title: Pooled input ChIPSeq

city: Cambridge

first: Zhenhua

last: Wu

address: 300 Technology Square floor 5

institute: H3 Biomedicine

data_processing:
The 75-nt sequence reads are generated by Illumina sequencing (using NextSeq 500)
ChIP-seq reads were aligned to the hg19 genome assembly using BWA with default settings
Data were filtered using the following specifications: Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis
peaks were called using macs2 version 2.1.1.20160309 with the following setting: Minimum FDR (q-value) cutoff -q (0.01), Effective genome size -g (hs), --bdg (True), --format (BAM), -c (pooled input is used as control)
treatment pileup bedgraph generated by macs2 is normalized to 10M totoal reads by dividing the number in "tags after filtering in treatment" field from the _peaks.xls file produced by macs2 times 10M
Genome_build: hg19
Supplementary_files_format_and_content: big wig files are converted from the normalized bedgraph file. The score respresents the normalized extended reads pileup signal

growth_protocol: MCF cell were maintained in DMEM supplemented with 10% FBS, 4 mM L-glutamine and 1x non-essential amino acids.  Cells were then washed 3 times in PBS and cultured for 72 hours in phenol red-free DMEM media supplemented with 10% charcoal-stripped serum prior to treatment.

extract_protocol:
Cells were formaldehyde fixed for 15 minutes (1% formaldehyde, 100 mM NaCl, 0.1 mM EDTA pH8.0, 5 mM Hepes pH 7.9).  Fixation was stopped with 2.5M glycine and cells were washed 2X in PBS/0.5% Igepal CA-630.  Cell pellets were snap frozen and chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

treatment_protocol: Cells were treated with indicated compounds for 45 minutes before harvesting.

tag: chip antibody

value: breast cancer cell line


title: ERalpha s6 5942 ChIPSeq

status: Public on Jun 12 2018

type: SRA

state: MA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

value: Estrogen Receptor alpha (Santa Cruz, sc-543, lot F1716)

tag: cell type

tag: treatment


title: ERalpha s10 E2 ChIPSeq


title: S5.H5

city: San Francisco

first: Alex

middle: Aaron

last: Pollen

state: California

address: 35 Medical Center Way

department: Neurology

institute: UCSF

library_source: transcriptomic

data_processing:
Trim Galore 3.7
HISAT2
subread-1.5.0 function featureCounts
GRCh38.79.gtf
Genome_build: GRCh38.p2/Clint_PTRv2; UCSC: panTro6; GCF_002880755.1
Supplementary_files_format_and_content: log(CPM+1)

molecule: total RNA

organism: Pan troglodytes

source_name: chimp_iPS-derived cerebral organoid

growth_protocol: Cerebral organoids from Kadoshima et al., 2013

extract_protocol:
Fluidigm C1 small IFC (100-5759; 100-6201);  SMARTer® Ultra™ Low RNA Kit (634832)
Nextera XT tagmentation kit (FC-131-096)

tag: donor id

tag: clone id

tag: age (weeks)

tag: date captured

tag: Sex

value: Male

value: iPS-derived cerebral organoid

tag: organoid id

tag: capture plate

tag: capture chamber


title: ERalpha s9 Fulv ChIPSeq

value: Fulvestrant


title: S69.A6


title: S5.F1


title: ERalpha s7 s5942 ChIPSeq

value: Saturated H3B-5942


title: S58.A2


title: ERalpha s8 Tam ChIPSeq

value: Tamoxifen


title: SM2_3_W8_1_S16

city: Manchester

first: Adam

last: Stevens

address: Oxford Road

department: Medicine

country: United Kingdom

institute: University of Manchester

description:
PolyA RNA
processed data file: Full_normalised_data.csv

data_processing:
Ordered BAM files were generated against the human genome feature file Homo_sapiens.GRCh38.90.gtf downloaded from Ensembl (ftp://ftp.ensembl.org/pub/current_gtf).
Data analysis was performed using Qlucore Omics Explorer 3.3 (Qlucore, Lund, Sweden) with a FPKM (Fragments Per Kilobase Million) cut-off of 10.
To identify significant differentially regulated transcripts, RNAseq expression data analysis was carried out by applying a group ANOVA with p<0.01 to the entire dataset. For illustration of the comparisons between the effect on transcription with EVI1-WT and EVI1-AQA in relation to untransfected cells and empty vector-transfected control cells with and without DNA damage, values were normalized to the mean of 0 and a variance of one. In addition, differences between expression levels at individual conditions were assessed by two group comparison (t-test).
Genome_build: Homo_sapiens.GRCh38.90.gtf
Supplementary_files_format_and_content: Full_normalised_data.csv: Comma-separated text file of FPKM normalised (mean centered) for batch.

source_name: Transfected HEK293

growth_protocol: Cells were plated in 6-well plates and co-transfected with pCMV-EVI1-flag effector plasmids (EVI1-WT or EVI1-AQA), PLZF-luciferase or FOS-luciferase and TK-renilla luciferase reporter plasmid. Comparable expression of EVI1-WT and EVI1-AQA in HEK293 cells was monitored by RT-PCR. After 48 hours, cells were lysed and firefly and renilla luciferase activities were assayed using the Dual-luciferase reporter assay (Promega) measured on a Victor plate reader (Perkin Elmer).

extract_protocol:
PolyA RNA
Libraries were prepared with the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit for Illumina (FWD) using an input of 200 ng and performing 14 cycles of amplification.
Indexed libraries were then quantified using the Kapa Illumina Library quantification kit (Cat 07960336001) and pooled. 1 x 75bp sequence reads were generated by clustering 2.0pM of the library pool on a NextSeq500 High throughput run.

treatment_protocol: Transfection experiments were exposed to 150 uM H2O2 or left untreated for 8 h.

tag: transfected plasmid

value: EVI1 WT

value: Untreated

tag: batch


title: ERalpha s3 s6545 ChIPSeq

value: Saturated H3B-6545


title: SM2_1_U8_1_S38

value: Untransfected


title: S5.B2


title: ERalpha s5 RAD1901 ChIPSeq


title: S5.A5


title: S5.A1


title: S5.D3


title: S188.F3


title: S191.G8


title: ERalpha s1 DMSO ChIPSeq

value: DMSO


title: S188.C2


title: ERalpha s2 6545 ChIPSeq


title: S186.D10


title: S187.G11


title: S188.B3


title: S5.D5


title: S186.B4


title: ERalpha s4 800 ChIPSeq


title: S176.E5


title: S176.B10


title: S169.C7


title: S150.A9


title: S14.A4


title: S12.G10


title: S12.C10


title: E14.5_FT 19_ROW40

city: Geneva

first: Denis

last: Jabaudon

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

data_processing:
aligned to UCSC mm10 avec TopHat v. 2.0.11
number of reads per feature counted with Htseq v.0.6.1
Cells were filtered according to pictures of single wells of C1 chip (considering presence of cell)
Cells were filtered with following steps: -3 standard deviation from highly stable genes (determined with the criteria: genes expressed in >95% of cells), subpalial markers <50 RPM
Genes were filtered with following steps: Filtered genes of analysis of the paper: DOI: 10.1126/science.aad8361
Genome_build: mm10
Supplementary_files_format_and_content: .txt file containing expression value

organism: Mus musculus

source_name: Cortical Neurons

extract_protocol:
Fluidigm C1 in-chip extracion
Nextera XT

tag: developmental age

tag: strain

tag: injection

value: FlashTag


title: E14.5_FT 19_ROW39


title: E14.5_FT 19_ROW21


title: E14.5_FT 19_ROW29


title: E14.5_FT 19_ROW28


title: E14.5_FT 19_ROW32


title: E14.5_FT 19_ROW35


title: E14.5_FT 19_ROW25


title: E14.5_FT 19_ROW17


title: E14.5_FT 19_ROW24


title: E14.5_FT 19_ROW18


title: E14.5_FT 19_ROW14


title: E14.5_FT 19_ROW12


title: E14.5_FT 19_ROW13


title: E14.5_FT 19_ROW08


title: E14.5_FT 19_ROW07


title: E14.5_FT 19_ROW09


title: E14.5_FT 19_ROW33


title: E14.5_FT 19_ROW38


title: S169.G6


title: E14.5_FT 18_ROW39


title: E14.5_FT 18_ROW40


title: E14.5_FT 19_ROW01


title: E14.5_FT 18_ROW37


title: E14.5_FT 18_ROW38


title: E14.5_FT 18_ROW33


title: E14.5_FT 18_ROW11


title: E14.5_FT 18_ROW24


title: E14.5_FT 18_ROW19


title: E14.5_FT 18_ROW21


title: E14.5_FT 18_ROW23


title: E14.5_FT 18_ROW32


title: E14.5_FT 18_ROW03


title: E14.5_FT 18_ROW20


title: E14.5_FT 17_ROW31


title: E14.5_FT 17_ROW36


title: E14.5_FT 17_ROW33


title: E14.5_FT 18_ROW22


title: E14.5_FT 17_ROW28


title: E14.5_FT 17_ROW27


title: E14.5_FT 17_ROW25


title: E14.5_FT 17_ROW22


title: E14.5_FT 17_ROW23


title: E14.5_FT 17_ROW26


title: E14.5_FT 17_ROW21


title: E14.5_FT 17_ROW14


title: E14.5_FT 18_ROW36


title: Tmem258-shRNA-LSB30-18h-B

first: Daniel

middle: Bartholomew

last: Graham

address: 415 Main St.

department: Infectious Disease and Microbiome

institute: Broad Institute

data_processing:
Alignment with Tophat 2.0.14 + Bowtie 1.1.2 + Samtools 0.0.19
Counting of genes with htseq-count
QC with RSeqC read_distribution.py + custom scripts, alignment file needs to have header reformatted to run with RSeqC (chromosome names
Differential gene expression with EdgeR + limma
Genome_build: mm9

source_name: bone marrow derived macrophages

growth_protocol: Bone marrow was seeded in media (DMEM with 10% FBS, GlutaMAX 1x, MEM non-essential amino acids 1x, penicillin-streptomycin 100 U/mL and 100 µg/mL, respectively, and GM-CSF (4% TOPO-derived media)) in a 24-well plate. On day 2 after seeding, cells were transduced with equal volume shRNA lentiviral supernatant. On day 5, cells were selected with 3 µg/mL puromycin for an additional 2 days.

extract_protocol:
Total RNA, column purified, DNase treated (Qiagen Rneasy mini kit).
Tag-Seq (Shishkin, A.A., Giannoukos, G., Kucukural, A., Ciulla, D., Busby, M., Surka, C., Chen, J., Bhattacharyya, R.P., Rudy, R.F., Patel, M.M., Novod, N., Hung, D.T., Gnirke, A., Garber, M., Guttman, M., Livny, J., 2015. Simultaneous generation of many RNA-seq libraries in a single reaction. Nat Meth 12, 323–325. doi:10.1038/nmeth.3313)

treatment_protocol: On day 7, the cells were stimulated in media supplemented with 10 ng/mL IFNg and 50 ng/mL LPS.

tag: tissue

value: bone marrow derived macrophages

tag: shRNA

value: LPS+IFNg

tag: treatment time

tag: replicate

value: B


title: Tmem258-shRNA-LSB30-6h-B

tag: treatment


title: Tmem258-shRNA-LSB31-18h-B


title: Tmem258-shRNA-LSB31-18h-A

value: A


title: Tmem258-shRNA-LSB31-6h-B


title: E14.5_FT 18_ROW08


title: Tmem258-shRNA-LSB30-18h-A


title: Tmem258-shRNA-LSB30-6h-A


title: E14.5_FT 17_ROW06


title: E14.5_FT 17_ROW09


title: E14.5_FT 17_ROW11


title: Tmem258-shRNA-LSB31-6h-A


title: E14.5_FT 18_ROW01


title: Nos2-shRNA-LSB26-18h-B


title: E14.5_FT 16_ROW32


title: E14.5_FT 16_ROW31


title: E14.5_FT 17_ROW05


title: Dnmt3a-shRNA-LSB53-18h-B


title: Sbno2-shRNA-LSB41-18h-B


title: E14.5_FT 16_ROW29


title: E14.5_FT 16_ROW28


title: Nos2-shRNA-LSB27-18h-A


title: E14.5_FT 16_ROW25


title: E14.5_FT 16_ROW24


title: Dnmt3a-shRNA-LSB52-18h-A


title: E14.5_FT 16_ROW22


title: Sbno2-shRNA-LSB41-18h-A


title: Dnmt3a-shRNA-LSB53-18h-A


title: Nos2-shRNA-LSB27-18h-B


title: E14.5_FT 16_ROW21


title: Nos2-shRNA-LSB26-18h-A


title: Sbno2-shRNA-LSB40-18h-A


title: E14.5_FT 16_ROW19


title: Sbno2-shRNA-LSB40-18h-B


title: Nos2-shRNA-LSB27-6h-B


title: E14.5_FT 16_ROW16


title: Nos2-shRNA-LSB26-6h-B


title: E14.5_FT 16_ROW14


title: E14.5_FT 16_ROW36


title: Dnmt3a-shRNA-LSB53-6h-B


title: Dnmt3a-shRNA-LSB52-6h-B


title: Sbno2-shRNA-LSB41-6h-B


title: E14.5_FT 16_ROW11


title: E14.5_FT 16_ROW12


title: E14.5_FT 16_ROW10


title: Sbno2-shRNA-LSB40-6h-B


title: E14.5_FT 16_ROW06


title: Nos2-shRNA-LSB27-6h-A


title: Dnmt3a-shRNA-LSB52-18h-B


title: E14.5_FT 16_ROW23


title: E14.5_FT 16_ROW04


title: Nos2-shRNA-LSB26-6h-A


title: Dnmt3a-shRNA-LSB53-6h-A


title: E14.5_FT 16_ROW02


title: E14.5_FT 15_ROW36


title: E14.5_FT 15_ROW39


title: E14.5_FT 15_ROW33


title: E14.5_FT 15_ROW32


title: Sbno2-shRNA-LSB40-6h-A


title: E14.5_FT 15_ROW31


title: Dnmt3a-shRNA-LSB52-6h-A


title: Prdx5-shRNA-LSB36-18h-B


title: Prdx5-shRNA-LSB37-18h-B


title: E14.5_FT 15_ROW28


title: Keap1-shRNA-LSB29-18h-B


title: Sbno2-shRNA-LSB41-6h-A


title: LacZ-shRNA-LSB49-18h-B

description: LacZ_LSB49_18h_repB was not included in the analysis due to QC issues.


