets with any “Undetermined” value, or Cq-Conf<0.8, or Amp_Score<1.24 are disregarded in subsequent analyses.
In the Non-Normalized data matrix 3 values are given for each sample: CT values on base 2 exponent. Cq confidence CQ_CONF. Amplification score AMP_SCORE. In the Normalized data matrix, we have CT_QNORM which CT values from the Non-Normalized data matrix that have CQ_CONF>0.8 and AMP_SCORE>1.24 (otherwise they are null-valued) and then quantile normalized.

label: FAM

source_name: PAXgene whole blood

label_protocol: Not applicable.

extract_protocol: Total RNA from 1 mL of serum that was prepared from PAXgene whole blood of patients was isolated using the Plasma/Serum Circulating and Exosomal RNA Purification Kit (Norgen Biotek). We averaged around 4 ng/ul of total RNA in 20 ul measured by RiboGreen. Isolated RNA was reverse-transcribed and the product was pre-amplified using Megaplex PreAmp Primers and TaqMan PreAmp Master Mix (Applied Biosystems).


title: Subject 6032198-M, microRNA, Normal Pregnancy


title: Subject 3044380-M, microRNA, Normal Pregnancy


title: Subject 3070934-M, microRNA, Normal Pregnancy


title: Subject 9096035-M, microRNA, Normal Pregnancy


title: Subject 5061842-M, microRNA, Preeclampsia Pregnancy


title: Subject 7016148-M, microRNA, Preeclampsia Pregnancy


title: Subject 7013951-M, microRNA, Normal Pregnancy


title: Subject 3066295-M, microRNA, Normal Pregnancy


title: Subject 2076690-M, microRNA, Normal Pregnancy


title: Subject 7044864-M, microRNA, Normal Pregnancy


title: Subject 1090275-M, microRNA, Normal Pregnancy


title: Subject 7068972-M, microRNA, Normal Pregnancy


title: Subject 3018175-M, microRNA, Normal Pregnancy


title: Subject 8046764-M, microRNA, Preeclampsia Pregnancy


title: Subject 6017807-M, microRNA, Normal Pregnancy


title: Subject 6072206-M, microRNA, Normal Pregnancy


title: Subject 9005775-M, microRNA, Normal Pregnancy


title: Subject 3035464-M, microRNA, Preeclampsia Pregnancy


title: Subject 7016015-M, Preeclampsia Pregnancy


title: Subject 6094898-M, Normal Pregnancy


title: Subject 3064425-M, Normal Pregnancy


title: Subject 3049942-M, microRNA, Normal Pregnancy


title: Subject 4020549-M, microRNA, Normal Pregnancy


title: Subject 3079044-M, microRNA, Normal Pregnancy


title: Subject 2040546-M, microRNA, Preeclampsia Pregnancy


title: Subject 9095285-M, microRNA, Normal Pregnancy


title: Subject 8007807-M, microRNA, Normal Pregnancy


title: Subject 7013727-M, microRNA, Preeclampsia Pregnancy


title: Subject 1039695-M, microRNA, Normal Pregnancy


title: Subject 8056467-M, microRNA, Preeclampsia Pregnancy


title: Subject 9052839-M, microRNA, Normal Pregnancy