title: TAW121, Replicate 2

city: Cambridge

first: Alan

last: Grossman

address: 31 Ames St.

department: Biology

institute: MIT

hyb_protocol: Salmon testes DNA and yeast tRNA were added, and each cDNA sample was hybridized to a DNA microarray at 42 °C overnight.

scan_protocol: Scanned on a GenePix 4000B scanner. Images were quantified using GenePix 3.0 (Axon Instruments).

data_processing: Loess normalized and background subtracted using the R statistical software package Linear Models for Microarray Data (LIMMA). [RGbkgd <- backgroundCorrect(RG, method=normexp, offset=50); normalizeWithinArrays(RGbkgd)]

organism: Bacillus subtilis

label_protocol: 10 µg of each RNA sample was reverse transcribed using Superscript II reverse transcriptase (Invitrogen), random hexamers, and aminoallyl-dUTP (Ambion). The cDNA was labeled by conjugation to monofunctional Cy3 or Cy5 dyes (Amersham) for reference or experimental samples, respectively. Each experimental sample was mixed with an aliquot of reference sample.

growth_protocol: Cells were grown to mid-log phase in batch culture at 37 °C in minimal media supplemented with 1% (w/v) arabinose, 0.5% (w/v) xylose, 0.1 mM IPTG, 40 µg/ml tryptophan, and 40 µg/ml phenylalanine.

extract_protocol: Cultures were fixed with an equal volume of -20C methanol. RNA was extracted using the Qiagen RNeasy kit according to the manufacturer's instructions.

tag: replication genotype

value: oriC- oriN+

tag: dnaa, sda, and spo0a genotype

value: Pspank-dnaA deltasda

source_name: Reference RNA

tag: reference rna

value: Includes pooled total RNA from B. subtilis cultures grown in defined minimal medium and cultures treated with DNA-damaging agents, as described in PMID 19737352


title: TAW121, Replicate 3

status: Public on Feb 16 2018

type: RNA

state: MA

country: USA

molecule: total RNA


title: TAW106, Replicate 2

value: Pspank-dnaA deltaspo0A


title: HSC-3 MMP-8

city: Oulu

first: Pirjo

last: Åström

address: Aapistie 5A

country: Finland

institute: University of Oulu

description: HSC-3 cell line is an aggressive human oral tongue squamous cell carcinoma cell line labeled with RFP by stable transduction with commercial lentiviral particles containing human MMP8 gene sequence.

hyb_protocol: The cRNA was fragmented to 35 to 200 nt prior to hybridization to Affymetrix Human Genome U133 Plus 2.0 arrays containing approximately 55 000 human transcripts. The array was washed and stained with streptavidin-phycoerythrin (Molecular Probes, Eugene, OR). Finally, biotinylated anti-streptavidin (Vector Laboratories Inc., Burlingame, CA) was used to amplify the staining signal and a second staining was performed with streptavidin-phycoerythrin.

scan_protocol: The arrays were scanned on a GeneChip Scanner 3000.

data_processing: The expression data was analyzed using dChip software.

label: biotin

organism: Homo sapiens

label_protocol: Three RNA samples were pooled; the pools contained an equal amount of RNA from each sample. In total, 1 µg of total RNA was used as a template to synthesize biotinylated cRNA by means of the GeneChip 3’IVT Express kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.

growth_protocol: HSC-3 (Japan Health Sciences Foundation, Japan) cells were cultured in a 1:1 DMEM/F-12 medium supplemented with 100 U/ml penicillin, 100 µg/ml streptomycin, 250 ng/ml fungizone, 50 µg/ml ascorbic acid and 0.4 µg/ml hydrocortisone and 10% heat inactivated fetal bovine serum. HSC-3 cells transduced with commercial lentiviral particles containing a non-coding control sequence or MMP8 and selected with puromycin.

extract_protocol: The cells were harvested for RNA extraction using a Qiagen RNA kit (Hilden, Germany).

treatment_protocol: The cells were seeded into uncoated 6-well plates (three wells each). The next day the cells were harvested for RNA extraction.

tag: line

value: oral tongue squamous cell carcinoma line HSC-3

tag: phenotype

value: stationary

tag: genotype/variation

value: MMP-8 overexpression


title: TAW106, Replicate 3


title: Patient C time 0 repeat 1

city: BETHESDA

first: PING

last: JIN

state: MD

address: 9000 ROCKVILLE PIKE

department: DTM

institute: CC/DTM/NIH

description:
C1
Gene expression data from Patient C time 0.

hyb_protocol: Biotinylated cRNA were hybridized on the arrays for 18h according to the manufacturer’s directions.

scan_protocol: Arrays were scanned (Affymetrix 3000 7G) according to manufacturer's instructions.

data_processing: Arrays data were imported into Partek Genomics Suite using RMA normalization after background subtraction. One-way ANOVA was used to identify differentially expressed genes among the 4 T cell subtypes with a significant cut off of pFDR<0.01. Differentially expressed probe sets were selected using a false discovery rate cutoff of 0.01 without specifying a fold change criterion.

source_name: PBMCs, Time 0, Patient C

label_protocol: Biotinylated cRNA were prepared according to the GeneChip 3' IVT PLUS Reagent Kit user guide from 300 ng total RNA (Applied Biosystems).

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

treatment_protocol:
Whole PBMCs (not CD8-enriched) from 3 patients (Patients C, M, and P) were activated with anti-CD3 and retrovirally-transduced with CD19 CAR and expanded in presence or absence of pharmacologic inhibitor of Akt.
PBMCs were enriched for 1E6 CD8+ T cells using Miltenyi negative selection kit.

tag: starting cell type

value: PBMCs

tag: treatment

tag: time

value: Time 0

tag: enriched cell type

value: CD8+ T cells

tag: patient id

value: C


title: SpleenTRNurr77High_rep1_207

type: SRA

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

library_source: transcriptomic

data_processing:
fastq quality read filtering (>80% with Sanger Q>20)
cell barcode demultiplexing (custom script)
mapping with tophat2 on the mm10 transcriptome
filtering out low alignment score reads and multiple mapping reads (samtools)
duplication filtering using unique molecular identifiers (custom scripts). UMI sequence is at the 4rth position in the read ID (separation by ":")
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

organism: Mus musculus

source_name: spleen

growth_protocol: Live cells were sorted by flow cytometry from the spleen of mice (carrying Foxp3 and Nr4a1 reporter genes).

extract_protocol:
Spleen were mechanically dissociated to single cell suspensions. Tregs were sorted by flow cytometry as DAPI- TCRb+ CD4+ FoxP3-Thy1.1+ cells in 3 different bins of Nr4a1-GFP expression (low=0-20%, med=40-60%, high=80-100%). Single cells were then encapsulated in nanodroplets according to the InDrops protocol.
mRNA was reverse transcribed using adapters containing oligo dT in each droplet. The emulsion was then broken and linear amplification was performed by in vitro transcription. Illumina adapters were added by reverse transcription and PCR. Library were sequenced using a NextSeq500.

tag: tissue

value: spleen

tag: library name

tag: sample type

tag: strain

value: B6 Nr4a1-Gfp Foxp3-Ires-Thy1.1

tag: Sex

value: male

tag: age (months)

tag: total number of reads

tag: number of mapped reads

tag: number of unique reads (umi)


title: Patient M time 0 repeat 1

description:
M1
Gene expression data from Patient M time 0.

source_name: PBMCs, Time 0, Patient M

value: M


title: TAW106, Replicate 1

tag: replication genotype

tag: dnaa, sda, and spo0a genotype

tag: reference rna


title: SpleenTRNurr77High_rep1_209


title: Patient C time 0 repeat 3

description:
C3
Gene expression data from Patient C time 0.

tag: starting cell type


title: SpleenTRNurr77High_rep1_208


title: BACE457_40Tun_88

city: Bellinzona

first: Andrea

last: Rinaldi

state: Ticino

address: via vela 6

country: Switzerland

institute: IOR - oncology institute of southern switzerland

hyb_protocol: Whole Genome Gene Expression Direct Hybridization

scan_protocol: Illumina HiScan

data_processing: The data were normalised using quantile method

source_name: HEK-293 (human embryonic kidney)

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

growth_protocol: in vitro

extract_protocol: RNA extraction was performed using a commercially available kit (RNeasy, Qiagen, Frederick,MD) according to the manufacturer's recommendations. RNA quality was confirmed based on a RNA integrity number >8 by use of an electrophoresis bioanalyzer (2100 Agilent Bioanalyzer).

tag: cell line

value: HEK-293 (human embryonic kidney)

tag: treatment

value: 40 ng/ml Tun

tag: er stress-inducing drug

value: yes

tag: expressing model polypeptides

value: no


title: SpleenTRNurr77High_rep1_206

tag: tissue


title: BACE457_TG_95

value: 25 nM TG


title: TAW118, Replicate 3

value: oriC- oriN+

value: deltadnaA deltasda

value: Includes pooled total RNA from B. subtilis cultures grown in defined minimal medium and cultures treated with DNA-damaging agents, as described in PMID 19737352


title: TAW121, Replicate 1

value: Pspank-dnaA deltasda


title: BACE457_TG_102


title: BACE457_40Tun_93


title: BACE457_40Tun_100


title: BACE457_5Tun_63

value: 5 ug/ml Tun


title: BACE457_TG_109


title: BACE457_5Tun_55


title: BACE457_5Tun_59


title: SpleenTRNurr77High_rep1_205

tag: library name


title: SpleenTRNurr77High_rep1_204

tag: sample type


title: SpleenTRNurr77High_rep1_203

tag: strain


title: SpleenTRNurr77High_rep1_202

tag: Sex


title: TAW118, Replicate 2


title: SpleenTRNurr77High_rep1_201

tag: age (months)


title: TAW97, Replicate 2

growth_protocol: Cells were grown to mid-log phase in batch culture at 37 °C in minimal media supplemented with 1% (w/v) arabinose, 0.5% (w/v) xylose, 0.1 mM IPTG, 40 µg/ml tryptophan, 40 µg/ml phenylalanine, and 120 µg/ml threonine.

value: Pspank-dnaA Pspank-sda


title: TAW97, Replicate 3


title: SpleenTRNurr77High_rep1_200

tag: total number of reads


title: TAW118, Replicate 1


title: TAW86, Replicate 3

value: deltadnaA Pspank-sda


title: BACE457_Tet_36

value: 100 ng/ml Tet


title: SpleenTRNurr77High_rep1_198

value: spleen

tag: number of mapped reads


title: TAW97, Replicate 1


title: BACE457_mock_108

value: mock


title: TAW86, Replicate 2


title: BACE457_Tet_34


title: BACE457DELTA_mock_29


title: BACE457_Tet_32


title: BACE457DELTA_Tet_28


title: SpleenTRNurr77High_rep1_199

value: B6 Nr4a1-Gfp Foxp3-Ires-Thy1.1

value: male

tag: number of unique reads (umi)


title: BACE457_mock_31

value: HEK-293 (human embryonic kidney)


title: TAW86, Replicate 1

tag: replication genotype


title: BACE457_mock_74


title: SpleenTRNurr77High_rep1_197


title: BACE457DELTA_Tet_30


title: BACE457DELTA_mock_27


title: CD3delta_qqq_mock_23

description: CD3δ qqq


title: BB668, Replicate 3

value: wild type (oriC+)

tag: dnaa, sda, and spo0a genotype

value: deltasda


title: BACE457DELTA_mock_25

value: no

value: yes


title: CD3delta_Tet_22

description: CD3δ qqq


title: BACE457DELTA_Tet_26


title: CD3delta_qqq_Tet_24

description: CD3δ qqq


title: SpleenTRNurr77High_rep1_196


title: SpleenTRNurr77High_rep1_195


title: SpleenTRNurr77High_rep1_194


title: BB668, Replicate 1

tag: reference rna


title: SpleenTRNurr77High_rep1_230


title: CD3delta_qqq_mock_19

description: CD3δ qqq


title: CD3delta_Tet_18


title: CD3delta_qqq_mock_21

description: CD3δ qqq


title: CD3delta_Tet_16


title: CD3delta_mock_17


title: CD3delta_mock_15


title: SpleenTRNurr77High_rep1_192


title: BB668, Replicate 2


title: SpleenTRNurr77High_rep1_190


title: SpleenTRNurr77High_rep1_191


title: AG174, Replicate 3

value: wild type


title: AG174, Replicate 2


title: AG174, Replicate 1


title: SpleenTRNurr77High_rep1_193


title: SpleenTRNurr77High_rep1_189


title: TAW5 no IPTG, Replicate 4

growth_protocol: Cells were grown to mid-log phase in batch culture at 37 °C in minimal media supplemented with 1% (w/v) arabinose, 0.5% (w/v) xylose, 40 µg/ml tryptophan, and 40 µg/ml phenylalanine.