title: Luc-shRNA-LSB48-18h-B


title: E14.5_FT 15_ROW26


title: Prdx5-shRNA-LSB37-18h-A


title: Keap1-shRNA-LSB28-18h-B


title: E14.5_FT 15_ROW21


title: E14.5_FT 15_ROW19


title: Keap1-shRNA-LSB29-18h-A


title: E14.5_FT 15_ROW15


title: E14.5_FT 15_ROW09


title: Keap1-shRNA-LSB28-18h-A


title: E14.5_FT 16_ROW01


title: E14.5_FT 15_ROW08


title: E14.5_FT 15_ROW35


title: LacZ-shRNA-LSB49-18h-A


title: E14.5_FT 15_ROW24


title: E14.5_FT 15_ROW07


title: E14.5_FT 15_ROW01


title: Prdx5-shRNA-LSB37-6h-B

value: LacZ


title: E14.5_FT 14_ROW40


title: Keap1-shRNA-LSB29-6h-B


title: Prdx5-shRNA-LSB36-18h-A


title: Keap1-shRNA-LSB28-6h-B


title: E14.5_FT 14_ROW37


title: LacZ-shRNA-LSB49-6h-B


title: E14.5_FT 14_ROW35


title: Prdx5-shRNA-LSB37-6h-A


title: Keap1-shRNA-LSB29-6h-A


title: E14.5_FT 14_ROW33


title: Prdx5-shRNA-LSB36-6h-A

value: Luc


title: Luc-shRNA-LSB48-6h-B


title: Luc-shRNA-LSB48-18h-A


title: Keap1-shRNA-LSB28-6h-A


title: E14.5_FT 14_ROW36


title: E14.5_FT 14_ROW23


title: E14.5_FT 14_ROW24


title: LacZ-shRNA-LSB49-6h-A


title: E14.5_FT 14_ROW26


title: Luc-shRNA-LSB48-6h-A


title: E14.5_FT 14_ROW19


title: Tmem258-shRNA-LSB30-2h-B


title: Tmem258-shRNA-LSB31-2h-B


title: E14.5_FT 14_ROW17


title: E14.5_FT 14_ROW39


title: E14.5_FT 14_ROW18


title: Prdx5-shRNA-LSB36-6h-B


title: E14.5_FT 14_ROW30


title: Tmem258-shRNA-LSB31-0h-B


title: Tmem258-shRNA-LSB31-2h-A


title: Tmem258-shRNA-LSB30-0h-B


title: E14.5_FT 14_ROW28


title: Tmem258-shRNA-LSB31-0h-A


title: E14.5_FT 14_ROW16


title: E14.5_FT 14_ROW14


title: Tmem258-shRNA-LSB30-2h-A


title: E14.5_FT 14_ROW15


title: E14.5_FT 14_ROW11


title: E14.5_FT 14_ROW10


title: E14.5_FT 14_ROW08


title: Nos2-shRNA-LSB27-2h-B


title: Tmem258-shRNA-LSB30-0h-A


title: E14.5_FT 13_ROW38


title: Dnmt3a-shRNA-LSB52-2h-B


title: Nos2-shRNA-LSB26-2h-B


title: E14.5_FT 13_ROW37


title: Sbno2-shRNA-LSB40-2h-B


title: Sbno2-shRNA-LSB41-2h-B


title: E14.5_FT 13_ROW36


title: Nos2-shRNA-LSB26-2h-A


title: Dnmt3a-shRNA-LSB53-2h-A


title: E14.5_FT 13_ROW33


title: E14.5_FT 13_ROW34


title: Nos2-shRNA-LSB27-2h-A


title: E14.5_FT 13_ROW30


title: Sbno2-shRNA-LSB41-2h-A


title: Nos2-shRNA-LSB27-0h-B


title: Dnmt3a-shRNA-LSB53-0h-B


title: Dnmt3a-shRNA-LSB52-2h-A


title: E14.5_FT 14_ROW06


title: E14.5_FT 13_ROW21


title: E14.5_FT 13_ROW18


title: E14.5_FT 13_ROW26


title: E14.5_FT 13_ROW29


title: Dnmt3a-shRNA-LSB52-0h-B


title: E14.5_FT 13_ROW20


title: E14.5_FT 13_ROW23


title: E14.5_FT 14_ROW05


title: Dnmt3a-shRNA-LSB53-2h-B


title: E14.5_FT 13_ROW16


title: Sbno2-shRNA-LSB41-0h-B


title: E14.5_FT 13_ROW14


title: Nos2-shRNA-LSB27-0h-A


title: Sbno2-shRNA-LSB40-0h-B


title: E14.5_FT 13_ROW12


title: E14.5_FT 13_ROW04


title: Dnmt3a-shRNA-LSB53-0h-A


title: E14.5_FT 12_ROW39


title: E14.5_FT 13_ROW01


title: Dnmt3a-shRNA-LSB52-0h-A


title: Sbno2-shRNA-LSB40-2h-A


title: E14.5_FT 12_ROW38


title: Nos2-shRNA-LSB26-0h-B


title: Sbno2-shRNA-LSB41-0h-A


title: Sbno2-shRNA-LSB40-0h-A


title: E14.5_FT 12_ROW37


title: E14.5_FT 12_ROW35


title: Prdx5-shRNA-LSB37-2h-B


title: E14.5_FT 12_ROW34


title: Prdx5-shRNA-LSB36-2h-B


title: E14.5_FT 12_ROW33


title: Keap1-shRNA-LSB29-2h-B


title: E14.5_FT 12_ROW29


title: Keap1-shRNA-LSB28-2h-B


title: E14.5_FT 12_ROW28


title: Luc-shRNA-LSB48-2h-B


title: E14.5_FT 12_ROW27


title: Keap1-shRNA-LSB29-2h-A


title: Prdx5-shRNA-LSB37-2h-A


title: LacZ-shRNA-LSB49-2h-B


title: Prdx5-shRNA-LSB36-2h-A


title: Nos2-shRNA-LSB26-0h-A


title: E14.5_FT 12_ROW26


title: E14.5_FT 12_ROW23


title: E14.5_FT 12_ROW19


title: E14.5_FT 12_ROW14


title: E14.5_FT 12_ROW11


title: LacZ-shRNA-LSB49-2h-A


title: Keap1-shRNA-LSB28-2h-A


title: Luc-shRNA-LSB48-2h-A


title: Prdx5-shRNA-LSB37-0h-B


title: Prdx5-shRNA-LSB36-0h-B


title: E14.5_FT 12_ROW09


title: Keap1-shRNA-LSB29-0h-B


title: E14.5_FT 12_ROW07


title: E14.5_FT 12_ROW06


title: Keap1-shRNA-LSB28-0h-B


title: Luc-shRNA-LSB48-0h-B


title: LacZ-shRNA-LSB49-0h-B


title: E14.5_FT 12_ROW05


title: E14.5_FT 12_ROW16


title: Keap1-shRNA-LSB28-0h-A


title: Prdx5-shRNA-LSB36-0h-A


title: LacZ-shRNA-LSB49-0h-A


title: E14.5_FT 12_ROW02


title: Keap1-shRNA-LSB29-0h-A


title: E14.5_FT 11_ROW40


title: Luc-shRNA-LSB48-0h-A


title: E14.5_FT 11_ROW39


title: E14.5_FT 11_ROW38


title: E14.5_FT 11_ROW36


title: E14.5_FT 11_ROW34


title: Prdx5-shRNA-LSB37-0h-A


title: E14.5_FT 11_ROW29


title: E14.5_FT 11_ROW28


title: D538G Ral1901 rep3

type: RNA

hyb_protocol: Samples were hybridized for 16 hours at 45 C, 60 RPMs onto U133 Plus 2.0 human genome arrays

scan_protocol: After washing the chips in the Affymetrix Fluidics System 450, they were scanned using the GeneChip 30007G Scanner

data_processing: The data were analyzed with robust multi-array average (RMA) using default analysis settings

label: biotin

label_protocol: Standard Affymetrix protocol

growth_protocol: Engineered MCF7 lines were cultured in media supplemented with 10% FBS.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit.

treatment_protocol: Cells were treated with DMSO or test compounds for ~16h.

tag: cell line

tag: er-alpha mutation


title: D538G Fulvestrant rep2


title: E14.5_FT 11_ROW22


title: D538G Ral1901 rep2


title: E14.5_FT 11_ROW21


title: E14.5_FT 11_ROW33


title: D538G DMSO rep2


title: D538G Ral1901 rep1


title: D538G Fulvestrant rep1


title: D538G Fulvestrant rep3


title: Y537S Fulvestrant rep3


title: D538G DMSO rep1


title: D538G DMSO rep3


title: Y537S Ral1901 rep3


title: E14.5_FT 11_ROW16


title: E14.5_FT 11_ROW17


title: Y537S Ral1901 rep2


title: Y537S Ral1901 rep1


title: E14.5_FT 11_ROW10


title: Y537S Fulvestrant rep1


title: E14.5_FT 10_ROW32

value: Kir-Gfp electroporation


title: E14.5_FT 11_ROW18


title: E14.5_FT 10_ROW39


title: E14.5_FT 10_ROW30


title: E14.5_FT 10_ROW29


title: E14.5_FT 10_ROW24


title: E14.5_FT 10_ROW02


title: E14.5_FT 9_ROW39


title: WT Fulvestrant rep2

value: wild type


title: Y537S DMSO rep2


title: Y537S DMSO rep3


title: WT Fulvestrant rep3

value: Fulvestrant


title: WT Ral1901 rep2


title: E14.5_FT 9_ROW26


title: S22 SS22.P10

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

description: bone marrow FrA plate 11 cell 42

data_processing: The file SCC_GEO_Jensen_2016_Raw.csv contains the raw Ct values. Ct values calculated and exported using Fluidigm Biomark software. Data normalised by subtraction of the median Ct per cell followed by z-score scaling.

label: FAM

label_protocol: Upon thawing, Taq/SSIII enzyme reaction mix (CellsDirect One-Step RT-qPCR kit, Invitrogen) and 96 TaqMan assays at a final dilution of 0.025x were added to each well, excluding 4 wells where no-reverse-transcription control of Taq enzyme (Invitrogen) reaction mix was added. Pre-amplification cycling was preformed according to previously described protocols (Pina et al. 2012) with minor alterations, the first cycle, 50°C at 15min, was extended to 60min.The pre-amplified single-cells were loaded on to a 96.96 Dynamic Array Chip for Gene Expression (Fluidigm) with 96 TaqMan assays and analysed on BioMark HD (Fluidigm).

extract_protocol: Cells were sorted into 96 well plates with 4µl lysis buffer (10%NP40, 10mM dNTP, 0.1M DTT, RNAsout (Invitrogen) and nuclease free water) and immediately frozen at -80°C.

