title: rep2_rna-seq

city: University Park

first: Nabeel

last: Ahmed

state: PENNSYLVANIA

address: 407 Chemistry Building

department: The Huck Institutes of the Life Sciences

institute: Pennsylvania State University

data_processing:
The raw reads were trimmed of the 3’ custom adapter CTGTAGGCACCATCAATTCGTATGCCGTCTTCTGCTTG using cutadapt (v1.1).
The low quality reads were filtered using PRINSEQ (v0.20.4), and reads shorter than 20 nucleotides were discarded
The processed reads were first aligned to the ribosomal RNA sequences using Bowtie 2 (v2.2.3). The unaligned reads were then aligned to the S. cerevisae assembly R64-1-1 (UCSC: sacCer3) using Tophat (v2.0.13) with up to two mismatches allowed.
Gene annotations were obtained from Saccharomyces Genome Database (http://www.yeastgenome.org/) on October 30, 2014.
The processed reads were mapped to sacCer3 reference genome. To maintain the accuracy of read assignment, transcripts in which multiple mapped reads constitute more than 0.1% of total reads mapping to the CDS region were not considered in the analysis. A-site positions in ribosome profiling reads were assigned according to the offset table generated using a Linear Programming algorithm which maximizes the reads between the second and stop codon of transcripts. The offset table for S. cerevisiae is given in Table S1 of the study. RPKM values were calculated for transcripts in RNA-Seq data by counting the reads whose 5′ ends were within the coding region of the transcript.
Genome_build: sacCer3
Supplementary_files_format_and_content: tab delimited file with gene name and RPKM values for the RNA-Seq sample and the corresponding Ribosome profiling sample published in GSE75322

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: 200 mL of yeast cells grown in YPD, at 30°C to an optical density (OD600) of 0.5

extract_protocol: Thawed cell lysates are cleared by centrifugation (20,000xg, 5 min, 4°C) and RNA extraction is performed using the hot acid phenol method (for details see Becker et al. 2013). 10 µg of extracted RNA was depleted for rRNA using the kit RiboMinus, Yeast Module (Invitrogen) and fragmented for 30 min using the NEBNext Magnesium RNA Fragmentation Module (NEB).  5 pmol of dephosphorylated mRNA footprints were linked to the 1 µg linker L1’ by incubation with 200 U T4 RNA Ligase 2, truncated (NEB) at 37°C for 2.5 h in buffer containing 20 mM Tris pH7, 20% PEG MW 8000, 10% DMSO, 20 U SUPERase·In. Linked footprints were size-selected by gel electrophoresis. Reverse transcription was carried out with 200 U SuperScript III (Invitrogen), 20 U SUPERase·In, 10 nmol dNTP, 25 pmol Linker L1’L2’, 100 nmol DTT in 20 µl of 1x FSB buffer (Invitrogen). Circularization by incubation with CircLigase (Epicentre) was performed two times for one hour each (a second aliquot of CircLigase was added after one hour) and the product was directly used for amplification by PCR.

treatment_protocol: Cells were filtered (All-Glass Filter 90mm, Millipore), flash frozen in liquid nitrogen and lysed by mixer milling (2 min, 30 Hz, MM400, Retsch) with 600 µL of lysis buffer (20 mM Tris-HCl pH 8.0, 140 mM KCl, 6 mM MgCl2, 0.1% NP-40, 0.1 mg/ml CHX, 1 mM PMSF, 2x protease inhibitors (Complete EDTA-free, Roche), 0.02 U/ml DNaseI (recombinant DNaseI, Roche), 20 mg/mL leupeptin, 20 mg/mL aprotinin, 10 mg/mL E-64, 40 mg/mL bestatin).


title: H37Rv_3SQ109_D1_rep3

status: Public on Aug 07 2018

type: SRA

city: Seattle

first: Shuyi

last: Ma

state: Washington

address: 1900 9th Avenue

department: Department of Pediatrics

country: USA

institute: University of Washington

library_source: transcriptomic

data_processing:
Raw FASTQ read data processing was carried out using a custom processing pipeline that harnesses the Bowtie 2 utilities, which is available at https://github.com/sturkarslan/DuffyNGS, and https://github.com/sturkarslan/DuffyTools, as previously described (PMID: 25784701)
The pipeline consists of 2 stages: 1) a pre-alignment filtering step to remove unwanted transcripts such as rRNA, and 2) a genomic alignment step using Bowtie2 with the command line option 'very-sensitive.'
BAM files from step 2 are combined into read depth wiggle tracks that record both uniquely mapped and multiply mapped reads from each of the forward and reverse strangs of the genome. Multiply mapped reads are prorated over all highest-quality aligned locations. Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.
Genome_build: MT_H37Rv_V3
Supplementary_files_format_and_content: Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.

molecule: total RNA

organism: Mycobacterium tuberculosis

source_name: H37Rv Mycobacterium tuberculosis

growth_protocol: Mycobacteria tuberculosis strain H37Rv (ATCC 27294) were grown on Middlebrook 7H9 medium (Difco) with 0.05% Tween 80 and ADC supplement.

extract_protocol:
RNA was isolated using published protocols (Rustad TR, Harrell MI, Liao R, Sherman DR (2008) The Enduring Hypoxic Response of Mycobacterium tuberculosis. PLoS ONE 3(1): e1502). In summary, frozen cell pellets Pellets were resuspended in Trizol, transferred to a tube containing Lysing Matrix B (QBiogene, Inc.), and vigorously shaken at max speed for 30 sec in a FastPrep 120 homogenizer (Qbiogene) three times, with cooling on ice between steps. This mixture was centrifuged at max speed for 1 min and the supernatant was transferred to a tube containing 300 mL chloroform and Heavy Phase Lock Gel (Eppendorf North America, Inc.), inverted for one minute, and centrifuged at max speed. The aqueous phase was then precipitated with 270 mL isopropanol and 270 mL high salt solution (0.8M Na citrate, 1.2M NaCl). RNA was cleaned using an RNeasy kit following manufacturer’s recommendations (Qiagen). Messenger RNA was enriched using the RiboZero rRNA removal (bacteria) magnetic kit (Illumina Inc.) according to manufacturer's instructions.
Libraries were prepared for Illumina sequencing using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer's instructions and using the AMPure XP reagent (Agencourt Bioscience Corporation) for size selection and cleanup of adaptor-ligated DNA. We used the NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) to barcode the libraries associated with each replicate and multiplexing up to 48 libraries per sequencing run. The prepared libraries were quantified using the Kapa qPCR quantification kit, and were sequenced at the University of Washington Northwest Genomics Center with the Illumina NextSeq 500 High Output v2 Kit (Illumina Inc).

treatment_protocol: Bacteria were harvested at 0, 1 days after being exposed to concentrations of SQ109 (0μM, 3μM) (as indicated in each sample title).

tag: drug dose

value: 3 μM

tag: days post drug


title: H37Rv_3SQ109_D1_rep1


title: H37Rv_3SQ109_D1_rep4


title: H37Rv_3SQ109_D0_rep4


title: H37Rv_3SQ109_D0_rep2


title: H37Rv_3SQ109_D0_rep1


title: H37Rv_3SQ109_D0_rep3


title: H37Rv_0SQ109_D1_rep4

value: 0 μM


title: Day7 rep1

city: Jingzhou

first: Tinghua

last: Huang

address: Jingmi Road #266

country: China

institute: Yangtze University

data_processing:
Illumina Casava1.7 software used for basecalling.
Data filtering is carried out to obtain clean reads to remove low quality reads present in the raw reads. The procedure includes following steps: 1) Remove reads in which the unknown bases (N) is presented; 2) Remove low quality reads, if the reads have low quality base (base with quality value ≤5), the reads were removed. Bowtie1 [49] was used to map clean reads to reference genes set, which was extracted from the NCBI reference sequence database [50]. The calculated reads count per gene per length were used for comparing the difference of gene expression among samples.
Using R version 3.4.2 software (limma pakage) to find differential genes
Functional annotation of genes with the same expression type was performed using the DAVID annotation tool.
Using innateDB to Analyze the Immune Response Pathway

organism: Sus scrofa

source_name: Whole blood

growth_protocol: The piglets of Duroc × Landrace × Yorkshire crossbred were used. Piglets were raised in climate-controlled, fully enclosed isolation facilities.

extract_protocol:
Total RNA were extrated by PAXgene blood RNA kit using the standard protocols. All samples were quantified using a NanoDrop 2000 (Thermo-Fisher Scientific, Waltham, MA, USA), and assessed with an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). The RNA integrity number (RIN) of each sample was >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The pigs were tested fecal negative for Salmonella three times before intranasal challenge with 109 colony forming units (cfu) of Salmonella enterica serovar Typhimurium LT2 at four weeks of age.

tag: breed

value: Duroc x Landrace x Yorkshire

tag: tissue

value: Peripheral blood

tag: agent

tag: time

value: Day 7


title: Day2 rep3

value: Salmonella enterica serovar Typhimurium LT2

value: Day 2


title: Day7 rep2


title: Day7 rep4


title: Day7 rep3


title: Day2 rep4


title: implantation failure_6

type: RNA

city: Mumbai

first: Indira

last: Hinduja

address: 15, Dr. G. Deshmukh Marg

country: India

institute: Jaslok Hospital and Research centre

description: endometrial biopsy during implantation window undergoing long protocol of ovarian stimulation from an implantation failure pateint having previous 2 IVF failures with unexplained infertility.

hyb_protocol: 750ng of normalized cRNA (aRNA) was hybridized to 'Illumina Human HT-12' bead chip as per Standard Illumina hybridization protocol

scan_protocol: Hybridized bead chip was scanned by 'i Scan' using Standard Illumina scanning protocol

data_processing: The data was analysed using Genome studio software 2011. Quantile normalization method was used to normalize the raw data.

label: biotin

organism: Homo sapiens

source_name: endometrial tissue during implantation window

label_protocol: Biotinylated aRNA was prepared by using Epicentre TargetAmp Nano-g Biotin-aRNA Labeling Kit for the Illumina  System. In this, 500ng total RNA was reverse transcribed to obtain first and second strand of cDNA and subjected to in-vitro transcription of biotin labeled amlified RNA (aRNA) as described in the manfacturer's instruction.