value: oriC- oriN+

value: Pspank-dnaA


title: SpleenTRNurr77High_rep1_188


title: TAW5 no IPTG, Replicate 3

value: Includes pooled total RNA from B. subtilis cultures grown in defined minimal medium and cultures treated with DNA-damaging agents, as described in PMID 19737352


title: CD3delta_mock_13


title: alpha1AT-C-D64A_mock_11


title: CD3delta_Tet_14


title: alpha1AT-C-D64A_Tet_8


title: alpha1AT-C-D64A_Tet_10


title: alpha1AT-C-D64A_Tet_12


title: alpha1AT-C-D64A_mock_9


title: SpleenTRNurr77High_rep1_187


title: WM266-4-ID3-3

city: heidelberg

first: Lionel

last: Larribere

address: im neuenheimer Feld

country: Germany

institute: DKFZ

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: melanoma patient

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: mRNA was isolated with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Clean-up and DNase I treatment was included. Quality control was performed with Agilent Bioanalyser.

tag: source

value: generated at DKFZ

tag: genotype/variation

value: ID3 overexpressing


title: TAW5 no IPTG, Replicate 2


title: WM266-4-EV-3

description: replicate 3

tag: cell line

value: control


title: WM266-4-ID3-1

description: replicate 1


title: WM266-4-EV-1

description: replicate 1


title: WM266-4-Vem-2

description: replicate 2

value: ATCC

tag: treatment

value: vemurafenib


title: WM266-4-EV-2

description: replicate 2


title: WM266-4-ID3-2

description: replicate 2


title: SpleenTRNurr77High_rep1_186

value: spleen


title: SpleenTRNurr77High_rep1_185

value: B6 Nr4a1-Gfp Foxp3-Ires-Thy1.1


title: WM266-4-DMSO-3

description: replicate 3

value: DMSO


title: SpleenTRNurr77High_rep1_184

value: male


title: TAW5 +HPUra, Replicate 2

treatment_protocol: HPUra was added to a final concentration of 38 µg/ml, and cells were harvested 1 hour later


title: TAW5 no IPTG, Replicate 1


title: TAW5 +HPUra, Replicate 3


title: WM266-4-DMSO-1

description: replicate 1


title: SpleenTRNurr77High_rep1_183


title: TAW5, Replicate 15


title: Skmel 28_Vem-3

description: replicate 3


title: SpleenTRNurr77High_rep1_182


title: Skmel 28_Vem-2

description: replicate 2


title: SpleenTRNurr77High_rep1_181


title: TAW5, Replicate 14


title: TAW5, Replicate 13


title: WM266-4-DMSO-2

description: replicate 2


title: SpleenTRNurr77High_rep1_180


title: WM266-4-Vem-3

description: replicate 3


title: Skmel 28_Vem-1

description: replicate 1


title: TAW5 +HPUra, Replicate 1


title: SpleenTRNurr77High_rep1_179


title: CD3delta_qqq_Tet_20

description: CD3δ qqq

value: HEK-293 (human embryonic kidney)

value: 100 ng/ml Tet

tag: er stress-inducing drug

tag: expressing model polypeptides


title: Skmel 28_DMSO-3

description: replicate 3


title: SpleenTRNurr77High_rep1_178

tag: tissue

tag: library name


title: Skmel 28_DMSO-1

description: replicate 1


title: TAW5, Replicate 11


title: TAW5, Replicate 12


title: Skmel 28_DMSO-2

description: replicate 2


title: TAW5, Replicate 10


title: A375_Vem-3

description: replicate 3


title: A375 _DMSO-2

description: replicate 2


title: A375 _DMSO-3

description: replicate 3


title: SpleenTRNurr77High_rep1_177

tag: sample type

tag: strain


title: A375_Vem-1

description: replicate 1


title: A375_Vem-2

description: replicate 2


title: TAW5, Replicate 9


title: TAW5, Replicate 8


title: SpleenTRNurr77High_rep1_175

tag: Sex

tag: age (months)


title: SpleenTRNurr77High_rep1_174

tag: total number of reads

tag: number of mapped reads


title: TAW5, Replicate 7

tag: replication genotype


title: TAW5, Replicate 5

tag: dnaa, sda, and spo0a genotype


title: TAW5, Replicate 6

tag: reference rna


title: SpleenTRNurr77High_rep1_173

tag: number of unique reads (umi)


title: SpleenTRNurr77High_rep1_176


title: SpleenTRNurr77High_rep1_172


title: TAW5, Replicate 4


title: 681

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

hyb_protocol: The HT_MG-430A Array plate consists of 96 single MG-430A arrays arranged into standard SBS 96 well plate format.  All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.

scan_protocol: Scanned images were subjected to visual inspection and a chip quality report was generated by the Affymetrix's GeneChip Operating System (GCOS) and Expression console (Affymetrix).

data_processing: The image data was processed using the Affymetrix GCOS algorithm utilizing quantile normalization or the Robust Multiarray method (RMA) to determine the specific hybridizing signal for each gene.

source_name: heart

label_protocol: All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays.

growth_protocol: 16 week male mice maintained on 12 hr light dark cycle fed a chow diet

extract_protocol: Qiazol with homogenization followed by Rneasy spin columns with option Dnase per manufacturers protocol

tag: gender

value: Male

tag: age

value: 112 weeks


title: 674

value: 110 weeks


title: SpleenTRNurr77High_rep1_170


title: 683

value: 113 weeks


title: 670

value: 109 weeks


title: 664

value: 107 weeks


title: 676

value: 111 weeks


title: TAW5, Replicate 3

value: oriC- oriN+

value: Pspank-dnaA

value: Includes pooled total RNA from B. subtilis cultures grown in defined minimal medium and cultures treated with DNA-damaging agents, as described in PMID 19737352


title: TAW5, Replicate 2


title: TAW5, Replicate 1


title: 656

value: 105 weeks


title: 668

value: 108 weeks


title: 661

value: 106 weeks


title: 653

value: 104 weeks


title: AIG200 no IPTG, Replicate 3

value: deltadnaA


title: SpleenTRNurr77High_rep1_168

value: spleen

value: B6 Nr4a1-Gfp Foxp3-Ires-Thy1.1

value: male


title: 647

value: Male

value: 102 weeks


title: 636

value: 99 weeks


title: 652

value: 103 weeks


title: 642

value: 101 weeks


title: 640

value: 100 weeks


title: 633

value: 98 weeks


title: 629

value: 97 weeks


title: 622

value: 95 weeks


title: SpleenTRNurr77High_rep1_167


title: SpleenTRNurr77High_rep1_166


title: 618

value: 94 weeks


title: AIG200 no IPTG, Replicate 1

value: oriC- oriN+

value: Includes pooled total RNA from B. subtilis cultures grown in defined minimal medium and cultures treated with DNA-damaging agents, as described in PMID 19737352


title: AIG200 +HPUra, Replicate 3


title: SpleenTRNurr77High_rep1_165


title: SpleenTRNurr77High_rep1_164


title: AIG200 +HPUra, Replicate 1


title: AIG200 +HPUra, Replicate 2


title: AIG200 no IPTG, Replicate 2


title: 600

value: 90 weeks


title: 624

value: 96 weeks


title: 611

value: 93 weeks


title: 610

value: 92 weeks


title: 586

value: 86 weeks


title: SpleenTRNurr77High_rep1_162

value: spleen

value: B6 Nr4a1-Gfp Foxp3-Ires-Thy1.1

value: male


title: SpleenTRNurr77High_rep1_171


title: AIG200, Replicate 9

value: deltadnaA


title: AIG200, Replicate 7


title: AIG200, Replicate 8


title: AIG200, Replicate 6


title: 590

value: Male

value: 87 weeks


title: SpleenTRNurr77High_rep1_163


title: 593

value: 88 weeks


title: 581

value: 85 weeks


title: 597

value: 89 weeks


title: SpleenTRNurr77High_rep1_158


title: 606

value: 91 weeks


title: SpleenTRNurr77High_rep1_159


title: 566

value: 81 weeks


title: 569

value: 82 weeks


title: 576

value: 83 weeks


title: 564

value: 80 weeks


title: SpleenTRNurr77High_rep1_161


title: 560

value: 78 weeks


title: SpleenTRNurr77High_rep1_160


title: 578

value: 84 weeks


title: 562

value: 79 weeks


title: AIG200, Replicate 4

value: oriC- oriN+

value: Includes pooled total RNA from B. subtilis cultures grown in defined minimal medium and cultures treated with DNA-damaging agents, as described in PMID 19737352


title: 556

value: 77 weeks


title: 546

value: 74 weeks


title: SpleenTRNurr77High_rep1_157

value: spleen

value: B6 Nr4a1-Gfp Foxp3-Ires-Thy1.1

value: male


title: 549

value: Male

value: 75 weeks


title: AIG200, Replicate 3

value: deltadnaA


title: 552

value: 76 weeks


title: SpleenTRNurr77High_rep1_156


title: AIG200, Replicate 2


title: AIG200, Replicate 5


title: 544

value: 73 weeks


title: 540

value: 72 weeks


title: SpleenTRNurr77High_rep1_154


title: SpleenTRNurr77High_rep1_155


title: SpleenTRNurr77High_rep1_153


title: AIG200, Replicate 1


title: SpleenTRNurr77High_rep1_150


title: 527

value: 69 weeks


title: SpleenTRNurr77High_rep1_151


title: 524

value: 68 weeks


title: 518

value: 67 weeks


title: 533

value: 70 weeks


title: 510

value: 66 weeks


title: SpleenTRNurr77High_rep1_149


title: SpleenTRNurr77High_rep1_152


title: SpleenTRNurr77High_rep1_148


title: SpleenTRNurr77High_rep1_147


title: 498

value: 63 weeks


title: 536

value: 71 weeks


title: 502

value: 64 weeks


title: 493

value: 61 weeks


title: 505

value: 65 weeks


title: 483

value: 59 weeks


title: 487

value: Male

value: 60 weeks


title: 496

value: 62 weeks


title: FXS Neuron_mock.1_RNA-seq

city: CAMBRIDGE

first: Shawn

last: Liu

address: 455 MAIN STREET

institute: Whitehead Institute for Biomedical Research

data_processing:
The resulting 40 bp single-end reads from Illumina had good quality by checking with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).  Reads were mapped to hg19 using TopHat v2.1.1 with options as “solexa1.3-quals” mode and “no-novel-juncs”. The gene model for TopHat was created by merging knownGene in gtf format with kgXref table, downloaded from the UCSC table browser. The read counts were obtained using the featureCounts function from Subread package with strandness option as –s 2.  Reads were normalized with DESeq2.  The biological replicates in the neuron samples, processed at different time periods, have batch effect as suggested by principle component analysis. Consequently, Combat was used for reducing this batch effect.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files from featureCount

molecule: polyA RNA

growth_protocol: FXS iPSCs were cultured either with mTeSR™1 medium (STEMCELL, #85850) or on irradiated mouse embryonic fibroblasts (MEFs) with standard hESCs medium. Neurons were derived from FXS iPSCs with a previously reported differentiation protocol (Shi, Y., et al, Nature Protocol, 2012) and cultured on N2B27 medium.