treatment_protocol: Single cell suspension of BM cells were FACS sorted to obtain CLP and FrA cells

tag: genotype

value: wt

value: bone marrow

tag: cell subtype

value: FrA Gfra2+ Bst1+


title: Y537S Fulvestrant rep2


title: WT Ral1901 rep3


title: Y537S DMSO rep1


title: WT Ral1901 rep1


title: E14.5_FT 9_ROW21


title: WT Fulvestrant rep1


title: S23 SS23.P10

description: bone marrow FrA plate 11 cell 40


title: Vehicle Fulvestrant rep3

value: vehicle


title: S26 SS26.P10

description: bone marrow FrA plate 11 cell 39


title: WT DMSO rep1


title: S24 SS24.P10

description: bone marrow FrA plate 11 cell 38


title: E14.5_FT 9_ROW29


title: WT DMSO rep2


title: E14.5_FT 9_ROW13


title: S27 SS27.P10

description: bone marrow FrA plate 11 cell 37


title: E14.5_FT 9_ROW12


title: S19 SS19.P10

description: bone marrow FrA plate 11 cell 36


title: S25 SS25.P10

description: bone marrow FrA plate 11 cell 41


title: Vehicle Fulvestrant rep1


title: Vehicle Ral1901 rep3


title: E14.5_FT 8_ROW39


title: Vehicle Fulvestrant rep2


title: S29 SS29.P10

description: bone marrow FrA plate 11 cell 33


title: Vehicle Ral1901 rep2


title: E14.5_FT 8_ROW27


title: S20 SS20.P10

description: bone marrow FrA plate 11 cell 34


title: S30 SS30.P10

description: bone marrow FrA plate 11 cell 31


title: Vehicle Ral1901 rep1


title: S21 SS21.P10

description: bone marrow FrA plate 11 cell 32


title: E14.5_FT 8_ROW21


title: Vehicle DMSO rep3


title: S16 SS16.P10

description: bone marrow FrA plate 11 cell 30


title: Knockout 4 month old male K12

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

description: Knockout 4 month old male K12

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to mm10 using Tophat
number of read counts was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

source_name: Whole heart RNA

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

value: NBCe1 knockout


title: E14.5_FT 8_ROW02


title: S31 SS31.P10

description: bone marrow FrA plate 11 cell 29


title: S17 SS17.P10

description: bone marrow FrA plate 11 cell 28


title: S32 SS32.P10

description: bone marrow FrA plate 11 cell 27


title: Knockout 4 month old male K11

description: Knockout 4 month old male K11


title: S28 SS28.P10

description: bone marrow FrA plate 11 cell 35


title: E14.5_FT 7_ROW34


title: E14.5_FT 7_ROW40


title: Vehicle DMSO rep1


title: Vehicle DMSO rep2


title: S13 SS13.P10

description: bone marrow FrA plate 11 cell 24


title: S14 SS14.P10

description: bone marrow FrA plate 11 cell 22


title: WT DMSO rep3


title: E14.5_FT 7_ROW28


title: S34 SS34.P10

description: bone marrow FrA plate 11 cell 23


title: E14.5_FT 7_ROW13


title: S35 SS35.P10

description: bone marrow FrA plate 11 cell 21


title: S33 SS33.P10

description: bone marrow FrA plate 11 cell 25


title: Knockout 4 month old male K9

description: Knockout 4 month old male K9


title: Knockout 4 month old male K8

description: Knockout 4 month old male K8


title: S15 SS15.P10

description: bone marrow FrA plate 11 cell 20


title: E14.5_FT 6_ROW34


title: E14.5_FT 6_ROW10


title: S18 SS18.P10

description: bone marrow FrA plate 11 cell 26


title: Knockout 4 month old male K10

description: Knockout 4 month old male K10


title: S36 SS36.P10

description: bone marrow FrA plate 11 cell 19


title: S10 SS10.P10

description: bone marrow FrA plate 11 cell 18


title: S37 SS37.P10

description: bone marrow FrA plate 11 cell 17


title: S38 SS38.P10

description: bone marrow FrA plate 11 cell 15


title: Wild-type 4 month old male W6

description: Wild-type 4 month old male W6


title: E14.5_FT 5_ROW36


title: Wild-type 4 month old male W5

description: Wild-type 4 month old male W5


title: S11 SS11.P10

description: bone marrow FrA plate 11 cell 16


title: S12 SS12.P10

description: bone marrow FrA plate 11 cell 14


title: S39 SS39.P10

description: bone marrow FrA plate 11 cell 13


title: S07 SS7.P10

description: bone marrow FrA plate 11 cell 12


title: Wild-type 4 month old male W4

description: Wild-type 4 month old male W4


title: E14.5_FT 5_ROW27


title: E14.5_FT 5_ROW33


title: Wild-type 4 month old male W3

description: Wild-type 4 month old male W3


title: S40 SS40.P10

description: bone marrow FrA plate 11 cell 11


title: Knockout 4 month old male K7

description: Knockout 4 month old male K7


title: S41 SS41.P10

description: bone marrow FrA plate 11 cell 9


title: S08 SS8.P10

description: bone marrow FrA plate 11 cell 10


title: E14.5_FT 5_ROW22


title: Wild-type 4 month old male W2

description: Wild-type 4 month old male W2


title: S09 SS9.P10

description: bone marrow FrA plate 11 cell 8


title: S42 SS42.P10

description: bone marrow FrA plate 11 cell 7


title: S04 SS4.P10

description: bone marrow FrA plate 11 cell 6


title: E14.5_FT 4_ROW40


title: S05 SS5.P10

description: bone marrow FrA plate 11 cell 5


title: S01 SS1.P10

description: bone marrow FrA plate 11 cell 3


title: S06 SS6.P10

description: bone marrow FrA plate 11 cell 4


title: E14.5_FT 4_ROW39


title: S03 SS3.P10

description: bone marrow FrA plate 11 cell 1


title: S22 SS22.P9

description: bone marrow CLP plate 10 cell 42

value: CLP Ly6d+Gfra2+


title: E14.5_FT 4_ROW38


title: E14.5_FT 4_ROW37


title: S23 SS23.P9

description: bone marrow CLP plate 10 cell 40


title: S25 SS25.P9

description: bone marrow CLP plate 10 cell 41


title: S26 SS26.P9

description: bone marrow CLP plate 10 cell 39


title: E14.5_FT 4_ROW33


title: Wild-type 4 month old male W1

description: Wild-type 4 month old male W1


title: E14.5_FT 4_ROW36


title: E14.5_FT 5_ROW18


title: S19 SS19.P9

description: bone marrow CLP plate 10 cell 36


title: S27 SS27.P9

description: bone marrow CLP plate 10 cell 37


title: S24 SS24.P9

description: bone marrow CLP plate 10 cell 38


title: E14.5_FT 4_ROW32


title: SCC-9 Ctl

city: Guangzhou

first: Guokai

last: Pan

address: 107 Yanjiang West Road

department: Department of Oral and Maxillofacial Surgery

country: China

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

description:
Human tongue squamous cell carcinoma (TSCC) cell line
Gene expression data

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) was applied for hybridization as described by the manufacturer. Slides were hybridized at 65°C for 17h in Agilent's SureHyb Hybridization Chambers.

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Agilent Microarray Scanner (Agilent p/n G2565BA) , then the data were extracted using Agilent Feature Extraction Software

data_processing: Data was extracted using Agilent Feature Extraction software. Results were provided in the Raw Data Files. Normalization was performed using the Agilent GeneSpring GX v12.0 software. Differentially expressed genes were identified through Fold Change filtering.

source_name: SCC9 control group

label_protocol: Quick Amp Labeling Kit (Agilent p/n 5190-0442) was used for sample labeling.

growth_protocol: Two human tongue squamous cell carcinoma cell lines Cal-27 and Scc-9 were obtained from the American Type Culture Collection. Cal-27 cells were cultivated in Dulbecco’s modified Eagle’s medium (Gibco, Rockville, MD, USA) supplemented with 10% fetal bovine serum (Invitrogen, Carlsbad, CA, USA). Scc-9 cells were cultivated in Dulbecco’s modifed Eagle’s medium-F12 (Gibco) supplemented with 10% fetal bovine serum. Cells were cultured at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: CAL-27 and SCC-9 cells, with stably transduced with shRNA targeted LINC01011, were treated with the IC50 of cisplatin (Sigma, USA) for 24 hours for a mRNA microarray assay. Sample labeling and array hybridization were performed by  Agilent Whole Human Genome microarrays (Agilent Technologies, Santa Clara, CA)  according to the Agilent Whole Genome Oligo Microarrays protocol (Arraystar, Inc., Rockville, MD, USA). After quantile normalization of the raw data, the genes detected were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through P value/FDR filtering.

value: SCC-9 cells


title: S02 SS2.P10

description: bone marrow FrA plate 11 cell 2


title: S28 SS28.P9

description: bone marrow CLP plate 10 cell 35


title: S29 SS29.P9

description: bone marrow CLP plate 10 cell 33


title: E14.5_FT 4_ROW31


title: SCC-9 ShRNA2

source_name: SCC9 shRNA2 group


title: S21 SS21.P9

description: bone marrow CLP plate 10 cell 32


title: E14.5_FT 4_ROW30


title: S16 SS16.P9

description: bone marrow CLP plate 10 cell 31


title: CAL-27 Ctl

source_name: CAL27 control group

value: CAL-27 cells


title: S31 SS31.P9

description: bone marrow CLP plate 10 cell 30


title: SCC-9 ShRNA5

source_name: SCC9 shRNA5 group


title: PD-L1-24

city: South San Francisco

first: Craig

last: Cummings

state: CA

address: 1 DNA Way

department: Oncology Biomarker Development

institute: Genentech/Roche

data_processing:
bcl2fastq2 v2.20
fastq-mcf --max-ns 4 --qual-mean 25 -H -p 5 -q 7 -l 25 -l 25
Read alignment: GSNAP version 2013-10-10 (parameters: -M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap)
Genentech in-house RNA-Seq pipeline
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited with four columns: (Entrez gene ID, raw read count, gene feature width [exonic], RPKM)

source_name: tumor

extract_protocol:
High Pure FFPET RNA Isolation Kit
Illumina TruSeq RNA Access Library Prep Kit

tag: timepoint

value: on treatment

value: post-tracer tumor biopsies


title: PD-L1-19


title: E14.5_FT 4_ROW18


title: S20 SS20.P9

description: bone marrow CLP plate 10 cell 34


title: E14.5_FT 11_ROW13

value: FlashTag


title: E14.5_FT 4_ROW15


title: PD-L1-16


title: PD-L1-15


title: CAL-27 ShRNA2

source_name: CAL27 shRNA2 group


title: S33 SS33.P9

description: bone marrow CLP plate 10 cell 26


title: S18 SS18.P9

description: bone marrow CLP plate 10 cell 27


title: S13 SS13.P9

description: bone marrow CLP plate 10 cell 25


title: CAL-27 ShRNA5

source_name: CAL27 shRNA5 group


title: E14.5_FT 4_ROW08


title: PD-L1-14


title: S34 SS34.P9

description: bone marrow CLP plate 10 cell 24


title: E14.5_FT 4_ROW10


title: PD-L1-10


title: S35 SS35.P9

description: bone marrow CLP plate 10 cell 22


title: S15 SS15.P9

description: bone marrow CLP plate 10 cell 21


title: E14.5_FT 3_ROW39


title: E14.5_FT 3_ROW35


title: PD-L1-08


title: S10 SS10.P9

description: bone marrow CLP plate 10 cell 20


title: S14 SS14.P9

description: bone marrow CLP plate 10 cell 23


title: S32 SS32.P9

description: bone marrow CLP plate 10 cell 28


title: S11 SS11.P9

description: bone marrow CLP plate 10 cell 18


title: S37 SS37.P9

description: bone marrow CLP plate 10 cell 19


title: PD-L1-18


title: S38 SS38.P9

description: bone marrow CLP plate 10 cell 17


title: PD-L1-02


title: E14.5_FT 3_ROW23


title: S39 SS39.P9

description: bone marrow CLP plate 10 cell 15


title: S12 SS12.P9

description: bone marrow CLP plate 10 cell 16


title: E14.5_FT 3_ROW22


title: S07 SS7.P9

description: bone marrow CLP plate 10 cell 14


title: S40 SS40.P9

description: bone marrow CLP plate 10 cell 13


title: PD-L1-06


title: E14.5_FT 3_ROW20


title: S13.F11

source_name: human_iPS-derived cerebral organoid

tag: donor id

tag: clone id

tag: age (weeks)