extract_protocol: Total RNA was extracted using trizol method as per manufacture's instruction. It was followed by Dnase treatment using DNAse enzyme. Quality control of RNA was performed by Agilent 2100 bioanalyzer and RNA was quantified using Qubit Ribogreen quantitation @ SPPL. RNA integrity number (RIN) in the range of 7.5-10 was considered to have good quality

treatment_protocol: After collection of endometrial tissue with the help of Gynetics catheter in sterile environment, it was washed with phosphate buffer saline at pH7.0, homogenized in liquid nitrogen and dissolved in trizol solution.

value: endometrium

tag: sample group and identifier

tag: age

tag: sample collection day

tag: stimulation protocol

value: GnRH agonist long protocol


title: implantation failure_5


title: implantation failure_3

description: endometrial biopsy during implantation window undergoing long protocol of ovarian stimulation from an implantation failure pateint having previous 4 IVF failures with unexplained infertility.


title: H37Rv_3SQ109_D1_rep2


title: implantation failure_1


title: oocyte donor_5

description: endoemtrial biopsy during implantation window from oocyte donor with healthy proven fertility undergoing long protocol of ovarian stimulation


title: H37Rv_0SQ109_D1_rep3


title: implantation failure_2


title: oocyte donor_6


title: oocyte donor_2


title: implantation failure_4

description: endometrial biopsy during implantation window undergoing long protocol of ovarian stimulation from an implantation failure pateint having previous 5 IVF failures with unexplained infertility.


title: oocyte donor_4


title: oocyte donor_3


title: H37Rv_0SQ109_D1_rep2


title: Day2 rep1


title: Day0 rep3

value: Day 0


title: H37Rv_0SQ109_D1_rep1


title: H37Rv_0SQ109_D0_rep3


title: H37Rv_0SQ109_D0_rep4


title: Day0 rep2


title: Day0 rep1


title: H37Rv_0SQ109_D0_rep1


title: Day2 rep2


title: oocyte donor_1


title: rep1_rna-seq

extract_protocol:
Thawed cell lysates are cleared by centrifugation (20,000xg, 5 min, 4°C) and RNA extraction is performed using the hot acid phenol method (for details see Becker et al. 2013)
10 µg of extracted RNA was depleted for rRNA using the kit RiboMinus, Yeast Module (Invitrogen) and fragmented for 30 min using the NEBNext Magnesium RNA Fragmentation Module (NEB).  5 pmol of dephosphorylated mRNA footprints were linked to the 1 µg linker L1’ by incubation with 200 U T4 RNA Ligase 2, truncated (NEB) at 37°C for 2.5 h in buffer containing 20 mM Tris pH7, 20% PEG MW 8000, 10% DMSO, 20 U SUPERase·In. Linked footprints were size-selected by gel electrophoresis. Reverse transcription was carried out with 200 U SuperScript III (Invitrogen), 20 U SUPERase·In, 10 nmol dNTP, 25 pmol Linker L1’L2’, 100 nmol DTT in 20 µl of 1x FSB buffer (Invitrogen). Circularization by incubation with CircLigase (Epicentre) was performed two times for one hour each (a second aliquot of CircLigase was added after one hour) and the product was directly used for amplification by PCR.

tag: strain

tag: genotype/variation

value: wild type


title: Day0 rep4


title: H37Rv_0SQ109_D0_rep2


title: spleen_WT_UnImm 4

status: Public on Aug 06 2018

city: Albany

first: Andrew

middle: Arthur

last: Reilly

state: NY

address: 150 New Scotland Ave

department: Genetics

institute: Wadsworth Cntr, NYS Dept of Health

description: gene expression data unImm

hyb_protocol: Standard Affimetrix

scan_protocol: Standard Affimetrix, using 5.5ug cDNA (3.5 for #169)

data_processing:
Standard Affimetrix
Gene Set Enrichment Analysis using Molecular Signatures Database v5.0 (MSigDB).

organism: Mus musculus

label_protocol: Affimetrix Biotin

growth_protocol: Mice were young adult F1 B6/CBA hybrid females, maintained under standard conditions.

extract_protocol: Spleens were dissociated by mechanical disruption and red blood cells were removed by hypotonic lysis in 0.15 M ammonium chloride. Splenocytes were lysed in RLT buffer (Qiagen, Valencia, CA) and cell lysates were homogenized using a QIAshredder homogenizer (Qiagen). Cellular RNA was purified using RNeasy columns (Qiagen) and residual genomic DNA was digested with RQ1 DNase (Promega, Madison, WI). RNA was precipitated and re-suspended in sterile water. RNA integrity was verified by agarose gel electrophoresis. RNA quality and concentration were measured using an Agilent 2100 Bioanalyzer (Life Technologies). cRNA was prepared according to the Affymetrix standard protocol as described (54) and hybridized to Affymetrix Mouse Gene 2.0 ST by SUNYMAC (Syracuse, NY.)

treatment_protocol: A combination of three non-overlapping HTT Exon1 coded peptides (AAs 1-17, 49-60, 74-88), conjugated to KLH, was delivered with alum adjuvant. Mice were primed at 6-12 weeks (R6/1) or 15-24 weeks (zQ175), and boosted twice at monthly/ bimonthly intervals, with spleen collection 10 days after the second boost.

value: spleen

tag: gentype

value: CBA/B6 F1

value: adult


title: spleen_WT_UnImm 5

description: gene expression data unImm


title: spleen_WT_imm_TriPep 2

description: gene expression data post-immunization

source_name: spleenocytes 10 days after final boost


title: spleen_zQ175_UnImm 1

description: gene expression data unImm

value: HD zQ175


title: spleen_WT_imm_TriPep 3

description: gene expression data post-immunization


title: spleen_R61_UnImm 2

description: gene expression data unImm

value: HD R6/1


title: spleen_zQ175_UnImm 4

description: gene expression data unImm


title: spleen_WT_UnImm 2

description: gene expression data unImm


title: spleen_zQ175_UnImm 3

description: gene expression data unImm


title: spleen_WT_UnImm 1

description: gene expression data unImm


title: spleen_zQ175_imm_TriPep 4

description: gene expression data post-immunization


title: spleen_WT_imm_TriPep 4

description: gene expression data post-immunization


title: spleen_R61_UnImm 5

description: gene expression data unImm


title: spleen_R61_UnImm 1

description: gene expression data unImm


title: spleen_R61_imm_TriPep 5

description: gene expression data post-immunization


title: spleen_zQ175_imm_TriPep 5

description: gene expression data post-immunization


title: spleen_zQ175_imm_TriPep 1

description: gene expression data post-immunization


title: spleen_zQ175_UnImm 2

description: gene expression data unImm


title: spleen_R61_UnImm 3

description: gene expression data unImm


title: spleen_WT_UnImm 3

description: gene expression data unImm


title: spleen_zQ175_imm_TriPep 3

description: gene expression data post-immunization


title: spleen_R61_imm_TriPep 4

description: gene expression data post-immunization


title: spleen_WT_imm_TriPep 1

description: gene expression data post-immunization


title: spleen_R61_imm_TriPep 1

description: gene expression data post-immunization


title: spleen_R61_imm_TriPep 3

description: gene expression data post-immunization


title: 578_Vglut3-/-

city: Boston

first: Lisa

middle: V

last: Goodrich

state: MA

address: 220 Longwood Avenue

department: Neurobiology

institute: Harvard Medical School

data_processing:
short and poor quality reads were trimmed using Trimmomatic (v0.33)
alignment to the mouse genome was done using STAR (v2.4.0)
counts for reads aligned to the mouse transcriptome was generated using featureCounts program in the Subread package (v1.4.6)
trimmed mean of M-values (TMM) normalization was done on raw read counts using EdgeR (3.14.0)
log-transformation was done after scaling total read counts within each cell to 1 million in Seurat (v1.4.0.12)
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated text file with raw and log-transformed counts for the genes and single cell samples on which the final interpretation of the study is based.

molecule: polyA RNA

source_name: Spiral ganglion neuron

extract_protocol:
RNA was extracted by adding lysis buffer to each neuron and reverse-transcribed immediately as described in the Smart-seq2 protocol
Smart-seq2 (Picelli et al., Nat Protoc. 2014 Jan;9(1):171-81. doi: 10.1038/nprot.2014.006)