extract_protocol:
RNA extraction was performed with Trizol and Direct-zol RNA MiniPrep Plus kit from Zym Research
Illumina TruSeq Stranded RNA

treatment_protocol: FXS neurons after 4-week withdrawal of FGF were harvested for RNA extraction.

tag: cell type

value: neurons derived from FXS iPSCs

tag: genotype

value: Neurons derived from FX52 mock iPSCs


title: 481

value: 58 weeks


title: FXS Neuron_dC-T.2.2_RNA-seq

value: Neurons derived from FX52 iPSCs infected with lentiviruses expressing dCas9-Tet1-P2A-tBFP (dC-T) and a mCherry-expressing sgRNA targeting CGG repeats


title: FXS Neuron_mock.2_RNA-seq


title: 475

value: 57 weeks


title: SpleenTRNurr77High_rep1_146

value: spleen

value: B6 Nr4a1-Gfp Foxp3-Ires-Thy1.1

value: male


title: 473

value: 56 weeks


title: FXS Neuron_dC-T.1_RNA-seq


title: 407

value: 52 weeks

value: BUB/BnJ


title: 456

value: 55 weeks

value: I/LnJ


title: SpleenTRNurr77High_rep1_145


title: 423

value: 53 weeks

value: MA/MyJ


title: 394

value: Male

value: 50 weeks


title: 448

value: 54 weeks

value: RIIIS/J


title: 397

value: 51 weeks


title: FXS iPSC_mock_RNA-seq

value: FXS iPSC line containing about 450 CGG repeats in the 5' UTR region of FMR1

value: FX52 mock iPSCs


title: SpleenTRNurr77High_rep1_143

value: spleen


title: FXS iPSC_dC-T_RNA-seq

value: FX52 iPSCs infected with lentiviruses expressing dCas9-Tet1-P2A-tBFP (dC-T) and a mCherry-expressing sgRNA targeting CGG repeats


title: FXS Neuron_dC-T.2.1_RNA-seq

value: neurons derived from FXS iPSCs

value: Neurons derived from FX52 iPSCs infected with lentiviruses expressing dCas9-Tet1-P2A-tBFP (dC-T) and a mCherry-expressing sgRNA targeting CGG repeats


title: SpleenTRNurr77High_rep1_141

value: B6 Nr4a1-Gfp Foxp3-Ires-Thy1.1

value: male


title: 334

value: 47 weeks

value: LG/J


title: 377

value: 49 weeks

value: SEA/GnJ


title: 320

value: Male

value: 46 weeks


title: SpleenTRNurr77High_rep1_142


title: FXS neuron_dC-dT_ChIP-BS-seq

description: Chip-Seq then Bisulfite conversion

library_source: genomic

data_processing:
The adapter sequences in the Illumina reads identified with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) were removed with Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). BS-Seq aligner Bismark was used for assigning reads to human genome hg19 and calling methylation with bismark_methylation_extractor. To increase the number of uniquely mapped reads, after the first bismark alignment, 5 bases from the 5’ and one base from the 3’ of the unmapped reads were trimmed based on FastQC analysis. The resulting trimmed reads were then aligned to genome with bismark. In both cases, bismark was ran with the options “--non_directional -un --ambiguous --bowtie2 -N 1 -p 4 --score_min L,-6,-0.3 --solexa1.3-quals”.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_sorted.bismark.cov: Tab-delimited text files from bismark: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>

molecule: genomic DNA

source_name: FXS neurons

growth_protocol: FXS iPSCs were cultured either with mTeSR™1 medium (STEMCELL, #85850) or on irradiated mouse embryonic fibroblasts (MEFs) with standard hESCs medium.

extract_protocol:
Collected cells were washed with PBS twice, and then re-suspended in 3.5 ml of sonication buffer. Sonication was performed for 10 cycles with 0.5 min pulse on and 1 min rest, and 24 watts in ice-water mixture. Then cell lysate was spun down with 14,000 x rpm for 10 min at 4 °C. 50 ul of supernatant was saved as input for gDNA. 10 ul of anti-CTCF antibody (EMD Millipore: 07729) was added and incubate overnight at 4 °C. 50 ul protein G dynabeads was added into antibody-cell lysate mixture and incubate overnight at 4 °C. Then beads were washed with sonication buffer, sonication buffer with high salt (500 mM NaCl), LiCl wash buffer, and TE buffer. Bound protein-DNA complex was eluted from beads by incubation in a 65 °C oven for 15 min, and then reverse cross-linked under 65 °C over-night. The bound DNA was purified with Qiagen QIAquick PCR Purification Kit.
EpiNext High-Sensitivity Bisulfite-Seq Kit.

treatment_protocol: Cells were cross-linked by 1% formaldehyde in the medium for 10 min in room temperature, and then quenched by adding 0.125 M Glycine for 5 min.

value: Neurons derived from FXS iPSCs

value: Infected with catalytically inactive Tet1 (dC-dT) and sgRNA targeting CGG repeats

tag: chip antibody

value: Mouse monoclonal anti-Cas9


title: FXS neuron_dC-T_ChIP-BS-seq

description: Chip-Seq then Bisulfite conversion

value: Infected with lentiviruses expressing dCas9-Tet1-P2A-tBFP (dC-T) and a mCherry-expressing sgRNA targeting CGG repeats


title: 338

value: 48 weeks

value: NON/ShiLtJ


title: 296

value: 43 weeks

value: NOD/ShiLtJ


title: 303

value: 44 weeks

value: CE/J


title: 313

value: 45 weeks

value: A/J


title: FXS iPSC_dC-T_ChIP-BS-seq

description: Chip-Seq then Bisulfite conversion

source_name: FXS iPSCs

value: FXS iPSC line containing about 450 CGG repeats in the 5' UTR region of FMR1


title: SpleenTRNurr77High_rep1_139

tag: tissue

value: spleen

value: B6 Nr4a1-Gfp Foxp3-Ires-Thy1.1

value: male


title: 281

value: Male

value: 40 weeks

value: PL/J


title: FXS iPSC_dC-dT_ChIP-BS-seq

description: Chip-Seq then Bisulfite conversion

value: Infected with catalytically inactive Tet1 (dC-dT) and sgRNA targeting CGG repeats

value: Mouse monoclonal anti-Cas9


title: 289

value: 42 weeks


title: SpleenTRNurr77High_rep1_138

tag: library name


title: SpleenTRNurr77High_rep1_169

tag: sample type


title: 286

value: 41 weeks

tag: strain

value: BTBR T<+> tf/J


title: 240

value: 39 weeks


title: 238

value: 38 weeks

value: CAST/EiJ


title: 218

value: 35 weeks

value: NZW/LacJ


title: 230

value: 37 weeks


title: SpleenTRNurr77High_rep1_137

value: spleen

tag: Sex


title: SpleenTRNurr77High_rep1_135

value: B6 Nr4a1-Gfp Foxp3-Ires-Thy1.1

tag: age (months)


title: SpleenTRNurr77High_rep1_136

value: male

tag: total number of reads


title: 224

value: Male

value: 36 weeks

value: NZB/BlNJ


title: 206

value: 34 weeks

value: CBA/J


title: SpleenTRNurr77High_rep1_134

tag: number of mapped reads


title: SpleenTRNurr77High_rep1_140


title: SpleenTRNurr77High_rep1_133


title: SpleenTRNurr77High_rep1_132


title: SpleenTRNurr77High_rep1_131


title: SpleenTRNurr77High_rep1_130


title: 137

value: 32 weeks

value: FVB/NJ


title: 101

value: 30 weeks


title: 88

value: 28 weeks

value: SWR/J


title: 98

value: 29 weeks


title: 57

value: 24 weeks

value: AKR/J


title: 80

value: 27 weeks


title: SpleenTRNurr77High_rep1_129

value: spleen


title: 107

value: 31 weeks

value: BALB/cJ


title: 61

value: Male

value: 25 weeks

value: SM/J


title: SpleenTRNurr77High_rep1_128

value: B6 Nr4a1-Gfp Foxp3-Ires-Thy1.1

value: male


title: 40

value: 22 weeks


title: 202

value: 33 weeks

value: KK/HlJ


title: 45

value: 23 weeks

value: LP/J


title: 34

value: 21 weeks


title: 19

value: 18 weeks


title: 32

value: 20 weeks


title: 25

value: 19 weeks


title: 9

value: 16 weeks


title: 74

value: 26 weeks


title: 16

value: 17 weeks


title: SpleenTRNurr77High_rep1_126

value: spleen


title: SpleenTRNurr77High_rep1_127


title: 3

value: Male


title: SpleenTRNurr77High_rep1_124


title: SpleenTRNurr77High_rep1_125


title: SpleenTRNurr77High_rep1_121


title: SpleenTRNurr77High_rep1_120


title: CD172a KO Rep1 Sp

city: St. Louis

first: David

middle: Alexander

last: Anderson III

state: Missouri

address: 660. S Euclid Ave., Campus Box 8118

department: Pathology and Immunology

institute: Washington University School of Medicine

description: Homeostatic spleen

hyb_protocol: Hybridiztion to Mouse Gene 1.0 ST array

scan_protocol: Not provided

data_processing: ArrayStar(DNASTAR) Quantile Normalization. Control set genes omitted. Normalization was conducted separately for splenic DCs and bone marrow Flt3l DC samples, which represent independent expriments. All data are included together in matrix file but should be treated as independent experiments.

label: Biotin

source_name: CD172a+ DCs from mouse 16

label_protocol: Ovation Pico WTA System (NuGEN)

growth_protocol: For homeostasis experiments, For activation experiments, whole bone marrow isolated from mice, grown at a density of 2 million per ml of complete IMDM media in 5% Flt3l for 9 days. On day 9, cells were treated with gamma interferon for 22 hours, followed by 4 hour treatment with LPS.

extract_protocol: Total RNA isolated with EZNA MicroElute RNA Kit and treated with DNase using TURBO DNA-free kit (Invitrogen).

treatment_protocol: Activaed Flt3l cultures were sorted for CD24+ and CD172a+ subsets.

value: Ciita -/-, Zbtb46 GFP/+

value: CD172a+ dendritic cells (DCs)


title: SpleenTRNurr77High_rep1_118

value: B6 Nr4a1-Gfp Foxp3-Ires-Thy1.1

value: male


title: CD172a WT Rep2 BM

description: Activated with gamma interferon and LPS

source_name: BM Flt3l CD172a DCs from mouse 56

value: Ciita +/+, Zbtb46 GFP/+

value: BM Flt3l CD172a dendritic cells (DCs)


title: CD24 KO Rep2 Sp

description: Homeostatic spleen

source_name: CD24+ DCs from mouse 25

value: CD24+ dendritic cells (DCs)


title: CD172a WT Rep1 Sp

description: Homeostatic spleen

source_name: CD172a+ DCs from mouse 37


title: CD24 WT Rep2 Sp

description: Homeostatic spleen

source_name: CD24+ DCs from mouse 50


title: SpleenTRNurr77High_rep1_119


title: SpleenTRNurr77High_rep1_123


title: CD24 WT Rep1 BM

description: Activated with gamma interferon and LPS

source_name: BM Flt3l CD24 DCs from mouse 54

value: BM Flt3l CD24 dendritic cells (DCs)


title: CD24 KO Rep1 Sp

description: Homeostatic spleen

source_name: CD24+ DCs from mouse 16


title: CD172a WT Rep2 Sp

description: Homeostatic spleen

source_name: CD172a+ DCs from mouse 50


title: CD172a KO Rep2 Sp

description: Homeostatic spleen

source_name: CD172a+ DCs from mouse 25


title: SpleenTRNurr77High_rep1_122


title: CD24 WT Rep1 Sp

description: Homeostatic spleen

source_name: CD24+ DCs from mouse 37


title: CD172a WT Rep1 BM

description: Activated with gamma interferon and LPS

source_name: BM Flt3l CD172a DCs from mouse 54


title: CD172a KO Rep2 BM

description: Activated with gamma interferon and LPS

source_name: BM Flt3l CD172a DCs from mouse 78


title: SpleenTRNurr77High_rep1_117

source_name: spleen


title: CD24 WT Rep2 BM

description: Activated with gamma interferon and LPS

source_name: BM Flt3l CD24 DCs from mouse 56


title: SpleenTRNurr77High_rep1_115


title: CD24 KO Rep1 BM

description: Activated with gamma interferon and LPS

source_name: BM Flt3l CD24 DCs from mouse 53


title: CD24 KO Rep2 BM

description: Activated with gamma interferon and LPS

source_name: BM Flt3l CD24 DCs from mouse 78


title: A498 ROC-325, biological rep 2

city: Tucson

first: Jennifer

last: Carew

state: Arizona

address: University of Arizona Cancer Center, 1515 N. Campbell Ave

institute: USA

description: Gene expression data

hyb_protocol: 300 ng of total RNA per sample was amplified and hybridized to GeneChip® Human Gene 1.0 ST arrays (Affymetrix, Inc., Santa Clara, CA) according to the manufacturer’s instructions.