tag: date captured

tag: Sex

value: Male

tag: cell type

value: iPS-derived cerebral organoid

tag: organoid id

tag: capture plate


title: PD-L1-01

tag: tissue


title: E14.5_FT 3_ROW17

tag: developmental age

tag: strain

tag: injection


title: S41 SS41.P9

description: bone marrow CLP plate 10 cell 11


title: S09 SS9.P9

description: bone marrow CLP plate 10 cell 10


title: S04 SS4.P9

description: bone marrow CLP plate 10 cell 9


title: S13.D7

tag: capture chamber


title: E14.5_FT 3_ROW16


title: S08 SS8.P9

description: bone marrow CLP plate 10 cell 12


title: S101.E4


title: S101.A1


title: S05 SS5.P9

description: bone marrow CLP plate 10 cell 8


title: S44 20Cell.P9

description: 20 cell control plate 10


title: S45 SS45.P9

description: bone marrow CLP plate 10 cell 6


title: S101.A10


title: S164.G3


title: E14.5_FT 2_ROW22


title: E14.5_FT 2_ROW13


title: S164.D4


title: E14.5_FT 1_ROW35


title: S02 SS2.P9

description: bone marrow CLP plate 10 cell 3


title: S01 SS1.P9

description: bone marrow CLP plate 10 cell 5


title: S46 SS46.P9

description: bone marrow CLP plate 10 cell 4


title: S148.G4


title: S47 SS47.P9

description: bone marrow CLP plate 10 cell 2


title: S22 SS22.P8

description: bone marrow CLP plate 9 cell 45

value: CLP Ly6d-Gfra2-


title: S25 SS25.P8

description: bone marrow CLP plate 9 cell 44


title: E14.5_FT 1_ROW07

value: Kir-Gfp electroporation


title: E14.5_FT 2_ROW40


title: E14.5_FT 2_ROW34


title: S148.E4


title: S43 10Cell.P9

description: 10 cell control plate 10


title: S23 SS23.P8

description: bone marrow CLP plate 9 cell 43


title: S06 SS6.P9

description: bone marrow CLP plate 10 cell 7


title: S148.E10


title: S26 SS26.P8

description: bone marrow CLP plate 9 cell 42


title: S24 SS24.P8

description: bone marrow CLP plate 9 cell 41


title: E14.5_FT 10_ROW33


title: S19 SS19.P8

description: bone marrow CLP plate 9 cell 39


title: S27 SS27.P8

description: bone marrow CLP plate 9 cell 40


title: S28 SS28.P8

description: bone marrow CLP plate 9 cell 38


title: E14.5_FT 10_ROW18


title: S03 SS3.P9

description: bone marrow CLP plate 10 cell 1


title: S21 SS21.P8

description: bone marrow CLP plate 9 cell 36


title: S98.C10

value: Female


title: E14.5_FT 10_ROW16


title: S98.A11


title: E14.5_FT 10_ROW14


title: E14.5_FT 10_ROW37


title: E14.5_FT 10_ROW04


title: S16 SS16.P8

description: bone marrow CLP plate 9 cell 34


title: S31 SS31.P8

description: bone marrow CLP plate 9 cell 33


title: E14.5_FT 9_ROW40


title: S30 SS30.P8

description: bone marrow CLP plate 9 cell 35


title: S157.H1


title: S17 SS17.P8

description: bone marrow CLP plate 9 cell 32


title: S157.G11


title: S18 SS18.P8

description: bone marrow CLP plate 9 cell 30


title: S32 SS32.P8

description: bone marrow CLP plate 9 cell 31


title: S33 SS33.P8

description: bone marrow CLP plate 9 cell 29


title: S13 SS13.P8

description: bone marrow CLP plate 9 cell 28


title: S157.G4


title: S35 SS35.P8

description: bone marrow CLP plate 9 cell 25


title: S14 SS14.P8

description: bone marrow CLP plate 9 cell 26


title: E14.5_FT 9_ROW38


title: S34 SS34.P8

description: bone marrow CLP plate 9 cell 27


title: S98.G1


title: S157.D8


title: S29 SS29.P8

description: bone marrow CLP plate 9 cell 37


title: E14.5_FT 9_ROW37


title: S15 SS15.P8

description: bone marrow CLP plate 9 cell 24


title: S157.H10


title: E14.5_FT 9_ROW36


title: S157.C6


title: E14.5_FT 9_ROW32


title: S36 SS36.P8

description: bone marrow CLP plate 9 cell 23


title: S10 SS10.P8

description: bone marrow CLP plate 9 cell 22


title: S157.C3


title: S37 SS37.P8

description: bone marrow CLP plate 9 cell 21


title: E14.5_FT 9_ROW19


title: S11 SS11.P8

description: bone marrow CLP plate 9 cell 20


title: S146.H5


title: S12 SS12.P8

description: bone marrow CLP plate 9 cell 18


title: S38 SS38.P8

description: bone marrow CLP plate 9 cell 19


title: E14.5_FT 9_ROW10


title: S146.H2


title: S146.F2


title: E14.5_FT 9_ROW09


title: S08 SS8.P8

description: bone marrow CLP plate 9 cell 14


title: E14.5_FT 9_ROW08


title: S07 SS7.P8

description: bone marrow CLP plate 9 cell 16


title: S40 SS40.P8

description: bone marrow CLP plate 9 cell 15


title: S143.E3


title: E14.5_FT 9_ROW07


title: S43 10Cell.P8

description: 10 cell control plate 9


title: E14.5_FT 9_ROW04


title: S04 SS4.P8

description: bone marrow CLP plate 9 cell 10


title: S41 SS41.P8

description: bone marrow CLP plate 9 cell 13


title: S09 SS9.P8

description: bone marrow CLP plate 9 cell 12


title: S42 SS42.P8

description: bone marrow CLP plate 9 cell 11


title: S202.F5


title: S05 SS5.P8

description: bone marrow CLP plate 9 cell 9


title: E14.5_FT 9_ROW03


title: S201.H3


title: E14.5_FT 8_ROW40


title: S44 20Cell.P8

description: 20 cell control plate 9


title: S45 SS45.P8

description: bone marrow CLP plate 9 cell 7


title: S39 SS39.P8

description: bone marrow CLP plate 9 cell 17


title: S06 SS6.P8

description: bone marrow CLP plate 9 cell 8


title: E14.5_FT 8_ROW34


title: S201.C9


title: S01 SS1.P8

description: bone marrow CLP plate 9 cell 6


title: E14.5_FT 8_ROW33


title: S201.F7


title: S143.C8


title: S47 SS47.P8

description: bone marrow CLP plate 9 cell 3


title: S17 SS17.P9

description: bone marrow CLP plate 10 cell 29


title: S201.A5


title: S02 SS2.P8

description: bone marrow CLP plate 9 cell 4


title: E14.5_FT 8_ROW29


title: S03 SS3.P8

description: bone marrow CLP plate 9 cell 2


title: E14.5_FT 8_ROW20


title: S48 SS48.P8

description: bone marrow CLP plate 9 cell 1


title: S168.H3


title: E14.5_FT 8_ROW18


title: S170.E10


title: E14.5_FT 8_ROW17


title: S166.A4


title: S22 SS22.P7

description: bone marrow FrA plate 8 cell 44

value: FrA Gfra2- Bst1-


title: S23 SS23.P7

description: bone marrow FrA plate 8 cell 42

value: wt


title: S46 SS46.P8

description: bone marrow CLP plate 9 cell 5

value: bone marrow


title: S26 SS26.P7

description: bone marrow FrA plate 8 cell 41


title: S163.F1


title: E14.5_FT 8_ROW12


title: S27 SS27.P7

description: bone marrow FrA plate 8 cell 39


title: S24 SS24.P7

description: bone marrow FrA plate 8 cell 40


title: S163.E7


title: S19 SS19.P7

description: bone marrow FrA plate 8 cell 38


title: S28 SS28.P7

description: bone marrow FrA plate 8 cell 37


title: S20 SS20.P7

description: bone marrow FrA plate 8 cell 36


title: S163.C1


title: S29 SS29.P7

description: bone marrow FrA plate 8 cell 35


title: S163.B5


title: S21 SS21.P7

description: bone marrow FrA plate 8 cell 34


title: E14.5_FT 8_ROW05


title: S30 SS30NoRT.P7

description: bone marrow FrA plate 8 cell 33


title: S16 SS16.P7

description: bone marrow FrA plate 8 cell 32


title: S25 SS25.P7

description: bone marrow FrA plate 8 cell 43


title: S75.D12


title: E14.5_FT 7_ROW39


title: E14.5_FT 8_ROW04


title: S73.G7


title: E14.5_FT 7_ROW38


title: S31 SS31.P7

description: bone marrow FrA plate 8 cell 31


title: S18 SS18.P7

description: bone marrow FrA plate 8 cell 28


title: S33 SS33.P7

description: bone marrow FrA plate 8 cell 27


title: E14.5_FT 7_ROW30


title: E14.5_FT 8_ROW07


title: S73.B5


title: S13 SS13.P7

description: bone marrow FrA plate 8 cell 26


title: S73.H3


title: S77.E4


title: S14 SS14.P7

description: bone marrow FrA plate 8 cell 24


title: S34 SS34.P7

description: bone marrow FrA plate 8 cell 25


title: S35 SS35.P7

description: bone marrow FrA plate 8 cell 23


title: S15 SS15.P7

description: bone marrow FrA plate 8 cell 22


title: E14.5_FT 7_ROW21


title: E14.5_FT 7_ROW18


title: S36 SS36NoRT.P7

description: bone marrow FrA plate 8 cell 21


title: S77.C8


title: S10 SS10.P7

description: bone marrow FrA plate 8 cell 20


title: S77.B4


title: S37 SS37.P7

description: bone marrow FrA plate 8 cell 19


title: E14.5_FT 7_ROW15


title: S38 SS38.P7

description: bone marrow FrA plate 8 cell 17


title: S11 SS11.P7

description: bone marrow FrA plate 8 cell 18


title: S32 SS32.P7

description: bone marrow FrA plate 8 cell 29


title: S77.A5


title: E14.5_FT 7_ROW07


title: S12 SS12.P7

description: bone marrow FrA plate 8 cell 16


title: E14.5_FT 7_ROW24


title: S39 SS39.P7

description: bone marrow FrA plate 8 cell 15


title: S07 SS7.P7

description: bone marrow FrA plate 8 cell 14


title: S10.C10


title: E14.5_FT 7_ROW02


title: S10.A10


title: E14.5_FT 6_ROW40


title: S17 SS17.P7

description: bone marrow FrA plate 8 cell 30


title: S08 SS8.P7

description: bone marrow FrA plate 8 cell 12


title: S6.H2


title: S09 SS9.P7

description: bone marrow FrA plate 8 cell 10


title: S6.F9


title: E14.5_FT 6_ROW39


title: S43 10Cell.P7

description: 10 cell control plate 8


title: S04 SS4.P7

description: bone marrow FrA plate 8 cell 9


title: E14.5_FT 6_ROW38


title: S6.D11


title: S6.D8


title: E14.5_FT 6_ROW30


title: S6.B7


title: S06 SS6.P7

description: bone marrow FrA plate 8 cell 7


title: S44 20Cell.P7

description: 20 cell control plate 8


title: S41 SS41.P7

description: bone marrow FrA plate 8 cell 11


title: S47 SS47.P7

description: bone marrow FrA plate 8 cell 2


title: E14.5_FT 6_ROW37


title: S03 SS3.P7

description: bone marrow FrA plate 8 cell 1


title: S22 SS22.P6

description: bone marrow CLP plate 7 cell 44

value: CLP Ly6d+Gfra2-


title: S25 SS25.P6

description: bone marrow CLP plate 7 cell 43


title: S46 SS46.P7

description: bone marrow FrA plate 8 cell 4


title: S8.B2


title: E14.5_FT 6_ROW12


title: S6.A3


title: S23 SS23.P6

description: bone marrow CLP plate 7 cell 42


title: E14.5_FT 6_ROW09


title: S11.C6


title: S24 SS24.P6

description: bone marrow CLP plate 7 cell 40


title: S45 SS45.P7

description: bone marrow FrA plate 8 cell 6


title: E14.5_FT 6_ROW31


title: S26 SS26.P6

description: bone marrow CLP plate 7 cell 41


title: E14.5_FT 6_ROW08


title: E14.5_FT 6_ROW03


title: E14.5_FT 6_ROW16


title: S6.E11


title: E14.5_FT 6_ROW01


title: S21 SS21.P6

description: bone marrow CLP plate 7 cell 34


title: S29 SS29.P6

description: bone marrow CLP plate 7 cell 35


title: E14.5_FT 5_ROW39


title: S19 SS19.P6

description: bone marrow CLP plate 7 cell 38


title: S28 SS28.P6

description: bone marrow CLP plate 7 cell 37


title: S27 SS27.P6

description: bone marrow CLP plate 7 cell 39


title: S05 SS5.P7

description: bone marrow FrA plate 8 cell 8


title: S20 SS20.P6

description: bone marrow CLP plate 7 cell 36


title: S16 SS16.P6

description: bone marrow CLP plate 7 cell 32


title: E14.5_FT 5_ROW32


title: E14.5_FT 5_ROW38


title: S30 SS30.P6

description: bone marrow CLP plate 7 cell 33


title: S31 SS31.P6

description: bone marrow CLP plate 7 cell 31


title: E14.5_FT 5_ROW29


title: S17 SS17.P6

description: bone marrow CLP plate 7 cell 30


title: S18 SS18.P6

description: bone marrow CLP plate 7 cell 28


title: S32 SS32.P6

description: bone marrow CLP plate 7 cell 29


title: E14.5_FT 5_ROW26


title: E14.5_FT 5_ROW24


title: S01 SS1.P7

description: bone marrow FrA plate 8 cell 5


title: S34 SS34.P6

description: bone marrow CLP plate 7 cell 25


title: S14 SS14.P6

description: bone marrow CLP plate 7 cell 24


title: S35 SS35.P6

description: bone marrow CLP plate 7 cell 23


title: S15 SS15.P6

description: bone marrow CLP plate 7 cell 22


title: S36 SS36.P6

description: bone marrow CLP plate 7 cell 21


title: S40 SS40.P7

description: bone marrow FrA plate 8 cell 13


title: E14.5_FT 5_ROW21


title: S02 SS2.P7

description: bone marrow FrA plate 8 cell 3


title: S10 SS10.P6

description: bone marrow CLP plate 7 cell 20


title: E14.5_FT 5_ROW04


title: E14.5_FT 5_ROW17


title: E14.5_FT 5_ROW20


title: S33 SS33.P6

description: bone marrow CLP plate 7 cell 27


title: E14.5_FT 5_ROW10


title: E14.5_FT 5_ROW02


title: S12 SS12.P6

description: bone marrow CLP plate 7 cell 16


title: S38 SS38.P6

description: bone marrow CLP plate 7 cell 17


title: S40 SS40.P6

description: bone marrow CLP plate 7 cell 13


title: S39 SS39.P6

description: bone marrow CLP plate 7 cell 15