tag: genotype

tag: tonotopic location

value: Middle


title: spleen_R61_imm_TriPep 2

description: gene expression data post-immunization


title: spleen_R61_UnImm 4

description: gene expression data unImm


title: spleen_zQ175_UnImm 5

description: gene expression data unImm


title: spleen_zQ175_imm_TriPep 2

description: gene expression data post-immunization


title: 554_Wildtype

value: Wildtype

value: Base


title: 556_Wildtype


title: 552_Wildtype


title: 538_Wildtype


title: 541_Wildtype


title: 546_Wildtype


title: 539_Wildtype


title: 532_Wildtype


title: 551_Wildtype


title: 545_Wildtype


title: 535_Wildtype


title: 537_Wildtype


title: 544_Wildtype


title: 530_Wildtype


title: 533_Wildtype


title: 543_Wildtype


title: 529_Wildtype


title: 528_Wildtype


title: 524_Wildtype


title: 523_Wildtype


title: 526_Wildtype


title: 555_Wildtype


title: 527_Wildtype


title: 519_Wildtype


title: 520_Wildtype


title: 518_Wildtype


title: 517_Wildtype


title: 521_Wildtype


title: 522_Wildtype


title: 510_Wildtype


title: 506_Wildtype


title: 504_Wildtype


title: 516_Wildtype


title: 498_Wildtype


title: 497_Wildtype


title: 496_Wildtype


title: 500_Wildtype


title: 492_Wildtype


title: 486_Wildtype


title: 488_Wildtype


title: 483_Vglut3-/-


title: 493_Wildtype


title: 472_Vglut3-/-


title: 495_Wildtype


title: 471_Vglut3-/-


title: 466_Wildtype


title: 467_Wildtype


title: 470_Vglut3-/-


title: 465_Wildtype


title: 464_Wildtype


title: 462_Wildtype


title: 463_Wildtype


title: 460_Wildtype

value: Apex


title: 454_Wildtype


title: 453_Wildtype


title: 502_Wildtype


title: 452_Wildtype


title: 474_Vglut3-/-


title: 447_Wildtype


title: 448_Wildtype


title: 449_Wildtype


title: 444_Wildtype


title: 451_Wildtype


title: 445_Wildtype


title: 442_Wildtype


title: 440_Wildtype


title: 437_Wildtype


title: 443_Wildtype


title: 441_Wildtype


title: 436_Wildtype


title: 430_Wildtype


title: 432_Wildtype


title: 429_Wildtype


title: 435_Wildtype


title: 431_Wildtype


title: 428_Wildtype


title: 427_Wildtype


title: 425_Wildtype


title: 424_Wildtype


title: 422_Wildtype


title: 421_Wildtype


title: 419_Wildtype


title: 439_Wildtype


title: 418_Wildtype


title: 416_Wildtype


title: 438_Wildtype


title: 413_Wildtype


title: 412_Wildtype


title: 415_Wildtype


title: 411_Wildtype


title: 410_Wildtype


title: 407_Wildtype


title: 408_Wildtype


title: 406_Wildtype


title: 395_Wildtype


title: 391_Wildtype


title: 396_Wildtype


title: 490_Wildtype


title: 393_Wildtype


title: 426_Wildtype


title: 389_Wildtype


title: 387_Wildtype


title: 384_Wildtype


title: 382_Wildtype


title: 417_Wildtype


title: 414_Wildtype


title: 378_Wildtype


title: 376_Wildtype


title: 373_Wildtype


title: 372_Wildtype


title: 370_Wildtype


title: 371_Wildtype


title: 365_Wildtype


title: 405_Wildtype


title: 364_Wildtype


title: 362_Wildtype


title: 358_Wildtype


title: 357_Wildtype


title: 356_Vglut3-/-


title: 355_Vglut3-/-


title: 385_Wildtype


title: 351_Vglut3-/-


title: 353_Vglut3-/-


title: 352_Vglut3-/-


title: 350_Vglut3-/-


title: 349_Vglut3-/-


title: 380_Wildtype


title: 344_Vglut3-/-


title: 345_Vglut3-/-


title: 343_Vglut3-/-


title: 342_Vglut3-/-


title: 338_Vglut3-/-


title: 368_Wildtype


title: 337_Vglut3-/-


title: 334_Vglut3-/-


title: 335_Vglut3-/-


title: 328_Vglut3-/-


title: 360_Wildtype


title: 333_Vglut3-/-


title: 321_Vglut3-/-


title: 320_Vglut3-/-


title: 316_Vglut3-/-


title: 286_Vglut3-/-


title: 311_Vglut3-/-


title: 354_Vglut3-/-


title: 310_Vglut3-/-


title: 282_Vglut3-/-


title: 249_Vglut3-/-


title: 260_Vglut3-/-


title: 264_Vglut3-/-


title: 256_Vglut3-/-


title: 246_Vglut3-/-


title: 252_Vglut3-/-


title: 261_Vglut3-/-


title: 225_Wildtype


title: 322_Vglut3-/-


title: 203_Wildtype


title: 214_Wildtype


title: 201_Wildtype


title: 193_Wildtype


title: 196_Wildtype


title: 194_Wildtype


title: 216_Wildtype


title: 213_Wildtype


title: 191_Wildtype


title: 285_Vglut3-/-


title: 179_Wildtype


title: 557_Wildtype


title: 164_Wildtype


title: 173_Wildtype


title: 149_Wildtype


title: 227_Wildtype


title: 146_Wildtype


title: 142_Wildtype


title: 147_Wildtype


title: 141_Wildtype


title: 134_Wildtype


title: 138_Wildtype


title: 131_Wildtype


title: 125_Wildtype


title: 202_Wildtype


title: 124_Wildtype


title: 122_Wildtype


title: 188_Wildtype


title: 174_Wildtype


title: 114_Wildtype


title: 119_Wildtype


title: 120_Wildtype


title: 106_Wildtype


title: 103_Wildtype


title: 116_Wildtype


title: 100_Wildtype


title: 99_Wildtype


title: 94_Wildtype


title: 96_Wildtype


title: 172_Wildtype


title: 80_Wildtype


title: 91_Wildtype


title: 90_Wildtype


title: 76_Wildtype


title: 75_Wildtype


title: 79_Wildtype


title: 64_Wildtype


title: 78_Wildtype


title: 60_Wildtype


title: 59_Wildtype


title: 58_Wildtype


title: 54_Wildtype


title: 36_Wildtype


title: 53_Wildtype


title: 107_Wildtype


title: 32_Wildtype


title: 28_Wildtype


title: 26_Wildtype


title: 835368p_1

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

data_processing:
Single-end 50 bp reads generated on Illumina HiSeq were aligned to the mouse genome  using TopHat v2.1.1 (Trapnell et al., 2009). Read counts were obtained using subread v1.5.2 (Yang Liao et al., 2013), normalised and tested for differential gene expression using the Bioconductor package DESeq2 v1.14.1 (Michael Love 2014).
Multiple testing corrections were applied using the Benjamini-Hochberg method (Benjamini and Hochberg, 1995). Genes were selected as differentially expressed such that FDR < 0.01.
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: subread-count gene counts

source_name: Intestine

growth_protocol: The mice were kept under standard conditions (12 h light/dark cycle).

extract_protocol:
Small intestine was fractionated, EpCAM+tdTom+ and EpCAM+tdTom- live cells were collected directly into the lysis buffer and RNA was extracted immediately following the sort (RNeasy Micro Plus Kit, Qiagen).
TruSeq Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: Atoh1(WT)CreERT2 R26RtdTom mice were injected with 1 mg tamoxifen per day on 3 consecutive days for maximal labelling of all secretory lineages with a fluorescent lineage marker tdTomato.

tag: group

value: tdTompositive

value: Intestine


title: 25_Wildtype


title: 834795n_5

value: tdTomnegative


title: 834795p_5


title: 835362n_2


title: 835368n_1


title: 835362p_2


title: 834790n_7


title: 23_Wildtype


title: 834790p_7


title: 18_Wildtype


title: 16_Wildtype


title: 13_Wildtype


title: 834784p_8


title: 10_Wildtype


title: 11_Wildtype


title: 834777n_3


title: 834767p_4


title: 1_Wildtype


title: 3_Wildtype


title: 927252P

source_name: colon

extract_protocol:
Small intestine and colon were fractionated, EpCAM+tdTom+ and EpCAM+tdTom- live cells were collected directly into the lysis buffer and RNA was extracted immediately following the sort (RNeasy Micro Plus Kit, Qiagen).
TruSeq Stranded mRNA Library Prep Kit (Illumina)

value: colon


title: 834777p_3


title: 927240P


title: 834795P


title: 12_Wildtype


title: 834767n_4


title: 15_Wildtype


title: 927252N


title: 834762p_6


title: 73929P


title: 834762n_6


title: 927246P


title: 927251N


title: 73929N


title: 73923P


title: 927246N


title: 927251P


title: RNA-Seq CDK6-WT, replicate 2

city: Vienna

first: Markus

last: Zojer

address: Josef-Baumanngasse

department: Institute for Pharmakology and Toxokology

country: Austria

institute: University of Veterinary Medicine

data_processing:
Alignment to genome version GRCm38 using BWA (ChIP-Seq) or STAR (RNA-Seq)
Adapter trimming and removing of low quality bases was performed using Trimmomatic
Counting of reads was done using featureCounts
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: raw count file (tab delimited); bigWig

source_name: BCR-ABL+ cell lines

growth_protocol: Cells were cultured in RPMI incl. 10% FCS,50 μmol/l 2-mercaptoethanol, 100 u/ml penicillin and 100 μg/ml streptomycin

extract_protocol:
QIAGEN RNeasy extraction kit
Phenol-Chloroform extraction
RNA-seq: SENSE mRNA-Seq Library Prep kit, 50 bp single-end, ChIP-seq: NEB Ultra DNA Library Prep kit;

value: Pre/Pro-B-cells


title: 834784n_8


title: WTSI7

source_name: Small intestine

extract_protocol:
Small intestine and colon were fractionated, EpCAM+tdTom+ live cells were collected directly into the lysis buffer and RNA was extracted immediately following the sort (RNeasy Micro Plus Kit, Qiagen).
TruSeq Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: Atoh1(WT)CreERT2 R26RtdTom and Atoh1(9S/T-A)CreERT2 R26RtdTom mice were injected with a single dose of 3 mg tamoxifen i.p.

tag: treatment

value: 3 mg tamoxifen

tag: Sex

value: female


title: 834795N


title: 927240N


title: 73979N


title: 73979P


title: RNA-Seq CDK6-WT, replicate 1


title: reconstituted Cdk6 replicate 3 input 3

library_source: genomic

molecule: genomic DNA

value: reconstituted Cdk6


title: reconstituted Cdk6 replicate 3 input 1


title: RNA-Seq CDK6-K43M, replicate 2


title: reconstituted Cdk6 replicate 3 input 2


title: WTSI3

value: male


title: 73923N


title: WTSI6


title: WTSI2


title: RNA-Seq CDK6-KO, replicate 2


title: RNA-Seq CDK6-KO, replicate 1


title: WTCOLON7

source_name: Colon


title: reconstituted Cdk6 replicate 2 input 2


title: reconstituted Cdk6 replicate 2 input 1


title: reconstituted Cdk6 replicate 2 input 3


title: RNA-Seq CDK6-K43M, replicate 1


title: reconstituted Cdk6 replicate 1 input 2


title: WTCOLON6


title: reconstituted Cdk6, replicate 3


title: WTSI5


title: reconstituted Cdk6 replicate 1 input 3


title: WTCOLON3


title: APSI7


title: WTCOLON5


title: WTSI4


title: reconstituted Cdk6 replicate 1 input 1


title: WTCOLON2


title: WTCOLON4


title: reconstituted Cdk6, replicate 2


title: reconstituted Cdk6, replicate 1


title: wt, replicate 2 input

value: wildtype


title: wt, replicate 1


title: APCOLON7


title: wt, replicate 1 input


title: APSI5


title: APSI2


title: APCOLON4


title: APSI6


title: APCOLON6


title: APSI3


title: APSI4


title: APCOLON5


title: wt, replicate 2


title: APCOLON2


title: Sleep-SH, biological rep3

city: Guelph

first: Elena

last: Tsimakouridze

address: 50 Stone Rd E

country: Canada

institute: University of Guelph

description: sham surgery

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Murine MOE430A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: MAS5 CHP files are Command Console CHP file version 1. Further data analysis performed with GeneSpring GX Software v. 11.5 using default Affymetrix settings.