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

data_processing: Affymetrix CEL files were imported into Partek® Genomics Suite™ 6.4 (Partek Inc., St. Louis, MO) using the default Partek normalization parameters and the robust multi-array average (RMA) analysis adjusted for probe sequence and GC content (GC-RMA). Data normalization was performed across all arrays using quantile normalization

source_name: A498 ROC-325 treated, 24h

label_protocol: Labeling was done using terminal deoxynucleotidyl transferase (TdT) in the presence of a proprietary biotinylated compound, GeneChip® DNA Labeling Reagent. Both components are also provided in the WT Terminal Labeling Kit. The final labeled DNA target is ready to be added to the cocktail for hybridizing to the arrays such as the GeneChip® Human Exon 1.0 ST Array.

growth_protocol: RCC cell lines were grown in 10% FBS RPMI media. Cells were cultured in a humified incubator at 37 C with 5% CO2.

extract_protocol: Total RNAs were isolated using the RNeasy Plus Mini Kit (Qiagen, Germantown, MD) and treated with TURBO DNA-free™ Kit (Applied Biosystems, Foster City, CA).

treatment_protocol: RCC cell lines were either untreated or treated with 5 uM ROC-325 for 24 h.

tag: cell line

value: renal cell carcinoma


title: A498 ROC-325, biological rep 1

description: Gene expression data


title: SpleenTRNurr77High_rep1_114


title: A498 Control, biological rep 3

description: Gene expression data

source_name: A498 untreated Control


title: SpleenTRNurr77High_rep1_113


title: SpleenTRNurr77High_rep1_112


title: A498 ROC-325, biological rep 3

description: Gene expression data


title: A498 Control, biological rep 2

description: Gene expression data


title: 786-O ROC-325, biological rep 3

description: Gene expression data

source_name: 786-O ROC-325 treated, 24h


title: CD172a KO Rep1 BM

description: Activated with gamma interferon and LPS

source_name: BM Flt3l CD172a DCs from mouse 53


title: SpleenTRNurr77High_rep1_110


title: SpleenTRNurr77High_rep1_144


title: 786-O ROC-325, biological rep 2

description: Gene expression data


title: SpleenTRNurr77High_rep1_116


title: A498 Control, biological rep 1

description: Gene expression data


title: SpleenTRNurr77High_rep1_111


title: 786-O Control, biological rep 1

description: Gene expression data

source_name: 786-O untreated Control


title: SpleenTRNurr77High_rep1_109


title: 786-O ROC-325, biological rep 1

description: Gene expression data


title: SpleenTRNurr77High_rep1_108


title: SpleenTRNurr77High_rep1_107


title: 46A1-s3

city: Kobe City

first: Michiyo

last: Koyanagi-Aoi

address: Chuo-ku, Kusunoki-cho 7-5-1

country: Japan

institute: Kobe University

description: gdT cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip primeview human gene expression array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Genechip Scanner 3000 7G system.

data_processing: The data were analyzed using the Gene Spring GX 13.1.1 software program (Agilent Technologies). We used RMA as summarization algorithm and performed quantile normalizaion. Baseline transformation was not performed.

source_name: gdT-derived iPS

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng of total RNA

growth_protocol: iPSCs were cultured in StemFit medium on plates coated with laminin-511 E8 fragments.

extract_protocol: Total RNA was isolated by Trizol reagent (Life Technologies) according to the manufacturer's instruction.

value: female

tag: origin

value: gdT cell

tag: method

value: Sendai virus


title: LPF2 (11)

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

country: France

institute: Institut Curie

description: MGH-U3 treated with LipofectaminRNAimax

hyb_protocol: Affymetrix microarrays were hybridized with 10µg of biotinylated cRNA according the supplier recommendations. Microarrays were washed and stained using FS450 fluidics upon a protocol provided by Affymetrix, corresponding to the GeneChip Human Exon 1.0 ST (Affymetrix) array

scan_protocol: Microarrays were scanned using a 7G, Affymetrix GCS3000 scanner, raw data were acquired with Affymetrix Genechip Command Console.

data_processing: Signal reconstruction was performed with the RMA algorithm as implemented in Bioconductor affy package on R statistical software using the Dai custom CDF package: HuEx10stv2_Hs_ENTREZG Brainarray Custom CDF EntrezG version 12.1.0

source_name: human bladder cancer cell line, MGH-U3

label_protocol: 100ng of total RNA were amplified to produced biotinylated complementary RNAs, as recommended by Affymetrix.

growth_protocol: The bladder cancer cells, MGH-U3, have been culture in DMEM 10% fetal bobine serum

extract_protocol: mRNAs were extracted and purified using RNeasy Mini kits (Qiagen).

treatment_protocol: MGH-U3 cells were transfected for 72h either with siRNA FGFR3 (Si1 FGFR3, Ambion, 144467), siRNA FGFR3 (Si2 FGFR3, Ambion, 144468),or a pool of siRNA FGFR3 (SiPool FGFR3, Dharmacon, L-0031333-00-0005) using LipofectaminRNAimax (Invitrogen) according to the manufacturer's instructions (reverse protocol)


title: LPF1 (12)

description: MGH-U3 treated with LipofectaminRNAimax


title: 786-O Control, biological rep 3

description: Gene expression data


title: SpleenTRNurr77High_rep1_106

tag: number of unique reads (umi)


title: SpleenTRNurr77High_rep1_105


title: 46C2-s4

description: gdT cells

tag: gender


title: 786-O Control, biological rep 2

description: Gene expression data


title: MNase-treated chromatin DNA_ThruPlex

city: Kashiwa

first: Fumihito

last: Miura

state: Chiba

address: Kashiwanoha 5-1-5

department: Graduate School of Frontier Sciences

institute: The University of Tokyo

data_processing:
The reads were mapped on the reference yeast genome with bowtie 0.12.7. The output format was specified to sam.
The sam file output was converted by using samtools 1.3.1 with view -Sb subcommand. The output format was specified in bam.
The bam file was sorted by using samtools 1.3.1 with sort subcommand.
The sorted bam file was converted to bedgraph format by using bedtools 2.26.0 with genomecov subcommand and option -5 and -bg.
Genome_build: Saccharomyces cerevisiae, S288C, R64-2-1
Supplementary_files_format_and_content: bedgraph

organism: Saccharomyces cerevisiae

source_name: MNase-DNA

growth_protocol: A colony was inoculated into 3 ml of YPD medium (1% (w/v) yeast extract, 2% (w/v) Bacto Peptone, 2% (w/v) glucose) and incubated overnight at 30 °C with shaking. The overnight culture was diluted in 15 ml of fresh YPD and the optical density at 600 nm was adjusted to 0.5. The diluted cells were grown at 30 °C for 2 h with shaking.

extract_protocol:
The cultured yeast cells were collected with centrifugation at 2,000 × g for 5 min, and re-suspended in 1 ml of spheroplast buffer that contained 1 M sorbitol; 50 mM Tris-HCl, pH 7.5; and 1 mM β-mercaptoethanol. The cell suspension was supplemented with 20 µl of 10 mg/ml Zymolyase-100T (Seikagaku Kogyo, Tokyo, Japan) and incubated at 30 °C for 10 min to make spheroplasts. The spheroplasts were collected by centrifugation at 2,000 × g for 5 min and resuspended in 1 ml of MNase digestion buffer (50 mM Tris-HCl, pH 7.6; 1 mM CaCl2; 0.2% (v/v) Triton X-100) containing 1× protease inhibitor (Nacalai Tesque, Kyoto, Japan). The lysate was digested with 50 units of micrococcal nuclease (Takara Bio Inc.). After incubation at 37 °C for 10 min, the digestion was stopped by adding 100 µl of 500 mM EDTA. The reaction mixture was then supplemented with 100 µl of 10% (w/v) SDS and 25 µl of 20 mg/ml Protease K (Qiagen), and incubated at 50 °C for 1 hr. Following phenol and phenol/chloroform extraction, nucleic acids were collected by isopropanol precipitation.
Two library construction methods were used. The one used ThruPlex kit according to manufacturees instruction, the other is based on TCS ligation.


title: MNase-treated chromatin DNA_CuAAC


title: ato_t4/t5_input_2 L3

city: Leuven

first: Mark

last: Fiers

address: Herestraat 49

department: Center for Brain and Disease

country: Belgium

institute: VIB

description: featurecounts.tsv

data_processing:
Basecalls performed with BaseSpace FastQ Version: 1.0.0
Raw reads adapter and low quality trimmed using fastq-mcf version 1.04.807
Read mapped to the genome using Tophat 2.0.12
Reads counted using FeatureCounts v1.4.4 (part of the subRead package)
Genome_build: DM3

organism: Drosophila melanogaster

source_name: L3 Brains

growth_protocol: The Drosophila stocks used in this experiment were keept at 25 degrees at standard conditions

extract_protocol: 500 L3 larvae of the desired genotype were dissect to collect 500 Brains. The Brains were deep frozen in liquid nitrogen and then homogenized. A 10% of the brain homogenates was used as input, the rest was immunuprecipated with anti-GFP antibodies to isolate t4/t5 ribosomes. The RNA bound to the ribosome was then purified, sonicated and sequenced.

treatment_protocol: Flies were keept under normal growing contions and they were not treated before dissection

tag: developmental stage

value: brains

value: ipcGal4, UASRpl10Ab::GFP; ato1

value: ato loss of function

tag: replicate-id


title: ato_t4/t5_input_2 L4

description: featurecounts.tsv

tag: genotype


title: SpleenTRNurr77High_rep1_104

value: spleen


title: SpleenTRNurr77High_rep1_103


title: ato_t4/t5_input_2 L1

description: featurecounts.tsv

tag: chip antibody


title: ato_t4/t5_input_1 L4

description: featurecounts.tsv

tag: tissue


title: SpleenTRNurr77High_rep1_102

tag: library name


title: ato_t4/t5_input_1 L3

description: featurecounts.tsv


title: SpleenTRNurr77High_rep1_101

tag: sample type


title: SpleenTRNurr77High_rep1_100

tag: strain


title: ato_t4/t5_input_1 L2

description: featurecounts.tsv


title: ato_t4/t5_input_2 L2

description: featurecounts.tsv


title: SpleenTRNurr77High_rep1_99

tag: Sex


title: SpleenTRNurr77High_rep1_97

tag: age (months)


title: SiPool FGFR3 (5)

description: MGH-U3 treated with SiPool FGFR3 (Dharmacon, L-0031333-00-0005)


title: wt_t4/t5_input_2 L4

description: featurecounts.tsv

value: ipcGal4, UASRpl10Ab::GFP

value: wild type


title: wt_t4/t5_input_2 L3

description: featurecounts.tsv


title: Si2 FGFR3 (4)

description: MGH-U3 treated with Si2 FGFR3 (Ambion, 144468)


title: LPF3 (10)

description: MGH-U3 treated with LipofectaminRNAimax


title: wt_t4/t5_input_2 L2

description: featurecounts.tsv


title: SpleenTRNurr77High_rep1_96

tag: total number of reads


title: RBM5 Knockdown Virus, biological rep3

city: Pittsburgh

first: Travis

middle: C.