title: S11 SS11.P6

description: bone marrow CLP plate 7 cell 18


title: S07 SS7.P6

description: bone marrow CLP plate 7 cell 14


title: S41 SS41.P6

description: bone marrow CLP plate 7 cell 11


title: S04 SS4.P6

description: bone marrow CLP plate 7 cell 9


title: S13 SS13.P6

description: bone marrow CLP plate 7 cell 26


title: S08 SS8.P6

description: bone marrow CLP plate 7 cell 12


title: E14.5_FT 4_ROW34


title: S09 SS9.P6

description: bone marrow CLP plate 7 cell 10


title: E14.5_FT 4_ROW24


title: S37 SS37.P6

description: bone marrow CLP plate 7 cell 19


title: S43 10Cell.P6

description: 10 cell control plate 7


title: S05 SS5.P6

description: bone marrow CLP plate 7 cell 8


title: S44 20Cell.P6

description: 20 cell control plate 7


title: S06 SS6.P6

description: bone marrow CLP plate 7 cell 7


title: E14.5_FT 4_ROW19


title: S45 SS45.P6

description: bone marrow CLP plate 7 cell 6


title: S01 SS1.P6

description: bone marrow CLP plate 7 cell 5


title: E14.5_FT 4_ROW16


title: S46 SS46.P6

description: bone marrow CLP plate 7 cell 4


title: S02 SS2.P6

description: bone marrow CLP plate 7 cell 3


title: E14.5_FT 3_ROW26


title: E14.5_FT 3_ROW24


title: E14.5_FT 3_ROW21


title: S03 SS3.P6

description: bone marrow CLP plate 7 cell 1


title: E14.5_FT 3_ROW14


title: S22 SS22.P5

description: bone marrow CLP plate 6 cell 42


title: E14.5_FT 3_ROW18


title: S25 SS25.P5

description: bone marrow CLP plate 6 cell 41


title: S26 SS26.P5

description: bone marrow CLP plate 6 cell 39


title: S24 SS24.P5

description: bone marrow CLP plate 6 cell 38


title: S19 SS19.P5

description: bone marrow CLP plate 6 cell 36


title: S23 SS23.P5

description: bone marrow CLP plate 6 cell 40


title: S28 SS28.P5

description: bone marrow CLP plate 6 cell 35


title: S27 SS27.P5

description: bone marrow CLP plate 6 cell 37


title: S20 SS20.P5

description: bone marrow CLP plate 6 cell 34


title: E14.5_FT 4_ROW20


title: E14.5_FT 3_ROW13


title: E14.5_FT 3_ROW01


title: S16 SS16.P5

description: bone marrow CLP plate 6 cell 31


title: E14.5_FT 2_ROW37


title: E14.5_FT 2_ROW36


title: S21 SS21.P5

description: bone marrow CLP plate 6 cell 32


title: S17 SS17.P5

description: bone marrow CLP plate 6 cell 29


title: S32 SS32.P5

description: bone marrow CLP plate 6 cell 28


title: S18 SS18.P5

description: bone marrow CLP plate 6 cell 27


title: E14.5_FT 2_ROW35


title: S31 SS31.P5

description: bone marrow CLP plate 6 cell 30


title: S33 SS33.P5

description: bone marrow CLP plate 6 cell 26


title: S47 SS47.P6

description: bone marrow CLP plate 7 cell 2


title: E14.5_FT 2_ROW33


title: S14 SS14.P5

description: bone marrow CLP plate 6 cell 23


title: E14.5_FT 2_ROW29


title: S29 SS29.P5

description: bone marrow CLP plate 6 cell 33


title: S35 SS35.P5

description: bone marrow CLP plate 6 cell 22


title: E14.5_FT 2_ROW24


title: E14.5_FT 2_ROW26


title: S34 SS34.P5

description: bone marrow CLP plate 6 cell 24


title: S15 SS15.P5

description: bone marrow CLP plate 6 cell 21


title: E14.5_FT 2_ROW23


title: S10 SS10.P5

description: bone marrow CLP plate 6 cell 20


title: S11 SS11.P5

description: bone marrow CLP plate 6 cell 18


title: S38 SS38.P5

description: bone marrow CLP plate 6 cell 17


title: S37 SS37.P5

description: bone marrow CLP plate 6 cell 19


title: S39 SS39.P5

description: bone marrow CLP plate 6 cell 15


title: S07 SS7.P5

description: bone marrow CLP plate 6 cell 14


title: E14.5_FT 2_ROW21


title: E14.5_FT 2_ROW17


title: S40 SS40.P5

description: bone marrow CLP plate 6 cell 13


title: S41 SS41.P5

description: bone marrow CLP plate 6 cell 11


title: S08 SS8.P5

description: bone marrow CLP plate 6 cell 12


title: E14.5_FT 2_ROW16


title: S13 SS13.P5

description: bone marrow CLP plate 6 cell 25


title: S04 SS4.P5

description: bone marrow CLP plate 6 cell 9


title: S43 10Cell.P5

description: 10 cell control plate 6


title: S09 SS9.P5

description: bone marrow CLP plate 6 cell 10


title: E14.5_FT 2_ROW14


title: S05 SS5.P5

description: bone marrow CLP plate 6 cell 8


title: E14.5_FT 2_ROW07


title: S06 SS6.P5

description: bone marrow CLP plate 6 cell 7


title: E14.5_FT 1_ROW40


title: S44 20Cell.P5

description: 20 cell control plate 6


title: E14.5_FT 1_ROW39


title: S01 SS1.P5

description: bone marrow CLP plate 6 cell 5


title: S02 SS2.P5

description: bone marrow CLP plate 6 cell 3


title: S47 SS47.P5

description: bone marrow CLP plate 6 cell 2


title: S46 SS46.P5

description: bone marrow CLP plate 6 cell 4


title: S03 SS3.P5

description: bone marrow CLP plate 6 cell 1


title: E14.5_FT 1_ROW38


title: S22 SS22.P4

description: bone marrow CLP plate 5 cell 42


title: S25 SS25.P4

description: bone marrow CLP plate 5 cell 41


title: S23 SS23.P4

description: bone marrow CLP plate 5 cell 40


title: E14.5_FT 1_ROW33


title: S24 SS24.P4

description: bone marrow CLP plate 5 cell 38


title: E14.5_FT 2_ROW10


title: MCF7 5942 rep2

data_processing:
FASTQ file sequenced by Illumina HiSeqTM4000
After sequencing ,the raw reads were filtered.Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads
Transcript per million (TPM) were calculated using kallisto with default settings
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files generated by Kallisto with fields: gene_name: name of gene; length: length of the gene; eff_length: effective length of the gene; est_counts: estimated read count; tpm: transcript per million

growth_protocol: MCF cell were maintained in DMEM supplemented with 10% FBS, 4 mM L-glutamine and 1x non-essential amino acids.

extract_protocol:
RNA was collected using Trizol extraction
Non-stranded polyA mRNA library constructed at BGI

treatment_protocol: Cells were treated with indicated compounds at 100nM with media and compounds refreshed after 3 daysfor a total of 6 days treatment before harvesting.

tag: cell line

tag: treatment


title: MCF7 5942 rep3


title: S19 SS19.P4

description: bone marrow CLP plate 5 cell 36

tag: genotype

tag: cell subtype


title: MCF7 5942 rep1


title: S27 SS27.P4

description: bone marrow CLP plate 5 cell 37


title: S45 SS45.P5

description: bone marrow CLP plate 6 cell 6


title: S28 SS28.P4

description: bone marrow CLP plate 5 cell 35


title: E14.5_FT 1_ROW31


title: E14.5_FT 1_ROW28


title: MCF7 Fulvestrant rep3

value: Fulvestrant


title: S20 SS20.P4

description: bone marrow CLP plate 5 cell 34


title: S29 SS29.P4

description: bone marrow CLP plate 5 cell 33


title: E14.5_FT 1_ROW25


title: S16 SS16.P4

description: bone marrow CLP plate 5 cell 31


title: E14.5_FT 1_ROW26


title: E14.5_FT 1_ROW34


title: S26 SS26.P4

description: bone marrow CLP plate 5 cell 39


title: S31 SS31.P4

description: bone marrow CLP plate 5 cell 30


title: S17 SS17.P4

description: bone marrow CLP plate 5 cell 29


title: MCF7 Fulvestrant rep1


title: S32 SS32.P4

description: bone marrow CLP plate 5 cell 28


title: E14.5_FT 1_ROW24


title: S12 SS12.P5

description: bone marrow CLP plate 6 cell 16


title: S18 SS18.P4

description: bone marrow CLP plate 5 cell 27


title: MCF7 Tamoxifen rep3

value: Tamoxifen


title: E14.5_FT 1_ROW23


title: S33 SS33.P4

description: bone marrow CLP plate 5 cell 26


title: S13 SS13.P4

description: bone marrow CLP plate 5 cell 25


title: S34 SS34.P4

description: bone marrow CLP plate 5 cell 24


title: S21 SS21.P4

description: bone marrow CLP plate 5 cell 32


title: S14 SS14.P4

description: bone marrow CLP plate 5 cell 23


title: E14.5_FT 1_ROW19


title: MCF7 Tamoxifen rep1


title: S35 SS35.P4

description: bone marrow CLP plate 5 cell 22


title: E14.5_FT 1_ROW09


title: MCF7 DMSO RNASeq rep3

value: DMSO


title: MCF7 Fulvestrant rep2


title: S15 SS15.P4

description: bone marrow CLP plate 5 cell 21


title: S10 SS10.P4

description: bone marrow CLP plate 5 cell 20


title: MCF7 DMSO RNASeq rep2


title: S37 SS37.P4

description: bone marrow CLP plate 5 cell 19


title: S11 SS11.P4

description: bone marrow CLP plate 5 cell 18


title: E14.5_FT 1_ROW08


title: Gdc810.30nM.rep2

source_name: Ishikawa

growth_protocol: Ishikawa cell were cultured in DMEM supplemented with 5% CSS, trypsinized, washed with basal media (DMEM/F12 + 15 mM HEPES) 3 times for 5 minutes each. Cells were then seeded at 800,000 cells/well in basal medium in a 6-well plate. Compounds were added seven hours post plating.

treatment_protocol: Cells were treated with indicated compounds at 3nM and 30nM for 24 hours before collection.

value: Ishikawa

tag: dosage


title: MCF7 DMSO RNASeq rep1


title: E14.5_FT 1_ROW06


title: E14.5_FT 1_ROW03


title: MCF7 Tamoxifen rep2


title: S12 SS12.P4

description: bone marrow CLP plate 5 cell 16


title: S40 SS40.P4

description: bone marrow CLP plate 5 cell 13


title: S39 SS39.P4

description: bone marrow CLP plate 5 cell 15


title: S07 SS7.P4

description: bone marrow CLP plate 5 cell 14


title: Gdc810.30nM.rep1


title: P3_E15.5_CT 3

data_processing:
aligned to UCSC mm10 avec TopHat v. 2.0.11
number of reads per feature counted with Htseq v.0.6.1
Genes were filtered with the following specification:  at least 10 Reads per Million in all samples
Genome_build: mm10
Supplementary_files_format_and_content: .txt file containing expression value

extract_protocol:
Qiagen Rneasy Plus Micro
Smarter+Nextera

tag: age

tag: electroporated plasmid

value: mcherry


title: E14.5_FT 1_ROW20


title: S08 SS8.P4

description: bone marrow CLP plate 5 cell 12


title: S41 SS41.P4

description: bone marrow CLP plate 5 cell 11


title: Gdc810.3nM.rep2


title: P3_E15.5_CT 2


title: S04 SS4.P4

description: bone marrow CLP plate 5 cell 9


title: Gdc810.3nM.rep1


title: P3_E15.5_CT 1


title: H3B9224.30nM.rep2


title: S38 SS38.P4

description: bone marrow CLP plate 5 cell 17


title: S09 SS9.P4

description: bone marrow CLP plate 5 cell 10


title: S44 20Cell.P4

description: 20 cell control plate 5


title: P3_E14.5_Kir 3

value: Kir-Gfp


title: S43 10Cell.P4

description: 10 cell control plate 5


title: H3B9224.30nM.rep1


title: P3_E14.5_Kir 2


title: H3B9224.3nM.rep2


title: S06 SS6.P4

description: bone marrow CLP plate 5 cell 7


title: S01 SS1.P4

description: bone marrow CLP plate 5 cell 5


title: P3_E14.5_Kir 1


title: S46 SS46.P4

description: bone marrow CLP plate 5 cell 4


title: S45 SS45.P4

description: bone marrow CLP plate 5 cell 6


title: P3_E14.5_CT 4


title: S02 SS2.P4

description: bone marrow CLP plate 5 cell 3


title: H3B5942.30nM.rep2


title: P3_E14.5_CT 3


title: H3B9224.3nM.rep1


title: S47 SS47.P4

description: bone marrow CLP plate 5 cell 2


title: S25 SS25.P3

description: bone marrow FrA plate 4 cell 40

value: FrA Gfra2+ Bst1-


title: S23 SS23.P3

description: bone marrow FrA plate 4 cell 39


title: H3B5942.30nM.rep1


title: S22 SS22.P3

description: bone marrow FrA plate 4 cell 41


title: P3_E14.5_CT 2


title: S05 SS5.P4

description: bone marrow CLP plate 5 cell 8


title: H3B5942.3nM.rep2


title: H3B5942.3nM.rep1


title: S27 SS27.P3

description: bone marrow FrA plate 4 cell 36


title: S26 SS26.P3

description: bone marrow FrA plate 4 cell 38


title: S24 SS24.P3

description: bone marrow FrA plate 4 cell 37


title: Tamoxifen.30nM.rep2


title: 1 CLP

first: Andrew

last: McKenzie

address: Francis Crick Ave

department: PNAC

institute: MRC LMB

data_processing:
Basecalling and quality control was performed using Illumina RTA softare on the Hiseq2500 and HiSEQ4000
Sequence Quality was assessed and reads were trimmed using Partek Flow
Reads were aligned to the mm10 genome assembly using Tophat2 in Partek Flow
RPKM were calculated using Partek gemonic stuite using RefSeq transcripts 82 - 2017 - 08 - 02
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: CLPs from the Bone Marrow of naïve mice

growth_protocol: Primary cells were used

extract_protocol:
RNA was harvested using Trizol reagent and Qiagen kits followed by Nugen Ovation for cDNA
Nugen Ovation Ultralow Library Systems

treatment_protocol: Where indicated mice were treated with IL-33 or PBS intranasally