source_name: Sleep-time SH mouse heart

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol:
The mice had either MI or SHAM surgeries. For MI-sleep and SH-sleep, sleep-time surgeries were performed between ZT01-ZT03. The animals were euthanized 8 hours after sleep-time MI and sleep-time SH at ZT11 For MI-wake and SH-wake, wake-time surgeries were performed between ZT13-ZT15. The animals were euthanized 8 hours after wake-time MI and wake-time SH at ZT23.
The hearts were collected and snap frozen in liquid Nitrogen.

value: heart


title: Sleep-MI, biological rep3

description: infarcted myocardium

source_name: Sleep-time MI mouse heart


title: Sleep-MI, biological rep2

description: infarcted myocardium


title: Sleep-SH, biological rep1

description: sham surgery


title: Biopsy of normal mucosa Patient4

city: Tokyo

first: Nobutake

last: Yamamichi

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Gastroenterology, Graduate School of Medicine

country: Japan

institute: The University of Tokyo

description: Duodenal 2nd port

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Agilent Technologies G2600D SG12494263.

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1. We performed quantile normalization without baseline shift.

source_name: Human duodenal normal mucosa

label_protocol: Cyanine-3 (Cy3) labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit.

extract_protocol: Total RNA was extracted (miRNeasy Mini kit, Qiagen) from tissue samples, and its integrity was verified by Nanodrop 1000 spectrometer.

treatment_protocol: One biopsy sample was obtained from each neoplasm and surrounding normal mucosa.

tag: gender

value: M

value: normal mucosa

tag: location

value: Duodenal 2nd port


title: Wake-MI, biological rep2

description: infarcted myocardium

source_name: Wake-time MI mouse heart

tag: tissue


title: Biopsy of normal mucosa Patient1

description: Duodenal 2nd port


title: Biopsy of tumor Patient4

description: Duodenal bulbus

source_name: Human duodenal adenoma

value: adenoma

value: Duodenal bulbus


title: PDX_KPT_H3K27ac

city: Houston

first: Michael

last: Gundry

state: Texas

address: One Baylor Plaza, N1030

institute: Baylor College of Medicine

data_processing:
75bp single-end sequencing reads were mapped to the hg19 genome using Bowtie2 with default paramaters
Normalized read densities (RPM/bp) were generated using bamliquidator (https://github.com/BradnerLab/pipeline/wiki/bamliquidator).
MACS version 1.4.2 peak finding algorithm was used to identify regions of ChIP-Seq enrichment (Feng et al., 2012) with -p 1e-9 -w -S --space=50 --nolambda parameters specified.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files represent RPM/bp normalized read density tracks. bed files represent MACS14 peak calls.

source_name: PDX2 patient derived xenograft

growth_protocol: All human AML cell lines were cultured in RPMI with 10% FBS. Due to impaired cell growth at low concentrations, IMS-M2 cells were maintained at concentrations between 2x10^5 and 2x10^6/ml.  PDX2 cells were cultured in IMDM supplemented with 10% FBS, 2% L-glutamine, 10ng/ml FLT3L, 10 ng/ml TPO and 10 ng/ml SCF at a concentration between 1 and 2.5x10^6/ml.

extract_protocol:
Cells were washed once with PBS and fixed with 1% paraformaldehyde for 10min. Glycine was added at a final concentration of 0.125M to stop the reaction. Cells were collected at 500 g for 10 min at 4 °C (subsequent work was performed on ice and used cool buffers and solutions unless otherwise specified) and washed twice with up to 0.5 ml ice-cold PBS supplemented with 1X Xpert Protease Inhibitor Cocktail Solution. Cells were pelleted, flash frozen and stored at -80C or used immediately for downstream applications.
ChIPmentation was carried out as previously described (Schmidl et al., 2015), with minor adaptions. Cell pellets were lysed in sonication buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 0.25% SDS, 1X protease inhibitors) and sonicated with a Covaris S220 sonicator for 9 min in a microTUBE until the size of fragments was in the range of 200–700 bp. Lysates were transferred to new tube and diluted 1:1.5 with equilibration buffer (10mM Tris, 233mM NaCl, 1.66% Triton X-100, 0.166% sodium deoxycholate, 1 mM EDTA, 1X protease inhibitors). Lysates were centrifuged at full speed for 10 min at 4 °C and the supernatant containing the sonicated chromatin was transferred to a new tube. The lysate was then brought to RIPA buffer conditions (final concentration: 10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, 1X protease inhibitors) to a volume of 100 μl per immunoprecipitation. The antibody was added to the lysates and incubated on a rotator overnight at 4 °C. Used antibodies were H3K4me3 (1 μg per immunoprecipitation, Cell Signaling clone C42D8), H3K27ac (1 μg per immunoprecipitation, Cell Signaling clone D5E4) and H3K27me3 (1 μg per immunoprecipitation, Cell Signaling clone C36B11). 5μl magnetic Protein A beads (Life Technologies) were washed twice and resuspended in 10ul of RIPA-LS supplemented with 0.1% BSA.  Blocked beads were added to immunopreciptated lysates and incubated for 2 hours on a rotator at 4 °C. Beads were washed subsequently with RIPA-LS (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate and 1X protease inhibitors) (twice), RIPA-HS (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 500 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate and 1X protease inhibitors) (twice) and RIPA-LiCl (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl, 1% Triton X-100, 0.5% sodium deoxycholate, 0.5% NP40 and 1X protease inhibitors) (twice). Beads were washed with cold Tris-Cl pH 8.0, to remove detergent, salts and EDTA. Beads were washed once more with cold Tris-Cl pH 8.0 but the reaction was not placed on a magnet to discard supernatant immediately. Instead, the whole reaction including beads was transferred to a new tube and then placed on a magnet to remove supernatant to decrease background. Beads were then resuspended in 25 μl of the tagmentation reaction mix (10 mM Tris pH 8.0, 5 mM MgCl2, 10% v/v dimethylformamide) containing 1 μl Tagment DNA Enzyme from the Nextera DNA Sample Prep Kit and incubated at 37 °C for 2 min in a thermocycler. The beads were washed with RIPA-LS (twice) and once with cold Tris-HCl pH 8. Beads were washed once more with cold Tris-HCl pH 8.0 but the reaction was not placed on a magnet to discard supernatant immediately. Instead, the whole reaction including beads was again transferred to a new tube and then placed on a magnet to remove supernatant. Beads were then incubated with 50 μl elution buffer (0.5% SDS, 300 mM NaCl, 5 mM EDTA and 10 mM Tris-HCl pH 8.0) containing 2 μl of Proteinase K for 1 h at 55 °C and 8 h at 65 °C, to revert formaldehyde cross-linking, and supernatant was transferred to a new tube. Finally, DNA was purified with Qiagen MinElute columns and eluted in 22ul of elution buffer (10mM Tris-HCl pH 8.0). Enrichment of the libraries was performed in a 50-μl reaction using 0.75 μM primers, 25μl NEBNext High-Fidelity 2X PCR Master Mix and 20ul of the purified library. Libraries were amplified for N+1 cycles, where N is equal to the rounded-up Cq value determined in a test qPCR reaction with 1ul of the library. Enriched libraries were purified using SPRI AMPure XP beads at a beads-to-sample ratio of 1:1, followed by a size selection using AMPure XP beads to recover libraries with a fragment length of 200–400 bp. Library preparation was performed using custom Nextera primers as described for ATAC-seq (Buenrostro et al., 2013). ChIP-seq libraries were run on an Illumina NextSeq 500 instrument (single end 75 bp reads).

value: PDX2 patient derived xenograft

tag: cell type

value: AML

value: 100nM Selinexor


title: IMS_KPT_H3K27ac

source_name: IMS-M2 cell line

tag: cell line


title: Wake-SH, biological rep1

description: sham surgery

source_name: Wake-time SH mouse heart


title: Wake-SH, biological rep3

description: sham surgery


title: APCOLON3


title: monkey_brain_ultraDeep_RNA-seq

city: Irvine

first: Yumei

last: Li

state: CA

address: 825 Health Sciences Road

department: Department of Biological Chemistry

institute: University of California, Irvine

data_processing:
RNA-seq reads were filtered by inhouse scripts to get high quality reads.
High-quality reads were aligned to the corresponding genome using HISAT2 (v2.0.5).
Genome_build: human: hg19, monkey: rheMac2, tree shrew: tupBel1, mouse: mm9, pig: susScr3
Supplementary_files_format_and_content: bigWig files were generated using wiggles (v1.2.0); scores represented read coverage.

molecule: cytoplasmic RNA

organism: Macaca mulatta

source_name: brain

extract_protocol:
Frozen tissue was fractioned using hypotonic buffer (Hepes 20mM; KCl 10mM; EDTA 1mM; Glycerol 10%; NP-40 0.2%). Briefly, 60-100 mg tissues were grinded in liquid nitrogen. 1000 μl hypotonic buffer was then added and the tissues were incubated on ice for 10 min. After using the Dounce tissue grinder with 10 strokes (sigma-D8938), lysed samples were centrifuged at 600 x g for 5 min to get the cytoplasmic fraction in the supernatant.
Strand-specific polyA+ RNA libraries were prepared for sequencing using standard Illumina protocols.

value: brain

tag: developmental stage

value: adult

value: wild type


title: Sleep-SH, biological rep2

description: sham surgery


title: Sleep-MI, biological rep1

description: infarcted myocardium


title: Biopsy of normal mucosa Patient3

description: Duodenal 2nd port

value: F


title: Wake-MI, biological rep3

description: infarcted myocardium


title: Wake-MI, biological rep1

description: infarcted myocardium


title: IMS_DMSO_H3K27ac


title: Biopsy of normal mucosa Patient2

description: Duodenal bulbus


title: Wake-SH, biological rep2

description: sham surgery


title: Biopsy of tumor Patient2

description: Duodenal 2nd port

source_name: Human duodenal adenocarcinoma

value: adenocarcinoma


title: PDX_DMSO_H3K27ac


title: Biopsy of tumor Patient3

description: Duodenal bulbus


title: adult hlk_ALL_sample-3

city: Padova

first: Chiara

last: Borga

address: Corso Stati Uniti,4

country: Italy

institute: University of Padua

description: Gene expression data

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Zebrafish Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000

data_processing: Microarray data (.CEL files) were normalized using the justRMA algorithm and analyzed using R-Bioconductor (Version 2.15.3)

organism: Danio rerio

source_name: GFP+_FACS purified ALL from total body

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol starting from 100 ng of  total RNA (GeneChip® 3’ IVT Express Kit Technical Manual, 2008, Affymetrix).