last: Jackson

state: Pennsylvania

address: 3550 Terrace Street

department: Critical Care Medicine

institute: University of Pittsburgh

description: Gene expression data from neurons with RBM5 knockdown

hyb_protocol: The Affymetrix GeneChip® Hybridization, Wash, and Stain kit was used for array processing. 5.2µg biotin-labeled fragmented ss-cDNA was added to 1X hybridization buffer containing oligo B2, hybridization controls, and DMSO.  Following incubation at 95°C and 45°C for 5 minutes each, 200µL hybridization mix was loaded onto each array. Arrays were incubated for 16h in a GeneChip 645 hybridization oven (Affymetrix) at 45°C with rotation at 60rpm.

scan_protocol: Arrays were scanned using the GeneArray® 3000 scanner (Affymetrix).

data_processing: Results were normalized by robust multi-array average (RMA). Gene level normalization and signal summarization and QC were performed in Expression Console Software (Affymetrix). The data was exported as CHP files and statistical anlaysis done in Transcriptome Analysis Software (TAC, Affymetrix).

organism: Rattus norvegicus

source_name: Cortical Neuron, DIV6, 60 MOI Lentivirus, RBM5 Targeting shRNA Vector

label_protocol: Amplified cRNA was made using second strand synthesis and in vitro transcription.  cDNA was produced by a subsequent reverse transcription and then fragmented. Fragments were biotin end-labeled in preparation for hybridization to the RTA.

growth_protocol: Neurons were plated in Neurobasal media + B27 supplement and given 1/2 media exchange on DIV3.

treatment_protocol: DIV6 neurons were harvested on ice. Cells were washed with ice-cold PBS (supplemented with 1mM DTT) and harvested on ice in 1mL Trizol.

value: Sprague Dawley

value: Primary Cortical Neuron

value: RBM5 knockdown

tag: age

value: Day In Vitro 6 Cells


title: Si1 FGFR3 (1)

description: MGH-U3 treated with Si1 FGFR3 ( Ambion, 144467)

tag: cell line


title: DDK-tagged rat RBM5 open reading frame overexpression virus, biological rep4

description: Gene expression data from neurons tranduced with a lentivirus to overexpression rat RBM5

source_name: Cortical Neuron, DIV6, 30 MOI Lentivirus, DDK-Tagged rat RBM5 ORF Vector

value: RBM5 Overexpression


title: ato_t4/t5_input_1 L1

description: featurecounts.tsv


title: SpleenTRNurr77High_rep1_98

value: B6 Nr4a1-Gfp Foxp3-Ires-Thy1.1

value: male

tag: number of mapped reads


title: wt_t4/t5_input_2 L1

description: featurecounts.tsv


title: Empty Vector Control Virus, biological rep4

description: Gene expression data from normal neurons tranduced with an empty-vector lentivirus (i.e. no recobminant experimental gene is expressed)

source_name: Cortical Neuron, DIV6, 30 MOI Lentivirus, Control Empty Vector

value: Wt (Control for overexpression)


title: 409B2

source_name: validated iPS

tag: origin

value: Fibro (HDF1388)

tag: method

value: Episomal plasmid


title: Empty Vector Control Virus, biological rep3


title: wt_t4/t5_input_1 L4

description: featurecounts.tsv


title: SpleenTRNurr77High_rep1_94

source_name: spleen

tag: number of unique reads (umi)


title: NT shRNA Control Virus, biological rep3

description: Gene expression data from normal neurons tranduced with a lentivirus to deliver non-targeting shRNA

source_name: Cortical Neuron, DIV6, 60 MOI Lentivirus, Control NT shRNA Vector

value: Wt (control for knockdown)


title: wt_t4/t5_input_1 L3

description: featurecounts.tsv

tag: developmental stage

value: brains


title: SpleenTRNurr77High_rep1_93


title: SpleenTRNurr77High_rep1_91


title: wt_t4/t5_input_1 L2

description: featurecounts.tsv

tag: replicate-id


title: ato_t4/t5_RIP_2 L4

description: featurecounts.tsv

value: anti-GFP

tag: genotype

value: ipcGal4, UASRpl10Ab::GFP; ato1


title: wt_t4/t5_input_1 L1

description: featurecounts.tsv

tag: chip antibody


title: SpleenTRNurr77High_rep1_90

tag: tissue

value: spleen


title: ato_t4/t5_RIP_2 L3

description: featurecounts.tsv

value: ato loss of function


title: SpleenTRNurr77High_rep1_89

tag: library name


title: ato_t4/t5_RIP_2 L2

description: featurecounts.tsv


title: SpleenTRNurr77High_rep1_88

tag: sample type


title: DDK-tagged rat RBM5 open reading frame overexpression virus, biological rep3

tag: strain


title: Empty Vector Control Virus, biological rep2


title: SpleenTRNurr77High_rep1_92

tag: Sex


title: SpleenTRNurr77High_rep1_86

tag: age (months)


title: SpleenTRNurr77High_rep1_87

tag: total number of reads


title: ato_t4/t5_RIP_2 L1

description: featurecounts.tsv


title: NT shRNA Control Virus, biological rep1

tag: age


title: RBM5 Knockdown Virus, biological rep1


title: DDK-tagged rat RBM5 open reading frame overexpression virus, biological rep1


title: ato_t4/t5_RIP_1 L3

description: featurecounts.tsv


title: RBM5 Knockdown Virus, biological rep2


title: SpleenTRNurr77High_rep1_85


title: ato_t4/t5_RIP_1 L2

description: featurecounts.tsv


title: SpleenTRNurr77High_rep1_84


title: ato_t4/t5_RIP_1 L1

description: featurecounts.tsv


title: SpleenTRNurr77High_rep1_95


title: wt_t4/t5_RIP_2 L4

description: featurecounts.tsv

value: ipcGal4, UASRpl10Ab::GFP

value: wild type


title: SpleenTRNurr77High_rep1_83


title: SpleenTRNurr77High_rep1_81


title: SpleenTRNurr77High_rep1_80


title: DDK-tagged rat RBM5 open reading frame overexpression virus, biological rep2

value: Sprague Dawley

value: Primary Cortical Neuron


title: ato_t4/t5_RIP_1 L4

description: featurecounts.tsv


title: SpleenTRNurr77High_rep1_79


title: wt_t4/t5_RIP_2 L1

description: featurecounts.tsv


title: wt_t4/t5_RIP_2 L3

description: featurecounts.tsv


title: wt_t4/t5_RIP_2 L2

description: featurecounts.tsv


title: wt_t4/t5_RIP_1 L4

description: featurecounts.tsv


title: SpleenTRNurr77High_rep1_78


title: wt_t4/t5_RIP_1 L3

description: featurecounts.tsv


title: wt_t4/t5_RIP_1 L2

description: featurecounts.tsv


title: SpleenTRNurr77High_rep1_75


title: wt_t4/t5_RIP_1 L1

description: featurecounts.tsv


title: SpleenTRNurr77High_rep1_74


title: SpleenTRNurr77High_rep1_76


title: SpleenTRNurr77High_rep1_73


title: SpleenTRNurr77High_rep1_77


title: SpleenTRNurr77High_rep1_72


title: SpleenTRNurr77High_rep1_70


title: SpleenTRNurr77High_rep1_69


title: SpleenTRNurr77High_rep1_68


title: SpleenTRNurr77High_rep1_65


title: SpleenTRNurr77High_rep1_63


title: SpleenTRNurr77High_rep1_64


title: SpleenTRNurr77High_rep1_62


title: SpleenTRNurr77High_rep1_61


title: SpleenTRNurr77High_rep1_71


title: SpleenTRNurr77High_rep1_59


title: SpleenTRNurr77High_rep1_60


title: SpleenTRNurr77High_rep1_67


title: SpleenTRNurr77High_rep1_66


title: NT shRNA Control Virus, biological rep2

value: Day In Vitro 6 Cells


title: SpleenTRNurr77High_rep1_58


title: Empty Vector Control Virus, biological rep1


title: SpleenTRNurr77High_rep1_55


title: SpleenTRNurr77High_rep1_57


title: Node_negative_Breast_tumor_330

city: Milan

first: Marco

last: Silvestri

address: via Amadeo 42

department: Department of Applied Research and Technological Development

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were log(2) transformed and robust spline normalized using the lumi package in R.

label_protocol: Biotinylated cRNA were prepared with the TotalPrep Amplification kit (Ambion) for Illumina arrays.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: age (yrs)

tag: size

tag: histotype

value: Altro

tag: pam

value: LumB


title: Node_negative_Breast_tumor_193

value: CDI


title: Node_negative_Breast_tumor_509


title: Node_negative_Breast_tumor_531


title: SpleenTRNurr77High_rep1_56

value: B6 Nr4a1-Gfp Foxp3-Ires-Thy1.1

value: male

tag: number of mapped reads

tag: number of unique reads (umi)