value: CLPs


title: 2 CLP


title: S19 SS19.P3

description: bone marrow FrA plate 4 cell 35


title: Tamoxifen.30nM.rep1


title: S03 SS3.P4

description: bone marrow CLP plate 5 cell 1


title: S28 SS28.P3

description: bone marrow FrA plate 4 cell 34


title: S20 SS20.P3

description: bone marrow FrA plate 4 cell 33


title: S17 SS17.P3

description: bone marrow FrA plate 4 cell 29


title: Tamoxifen.3nM.rep1


title: S31 SS31.P3

description: bone marrow FrA plate 4 cell 30


title: S32 SS32.P3

description: bone marrow FrA plate 4 cell 28


title: S16 SS16.P3

description: bone marrow FrA plate 4 cell 31


title: S29 SS29.P3

description: bone marrow FrA plate 4 cell 32


title: Fulvestrant.30nM.rep2


title: S13 SS13.P3

description: bone marrow FrA plate 4 cell 25


title: S33 SS33.P3

description: bone marrow FrA plate 4 cell 26


title: Fulvestrant.30nM.rep1


title: S34 SS34.P3

description: bone marrow FrA plate 4 cell 24


title: S35 SS35.P3

description: bone marrow FrA plate 4 cell 22


title: Fulvestrant.3nM.rep2


title: S15 SS15.P3

description: bone marrow FrA plate 4 cell 21


title: S10 SS10.P3

description: bone marrow FrA plate 4 cell 20


title: Fulvestrant.3nM.rep1


title: S14 SS14.P3

description: bone marrow FrA plate 4 cell 23


title: S37 SS37.P3

description: bone marrow FrA plate 4 cell 19


title: E2.30nM.rep2


title: S11 SS11.P3

description: bone marrow FrA plate 4 cell 18


title: S38 SS38.P3

description: bone marrow FrA plate 4 cell 17


title: E2.30nM.rep1


title: S18 SS18.P3

description: bone marrow FrA plate 4 cell 27


title: S39 SS39.P3

description: bone marrow FrA plate 4 cell 15


title: Tamoxifen.3nM.rep2


title: S12 SS12.P3

description: bone marrow FrA plate 4 cell 16


title: E2.3nM.rep2


title: S07 SS7.P3

description: bone marrow FrA plate 4 cell 14


title: E2.3nM.rep1


title: S08 SS8.P3

description: bone marrow FrA plate 4 cell 12


title: S09 SS9.P3

description: bone marrow FrA plate 4 cell 10


title: S40 SS40.P3

description: bone marrow FrA plate 4 cell 13


title: DMSO.DMSO.rep2


title: S41 SS41.P3

description: bone marrow FrA plate 4 cell 11


title: DMSO.DMSO.rep1


title: S04 SS4.P3

description: bone marrow FrA plate 4 cell 9


title: S05 SS5.P3

description: bone marrow FrA plate 4 cell 8


title: S43 10Cell.P3

description: 10 cell control plate 4


title: S44 20Cell.P3

description: 20 cell control plate 4


title: Liver_Nano_21d_rep5

city: Leioa

first: José María

last: Lacave

state: Bizkaia

address: Sarriena s/n

department: Zoology and Animal Cell Biology

country: Spain

institute: University of the Basque Country

hyb_protocol: Chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 1.65 ug. Volume: 100 uL. Temperature (oC): 65. Duration: 17 hours at 10 rpm in the hybridization oven.

scan_protocol: Scanned on a G2565CA DNA microarray scanner (Agilent Technologies), with ozone-barrier slide covers (Agilent P/N G2505-60550) SCAN C SETTINGS Dye Channel Scan RegionGreen 61 x 21,6 mm Scan resolution (um) 6 Tiff 20 bit

data_processing: Images (.tiff images) were quantified using Agilent Feature Extraction Software (ver. 10.7.3.1) (Agilent Technologies). The Feature Extraction software (FE) extracts the raw data from Cy3 (Green(g) channel) fluorescence signal (mean signal) from the spot which contains the probes (control features and biological or non control features) and from background. After processing of the raw signal it applies several algorithms for the calculation of the processed signal, which will be used in the analysis, and other useful data for the assessment of the quality of the processed data. The processed signal is corrected for background and microarray processing artifacts (Spatial detrending). For background correction it uses the negative control feature data, which corresponds to sequences with no expected hybridization, and it is an indication of unspecific binding or hybridization. Processed data were filtered based on present/absent calls. Entities retained in which 80 % of samplesin 1 out of any 6 conditions (3d Control, 3d Ionic, 3d Nano, 3w  Control, 3w Ionic, 3w Nano) have Present or Marginal Flag. More detailed data processing description is available on the series record.

organism: Danio rerio

source_name: Liver, Ag NPs, 21d

label_protocol: Amount of nucleic acid labeled: 100 ng. Agilent Protocol One-Color Microarray-Based Gene Expression analysis (Low Input Quick Amp Labeling) Version 6.5 May 2010. Samples are retrotranscribed (first strand synthesis) and labeled using Low imput Quick Amp Labeling kit, One color (Agilent Technologies, Cat. Nº 5190-2305) following manufacturer instructions. First, total RNA is retrotranscribed with AffinityScript Reverse Transcriptase (AffinityScript RT), an engineered thermostable mutant derived from Moloney Murine Leukemia Virus (MMLV) reverse transcriptase, using Oligo dT primers coupled to T7 promoter. Double stranded cDNA synthesized by AffinityScript RT is in vitro transcribed by T7 RNA pol in the presence of either Cy3-CTP or Cy5-CTP fluorophores to generate amplified and labeled cRNA. Labeled samples are purified with silica-based RNeasy spin columns (Qiagen). After labeling and purification, cRNA is quantify with NanoDrop ND-1000 spectrophotometer in order to determine the yield and specific activity of each reaction. Yield: µg of cRNA. Should be > 1.65 µg. Specific activity: pmol Cy3 per µg of cRNA. Should be >6. All the labeled samples where above those limits.

extract_protocol: Total RNA was extracted following the TRizol® extraction method (ThermoFisher Scientific). Concentration of RNA was measured in a Biophotometer (Eppendorf, Hamburg, Germany). RNA was purified with RNeasy mini kit (Qiagen, Venlo, The Netherlands). In addition, RNA quality was assessed in an Agilent 2100 Bioanalyzer (Agilent Technologies). Only RNA samples with a RIN value above 8.1 were used for microarray and qPCR analysis.

treatment_protocol: Samples were waterborne exposed to 0.01 mg/L of maltose-coated Ag NPs of 20 nm or ionic silver for 3 and 21 days

value: Liver

value: Wildtype AB/Tuebingen

tag: gender

value: Male

tag: days of exposure


title: HeLa Chromatin-associated RNA-seq poly(I:C) 3

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

data_processing:
Raw sequence files are QC assessed using FASTQC
Paired sequences were aligned to the human genome hg19 using bowtie2 (version version 2.2.7; parameters: --very-sensitive --no-unal --no-mixed --no-discordant)
BAM files were sorted and indexed using samtools (version 1.3)
Read counts were extracted from relevant regions using bedtools (version v2.23.0; parameters: multicov)
Human miRNA reference sequences were obtained from miRBase (version 21)
Read depths were determined using samtools (version 1.3; parameters: -d 1000000)
Genome_build: hg19_p4, annotation release 83 from Ensembl
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts for miRNA precursors and flanking regions

source_name: HeLa cells

growth_protocol: HeLa cells were grown in standard media (DMEM, 10%FBS, Pen/strept), 37C and 5%CO2

extract_protocol:
After enriching for the chromatin fraction, RNA was extracted using Trizol LS
Eight RNA samples were prepared for sequencing by BGI. Strand specific RNA Transcriptome sequencing, including ribo-zero rRNA depletion and random fragmentation and strand specific library construction, to be sequenced by Illumina HiSeq 4000, 100PE.

treatment_protocol: poly(I:C) at a final conc 1yg/ml was transfected in cells using Lipofectamine 2000

value: HeLa cells


title: Liver_Nano_21d_rep3


title: S06 SS6.P3

description: bone marrow FrA plate 4 cell 7


title: Liver_Nano_21d_rep2


title: S46 SS46.P3

description: bone marrow FrA plate 4 cell 4


title: S01 SS1.P3

description: bone marrow FrA plate 4 cell 5


title: Liver_Nano_21d_rep4


title: Liver_Ionic_21d_rep4

source_name: Liver, Ionic silver, 21d


title: HeLa Chromatin-associated RNA-seq poly(I:C) 4


title: Liver_Nano_21d_rep1


title: Liver_Ionic_21d_rep1


title: S02 SS2.P3

description: bone marrow FrA plate 4 cell 3


title: Liver_Ionic_21d_rep2


title: HeLa Chromatin-associated RNA-seq poly(I:C) 2


title: HeLa Chromatin-associated RNA-seq poly(I:C) 1


title: HeLa Chromatin-associated RNA-seq mock 3


title: S23 SS23.P2

description: bone marrow FrA plate 3 cell 40


title: S03 SS3.P3

description: bone marrow FrA plate 4 cell 1


title: S47 SS47.P3

description: bone marrow FrA plate 4 cell 2


title: S26 SS26.P2

description: bone marrow FrA plate 3 cell 39


title: S22 SS22.P2

description: bone marrow FrA plate 3 cell 42


title: Liver_Control_21d_rep5

source_name: Liver, Control 21d


title: Liver_Ionic_21d_rep5


title: S45 SS45.P3

description: bone marrow FrA plate 4 cell 6


title: S24 SS24.P2

description: bone marrow FrA plate 3 cell 38


title: HeLa Chromatin-associated RNA-seq mock 1


title: S27 SS27.P2

description: bone marrow FrA plate 3 cell 37


title: HeLa Chromatin-associated RNA-seq mock 4


title: S19 SS19.P2

description: bone marrow FrA plate 3 cell 36


title: Liver_Control_21d_rep3


title: S25 SS25.P2

description: bone marrow FrA plate 3 cell 41


title: S28 SS28.P2

description: bone marrow FrA plate 3 cell 35


title: Liver_Ionic_21d_rep3


title: Liver_Nano_3d_rep5

source_name: Liver, Ag NPs, 3d


title: Liver_Control_21d_rep1


title: S16 SS16.P2

description: bone marrow FrA plate 3 cell 31


title: Liver_Control_21d_rep4


title: S29 SS29.P2

description: bone marrow FrA plate 3 cell 33


title: S31 SS31.P2

description: bone marrow FrA plate 3 cell 30


title: S21 SS21.P2

description: bone marrow FrA plate 3 cell 32


title: S32 SS32.P2

description: bone marrow FrA plate 3 cell 28


title: Liver_Nano_3d_rep4


title: S18 SS18.P2

description: bone marrow FrA plate 3 cell 27


title: S20 SS20.P2

description: bone marrow FrA plate 3 cell 34


title: HeLa Chromatin-associated RNA-seq mock 2


title: S33 SS33.P2

description: bone marrow FrA plate 3 cell 26


title: S34 SS34.P2

description: bone marrow FrA plate 3 cell 24


title: S13 SS13.P2

description: bone marrow FrA plate 3 cell 25


title: S35 SS35.P2

description: bone marrow FrA plate 3 cell 22


title: S14 SS14.P2

description: bone marrow FrA plate 3 cell 23


title: S10 SS10.P2

description: bone marrow FrA plate 3 cell 20


title: S37 SS37.P2

description: bone marrow FrA plate 3 cell 19


title: S15 SS15.P2

description: bone marrow FrA plate 3 cell 21


title: S11 SS11.P2

description: bone marrow FrA plate 3 cell 18


title: S17 SS17.P2

description: bone marrow FrA plate 3 cell 29


title: Liver_Ionic_3d_rep5

source_name: Liver, Ionic silver, 3d


title: Liver_Nano_3d_rep1


title: Liver_Nano_3d_rep3


title: Liver_Nano_3d_rep2


title: Liver_Ionic_3d_rep4


title: S12 SS12.P2

description: bone marrow FrA plate 3 cell 16


title: S38 SS38.P2

description: bone marrow FrA plate 3 cell 17


title: Liver_Ionic_3d_rep3


title: S40 SS40.P2

description: bone marrow FrA plate 3 cell 13


title: S39 SS39.P2

description: bone marrow FrA plate 3 cell 15


title: S08 SS8.P2

description: bone marrow FrA plate 3 cell 12


title: Liver_Control_3d_rep5

source_name: Liver, Control 3d


title: S07 SS7.P2

description: bone marrow FrA plate 3 cell 14


title: S05 SS5.P2

description: bone marrow FrA plate 3 cell 8


title: S09 SS9.P2

description: bone marrow FrA plate 3 cell 10


title: S43 10Cell.P2

description: 10 cell control plate 3


title: S44 20Cell.P2

description: 20 cell control plate 3


title: S06 SS6.P2

description: bone marrow FrA plate 3 cell 7


title: S04 SS4.P2

description: bone marrow FrA plate 3 cell 9


title: S45 SS45.P2

description: bone marrow FrA plate 3 cell 6


title: S01 SS1.P2

description: bone marrow FrA plate 3 cell 5


title: Liver_Control_3d_rep3


title: Liver_Ionic_3d_rep1


title: Liver_Control_3d_rep2


title: Mus_12B-6: WT melatonin, biological rep 6

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 hybridized on Affymetrix GeneChip Mouse Gene 2.0 ST array,  according to manufacturer's instructions. GeneChips were washed and stained on the GeneAltas platform.

scan_protocol: GeneChips were scanned on the GeneAltas platform.

data_processing: The data were analyzed with GeneSpring GX Software v. 14.8 using default Affymetrix settings.

source_name: WT - melatonin

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

growth_protocol: The mice were collected at 4 weeks of age, 3 hours after lights off.

extract_protocol: Total RNA was extracted using Qiagen miRNeasy spin columns according to the manufacturer's instructions.