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

value: Leukemia

tag: genetic background

value: GFP+_FACS purified ALL


title: O3_KPT_H3K27ac

source_name: OCI-AML3 cell line


title: adult hlk_ALL_sample-2

description: Gene expression data


title: adult hMYC-1_ALL_sample-4

description: Gene expression data

value: rag2:hMYC;lck:eGFP double transgenic line


title: adult hlk_ALL_sample-1

description: Gene expression data


title: O3_DMSO_H3K27ac


title: adult hMYC-1_ALL_sample-3

description: Gene expression data


title: adult hMYC-1_ALL_sample-2

description: Gene expression data


title: Biopsy of tumor Patient1

description: Duodenal bulbus


title: adult hMYC-1_ALL_sample-1

description: Gene expression data


title: p2_pano rep1

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
Reads were mapped to the Ensembl annotation GRCh37/hg19 genome with Hisat2 (v2.0.0.0-beta) using default parameters. Only uniquely mapped reads were kept.
Coverage signal tracks (bigWigs) of primary alignments generated using Samtools (v1.2) and DeepTools2 (v2.0.0)
Primary alignments were assigned to features using featureCounts (v1.4.6-p2) with the GRCh37 Gencode annotation (release 19) as a reference.
Differential experesssion analysis was performed using DESeq2 (1.18.1) and only genes with FDR<0.05 in all patient samples were considered
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: bigWig files, containing RPKM normalized coverage signals of primary alignments; featureCounts count table output

source_name: primary dermal fibroblasts

growth_protocol: DMEM-Glutamax supplemented with 10% FBS, Pen/Strep

extract_protocol:
RNA was extracted using the Direct-zol RNA MiniPrep Kit (Zymo Research)
TruSeq Stranded mRNA Sample Prep Kit (Illumina)

tag: passage

value: skin

value: primary dermal fibroblasts

value: heterozygous MSL3 frameshift

value: female

tag: agent

value: pano


title: IMS_sgNPM1c_H3K27ac


title: IMS_sgCD45_H3K27ac


title: p2_dmso rep1

value: dmso


title: p2_pano rep2


title: p1_pano rep2

value: heterozygous MSL3 exon 11 skipped


title: O3_sgNPM1c_H3K4me3

value: AML


title: O3_sgNPM1c_H3K27ac


title: O3_sgNPM1c_H3K27me3


title: STAT1_repeat_non_stim_Fibroblast

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

data_processing:
Sequence reads were aligned using STAR aligner with GRCh37 reference genome.
HTSeq-count was used to generate count files.
For each individual, the fold change (FC) between unstimulated and stimulated conditions were calculated. Counts of duplicate samples of the same individual and treatment condition were tested for correlation and then averaged prior to computing the FC values. Genes with fold change higher than 1.5 fold in all the controls were used to filter the residual responsive genes to generate heatmaps.
Genome_build: Ensembl GRCh37
Supplementary_files_format_and_content: HTSeq-count is used to get the count files, followed by DESeq2 package in R for normalization and log2 transformation. GEO_normalized_log.xls contains: normalized and log2 transformed count files for all the samples

source_name: Fibroblast

extract_protocol:
Total RNA was isolated (RNeasy kit; QIAGEN) and RNA integrity was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies).
Poly (A)mRNA enrichment and cDNA library preparation was performed using a TruSeq Stranded mRNA Library Prep Kit (Illumina) in accordance with the manufacturer's recommendations. Paired-end sequencing was performed on HiSeq4000 (Illumina) with 150 cycles.

value: Fibroblast


title: STAT1_repeat_IFNa2b_treated_Fibroblast


title: adult hMYC-2_ALL_sample-1

description: Gene expression data


title: adult hMYC-2_ALL_sample-6

description: Gene expression data


title: adult hMYC-2_ALL_sample-2

description: Gene expression data


title: O3_sgCD45_H3K4me3


title: p1_pano rep1


title: adult hMYC-2_ALL_sample-4

description: Gene expression data


title: adult hMYC-2_ALL_sample-3

description: Gene expression data


title: Control2_IFNa2b_treated_Fibroblast


title: adult hMYC-2_ALL_sample-5

description: Gene expression data


title: O3_sgCD45_H3K27me3


title: Control 2

first: Maia

last: Inoue

address: 7-3-1, Hongo, Bunkyo-ku,

institute: The university of Tokyo

description: IonXpress_010.R_2015_11_19_00_10_01_user_Immunol-16-151119_ono_inoue

data_processing:
Data were acquired on an Ion Proton (Thermo Fisher)
The software used for the analysis was CLC Genomics Workbench ver. 8 (CLC).
The reads acquired were aligned to the Mm10 genome assembly.
Filtering parameters were as follows; Mismatch cost, 2; Insertion cost, 3; Deletion cost, 3; Length fraction, 0.8 and Similarity fraction, 0.8.
Empirical Analysis of DGE was performed for expression analysis.
Genome_build: Mm10
Supplementary_files_format_and_content: Xlsx file contains the EdgeR results as well as the read counts of individual genes in each sample.

source_name: iNKT cells

extract_protocol:
Total RNA was extracted using an RNeasy Plus Micro Kit (Qiagen).
cDNA was synthesized and amplified using a SMART-seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories).

value: Thymus

tag: strain

value: Stage 1 (CD24-NK1.1-T-bet-)

value: Prmt5 flox/D, Prmt5 flox/+ Cd4-Cre


title: Control 1

description: IonXpress_008.R_2015_11_19_00_10_01_user_Immunol-16-151119_ono_inoue


title: Prmt5 KO 2

description: IonXpress_011.R_2015_11_19_00_10_01_user_Immunol-16-151119_ono_inoue

value: Prmt5 flox/D Cd4-Cre


title: Control2_non_stim_Fibroblast


title: p1_dmso rep2


title: O3_sgCD45_H3K27ac


title: IMS_RNA_degron1_dTAG_3

data_processing:
Data was demultiplexed using bcl2fastq and aligned to the NCBI RefSeq build hg19 using hisat2.
Aligned SAM files were converted to .bam files for post-processing using samtools.
For genome visualization, aligned files were normalized and convered to bigWig files using Deeptools bamCoverage module
Transcript abundances were calculated using the cuffquant module of Cufflinks
FPKM values were calculated and normalized using cuffnorm
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files represent FPKM normalized read density tracks. Txt files represent normalized FPKM values and gene level differential expression statistics.

growth_protocol: All human AML cell lines were cultured in RPMI with 10% FBS. Due to impaired cell growth at low concentrations, IMS-M2 cells were maintained at concentrations between 2x10^5 and 2x10^6/ml. AML cells were cultured with in IMDM supplemented with 10% FBS, 2% L-glutamine, 10ng/ml FLT3L, 10ng/ml TPO and 10ng/ml SCF at a concentration between 1.5 and 3x10^6/ml

extract_protocol:
RNA was extracted using RNeasy micro kit
Illumina TruSeq Stranded mRNA Library Preparation Kit (Cat#RS-122-2101) was used with 200ng of total RNA for the construction of sequencing libraries. PolyA RNA libraries were prepared for sequencing using standard Illumina protocols

value: acute myeloid leukemia (AML)

tag: construct

value: Degron 1

value: 500nM dTAG-47


title: Prmt5 KO 1

description: IonXpress_009.R_2015_11_19_00_10_01_user_Immunol-16-151119_ono_inoue


title: STAT2_repeat_IFNa2b_treated_Fibroblast


title: p2_dmso rep2


title: p1_dmso rep1


title: p14_pano rep2

value: heterozygous MSL3 locus deletion


title: p14_pano rep1

value: skin


title: IMS_RNA_degron1_DMSO_3


title: STAT2_repeat_non_stim_Fibroblast


title: p14_dmso rep2

value: primary dermal fibroblasts


title: IMS_RNA_degron1_dTAG_1


title: IRF9_repeat_IFNa2b_treated_Fibroblast


title: STAT1_IFNa2b_treated_Fibroblast


title: IRF9_repeat_non_stim_Fibroblast


title: IMS_RNA_degron1_DMSO_2


title: p14_dmso rep1


title: STAT1_non-stim_Fibroblast


title: IMS_RNA_degron1_DMSO_1


title: control_pano rep2

value: unaffected control


title: O3_RNA_degron1_dTAG_2


title: control_dmso rep1

value: female


title: control_pano rep1

value: pano


title: IMS_RNA_degron1_dTAG_2


title: Control1_non_stim_Fibroblast


title: O3_RNA_degron1_DMSO_2


title: O3_RNA_degron1_dTAG_1


title: control_dmso rep2

value: dmso


title: STAT2_non_stim_Fibroblast


title: 4B2N1-DP2

city: Shanghai

first: Qing

address: 320 Yueyang Road

department: institute of biochemistry and cell biology

institute: Chinese Academy of Science

data_processing:
Library strategy: deep sequencing
QC control: FastQC version: 0.11.2
Trim: trimmomatic version: 0.36, parameters: PE AVGQUAL:20 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50
Alignment: All reads were aligned to the reference sequence using BWA-MEM with default parameters
Depth analysis: The hits of sgRNA, alignment score more than 30, were counted
Genome_build: reference sequence
Supplementary_files_format_and_content: bed of format contianed alignment results to reference sequences

source_name: haploid stem cells

growth_protocol: Haploid stem cells were maintained in DMEM (Millipore) with 15% FBS (Gibco), Penicillin-Streptomycin, NEAA, NUC, L-glutamine, β-mercaptoethanol, 1000 U/ml Lif, 1 μM PD03259010 (Selleck) and 3 μM CHIR99021 (Selleck).