title: Node_negative_Breast_tumor_681


title: Node_negative_Breast_tumor_10026

value: CLI


title: SpleenTRNurr77High_rep1_54


title: Node_negative_Breast_tumor_521


title: Node_negative_Breast_tumor_549


title: Node_negative_Breast_tumor_213


title: Node_negative_Breast_tumor_525


title: Node_negative_Breast_tumor_10040


title: Node_negative_Breast_tumor_10055


title: Node_negative_Breast_tumor_544


title: Node_negative_Breast_tumor_532


title: Node_negative_Breast_tumor_361


title: Node_negative_Breast_tumor_690


title: Node_negative_Breast_tumor_348

value: CDI+CLI


title: Node_negative_Breast_tumor_10049


title: Node_negative_Breast_tumor_10024


title: Node_negative_Breast_tumor_10021


title: SpleenTRNurr77High_rep1_52


title: SpleenTRNurr77High_rep1_51


title: Node_negative_Breast_tumor_419


title: SpleenTRNurr77High_rep1_49


title: Node_negative_Breast_tumor_536


title: SpleenTRNurr77High_rep1_50


title: Node_negative_Breast_tumor_10025


title: SpleenTRNurr77High_rep1_48


title: SpleenTRNurr77High_rep1_47


title: Node_negative_Breast_tumor_546


title: SpleenTRNurr77High_rep1_46


title: SpleenTRNurr77High_rep1_41


title: SpleenTRNurr77High_rep1_43


title: SpleenTRNurr77High_rep1_40


title: SpleenTRNurr77High_rep1_44


title: Node_negative_Breast_tumor_683


title: Node_negative_Breast_tumor_654


title: Node_negative_Breast_tumor_250


title: Node_negative_Breast_tumor_688


title: SpleenTRNurr77High_rep1_39


title: Node_negative_Breast_tumor_584


title: SpleenTRNurr77High_rep1_45


title: SpleenTRNurr77High_rep1_38


title: SpleenTRNurr77High_rep1_37


title: SpleenTRNurr77High_rep1_42


title: SpleenTRNurr77High_rep1_36


title: Node_negative_Breast_tumor_10027


title: SpleenTRNurr77High_rep1_33


title: SpleenTRNurr77High_rep1_34


title: Node_negative_Breast_tumor_463


title: Node_negative_Breast_tumor_10038


title: SpleenTRNurr77High_rep1_82


title: Node_negative_Breast_tumor_10058


title: Node_negative_Breast_tumor_159


title: Node_negative_Breast_tumor_589


title: SpleenTRNurr77High_rep1_31


title: SpleenTRNurr77High_rep1_30


title: Node_negative_Breast_tumor_657


title: SpleenTRNurr77High_rep1_29


title: SpleenTRNurr77High_rep1_28


title: SpleenTRNurr77High_rep1_27


title: SpleenTRNurr77High_rep1_35


title: Node_negative_Breast_tumor_184


title: Node_negative_Breast_tumor_593

value: LumA


title: Node_negative_Breast_tumor_10041


title: Node_negative_Breast_tumor_191


title: SpleenTRNurr77High_rep1_26


title: SpleenTRNurr77High_rep1_25


title: SpleenTRNurr77High_rep1_32


title: SpleenTRNurr77High_rep1_23


title: SpleenTRNurr77High_rep1_24


title: Node_negative_Breast_tumor_429


title: SpleenTRNurr77High_rep1_22


title: Node_negative_Breast_tumor_609


title: Node_negative_Breast_tumor_405


title: SpleenTRNurr77High_rep1_21


title: Node_negative_Breast_tumor_10053


title: Node_negative_Breast_tumor_513


title: Node_negative_Breast_tumor_511


title: Node_negative_Breast_tumor_592


title: SpleenTRNurr77High_rep1_20


title: Node_negative_Breast_tumor_334


title: Node_negative_Breast_tumor_430


title: Node_negative_Breast_tumor_510


title: SpleenTRNurr77High_rep1_18


title: Node_negative_Breast_tumor_10022


title: SpleenTRNurr77High_rep1_19


title: Node_negative_Breast_tumor_582


title: SpleenTRNurr77High_rep1_15


title: Node_negative_Breast_tumor_608


title: SpleenTRNurr77High_rep1_14


title: Node_negative_Breast_tumor_607


title: SpleenTRNurr77High_rep1_13


title: Node_negative_Breast_tumor_493


title: SpleenTRNurr77High_rep1_11


title: Node_negative_Breast_tumor_255


title: SpleenTRNurr77High_rep1_16


title: SpleenTRNurr77High_rep1_10


title: SpleenTRNurr77High_rep1_53


title: SpleenTRNurr77High_rep1_8


title: SpleenTRNurr77High_rep1_12


title: SpleenTRNurr77High_rep1_7


title: SpleenTRNurr77High_rep1_9


title: Node_negative_Breast_tumor_597


title: SpleenTRNurr77High_rep1_6


title: SpleenTRNurr77High_rep1_5


title: Node_negative_Breast_tumor_10034


title: SpleenTRNurr77High_rep1_17


title: SpleenTRNurr77High_rep1_3


title: Node_negative_Breast_tumor_387


title: Node_negative_Breast_tumor_591


title: Node_negative_Breast_tumor_613


title: Node_negative_Breast_tumor_601


title: Node_negative_Breast_tumor_10030


title: SpleenTRNurr77High_rep1_1


title: Node_negative_Breast_tumor_533


title: Node_negative_Breast_tumor_660


title: Node_negative_Breast_tumor_286


title: Node_negative_Breast_tumor_10001


title: Node_negative_Breast_tumor_556


title: SpleenTRNurr77High_rep1_2


title: Node_negative_Breast_tumor_10043


title: SpleenTRNurr77High_rep1_4


title: Node_negative_Breast_tumor_10002


title: Node_negative_Breast_tumor_471


title: Node_negative_Breast_tumor_10010


title: Node_negative_Breast_tumor_232


title: Node_negative_Breast_tumor_545


title: Node_negative_Breast_tumor_522


title: Node_negative_Breast_tumor_225


title: Node_negative_Breast_tumor_10005


title: Node_negative_Breast_tumor_10004


title: Node_negative_Breast_tumor_237


title: Node_negative_Breast_tumor_668


title: Node_negative_Breast_tumor_642


title: Node_negative_Breast_tumor_693


title: Node_negative_Breast_tumor_675

value: Basal


title: Node_negative_Breast_tumor_611


title: Node_negative_Breast_tumor_10056


title: CD8-E9-REP2

city: La Jolla

first: Christella

last: Widjaja

state: ca

address: 9500 Gilman Drive #0063

department: Medicine

institute: UCSD

description: replicate 2

scan_protocol: Standard Illumina scan protocol

data_processing: Data was normalized using quantile normalization and analyzed in Array Studio

source_name: Splenic CD8+ T lymphocytes

label_protocol: cRNA was labeled with Streptavidin-Cy3 according to standard Illumnia protocol

growth_protocol: Mouse spleens were homogenized and red blood cells were lysed with ACK lysis buffer. CD8+ T cells were isolated with Miltenyi CD8+ T cell Isolation Kit II. Cells were pre-treated with DMSO, 0.5 µM epoxomicin, or 1.0 µM of a novel proteasome activator E9 received from Dr. Huib Ovaa. Cells were then cultured for 3 days on 5 µg/ml immobilized antibodies against CD3 and CD28 in IL-2 containing media.

extract_protocol: RNA was extracted using Trizol reagent and cleaned up with Zymo RNA Clean and Concentrator kit according to the manufacturer's protocols. RNA quality was assessed with Agilent Bioanalyzer.

value: 6 weeks

tag: treatment


title: CD8-DMSO-REP1

description: replicate 1

value: spleen

value: DMSO


title: Node_negative_Breast_tumor_10037


title: Node_negative_Breast_tumor_10050


title: Node_negative_Breast_tumor_694


title: CD8-EPOX-REP1

description: replicate 1

value: 0.5 µM epoxomicin


title: CD8-E9-REP1

description: replicate 1

value: 1.0 µM of a novel proteasome activator E9


title: Node_negative_Breast_tumor_144


title: CD8-EPOX-REP2

description: replicate 2


title: Node_negative_Breast_tumor_651


title: CD8-DMSO-REP2

description: replicate 2


title: KO Room Temperature Brown fat, biological rep3

status: Public on Feb 15 2018

city: Ann Arbor

first: Jiandie

last: Lin

state: MI

address: 210 Washtenaw Avenue

department: Life Sciences Institute

institute: University of Michigan

description: Gene expression data from Nrg4 knockout liver, pool 2

hyb_protocol: Following labeling procedure, 2.53 ug of cDNA were hybridized at 48C on Mouse Gene ST 2.1 arrays, and were washed and stained using the Affymetrix GeneTitan system (software version 4.3.0.1592)

scan_protocol: Arrays were scanned using the Affymetrix GeneTitan system (software version 4.3.0.1592)

data_processing: Data was analyzed using the limma and oligo Bioconductor packages implemented in the R-statistical language version 3.3.0. RMA was used to fit log2 transformed expression values

source_name: Zbtb7b KO mouse brown fat

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA.

growth_protocol: Wild type and Zbtb7b knockout mice were maintained on standard rodent chow

treatment_protocol: Wild type and Zbtb7b knockout mice were kept at ambient room temperature (22C) or following cold exposure at 4C for 4 hrs. Brown adipose tissue was harvested for total RNA isolation and microarray analysis.

value: Brown fat

tag: genotype

value: Zbtb7b KO

tag: gender

value: Male

tag: cold exposure

value: Ambient room temperature


title: Node_negative_Breast_tumor_327


title: KO Cold Brown fat, biological rep2

tag: tissue

value: Cold exposure


title: KO Room Temperature Brown fat, biological rep2


title: WT Cold Brown fat, biological rep1

source_name: Wild type mouse brown fat

value: wild type


title: WT Cold Brown fat, biological rep2


title: KO Cold Brown fat, biological rep3


title: WT Cold Brown fat, biological rep3


title: WT Room Temperature Brown fat, biological rep3

description: Gene expression data from Nrg4 knockout liver, pool 1


title: KO Cold Brown fat, biological rep1


title: WT Room Temperature Brown fat, biological rep2

description: Gene expression data from wild type liver, pool 2


title: WT Room Temperature Brown fat, biological rep1

description: Gene expression data from wild type liver, pool 1


title: Node_negative_Breast_tumor_529


title: Patient 32_SN25

city: Maastricht

first: Lisa

middle: Maria

last: Hillen

state: Limburg

address: P. Debyelaan 25

department: Department of Pathology

country: Netherlands

institute: Maastricht University Medical Center

description:
raw data column in the raw_data.txt: Sp18
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

hyb_protocol: Samples were hybridized to NanoString PanCancer Pathway Panel probes according to manufacturer's instructions

scan_protocol: Samples were scanned on the nCounter System according to manufacturer's instructions.

data_processing:
The samples were dichotomized into a training set and a validation set. The training set included the 7 NCN and the 7 SN samples from the same 7 patients to minimize interindividual genomic background. The second group of samples included 8 NCN and 18 SN from different patients. All analyses were performed with R-/Bioconductor.  Each assay included 6 positive and 8 negative controls. A positive control normalization factor was calculated (with the geometric mean method). The negative controls were used to estimate background (mean + 2 × standard deviation). The average positive control normalization factor was low across assays with 1.04 (range: 0.71, 1.64). NanoString recommends a value between 0.3 and 3. The negative controls consistently produced a low value for the background (mean = 23.4; range: 6.68, 40.97). Testing for differential expression of the nCounter data in SN versus NCN was done using the limma and voom method in R (Green, Wilkins et al. 2016).
The voom procedure was used to non-parametrically estimate the mean-variance relationship of the log-transformed gene counts (Law, Chen et al. 2014). This procedure takes as input the raw counts; and total library size (total number of counts) per sample is used as a scaling factor to normalize the counts. The voom procedure generates precision weights, which are incorporated into the limma linear modelling procedure; and this removes the mean-variance relationship in the log-counts. The normalized log-counts were used in subsequent analyses.

source_name: skin spitz nevus

label_protocol: NanoString capture and reporter probe mix, Nat Biotechnol 2008;26:317-25.

extract_protocol: Serial sections, 5µm thick, were cut from FFPE tissue blocks using a microtome. One section per sample was mounted onto a glass slide and stained with Hematoxylin and Eosin (H&E), which served as corresponding reference section to obtain at least 70% tumor purity. For RNA and DNA isolation FFPE sections were collected in Eppendorf tubes, deparaffinized with xylol washing steps (1-4 times) and rehydrated in a graded alcohol series, starting at 100%, proceeding with 96% and completing with 70% ethanol. Each time tubes were washed with xylol/ethanol for 5 min in a centrifugation step for 5 min at 13000g. Subsequently the pellets were dried for 1 h at 56°C. RNA and DNA were isolated by AllPrep DNA/RNA FFPE kit (Qiagen, Hildesheim, Germany) according to the manufacturer's instructions. Purified RNA was measured in a spectrophotometer (Nanodrop, 2000; Thermo Scientific). Finally, another section was cut from the rest of FFPE block and stained with H&E, and the inclusion criteria were evaluated again on this section.

tag: patient id

value: Patient 32

value: skin spitz nevus

tag: dataset group

value: Validation Set SN


title: Patient 22_SN15

description:
raw data column in the raw_data.txt: Spad 5
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 22


title: Patient 31_SN24

description:
raw data column in the raw_data.txt: Sp13
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 31


title: Patient 25_SN18

description:
raw data column in the raw_data.txt: SPad1
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 25


title: Patient 24_SN17

description:
raw data column in the raw_data.txt: Sp5
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 24


title: Patient 28_SN21

description:
raw data column in the raw_data.txt: Sp2
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 28


title: Patient 29_SN22

description:
raw data column in the raw_data.txt: Sp11
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 29


title: Patient 23_SN16

description:
raw data column in the raw_data.txt: Spad 4
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 23


title: Patient 30_SN23

description:
raw data column in the raw_data.txt: Sp12
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 30


title: Patient 27_SN20

description:
raw data column in the raw_data.txt: Spad3
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 27


title: Patient 19_SN11

description:
raw data column in the raw_data.txt: Sp1
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 19


title: Patient 21_SN14

description:
raw data column in the raw_data.txt: KSPad
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 21


title: Patient 20_SN12

description:
raw data column in the raw_data.txt: Sp3
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 20


title: Patient 18_SN10

description:
raw data column in the raw_data.txt: Spad7
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 18


title: Patient 16_SN8

description:
raw data column in the raw_data.txt: Sp8
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 16


title: Patient 17_SN9

description:
raw data column in the raw_data.txt: SPad6
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 17


title: Patient 26_SN19

description:
raw data column in the raw_data.txt: Spad2
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 26

value: skin spitz nevus


title: Patient 14_NCN15

description:
raw data column in the raw_data.txt: NV11
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

source_name: skin nevocellular nevus

value: Patient 14

value: skin nevocellular nevus

value: Validation Set NCN


title: Patient 13_NCN14

description:
raw data column in the raw_data.txt: NV9
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 13


title: Patient 7_NCN7

description:
raw data column in the raw_data.txt: NV6
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 7

value: Training Set


title: Patient 7_SN7

description:
raw data column in the raw_data.txt: NV1
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).