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

tag: background strain

value: myocardium


title: S02 SS2.P2

description: bone marrow FrA plate 3 cell 3


title: Mus_11B-5: WT melatonin, biological rep 5


title: Liver_Control_3d_rep4


title: S03 SS3.P2

description: bone marrow FrA plate 3 cell 1


title: S41 SS41.P2

description: bone marrow FrA plate 3 cell 11


title: S22 SS22.P1

description: bone marrow FrA plate 2 cell 41

value: FrA Gfra2- Bst1-


title: Mus_10B-4: WT melatonin, biological rep 4


title: Mus_8B-2: WT melatonin, biological rep 2


title: Mus_7B-1: WT melatonin, biological rep 1


title: S25 SS25.P1

description: bone marrow FrA plate 2 cell 40

value: wt


title: S23 SS23.P1

description: bone marrow FrA plate 2 cell 39

value: bone marrow


title: S26 SS26.P1

description: bone marrow FrA plate 2 cell 38


title: Mus_9B-3: WT melatonin, biological rep 3


title: S24 SS24.P1

description: bone marrow FrA plate 2 cell 37


title: S46 SS46.P2

description: bone marrow FrA plate 3 cell 4


title: S47 SS47.P2

description: bone marrow FrA plate 3 cell 2


title: Mus_6A-6: WT control, biological rep 6

source_name: WT - control


title: S27 SS27.P1

description: bone marrow FrA plate 2 cell 36


title: S28 SS28.P1

description: bone marrow FrA plate 2 cell 34


title: S29 SS29.P1

description: bone marrow FrA plate 2 cell 32


title: S16 SS16.P1

description: bone marrow FrA plate 2 cell 30


title: S21 SS21.P1

description: bone marrow FrA plate 2 cell 31


title: S17 SS17.P1

description: bone marrow FrA plate 2 cell 28


title: S31 SS31.P1

description: bone marrow FrA plate 2 cell 29


title: S19 SS19.P1

description: bone marrow FrA plate 2 cell 35


title: S20 SS20.P1

description: bone marrow FrA plate 2 cell 33


title: S32 SS32.P1

description: bone marrow FrA plate 2 cell 27


title: S33 SS33.P1

description: bone marrow FrA plate 2 cell 25


title: S18 SS18.P1

description: bone marrow FrA plate 2 cell 26


title: Mus_5A-5: WT control, biological rep 5


title: S14 SS14.P1

description: bone marrow FrA plate 2 cell 22


title: S34 SS34.P1

description: bone marrow FrA plate 2 cell 23


title: S35 SS35.P1

description: bone marrow FrA plate 2 cell 21


title: Mus_1A-1: WT control, biological rep 1


title: Mus_4A-4: WT control, biological rep 4


title: Mus_10D-1: Waketime captopril-treated mI/R, biological rep 1

source_name: WT - waketime captopril mI/R

growth_protocol: The mice were collected at 14 days post-mI/R (10 weeks of age), 3 hours after lights off.

value: myocardium (left ventricle)


title: Mus_3A-3: WT control, biological rep 3


title: S10 SS10.P1

description: bone marrow FrA plate 2 cell 19


title: S15 SS15.P1

description: bone marrow FrA plate 2 cell 20


title: Mus_12D-3: Waketime captopril-treated mI/R, biological rep 3


title: Mus_2A-2: WT control, biological rep 2


title: Mus_9C-3: Sleeptime captopril-treated mI/R, biological rep 3

source_name: WT - sleeptime captopril mI/R


title: S13 SS13.P1

description: bone marrow FrA plate 2 cell 24


title: S11 SS11.P1

description: bone marrow FrA plate 2 cell 17


title: S38 SS38.P1

description: bone marrow FrA plate 2 cell 16


title: S37 SS37.P1

description: bone marrow FrA plate 2 cell 18


title: S12 SS12.P1

description: bone marrow FrA plate 2 cell 15


title: S39 SS39.P1

description: bone marrow FrA plate 2 cell 14


title: S40 SS40.P1

description: bone marrow FrA plate 2 cell 12


title: Mus_7C-1: Sleeptime captopril-treated mI/R, biological rep 1


title: S08 SS8.P1

description: bone marrow FrA plate 2 cell 11


title: S09 SS9.P1

description: bone marrow FrA plate 2 cell 9


title: S41 SS41.P1

description: bone marrow FrA plate 2 cell 10


title: S04 SS4.P1

description: bone marrow FrA plate 2 cell 8


title: S05 SS5.P1

description: bone marrow FrA plate 2 cell 7


title: Mus_6B-3: Placebo-treated mI/R, biological rep 3

source_name: WT - placebo mI/R


title: S45 SS45.P1

description: bone marrow FrA plate 2 cell 6


title: S06 SS6.P1

description: bone marrow FrA plate 2 cell 7


title: Mus_11D-2: Waketime captopril-treated mI/R, biological rep 2


title: Mus_5B-2: Placebo-treated mI/R, biological rep 2


title: Mus_1A-1: Sham control, biological rep 1

source_name: WT - sham


title: Mus_3A-3: Sham control, biological rep 3


title: Mus_2A-2: Sham control, biological rep 2


title: S01 SS1.P1

description: bone marrow FrA plate 2 cell 5


title: Mus_8C-2: Sleeptime captopril-treated mI/R, biological rep 2


title: S43 10Cell.P1

description: 10 cell control plate 2


title: Mus_5B-2: WT LBD, biological rep 2

source_name: WT - LBD

growth_protocol: The mice were collected at 12 weeks of age (after 4 weeks under a 12h light: 12h dark (LD) or 12h light: 4h blue: 8h dark (LBD) cycle), 7 hours after lights on.

extract_protocol: Total RNA was extracted using  Qiagen miRNeasy spin columns according to the manufacturer's instructions.


title: Mus_4B-1: WT LBD, biological rep 1


title: Mus_6B-3: WT LBD, biological rep 3


title: S02 SS2.P1

description: bone marrow FrA plate 2 cell 3


title: S44 20Cell.P1

description: 20 cell control plate 2


title: S47 SS47.P1

description: bone marrow FrA plate 2 cell 2


title: S22 SS22.P0

description: bone marrow CLP plate 1 cell 40

value: CLP Ly6d+Gfra2+


title: S03 SS3.P1

description: bone marrow FrA plate 2 cell 1


title: S26 SS26.P0

description: bone marrow CLP plate 1 cell 37


title: S25 SS25.P0

description: bone marrow CLP plate 1 cell 39


title: S24 SS24.P0

description: bone marrow CLP plate 1 cell 36


title: S23 SS23.P0

description: bone marrow CLP plate 1 cell 38


title: K562_I-CBP112_2uM_2

city: Majadahonda

first: Maria

last: Barrero

state: Madrid

address: Crta. Majadahonda-Pozuelo KM 2.2

institute: ISCIII

description:
Isolation of poly A+ RNA from total RNA
I-CBP112_2uM_2

data_processing:
RNA-seq processing:
RNA-seq analysis was performed with the nextpresso pipeline v1.4, using the following tools:
Read files were quality-checked with FastQC.
Reads were aligned to the human genome (GRCh37/hg19) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression calculated with Cufflinks 2.2.1
Homo sapiens GRCh37/hg19 transcript annotations from the UCSC Genome Browser were used
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: FPKM values obtained with Cuffnorm

source_name: K562 cells

growth_protocol: K562 cells wer grown in RPMI+10%FBS

extract_protocol:
Cells were trypsinized and total RNA was extracted using the RNeasy kit (Qiagen).
From 1 µg of total RNA PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit. Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced for 50 bases in a single-read format (Illumina HiSeq 2000).

treatment_protocol: K562 cells were treated for 48 hours with with 2 µM CBP30, 5μM CBP30 , 2 μM I-CBP112, 5 μM I-CBP112 or vehicle (DMSO). Two biological replicates were used per condition.

value: 2 μM I-CBP112


title: K562_I-CBP112_5uM_1

description:
Isolation of poly A+ RNA from total RNA
I-CBP112_5uM_1

value: 5 μM I-CBP112


title: K562_I-CBP112_5uM_2

description:
Isolation of poly A+ RNA from total RNA
I-CBP112_5uM_2


title: K562_I-CBP112_2uM_1

description:
Isolation of poly A+ RNA from total RNA
I-CBP112_2uM_1


title: S27 SS27.P0

description: bone marrow CLP plate 1 cell 35


title: Mus_1A-1: WT LD, biological rep 1

source_name: WT - LD


title: S19 SS19.P0

description: bone marrow CLP plate 1 cell 34


title: Mus_3A-3: WT LD, biological rep 3


title: S28 SS28.P0

description: bone marrow CLP plate 1 cell 33


title: S20 SS20.P0

description: bone marrow CLP plate 1 cell 32


title: S29 SS29.P0

description: bone marrow CLP plate 1 cell 31


title: K562_CBP30_5uM_1

description:
Isolation of poly A+ RNA from total RNA
CBP30_5uM_1

value: 5 μM CBP30


title: Mus_2A-2: WT LD, biological rep 2


title: Cell-Knockdown-Rep3 G3378-3 (Sample6)

city: Shanghai

first: Wenxi

last: Yu

state: N/A = Not Applicable

address: No.600, Yishan Road, Xuhui District, 200233 Shanghai, People's Republic of China

institute: Department of Oncology, Affiliated Sixth People's Hospital, Shanghai Jiaotong University

description: Gene expression data from HOS cells treated with DGKZ-silencing

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: HOS cells treated with DGKZ-silencing

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

growth_protocol: Cells were grown in DMEM-F12 growth medium mixed with 10.0% fetal bovine serum (FBS) that were purchased from Gibco (Gibco, USA). Cells were incubated in 5% atmospheric CO2 at 37 °C, passaged every three days, checked routinely.

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

treatment_protocol: HOS cells were treated with or without DGKZ-silencing and investigated by a microarray profiling

tag: sample type

value: Osteosarcoma, Female,Whilte,13 years old


title: S16 SS16.P0

description: bone marrow CLP plate 1 cell 30


title: Cell-Knockdown-Rep2 G3378-2 (Sample5)


title: Cell-Control-Rep1 G3377-2 (Sample2)

description: Gene expression data from HOS cells treated without DGKZ-silencing

source_name: HOS cells treated without DGKZ-silencing as a control


title: S31 SS31.P0

description: bone marrow CLP plate 1 cell 29


title: K562_DMSO_2

description:
Isolation of poly A+ RNA from total RNA
DMSO_2

value: DMSO


title: K562_DMSO_1

description:
Isolation of poly A+ RNA from total RNA
DMSO_1


title: K562_CBP30_2uM_1

description:
Isolation of poly A+ RNA from total RNA
CBP30_2uM_1

value: 2 μM CBP30


title: S17 SS17.P0

description: bone marrow CLP plate 1 cell 28


title: S18 SS18.P0

description: bone marrow CLP plate 1 cell 26


title: Mus_4B-1: Placebo-treated mI/R, biological rep 1


title: S33 SS33.P0

description: bone marrow CLP plate 1 cell 25


title: Cell-Control-Rep1 G3377-3 (Sample3)


title: Cell-Knockdown-Rep1 G3378-1 (Sample4)


title: DoubleMO-21hpf-rep3

city: Chicago

first: Erin

middle: A

last: Boyle Anderson

state: IL

department: Committee on Development, Regeneration and Stem Cell Biology

institute: University of Chicago

description:
PolyA RNA
Eyes were removed from the embryo prior to pooling and extracting RNA.
processed data file: final_gene_FPKM_tracking.tabular.txt

data_processing:
Illumina bcl2fastq software was used for basecalling.
All following steps were conducted on Galaxy. Data was groomed for quality using FASTQ Groomer (input ASCII range'#'(35)-'J'(74);input decimal range: 2-41). Reads were mapped to danRer10 using TopHat v2.1.0/Bowtie V 2.2.5.0).
Genome_build: danRer10 (GRCz10)
Supplementary_files_format_and_content: *_gene_FPKM tracking.tabular.txt: Tab-delimited text files include normalized abundance measurements.

source_name: whole embryo--eyes removed

extract_protocol:
10 pooled embryos for each condition at the relevant time point. RNA was extracted using Trizol.
RNA libraries were prepared for sequencing.

treatment_protocol: Whole embryos were injected with morpholinos targetting either Tbx5a, Tbx5b, or both at the single cell stage.

tag: strain/background

value: *AB

tag: genotype/variation

tag: developmental stage

value: Whole embryo with eyes removed


title: total RNA  of CAL-27 cells

hyb_protocol: each slide was hybridized with 100 ng Cy3-labeled RNA using a miRNA Complete Labeling and Hyb Kit (cat. #5190-0456, Agilent technologies, Santa Clara, CA, US) in a hybridization oven (cat. #G2545A, Agilent technologies, Santa Clara, CA, US) at 55℃ and 20 rpm for 20 h, according to the manufacturer’s instructions for hybridization of sections.After hybridization, slides were washed in staining dishes (cat. #121, Thermo Shandon, Waltham, MA, US) with a Gene Expression Wash Buffer Kit (cat. #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned with an Agilent Microarray Scanner (cat. #G2565BA, Agilent Technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, US) using the default settings.

data_processing: The raw data were normalized with a quantile algorithm using Gene Spring Software 11.0 (Agilent Technologies, Santa Clara, CA, US).

source_name: total RNA  of CAL-27 cells

label_protocol: miRNA molecules in different RNAs were labeled with an miRNA Complete Labeling and Hyb Kit (cat. #5190-0456, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions for labeling sections.

growth_protocol: Cal-27 cells and Cal-27res Cells (cisplatin-resistant CAL-27 cells) both were cultivated in Dulbecco’s modified Eagle’s medium (Gibco, Rockville, MD, USA) supplemented with 10% fetal bovine serum (Invitrogen, Carlsbad, CA, USA). Cells were cultured at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: cytosolic RNA, mitochondrial RNA and total RNA were extracted and checked for an RIN number to inspect the RNA integration with an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US).