extract_protocol:
Mouse genomic DNA of cells was isolated using the TIANamp Genomic DNA Kit (TIANGEN)
Amplicons library were prepared by Truseq Nano DNA Library Prep for deep sequencing.

value: haploid embryonic stem cells


title: STAT2_IFNa2b_treated_Fibroblast


title: O3_RNA_degron1_DMSO_1


title: Pt009_RNA_KPT

source_name: Primary leukemia Pt.009

value: 100nM Selinexor


title: Pt004_RNA_KPT

source_name: Primary leukemia Pt.004


title: O3_RNA_degron1_DMSO_3


title: IRF9_repeat_non_stim_B-cell

source_name: B-cell

value: B-cell


title: Pt004_RNA_DMSO


title: O3_RNA_degron1_dTAG_3


title: Control1_IFNa2b_treated_Fibroblast

value: Fibroblast


title: Control3_IFNa2b_treated_B-cell


title: Pt003_RNA_KPT

source_name: Primary leukemia Pt.003


title: Pt003_RNA_DMSO


title: Control3_non_stim_B-cell


title: Control2_IFNa2b_treated_B-cell


title: IMS_RNA_sgNPM1c_d3_3


title: IMS_RNA_sgNPM1c_d3_2


title: IRF9_non_stim_Fibroblast


title: CI-E4

data_processing:
Library strategy: WES
QC control: FastQC version: 0.11.2
Trim: trimmomatic version: 0.36, parameters: PE AVGQUAL:20 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50
Alignment: All reads were aligned to the mm10 genome assembly using BWA-MEM with default parameters
SNP/InDel analysis: SNV and InDel were called and annotated according to Sentieon(201611.02) pipelines
Genome_build: mm10
Supplementary_files_format_and_content: Vcf formate contianed SNP and indel summary for each samples.

extract_protocol:
Mouse genomic DNA of cells and mice was isolated using the TIANamp Genomic DNA Kit (TIANGEN)
Firstly, the genomic DNA randomly break into 150~300 bp by ultrasonic apparatus and purified with magnetic beads. Then, the product requires end repair, A-tailing, adapter ligation. The ligated products need to purify with magnetic beads again and obtain library through PCR amplification. The library was captured by Agilent Sure Select Mouse All Exon Kit and purified, amplified. The quality of sequencing library tested by Qubit and Agilent 2100 Bioanalyzer.

value: P7 pup

tag: generation

value: C57BL/6 X DBA2

value: tail


title: Control3_IFNa2b_treated_Fibroblast


title: Pt009_RNA_DMSO

value: acute myeloid leukemia (AML)


title: Control3_non_stim_Fibroblast


title: SAMPLE 12: GATA4 siRNA Rep 6

city: Helsinki

first: Tea

last: Soini

address: Biomedicum 2U, Tukholmankatu 8

department: Children's Hospital

country: Finland

institute: University of Helsinki

description: replicate 6

hyb_protocol: TargetAmp-Nano LAbeling Kit for Illumina Bead Expression BeadChip, 5/2013  Whole-Genome Gene Expression Direct Hybridization Assay Guide, Rev. A

scan_protocol: Standard Illumina Scanning protocol

data_processing: Quantile normalization was performed using Illumina Genome Studio software

source_name: HUH6 cell line

label_protocol: Illumina TotalPrep RNA Labeling Kit-protocol

growth_protocol: HUH6 cell line (Health Science Research Bank, Osaka, JP) was cultured in 37°C in Dulbecco's Modified Eagle's Medium (DMEM) (Lonza, Basel, CH) supplemented with 10% fetal calf serum, 2 mM L-glutamine, 100 units/mL penicillin, and 100 µg/mL streptomycin sulfate.

extract_protocol: RNA was extracted with Nucleospin RNA kit, followed by Nucleospin RNA clean-up kit (both from Macherey-Nagel, Dûren, Germany. RNA quality was  assessed  via Bioanalyzer (Agilent, Sanata Clara, CA). Array hybridization was performed using an Illumina Human HT-12_v4.0 oligonucleotide beadchip.

treatment_protocol: HUH6 cells were transfected in the absence of antibiotics with a pool of four siRNAs targeting GATA4 (target sequences: GGACAUAAUCACUGCGUAA, CGAUAUGUUUGACGACUUC, GAACCUGAAUAAAUC- UAAG, UAUCAGAGCUUGGCCAUGG) (siGENOME SMART pool reagent, catalog number L-008244-00-0010, Dharmacon, GE Healthcare) or with non-targeting control siRNA (NT, catalog number D-001810-01-20, Dharmacon) using Lipofectamine RNAiMAX reagent in Opti-MEM (Life Technologies). Final concentration of siRNA was 0.1 uM. After six hours of incubation with siRNA, normal growth medium was added to stop the transfection. Cells were lysed and RNA was extracted 72 h after beginning of transfection.

value: human hepatoblastoma

tag: genotype/variation

value: siRNA mediated GATA4 inhibition


title: Control2_non_stim_B-cell


title: IMS_RNA_sgNPM1c_d3_1


title: SAMPLE 11: GATA4 siRNA Rep 5

description: replicate 5


title: SAMPLE 9: GATA4 siRNA Rep 3

description: replicate 3


title: SAMPLE 10: GATA4 siRNA Rep 4

description: replicate 4


title: SAMPLE 8: GATA4 siRNA Rep 2

description: replicate 2


title: CI-E3


title: SAMPLE 6: Nontarget siRNA Rep 6

description: replicate 6

value: control nontargeting siRNA treatment


title: Control1_IFNa2b_treated_B-cell


title: IMS_RNA_sgCD45_d3_3


title: CI-E2


title: SAMPLE 5: Nontarget siRNA Rep 5

description: replicate 5


title: IMS_RNA_sgCD45_d3_2


title: CI-EC

value: E12.5 embryo


title: CI-E1


title: STAT2_repeat_IFNa2b_treated_B-cell


title: IMS_RNA_sgCD45_d3_1


title: SAMPLE 7: GATA4 siRNA Rep 1

description: replicate 1


title: IMS_RNA_sgCD19_d3_3


title: 4B2N1-E5


title: STAT2_IFNa2b_treated_B-cell


title: SAMPLE 3: Nontarget siRNA Rep 3

description: replicate 3


title: SAMPLE 4: Nontarget siRNA Rep 4

description: replicate 4


title: IMS_RNA_sgCD19_d3_2


title: SAMPLE 1: Nontarget siRNA Rep 1

description: replicate 1


title: 4B2N1-E4


title: 4B2N1-E3


title: Control1_non_stim_B-cell


title: STAT1_repeat_IFNa2b_treated_B-cell


title: IMS_RNA_sgCD19_d3_1


title: 4B2N1-E2


title: STAT2_repeat_non_stim_B-cell


title: STAT1_IFNa2b_treated_B-cell


title: 4B2N1-DP1


title: 4B2N1-EC


title: SAMPLE 2: Nontarget siRNA Rep 2

description: replicate 2


title: O3_RNA_sgNPM1c_d3_1


title: STAT1_repeat_non_stim_B-cell


title: 4B2N1-C3


title: STAT1_non_stim_B-cell


title: O3_RNA_sgCD45_d3_2


title: STAT2_non_stim_B-cell


title: BCG24hcon1

first: Ming

middle: zhe

state: Shanghai

address: 270 DongAn Road

department: Department of Gastric Surgery

institute: Fudan University Shanghai Cancer Center

hyb_protocol: Aligent SureHyb for hybridization

scan_protocol: Aligent DNA microarray scanner for scanning

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: gastric cancer cell line BGC823

label_protocol: Arraystar RNA flash labeling Kit for sample labeling.

growth_protocol: SGC7901 and BGC823 cells were routinely generated by re-plating d 4 in DMEM supplemented with 10% FBS

extract_protocol: RNA was harvested using Trizol reagent.RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: SGC7901 and BGC823 cells were exposed to hypoxia (1% oxygen) or normoxia (21% oxygen)for 24 hours

value: gastric cancer cell line BGC823

value: normoxia


title: SGC24hcon2

source_name: gastric cancer cell line SGC7901

value: gastric cancer cell line SGC7901


title: SGC24hcon1


title: O3_RNA_sgCD45_d3_1


title: 4B2N1-C2


title: BCG24hcon2


title: O3_RNA_sgCD19_d3_2


title: IRF9_non_stim_B-cell


title: 4B2N1-C1


title: O3_RNA_sgCD19_d3_1


title: SGC24h_QY_2

value: hypoxia


title: 4B2N1-C


title: O3_RNA_sgNPM1c_d3_2


title: SGC24h_QY_1


title: BCG24H_QY_2


title: KC_gd_d1_rep2

status: Public on Aug 05 2018

city: Bethesda

first: Fred

middle: P.