title: Patient 9_NCN9

description:
raw data column in the raw_data.txt: NV3
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 9


title: Patient 12_NCN13

description:
raw data column in the raw_data.txt: NV8
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 12


title: Patient 8_NCN8

description:
raw data column in the raw_data.txt: NV2
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 8


title: Patient 11_NCN12

description:
raw data column in the raw_data.txt: NV7
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 11


title: Patient 33_SN26

description:
raw data column in the raw_data.txt: Sp15
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 33

value: Validation Set SN


title: Patient 10_NCN11

description:
raw data column in the raw_data.txt: NV5
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 10


title: Patient 6_NCN6

description:
raw data column in the raw_data.txt: NV10
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 6


title: Patient 15_NCN16

description:
raw data column in the raw_data.txt: NV12
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 15


title: A8-SPIN-MET-RNA

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
MapSplice 0.7.4
RSEM upper quantile normalized
Genome_build: NCBI Build 36
Supplementary_files_format_and_content: text file with log 2 RSEM counts normalized to the upper quartile

source_name: SPINAL

extract_protocol:
QIAGEN RNAeasy
Illumina TruSeq polyA Select

value: breast cancer

tag: tumor location

value: SPINAL


title: Patient 6_SN6

description:
raw data column in the raw_data.txt: Ksp7
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: skin spitz nevus


title: A8-LIV-MET-RNA

source_name: LIVER

value: LIVER


title: Patient 1_NCN1

description:
raw data column in the raw_data.txt: NVK1
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 1

value: skin nevocellular nevus


title: Patient 1_SN1

description:
raw data column in the raw_data.txt: Ksp1
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).


title: Patient 5_NCN5

description:
raw data column in the raw_data.txt: NVK6
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 5


title: Patient 3_SN3

description:
raw data column in the raw_data.txt: Ksp4
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 3

value: Training Set


title: Patient 4_NCN4

description:
raw data column in the raw_data.txt: NVK5
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 4


title: A5-SKIN-Met-L-RNA

source_name: SKIN

extract_protocol:
Roche High Pure RNA Paraffin Kit
Illumina TruSeq RiboZero Gold

value: SKIN


title: Patient 5_SN5

description:
raw data column in the raw_data.txt: Ksp6
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).


title: Patient 3_NCN3

description:
raw data column in the raw_data.txt: NVK4
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).


title: Patient 2_SN2

description:
raw data column in the raw_data.txt: KSP3
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 2


title: A34-Primary-FFPE-RNA

source_name: PRIMARY

value: PRIMARY


title: Patient 4_SN4

description:
raw data column in the raw_data.txt: Ksp5
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).


title: Patient 2_NCN2

description:
raw data column in the raw_data.txt: NVK3
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).


title: A8-030222BSPIMET-RNA

source_name: breast cancer


title: KO Room Temperature Brown fat, biological rep1

description: Gene expression data from Nrg4 knockout liver, pool 2

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

value: Brown fat

value: Zbtb7b KO

value: Male

value: Ambient room temperature


title: A34-PancreasMet-RNA

source_name: PANCREAS

value: breast cancer

value: PANCREAS


title: A34-LN-Met-RNA

source_name: LYMPH NODE

value: LYMPH NODE


title: A34-LiverMet-L-RNA

value: LIVER


title: A34-LiverMet-R-RNA


title: A26-SoftTissueMet-RNA

source_name: SOFTTISSUE

value: SOFTTISSUE


title: A26-Primary-FFPE-RNA


title: A28-PT-FFPE-RNA


title: PAF_KO_2_RNA-seq

city: Houston

first: Bo

last: Xia

state: TX

address: 6670 Bertner Ave, R10-414D

institute: Houston Methodist

description: Intestinal adenoma

data_processing:
Sequenced reads were mapped to mm9 whole genome using tophat2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by Cuffdiff.
Genome_build: mm9
Supplementary_files_format_and_content: text file includes RPKM values for each Sample.

source_name: PAF knock out APC Min adenoma

extract_protocol:
RNA extract from mouse intestinal adenomas using Qaigen RNeasy mini kit
RNA libraries were prepared for sequencing using standard BGI and Illumina protocols

value: PAF KO; APC Min/+

value: small intestine

tag: disease state

value: adenoma


title: A26-Lung-Met-1-RNA

source_name: LUNG

value: LUNG


title: A23-PTcore-2009-FFPE-RNA


title: A8-LUNG-MET-RNA


title: A23-LN-Met-2010postT-FFPE-RNA


title: A2-Primary-FFPE-RNA


title: A17-Primary-FFPE-RNA


title: A15-LiverMet-RNA


title: A17-3-LivMet-1-RNA


title: A7-PRIMT020552B

extract_protocol:
QIAGEN RNAeasy
Illumina TruSeq RiboZero Gold


title: A15-ChestWallMet-RNA


title: A7-BRAIN-Met

source_name: BRAIN

value: BRAIN


title: A11-PT-FFPE-RNA


title: A8-OVA-MET-RNA

source_name: OVARY

value: OVARY


title: A5-SKIN-Met-R-RNA

value: SKIN


title: A5-PRIMT030065B-RNA

value: PRIMARY


title: A7-RIB-MET

source_name: RIB

value: RIB


title: A7-KIDNYMET

source_name: KIDNEY

value: KIDNEY


title: A4-PRIMT020306B-RNA


title: A30-Primary-FFPE-RNA


title: A4-LUL-MET-RNA


title: A4-LLL-MET-RNA


title: A30-LivMet-R-RNA


title: A30-BrainMet-R-RNA


title: A30-BrainMet-Occi-RNA


title: A30-LivMet-L-RNA


title: A30-BrainMet-L4-RNA


title: A28-LungMet-RUL-RNA


title: C57Bl/6 mouse whole bone marrow cells

city: Boston

first: Peter

last: Kharchenko

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

description: single-cell RNA-seq

data_processing:
dropEst pipeline was used for demultiplexing and read counting. The alignment was performed using tophat2 with mouse mm10 assembly and annotation.
Genome_build: mm10
Supplementary_files_format_and_content: Molecular count matrix, as written out by dropEst, with the list of genes (rows) and cell barcodes (columns) are provided as compressed text files.

source_name: bone marrow

extract_protocol:
Whole bone marrow cells were isolated from 11 weeks old C57Bl/6 male mice (Jackson Laboratory). Epiphysis/metaphysis fraction from long bones was collected, crushed, cut into small pieces, and digested using Collagenase I (STEMCELL Technologies) for 30 minutes at 37-degree agitation.  Bone marrow cells were filtered through a 70-micron filter. Red blood cells were lysed using Ack-lysis (ThermoFisher Scientific) on ice for five min, quenched with Media 199 (ThermoFisher Scientific) supplemented with 2% fetal bovine serum (ThermoFisher Scientific), and spun down at 500 g for 5 min. Cells were stained for 30 minutes with the red blood cell marker TER119 (Biolegend) and cells were sorted using DAPI (ThermoFisher Scientific) as a live/dead viability marker. Four hundred thousand live whole bone marrow cells (negative for TER119) were sorted into medium 199 (ThermoFisher Scientific). Before inDrop encapsulation cells were counted using a Cellometer (Nexcelom Bioscience). Cell viability is over 90%.
InDrop processing. Concentration of cells was adjusted to 300,000 cells/ml by adding PBS to the sorted cells. The cell suspension was then mixed 1:1 (v/v) with PBS containing 30% OptiPrep Density Gradient Medium (Sigma D1556) to obtain 150,000 cells/ml in 15% Optiprep. Using four microfluidics pumps and a polydimethylsiloxane (PDMS) microfluidic device, about 10,000 cells were co-encapsulated with barcoded polyacrylamide beads (V3) and a reverse transcription mixture containing Superscript III into water-in-oil droplets, according to a previously published protocol. The library preparation and quality control procedures were carried out as described previously. Indexed libraries were pooled and sequenced on a Next-seq 500 system (Illumina) at 2 pM concentrations.
single-cell RNA-seq (inDrop V3)

tag: strain

value: bone marrow


title: A28-PancreasMet-RNA


title: A28-DuraMaterMet-RNA

source_name: DURA

value: DURA


title: A28-LungMet-LLL-RNA

value: breast cancer


title: A28-LivMet-1-RNA


title: A28-AdrenalMet-RNA

source_name: ADRENAL

value: ADRENAL


title: A26-Lung-Met-2-RNA


title: A23-PleuraMet-RNA

source_name: PLEURA

value: PLEURA


title: A7-LIV-MET1

source_name: LIVER

value: LIVER


title: A23-BrainMet-RNA


title: A7-LUNG-MET1


title: A23-BrainMet-2-RNA


title: A20-LivMet-RNA


title: A23-BrainMet-3-RNA


title: A20-AdrenalMet-RNA


title: A20-BrainMet-RNA


title: A2-LivMet-RNA


title: A20-Primary-FFPE-RNA


title: A2-LN-Met-Subcarinal-RNA

source_name: SUBCARINAL LYMPH NODE

value: SUBCARINAL LYMPH NODE


title: A2-LungMet-RNA


title: A17-9-ChestMet-RNA


title: A15-LUNG-MET-RNA


title: A20-LungMet-R-RNA


title: A12-SkullMet-RNA

source_name: SKULL

value: SKULL


title: A12-PleuraMet-RNA


title: A12-RLL-MET-RNA

source_name: breast cancer


title: A15-LN-MET-RNA

value: LYMPH NODE


title: A12-LN-Met-subcarinal-RNA


title: A12-LIV-MET-RNA

source_name: PRIMARY


title: A11-RIB-MET-RNA


title: A11-LUNG-MET-RNA


title: A11-CELEB-MET-RNA


title: A1-SPIN-MET1

source_name: SPINAL

value: SPINAL


title: A20-LungMet-L-RNA

value: LUNG


title: A11-BRAIN-MET-RNA

value: BRAIN


title: A1-PRIMT-2


title: A1-LUNG-MET


title: A1-AX-LN-MET-RNA

source_name: AUXILLARY LYMPH NODE

value: AUXILLARY LYMPH NODE


title: A1-LIV-MET2


title: A15-MediastnMet-RNA


title: A1-ADRE-MET2


title: A12-PRIMT020076B-RNA


title: AB_1-4

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

data_processing:
alignment TopHat v2.0.14
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited gene counts

source_name: cultured cell

growth_protocol: hES cells were maintained in E8 medium and passaged in single cells for DE differentiatioin.

extract_protocol:
Cells were collected in Trizol for total RNA extraction using Qiagen RNeasy Plus reagents.
RNA-seq libraries were made by polyA selection of mRNA and directional RNA-seq library generation on the Apollo 324 system (IntegenX) at the biopolymers facility (Harvard Medical School).

treatment_protocol: Differentiation was started with activin A and CHIR99021 for 24 hours, then activin A only for 4 days. Base differentiation medium is Advanced RPMI 1640.