treatment_protocol: To construct stable cisplatin-resistant cell lines, CAL27 cells were treated with cisplatin (Sigma, St Louis, MO, USA) with concentrations that gradually increased from 10^-7 M to 10^-5 M. To isolate the mitochondrial, cytoplasmic and nuclear fractions, cells were washed twice with cold PBS, and the pellet was suspended in 0.2 ml of buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1.5 mM MgCl2, 1 mM EGTA, 1 mM EDTA, 1 mM dithiothreitol (DTT), 0.1 mM phenylmethylsulfonyl fluoride (PMSF), and 250 mM sucrose) containing a protease inhibitor cocktail. Then, the cells were homogenized with 12 strokes in a Dounce homogenizer, followed by centrifugation twice at 750 g for 5 min at 4°C to collect the nuclei and debris. The mitochondria-enriched heavy membrane pellet was collected with further centrifugation at 10,000 g for 15 min at 4°C; the supernatants were collected as the cytosolic fractions. Sample labeling and array hybridization were performed by Agilent human miRNA (8*60K) V19.0 microarrays.

value: CAL-27 cells


title: DoubleMO-21hpf-rep1

tag: tissue


title: DoubleMO-18hpf-rep2


title: S13 SS13.P0

description: bone marrow CLP plate 1 cell 24

tag: strain


title: K562_CBP30_2uM_2

description:
Isolation of poly A+ RNA from total RNA
CBP30_2uM_2


title: total RNA  of Cal-27res Cells

source_name: total RNA  of Cal-27res Cells


title: DoubleMO-18hpf-rep1


title: DoubleMO-21hpf-rep2


title: Tbx5bMO-21hpf-rep3


title: S34 SS34.P0

description: bone marrow CLP plate 1 cell 23


title: DoubleMO-18hpf-rep3


title: S14 SS14.P0

description: bone marrow CLP plate 1 cell 22


title: mitochondrial RNA of Cal-27res Cells

source_name: mitochondrial RNA of Cal-27res Cells


title: cytosolic RNA of Cal-27res Cells

source_name: cytosolic RNA of Cal-27res Cells


title: Tbx5bMO-21hpf-rep2


title: Tbx5bMO-21hpf-rep1


title: S35 SS35.P0

description: bone marrow CLP plate 1 cell 21


title: mitochondrial RNA of CAL-27 cells

source_name: mitochondrial RNA of CAL-27 cells


title: S15 SS15.P0

description: bone marrow CLP plate 1 cell 20


title: Tbx5bMO-18hpf-rep3


title: Tbx5bMO-18hpf-rep2


title: Tbx5bMO-18hpf-rep1


title: cytosolic RNA of CAL-27 cells

source_name: cytosolic RNA of CAL-27 cells


title: S32 SS32.P0

description: bone marrow CLP plate 1 cell 27


title: S10 SS10.P0

description: bone marrow CLP plate 1 cell 19


title: S37 SS37.P0

description: bone marrow CLP plate 1 cell 18


title: S11 SS11.P0

description: bone marrow CLP plate 1 cell 17


title: CAL-27_cisplatin-resistant_rep2

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labelled ds-cDNA in NimbleGen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: After being washed in an ozone-free environment, the slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).

data_processing: Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and mRNA level (*_RMA.calls) files were generated after normalization. All mRNA level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Differentially expressed LncRNAs and mRNAs with statistical significance were identified through Volcano Plot filtering. Hierarchical clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and pathway analysis were performed in the standard enrichment computation method.

source_name: Cisplatin-resistant CAL-27 cells

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from 5 μg of total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., USA). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). 1 μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

growth_protocol: CAL27 and CAL27-res cells were maintained in DMEM (GIBCO, Rockville, MD, USA) supplemented with 10% fetal bovine serum (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: To construct stable cisplatin-resistant cell lines, CAL27 cells were treated with cisplatin (Sigma, St Louis, MO, USA) with concentrations that gradually increased from 10^-7 M to 10^-5 M.


title: Tbx5aMO-21hpf-rep3


title: Tbx5aMO-21hpf-rep2


title: S38 SS38.P0

description: bone marrow CLP plate 1 cell 16


title: CAL-27_parental_rep2

source_name: Parental CAL-27 cells


title: 1 PBS Th2

source_name: Th2 from PBS treated (i/n) lung

tag: cell type

value: PBS


title: 2 PBS Th2


title: S12 SS12.P0

description: bone marrow CLP plate 1 cell 15


title: Tbx5aMO-21hpf-rep1


title: 1 IL-33 Th2

source_name: Th2 from IL-33 treated (i/n) lung


title: Tbx5aMO-18hpf-rep2


title: 2 IL-33 Th2


title: CAL-27_parental_rep1

tag: cell line


title: Tbx5aMO-18hpf-rep1


title: 1 PBS ILC2

source_name: ILC2 from PBS treated (i/n) lung

tag: treatment


title: S40 SS40.P0

description: bone marrow CLP plate 1 cell 12

tag: genotype


title: WT-21hpf-rep3

value: WT


title: 2 PBS ILC2


title: 1 IL-33 ILC2

source_name: ILC2 from IL-33 treated (i/n) lung


title: S09 SS9.P0

description: bone marrow CLP plate 1 cell 10

tag: cell subtype


title: WT-21hpf-rep2


title: CAL-27_cisplatin-resistant_rep1


title: WT-21hpf-rep1


title: 2 IL-33 ILC2


title: WT-18hpf-rep3


title: Tbx5aMO-18hpf-rep3


title: S43 10Cell.P0

description: 10 cell control plate 1


title: S39 SS39.P0

description: bone marrow CLP plate 1 cell 14


title: S07 SS7.P0

description: bone marrow CLP plate 1 cell 13


title: S05 SS5.P0

description: bone marrow CLP plate 1 cell 8


title: 1 PBS Gata3 neg Treg

source_name: Gata3 neg Treg from PBS treated (i/n) lung

value: Gata3- Treg


title: WT-18hpf-rep2


title: 2 PBS Gata3 neg Treg

source_name: Gata3 neg Treg from PBS  treated(i/n) lung


title: WT-18hpf-rep1


title: S44 20Cell.P0

description: 20 cell control plate 1


title: 1 IL-33 Gata3 neg Treg

source_name: Gata3 neg Treg from IL-33 treated (i/n) lung


title: S08 SS8.P0

description: bone marrow CLP plate 1 cell 11


title: prelim-Tbx5bMO-21hpf

description:
PolyA RNA
Whole embryo RNA was used.
processed data file: prelim_21hpf_gene_FPKM_tracking.tabular.txt

source_name: whole embryo

value: Tbx5b deficient

value: Whole embryo


title: 2 IL-33 Gata3 neg Treg


title: prelim-Tbx5bMO-18hpf

description:
PolyA RNA
Whole embryo RNA was used.
processed data file: prelim_18hpf_gene_FPKM_tracking.tabular.txt


title: S04 SS4.P0

description: bone marrow CLP plate 1 cell 9

value: wt

value: bone marrow


title: S45 SS45.P0

description: bone marrow CLP plate 1 cell 6

value: CLP Ly6d+Gfra2+


title: S06 SS6.P0

description: bone marrow CLP plate 1 cell 7


title: 1 PBS Gata3+ Treg

source_name: Gata3+ Treg from PBS treated (i/n) lung

value: Gata3+ Treg


title: Nedd9.wt.4

city: Philadelphia

first: Denise

middle: C

last: Connolly

state: PA

address: 333 Cottman Avenue

institute: Fox Chase Cancer Center

hyb_protocol: 1.65 ug of Cy-3 labeled cRNA targets is hybridized onto Agilent 4x44k whole genome arrays for 17 hours at 65º C and washed according to Agilent procedure.

scan_protocol: The hybridized slides are scanned at 5µm resolution on Agilent scanner (Agilent)  G2505B.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: C57BL/6JTgMISIIR-TAg;Nedd9-WT - replicate 4

label_protocol: 500 ng total RNA was amplified and labeled using Agilent QuickAmp labeling kit following the manufacturer protocol.

growth_protocol: Spontaneous tumor growth in mice  (n=4/group) was tracked by in vivo longitudinal magnetic resonance imaging. Mice were sacrificed after the tumor mass reached 2000 mm^3. Ovarian tisue samples were snap-frozen for analysis.

extract_protocol: Mouse tissue RNA samples were prepared using the RNeasy Mini Kit (QIAGEN) according to manufacturer’s instructions

value: ovarian tumor

value: female


title: prelim-Tbx5aMO-21hpf

value: Tbx5a deficient


title: S01 SS1.P0

description: bone marrow CLP plate 1 cell 5


title: Cell-Control-Rep1 G3377-1 (Sample1)

source_name: HOS cells treated without DGKZ-silencing as a control

value: Osteosarcoma, Female,Whilte,13 years old


title: 2 PBS Gata3+ Treg


title: prelim-Tbx5aMO-18hpf


title: 1 IL-33 Gata3+ Treg

source_name: Gata3+ Treg from IL-33 treated (i/n) lung


title: prelim-WT-21hpf


title: S46 SS46.P0

description: bone marrow CLP plate 1 cell 4


title: S02 SS2.P0

description: bone marrow CLP plate 1 cell 3


title: 2 IL-33 Gata3+ Treg


title: S47 SS47.P0

description: bone marrow CLP plate 1 cell 2


title: S03 SS3.P0

description: bone marrow CLP plate 1 cell 1


title: Nedd9.wt.1

source_name: C57BL/6JTgMISIIR-TAg;Nedd9-WT - replicate 1


title: S46 SS46.P1

description: bone marrow FrA plate 2 cell 4

value: FrA Gfra2- Bst1-


title: S07 SS7.P1

description: bone marrow FrA plate 2 cell 13


title: Nedd9.Null.4

source_name: C57BL/6JTgMISIIR-TAg;Nedd9-null - replicate 4


title: Nedd9.wt.2

source_name: C57BL/6JTgMISIIR-TAg;Nedd9-WT - replicate 2


title: MCoG cells_2

status: Public on Jun 11 2018

city: Kyoto

first: Leqian

address: 205 Room, International Science Innovation Building

country: Japan

institute: Kyoto university

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
RNA-seq reads were aligned to the mouse refference genome (hg19) using Tophat software
gene expression level was calculated Cufflink.
Genome_build: hg19
Supplementary_files_format_and_content: txt files reflect FPKM of each gene in Refseq.

source_name: human iPSCs

growth_protocol: human iPSCs 253G1 cultured in mTesR1 medium

extract_protocol:
Total RNA was isolated using the  RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions
The purifed mRNAs were used to construct the cDNA library with the NEB RNA library construct kit. The quality-ensured libraries were used for pair-end deep sequencing on Illumina HiSeq Sequencer.

tag: culture medium

value: mTesR 1

tag: passage

tag: substrates

value: Gelatin nanofiber

value: Monolayer


title: DCoG cells_2

value: Domed


title: prelim-WT-18hpf

value: *AB

value: WT


title: Nedd9.Null.2

source_name: C57BL/6JTgMISIIR-TAg;Nedd9-null - replicate 2

tag: gender


title: Nedd9.wt.3

source_name: C57BL/6JTgMISIIR-TAg;Nedd9-WT - replicate 3


title: P1TNSC7

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MD

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

data_processing:
Basecalling performed by RTA version 1.18.66.3
Demultiplexing performed by Bcl2fastq version 1.8.4
Adaptor trimming and quality control by Trimmomatic version 0.30
Read alignment performed by STAR version 2.5.1
Transcript quantification performed by RSEM version 1.2.22
Data normalized by median normalization
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file of RSEM values for each single cell

source_name: Patient triple negative single cell 7

growth_protocol: HuH-1 and HuH-7 were grown in DMEM medium plus 10% fetal bovine serum and 1% antibiotics. At 80% confluence, the cell were harvested for flow cytometry sorting

extract_protocol:
no RNA extraction step droplet-based single-cell RNA-seq (SMART-seq)
Cells were lysed in ice-cold lysis buffer. SMART-seq protolcol was performed on single or pooled sorted cells following the manufacturere's instructions with some modification. Briefly, whole transcriptome was amplified with the SMART-seq v4 Ultra Low Input RNA kit (Clonetech), purified (Beckman Coulter, A63881) and barcoded (Illumina, FC-131-1096). Finally, libraries were pooled and sequenced on Illumina Hiseq2500.

value: hepatcellular carcinoma

tag: cell surface marker

value: TripleNeg

tag: cell number

tag: cell status

value: single-cell


title: P1DPSC4

source_name: Patient EPCAM+CD24 positive single cell 4


title: P1DPSC3

source_name: Patient EPCAM+CD24 positive single cell 3


title: P1TNSC6

source_name: Patient triple negative single cell 6


title: P1DPSC5

source_name: Patient EPCAM+CD24 positive single cell 5


title: P1DPSC7

source_name: Patient EPCAM+CD24 positive single cell 7


title: P1DPSC6

source_name: Patient EPCAM+CD24 positive single cell 6


title: P1DPSC9

source_name: Patient EPCAM+CD24 positive single cell 9


title: P1DPSC2

source_name: Patient EPCAM+CD24 positive single cell 2


title: P1TNSC4

source_name: Patient triple negative single cell 4


title: P1TNSC5

source_name: Patient triple negative single cell 5


title: P1DPSC8

source_name: Patient EPCAM+CD24 positive single cell 8


title: MCoG cells_1


title: Nedd9.Null.3

source_name: C57BL/6JTgMISIIR-TAg;Nedd9-null - replicate 3


title: Nedd9.Null.1

source_name: C57BL/6JTgMISIIR-TAg;Nedd9-null - replicate 1


title: P1TNSC1

source_name: Patient triple negative single cell 1


title: P1TPSC4

source_name: Patient triple positive single cell 4

value: TriplePos


title: P1TPSC3

source_name: Patient triple positive single cell 3