last: Davis

state: MD

address: 9000 Rockville Pike

department: NIAMS

institute: NIH

description:
QC: pass
s250

data_processing:
We trimmed five nucleotides from the 5’ end of reads using seqtk (https://github.com/lh3/seqtk) to remove potential contaminating adapter sequence from the NuGen Ovation kit. We estimated the abundance of annotated genes using kallisto (v 0.43.1; Bray et al., 2015) to pseudo-align trimmed reads to the fly transcriptome (cDNA and ncRNA transcript sequences from ENSEMBL release 91, based on FlyBase release 2017_04), ERCC spike-ins, and the INTACT construct sequences GAL4-DBD, p65-AD, and UNC84_2XGFP.
ERCC, INTACT tag constructs, and rRNA genes were removed from the abundance tables and the estimated abundances of the remaining genes were renormalized to one million total transcripts.
We further analyzed high-quality libraries passing three criteria: > 8,500 genes detected, > 3ug cDNA yield, r>= 0.85 pearson correlation between replicates
We modeled transcript abundance (in high-quality libraries) as arising from a gene-specific mixture of on and off log-normal components (See manuscript for details). We used this model to transform transcript abundance into probabilities of expression (probability of arising from on state).
Genome_build: dm6. ENSEMBL BDGP.r91

molecule: nuclear RNA

organism: Drosophila melanogaster

growth_protocol: Split-GAL4 and GAL4 driver lines were used to express the INTACT reporter (UNC84-2XGFP) in defined cell populations

extract_protocol:
INTACT protocol: Adult flies were entrained to a 12:12 light:dark cycle, anesthetized by CO2 at ZT8 - ZT12, flash frozen in liquid N2 and decapitated by vigorous vortexing. Heads or wings/appendages were then collected on cooled metal sieves (H&C Sieving Systems: 1296, 1297, 1298, 1301). Both flies and purified frozen material can be stored indefinitely at -80degrees C. In a typical experiment 100 to 500 frozen heads were added to 5mls of 20mM Beta-glycerophosphate pH7, 200mM NaCl, 2mM EDTA, 0.5% NP40, 0.5mM spermidine, 0.15mM spermine, 1mM DTT, 1X complete protease inhibitor (Sigma: 5056489001), 3mg/ml BSA (ThermoFisher: AM2618), 1mg/ml torula RNA (ThermoFisher: AM7118), 0.6mg/ml carboxyl coated Dynabeads (ThermoFisher: 14306D) and 2 microgram anti-GFP antibody (ThermoFisher: G10362). Homogenization was carried out on ice by 50 tractions in a Dounce homogenizer using the tight pestle followed by filtration over a 10 micrometer cup filter (Partec: 0400422314). Released chromatin and broken nuclei were adsorbed to carboxyl coated magnetic beads for 30 minutes at 4 degrees C with constant rotation. After which the beads were removed on a magnetic stand, the supernatant diluted to 50mls with 20mM Beta-glycerophosphate pH7, 200mM NaCl, 2mM EDTA, 0.5% NP40, 0.5mM spermidine, 0.15mM spermine, 1mM DTT and 1X complete protease inhibitor (Sigma: 5056489001), filtered over a 1 micrometer cup filter (Pluriselect: 435000103) and split into two equal volumes. A 40% Optiprep (Sigma: D1556), 20mM Beta-glycerophosphate pH7, 2mM EDTA and 0.5% NP40 solution was then carefully placed under each aliquot. Followed by a lower layer of 50% Optiprep, 20mM Beta-glycerophosphate pH7, 2mM EDTA and 0.5% NP40. Nuclei were then pelleted on to the 50% layer for 30 minutes at 2300Xg. Purified nuclei were passed over a 10 micrometer cup filter, diluted to 10mls with 20mM Beta-glycerophosphate pH7, 200mM NaCl, 2mM EDTA, 0.5% NP40, 0.5mM spermidine, 0.15mM spermine, 1mM DTT and 1X complete protease inhibitor and incubated with 30 microliters of protein G Dynabeads (ThermoFisher: 10004D) for 40 minutes on ice with occasional agitation. Bead-bound nuclei were recovered on a magnet stand followed by a 20 minute incubation on ice in 9mls of 20mM Beta-glycerophosphate pH7, 300mM NaCl, 1M urea, 0.5% NP40, 2mM EDTA, 0.5mM spermidine, 0.15mM spermine, 1mM DTT, 1X complete protease inhibitor, 0.075mg/ml torula RNA and 0.05Units/ml Superasin (ThermoFisher: AM2696). Nuclei were then recovered on a magnet stand, resuspended in 1ml of the previous buffer, passed over a 10 micrometer cup filter, a 5 microliter aliquot was withdrawn for quantitation and the remainder of the sample solubilized in Arcturus Picopure RNA extraction buffer (ThermoFisher: KIT0204).
TAPIN-seq protocol: 100 to 3000 frozen heads were added to 5mls of sodium acetate ph8.5, 2.5mM MgCl2, 250mM sucrose, 0.5% NP-40, 0.6mM spermidine, 0.2mM spermine, 1mM DTT, 1X complete protease inhibitor, 0.5mg/ml torula RNA, 0.6mg/ml carboxyl coated Dynabeads and 2microgram anti-GFP antibody. Homogenization was carried out on ice by 50 tractions in a Dounce homogenizer using the tight pestle followed by filtration over either a 10 or 20 micrometer cup filter (Partec: 0400422314, 040042315). Released chromatin and broken nuclei were adsorbed to carboxyl coated magnetic beads for 30 minutes at 4 degrees C with constant rotation. Unbound antibody was removed by incubating the sample on ice for 20 minutes with 100 microliters of washed UNOsphere SUPra resin (Biorad: 1560218). After the resin was removed on a 10 micrometer cup filter and the carboxyl beads on a magnet stand, the nuclei-containing supernatant was mixed with an equal volume of 500mM sodium acetate ph8.5, 250mM sucrose, 6mM EGTA, 6mM EDTA, 0.6mM spermidine, 0.2mM spermidine, 1mM DTT, 1X complete protease inhibitor, 0.25mg/ml torula RNA and 30 microliters Protein A Dynabeads (ThermoFisher: 10002D). A 2 hour incubation on ice with occasional agitation was used to recover tagged nuclei. Bead-bound nuclei were then recovered on a magnet stand and washed twice with 250mM sodium acetate ph8.5, 250mM sucrose and 0.1% NP40. Nuclei were then released at 37 degrees C for 1 hour by incubation in 50 microliters of 10mM Tris pH7.5, 2.5mM MgCl2, 0.5mM CaCl2, 250mM sucrose, 0.1% NP40, 1mg/ml torula RNA, 40 units RNAsin (Promega: N2515), 2 units DNAseI (NEB: M0303L), 320 units IdeZ protease (NEB: P0770S). The sample was diluted to 100 microliters with 10mM Tris pH7.5, 2.5mM MgCl2, 0.5mM CaCl2, 250mM sucrose and 0.1% NP40, EGTA was added to 1mM and the suspension was rapidly triturated 100 times. After returning the sample to a magnet stand, 90 microliters of buffer containing released nuclei was removed and added to 1.5 microliters of Protein G Dynabeads that were previously resuspended in 10 microliters of 10mM Tris pH7.5, 2.5mM MgCl2, 0.5mM CaCl2, 250mM sucrose and 0.1% NP40. The second binding reaction was run for 1 to 3 hours on ice with occasional agitation, followed by 2 X 250 microliters washes in 10mM Tris pH7.5, 2.5mM MgCl2, 0.5mM CaCl2, 250mM sucrose and 0.1% NP40. Prior to the last wash a 5 microliter aliquot was removed for quantitation and the remainder of the sample was solubilized in Arcturus Picopure RNA extraction buffer.