tag: cell type

value: hES; day 4 of differentiation

tag: cell line

value: H9; day 4 of differentiation


title: AB_2-2

value: hES; day 2 of differentiation

value: H9; day 2 of differentiation


title: AB_2-0

value: undifferentiated hES


title: AB_4-2


title: AB_2-4


title: AB_4-1

value: hES; day 1 of differentiation

value: H9; day 1 of differentiation


title: AB_2-1


title: A11-LIV-MET-RNA

value: breast cancer


title: AB_4-3

value: hES; day 3 of differentiation

value: H9; day 3 of differentiation


title: AB_4-0


title: A12-AdrenalG-Met-RNA

value: ADRENAL


title: AB_1-1


title: AB_1-0


title: AB_2-3


title: AB_4-4


title: AB_1-2


title: A15-PRIMT070427B-RNA

value: PRIMARY


title: AB_1-3


title: miR-K12-3-3p HOK 4

city: Chicago

first: Afsar

last: Naqvi

state: IL

address: 801 S Paulina, Room 561B

department: Periodontics

institute: University of Illinois at Chicago

description: Primary gingival keratinocytes isolated from human oral mucosa

hyb_protocol: RNA samples were hybridized according to standard WT (whole transcript) PLUS target labeling protocol recommended by Affymetrix. We used Affymetrix HTA-2_0 arrays for transcriptome profiling

scan_protocol: After hybridization, each image was analyzed for the following quality metrics:  average signal present, signal intensity of species-specific house-keeping genes, relative signal intensities of labeling controls, and absolute signal intensities of hybridization controls.

data_processing:
Data was processed using Genomics Suite 6.6 statistical package (Partek, Inc).  The following parameters were applied for hybridization signal processing: Algorithm: RMA; Background Correction: RMA Background Correction; Normalization: Quantile Normalization; Log Probes using Base: 2; Probeset Summarization: Median Polish.
probe group file: VmiR_Microarray_HuGene2_121415_(HuGene-2_0-st)

label_protocol: RNA samples were labeled according to standard WT (whole transcript) PLUS target labeling protocol recommended by Affymetrix.

growth_protocol: Cells were cultured using DermaLife K Keratinocyte Medium Complete Kit (Lifeline Cell Technology, Frederick, MD), which contains basal medium, growth supplements (hormones, growth factors, and proteins, and penicillin/streptomycin to prevent bacterial growth.

extract_protocol: After 36 hours, cells were harvested for RNA isolation using miRNeasy kit according to manufacturer's protocol.

treatment_protocol: Transient transfections of miR-H1, miR-K12-3-3p or control mimic were performed using Lipofectaine 2000 reagent (Life Technologies, San Diego, CA) according to manufacturer’s instructions.

value: Primary Human Oral Keratinocytes (HOK)

tag: passages

value: 3-5 passages

tag: transfected with


title: miR-K12-3-3p HOK 3


title: miR-K12-3-3p HOK 2


title: miR-H1 HOK 4


title: Control mimic HOK 1

source_name: Control mimic_HOK

value: control mimic


title: Control mimic HOK 2


title: Control mimic HOK 4


title: miR-H1 HOK 3


title: Control mimic HOK 3


title: miR-K12-3-3p HOK 1


title: E18.5_2L1_PLACENTA_108.2463.4.1

first: Mana

last: Parast

state: California

address: 9500 Gilman drive #0695

department: Pathology

institute: University of California San Diego

description: SAMPLE 49

data_processing: The data were filtered for detection pValue > 0.01 and normalised using Robust Spline Normalisation with lumi in R

extract_protocol: Total RNA was purified using the MirVana RNA extraction kit (Ambion). Total RNA was quantified using the Ribogreen reagent (Lifetech, Inc.), and quality-controlled on a Bioanalyzer (Agilent). Two hundred nanograms of input total RNA was amplified and labeled using the TotalPrep kit (Ambion). The labeled product was then hybridized to Illumina HT12 arrays and scanned on a BeadArray Reader (Illumina, Inc.) according to the manufacturer’s instructions.

tag: origin

value: Placenta

tag: gestational age


title: miR-H1 HOK 1


title: E16.5_8R1_PLACENTA_108.2461.3.1

description: SAMPLE 48


title: E18.5_2L3_PLACENTA_108.2463.1.1

description: SAMPLE 50


title: E18.5_3L6_PLACENTA_108.2464.2.1

description: SAMPLE 54


title: Stomach cells with parietal cells isolated away

city: Houston.

first: Jason

middle: C

last: Mills

state: T

address: One Baylor Plaza

department: Gastroenterology, Medicine

institute: Baylor College of Medicine

hyb_protocol: Total RNA was hybridized to Affymetrix GeneChip Mouse Gene 2.0 ST Arrays according to manufacturers instructions

scan_protocol: Arrays were scanned with a GeneChip® Scanner 3000 laser confocal slide scanner

data_processing: Microarray data were analyzed using Partek Genomic Suite v6.6 (Partek Inc., St Louis, MO). Microarray CEL files were imported into Partek and normalized using RMA.

source_name: All cells except parietal cells from C57Bl/6 adult mouse stomach

label_protocol: Total RNA extracted and amplirifed, labeled, and fragmented (by Arctureus RiboAmp HS kit followed by the RNA Amplification and Labeling Kit from Enzo Life Sciences)

growth_protocol: Mice were grown in a temperature and light controlled mouse facility and co-caged whenever possible

extract_protocol: Total RNA was extracted, purified by RNEasy Mini Kit, and RNA integrity verified on Agilent Bioanalyzer

treatment_protocol: All treatments (listed in individual descriptions) were administered as daily intraperitoeal injections

value: All cells except parietal cells from full mouse stomach


title: E18.5_3L4_PLACENTA_108.2464.1.1

description: SAMPLE 53


title: E18.5_2L5_PLACENTA_108.2463.3.1

description: SAMPLE 52


title: E18.5_2L4_PLACENTA_108.2463.2.1

description: SAMPLE 51


title: Rapamycin treated full stomach, biological rep2

source_name: C57Bl/6 adult mouse injected with Rapamycin (0.6mg/20g mouse, 10 days)

value: whole stomach


title: E16.5_8L6_PLACENTA_108.2461.2.1

description: SAMPLE 47


title: miR-H1 HOK 2


title: Rapamycin and Tamoxifen treated full stomach, biological rep2

source_name: C57Bl/6 adult mouse injected with Rapamycin (0.6mg/20g mouse, 10 days) + Tamoxifen (5mg/20g mouse, 3 days)


title: Isolated Parietal Cells

source_name: Parietal cells isolated from C57Bl/6 adult mouse stomach

value: Parietal cells isolated from mouse stomach


title: E16.5_8L1_PLACENTA_108.2461.1.1

description: SAMPLE 46


title: Rapamycin treated full stomach, biological rep1


title: E16.5_20R1_PLACENTA_108.2462.2.1

description: SAMPLE 44


title: Rapamycin and Tamoxifen treated full stomach, biological rep1


title: E16.5_20L2_PLACENTA_108.2462.1.1

description: SAMPLE 43


title: Rapamycin treated full stomach, biological rep3


title: E14.5_31L2_PLACENTA_108.2460.2.1

description: SAMPLE 42


title: E14.5_31L1_PLACENTA_108.2460.1.1

description: SAMPLE 41


title: E16.5_20R2_PLACENTA_108.2462.3.1

description: SAMPLE 45


title: E14.5_30R4_PLACENTA_108.2459.4.1

description: SAMPLE 40


title: phaAstro_Br3

city: Stockholm

first: Anders

last: Lundin

address: Retzius väg 8

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

description: (total RNA >200nt)

data_processing:
RNASeq data was processed using the bcbio pipeline version 0.9.7
Hisat2 version 2.0.2-beta aligner was used to align reads to the human genome version hg38
Gene-level counts were derived using featureCounts version 1.4.4
Genome_build: hg38

source_name: Primary Adult Astrocyte

growth_protocol: ltNES cells grown according to Falk et al. 2012 using adherent culture of FGF2 and EGF supplmeneted media. NES-Astro grown adherently with FGF2, Heregulin1b, IGF1, and ActivinA supplemented media. Commertial lines grown according to manufacturer's instructions.

extract_protocol:
Cells detached using TryPLE and two rounds of washing step using PBS-/- followed by 300g centrifugation was peformed before RNA isolation using miRNeasy Kit
Libraries were prepared according to Illumina's instructions accompanying the Illumina TrueSeq Stranded mRNA LT Sample Prep Kit

value: Primary Adult Astrocyte

tag: donor gender

value: Male

tag: donor age


title: phaAstro_Br2

description: (total RNA >200nt)


title: E14.5_30L1_PLACENTA_108.2459.1.1

description: SAMPLE 37


title: E14.5_30R3_PLACENTA_108.2459.3.1

description: SAMPLE 39


title: Tamoxifen treated full stomach, biological rep1

source_name: C57Bl/6 adult mouse injected with Tamoxifen (5mg/20g mouse, 3 days)


title: Tamoxifen treated full stomach, biological rep2


title: E12.5_29R4_PLACENTA_108.2458.3.1

description: SAMPLE 36


title: Vehicle Control Full Stomach, biological rep2

source_name: C57Bl/6 adult mouse injected with sunflower oil


title: E12.5_27L3_PLACENTA_108.2457.2.1

description: SAMPLE 32


title: E11.5_26L4_PLACENTA_108.2456.2.1

description: SAMPLE 29


title: E12.5_27R1_PLACENTA_108.2457.3.1

description: SAMPLE 33


title: E12.5_27L1_PLACENTA_108.2457.1.1

description: SAMPLE 31


title: phaAstro_Br1

description: (total RNA >200nt)


title: Vehicle Control Full Stomach, biological rep1


title: E11.5_26R1_PLACENTA_108.2456.3.1

description: SAMPLE 30


title: E14.5_30L3_PLACENTA_108.2459.2.1

description: SAMPLE 38


title: E12.5_29L1_PLACENTA_108.2458.1.1

description: SAMPLE 34


title: E11.5_26L1_PLACENTA_108.2456.1.1

description: SAMPLE 28


title: E11.5_25L2_PLACENTA_108.2455.2.1

description: SAMPLE 26


title: E12.5_29L4_PLACENTA_108.2458.2.1

description: SAMPLE 35


title: E11.5_25R1_PLACENTA_108.2455.3.1

description: SAMPLE 27


title: Developing seeds_input rep2

city: guangzhou

first: yilong

last: hu

state: guangdong

address: No.723, xingke road, tianhe district

country: China

institute: south china botanical gardern, chinese academy of science

data_processing:
Quality control:Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA v0.7.12 and clean reads were aligned to the reference genome using BWA mem v 0.7.12.
Fragment size was estimated with MACS2 predicted method with default parameters(Model-based analysis of ChIP-Seq (MACS), Genome Biol).
Peak detection: To indentify regions of IP enrichment over background by useing the MACS2 version 2.1.0 (model-based analysis of ChIP-seq) (Zhang et al., 2008) peak finding algorithm
Genome_build: TAIR10; GCA_000001735.1
Supplementary_files_format_and_content: Peaks files are generated by MACS version 2.1.0.20150420

organism: Arabidopsis thaliana

source_name: Developing seeds_input

growth_protocol: Arabidopsi grown in full-spectrum white fluorescent light at 22°C under long day conditions (16 h light/8 h dark).

extract_protocol:
Lysates were clarified from sonicated nuclei and DNA-protein complexes were isolated with antibody.
Libraries were prepared according to the DNA Sample Kit . After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select DNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated DNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last,  PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: genotype/variation

value: pLEC1:LEC1-FLAG lec1-4

tag: development stage

value: seed mature stage

value: Developing seeds


title: developing seeds_LEC1_ChIP rep2

source_name: developing seeds_LEC1_ChIP

tag: chip antibody

value: anti-FLAG antibody (Sigma, F3165, lot#SLBQ7119V)


title: Developing seeds_input rep1

tag: tissue


title: developing seeds_LEC1_ChIP rep1


title: E10.5_24R5_PLACENTA_108.2454.3.1

description: SAMPLE 24


title: E11.5_25L1_PLACENTA_108.2455.1.1

description: SAMPLE 25


title: CCF_Br3

description: (total RNA >200nt)

source_name: Astrocytoma

value: Astrocytoma

value: Female


title: CCF_Br2

description: (total RNA >200nt)


title: CCF_Br1

description: (total RNA >200nt)