value: head

tag: genetic driver

tag: driver type

tag: external driver id

tag: intact reporter

tag: intact protocol

value: TAPIN


title: MBON_g1pedc_d1_rep2

description:
QC: suboptimal
s246


title: Lat_d1_rep1

description:
QC: suboptimal
s247

source_name: Lat


title: MBON_g1pedc_d1_rep1

description:
QC: suboptimal
s245


title: Pdf_d1_rep1

description:
QC: suboptimal
s241

source_name: Pdf

value: broad


title: Lat_d1_rep2

description:
QC: suboptimal
s248


title: lLNv_d1_rep1

description:
QC: suboptimal
s243

source_name: lLNv


title: lLNv_d1_rep2

description:
QC: suboptimal
s244


title: NPF_d1_rep4

description:
QC: suboptimal
s240

source_name: NPF


title: Pdf_d1_rep2

description:
QC: suboptimal
s242


title: NPF_d1_rep3

description:
QC: suboptimal
s239


title: CCAP_d1_rep2

description:
QC: suboptimal
s238

source_name: CCAP


title: IRF9_IFNa2b_treated_B-cell

value: B-cell


title: LPTC_HS.VS_d1_rep2

description:
QC: suboptimal
s236


title: T4.T5_d1_female_rep2

description:
QC: pass
s234


title: T4.T5_d1_female_rep1

description:
QC: pass
s233


title: KC_gd_d1_rep1

description:
QC: pass
s249


title: T4.T5_d1_male_rep2

description:
QC: pass
s232


title: T4.T5_d1_male_rep1

description:
QC: pass
s231


title: Muscles_Head_d2_rep1

description:
QC: suboptimal
s229


title: CCAP_d1_rep1

description:
QC: suboptimal
s237


title: Muscles_Head_d1_rep2

description:
QC: pass
s228


title: Muscles_Head_d1_rep1

description:
QC: pass
s227


title: Muscles_Head_d2_rep2

description:
QC: suboptimal
s230


title: BCG24H_QY_1

last: Ma

tag: treatment


title: Muscles_App_d1_rep1

description:
QC: pass
s225

tag: tissue


title: Dm12_d1_rep3

description:
QC: suboptimal
s223


title: Dm1_d1_rep2

description:
QC: pass
s222


title: LC10d_d1_rep2

description:
QC: suboptimal
s218


title: Dm1_d1_rep1

description:
QC: pass
s221


title: LC10bc_d1_rep2

description:
QC: suboptimal
s220


title: Mi15_d1_rep1

description:
QC: pass
s215


title: Mi9_d2_rep2

description:
QC: pass
s214


title: LC10bc_d1_rep1

description:
QC: suboptimal
s219


title: LPTC_HS.VS_d1_rep1

description:
QC: suboptimal
s235


title: Mi9_d1_rep1

description:
QC: pass
s211


title: Dm12_d1_rep4

description:
QC: pass
s224


title: Mi15_d1_rep2

description:
QC: pass
s216


title: VGlut_d1_rep2

description:
QC: pass
s210

source_name: VGlut


title: ChAT_d1_rep2

description:
QC: pass
s208

source_name: ChAT


title: ChAT_d1_rep1

description:
QC: pass
s207


title: Gad1_d1_rep2

description:
QC: pass
s206


title: Mi9_d1_rep2

description:
QC: pass
s212


title: Gad1_d1_rep1

description:
QC: pass
s205


title: PAM_2_d1_rep1

description:
QC: suboptimal
s203


title: PAM_6_d1_rep1

description:
QC: suboptimal
s201


title: VGlut_d1_rep1

description:
QC: pass
s209


title: PAM_6_d1_rep2

description:
QC: suboptimal
s202


title: T4.T5_d1_rep2

description:
QC: pass
s200


title: T4.T5_d1_rep1

description:
QC: pass
s199


title: Muscles_App_d1_rep2

description:
QC: pass
s226


title: LC10d_d1_rep1

description:
QC: suboptimal
s217


title: Mi9_d2_rep1

description:
QC: pass
s213


title: T5_d2_rep2

description:
QC: pass
s196


title: T4.T5_d2_rep1

description:
QC: pass
s197


title: T5_d2_rep1

description:
QC: pass
s195


title: T4.T5_d2_rep2

description:
QC: pass
s198


title: T5_d1_rep1

description:
QC: pass
s193


title: T5_d1_rep2

description:
QC: pass
s194


title: T4_d2_rep2

description:
QC: pass
s190


title: PAM_3_d1_rep2

description:
QC: pass
s188


title: PAM_3_d1_rep1

description:
QC: pass
s187


title: PAM_2_d1_rep2

description:
QC: suboptimal
s204


title: T4_d2_rep1

description:
QC: pass
s189


title: PAM_1_d1_rep2

description:
QC: pass
s184


title: MBON_bp1_d1_rep2

description:
QC: suboptimal
s186


title: PAM_5_d1_rep2

description:
QC: suboptimal
s182


title: PAM_1_d1_rep1

description:
QC: pass
s183


title: PAM_4_d1_rep2

description:
QC: pass
s180


title: PAM_8_d1_rep2

description:
QC: suboptimal
s178


title: PAM_9_d1_rep2

description:
QC: suboptimal
s176


title: PAM_9_d1_rep1

description:
QC: suboptimal
s175


title: PAM_7_d1_rep2

description:
QC: suboptimal
s174


title: PAM_7_d1_rep1

description:
QC: suboptimal
s173


title: T4_d1_rep1

description:
QC: pass
s191


title: KC_ab_c.p.s_d1_rep2

description:
QC: pass
s168


title: KC_ab_s_d1_rep1

description:
QC: pass
s169


title: KC_ab_c_d1_rep2

description:
QC: pass
s172


title: KC_ab_c.p.s_d1_rep1

description:
QC: pass
s167


title: KC_ab_c_d1_rep1

description:
QC: pass
s171


title: KC_apbp_m_d1_rep1

description:
QC: suboptimal
s163


title: KC_ab_p_d1_rep2

description:
QC: pass
s166


title: KC_apbp_m_d1_rep2

description:
QC: suboptimal
s164


title: KC_gd_d2_rep2

description:
QC: pass
s160


title: KC_apbp_ap_d1_rep2

description:
QC: suboptimal
s162


title: IRF9_repeat_IFNa2b_treated_B-cell

tag: cell type


title: KC_gd_d2_rep1

description:
QC: pass
s159


title: Dm3_d1_rep2

description:
QC: pass
s158


title: KC_ab_p_d1_rep1

description:
QC: pass
s165


title: Lawf1_d2_rep2

description:
QC: pass
s156


title: Dm3_d1_rep1

description:
QC: pass
s157


title: Tm20_d1_rep2

description:
QC: pass
s154


title: Tm20_d1_rep1

description:
QC: pass
s153


title: Dm8_d1_rep2

description:
QC: pass
s152


title: KC_ab_s_d1_rep2

description:
QC: pass
s170


title: Dm8_d1_rep1

description:
QC: pass
s151


title: Glia_Eg_d2_rep2

description:
QC: pass
s148


title: Tm29_d1_rep2

description:
QC: pass
s150


title: Tm29_d1_rep1

description:
QC: pass
s149


title: KC_apbp_ap_d1_rep1

description:
QC: suboptimal
s161


title: Glia_Eg_d3_rep2

description:
QC: pass
s146


title: Glia_Eg_d3_rep1

description:
QC: pass
s145


title: PAM_8_d1_rep1

description:
QC: suboptimal
s177


title: Glia_Eg_d2_rep1

description:
QC: pass
s147


title: Glia_Psg_d2_rep2

description:
QC: pass
s142


title: Glia_Eg_d1_rep2

description:
QC: pass
s144


title: Glia_Psg_d1_rep1

description:
QC: pass
s139


title: PB_6_d1_rep2

description:
QC: suboptimal
s136

source_name: Protocerebral bridge PB_6


title: Glia_Mg_d1_rep2

description:
QC: pass
s138


title: Glia_Psg_d2_rep1

description:
QC: pass
s141


title: PB_3_d1_rep2

description:
QC: pass
s134

source_name: Protocerebral bridge PB_3


title: Glia_Psg_d1_rep2

description:
QC: pass
s140


title: T4_d1_rep2

description:
QC: pass
s192


title: LPi-34_d1_rep1

description:
QC: pass
s131


title: LPi-34_d1_rep2

description:
QC: pass
s132


title: Lawf1_d2_rep1

description:
QC: pass
s155


title: PB_1_d1_rep2

description:
QC: pass
s130

source_name: Protocerebral bridge PB_1


title: PB_3_d1_rep1

description:
QC: pass
s133


title: PB_1_d1_rep1

description:
QC: pass
s129


title: Glia_Eg_d1_rep1

description:
QC: pass
s143


title: PB_5_d1_rep2

description:
QC: pass
s126

source_name: Protocerebral bridge PB_5


title: PB_2_d1_rep2

description:
QC: pass
s128

source_name: Protocerebral bridge PB_2


title: Pm3_d1_rep2

description:
QC: pass
s124


title: PB_5_d1_rep1

description:
QC: pass
s125


title: Pm3_d1_rep1

description:
QC: pass
s123


title: PB_4_d2_rep2

description:
QC: pass
s122

source_name: Protocerebral bridge PB_4


title: PB_4_d2_rep1

description:
QC: pass
s121


title: PB_2_d1_rep1

description:
QC: pass
s127


title: PB_6_d1_rep1

description:
QC: suboptimal
s135


title: Dm4_d1_rep1

description:
QC: pass
s117


title: PB_4_d1_rep1

description:
QC: pass
s119


title: PB_4_d1_rep2

description:
QC: pass
s120


title: LC4_d1_rep1

description:
QC: pass
s115


title: LC6_d2_rep2

description:
QC: pass
s114


title: LC6_d2_rep1

description:
QC: pass
s113


title: Dm4_d1_rep2

description:
QC: pass
s118


title: LPLC2_d1_rep1

description:
QC: pass
s109


title: LC6_d1_rep2

description:
QC: pass
s112


title: LPLC1_d1_rep2

description:
QC: pass
s108


title: LC6_d1_rep1

description:
QC: pass
s111


title: LPLC2_d1_rep2

description:
QC: pass
s110


title: LPLC1_d1_rep1

description:
QC: pass
s107


title: LC16_d2_rep2

description:
QC: pass
s106


title: LC16_d2_rep1

description:
QC: pass
s105


title: Glia_Mg_d1_rep1

description:
QC: pass
s137


title: LC16_d1_rep2

description:
QC: pass
s104


title: Dm4_d2_rep2

description:
QC: pass
s102


title: LC16_d1_rep1

description:
QC: pass
s103


title: LC10b_d1_rep2

description:
QC: pass
s100


title: LC10b_d1_rep1

description:
QC: pass
s099


title: LPC1_d2_rep2

description:
QC: pass
s098


title: Dm4_d2_rep1

description:
QC: pass
s101


title: LPC1_d2_rep1

description:
QC: pass
s097


title: LC4_d1_rep2

description:
QC: pass
s116


title: LC10a_d1_rep1

description:
QC: pass
s095


title: LC10a_d1_rep2

description:
QC: pass
s096


title: LPC1_d1_rep2

description:
QC: pass
s094


title: TmY5a_d1_rep1

description:
QC: pass
s089


title: LPC1_d1_rep1

description:
QC: pass
s093


title: TmY5a_d1_rep2

description:
QC: pass
s090


title: LLPC1_d1_rep2

description:
QC: pass
s092


title: LLPC1_d1_rep1

description:
QC: pass
s091


title: Mi15_d2_rep1

description:
QC: pass
s087


title: Mi15_d2_rep2

description:
QC: pass
s088


title: Pm4_d1_rep1

description:
QC: pass
s085


title: Dm11_d1_rep2

description:
QC: pass
s084


title: Dm9_d1_rep2

description:
QC: pass
s082


title: Pm4_d1_rep2

description:
QC: pass
s086


title: Dm11_d1_rep1

description:
QC: pass
s083


title: Dm9_d1_rep1

description:
QC: pass
s081


title: Dm10_d1_rep2

description:
QC: pass
s080


title: Dm10_d1_rep1

description:
QC: pass
s079


title: TmY3_d1_rep1

description:
QC: pass
s077


title: opticlobe_d2_rep2

description:
QC: pass
s075

source_name: dissected opticlobe after lamina removal

value: dissected

value: bulk


title: lamina_d1_rep2

description:
QC: pass
s074

source_name: lamina dissected from optic lobe

value: lamina dissected from optic lobe


title: opticlobe_d1_rep2

description:
QC: pass
s073

value: dissected opticlobe after lamina removal


title: lamina_d2_rep2

description:
QC: pass
s076


title: TmY3_d1_rep2

description:
QC: pass
s078


title: opticlobe_d2_rep1

description:
QC: pass
s071


title: lamina_d2_rep1

description:
QC: pass
s072


title: opticlobe_d1_rep1

description:
QC: pass
s069


title: R1-6_d1_rep4

description:
QC: pass
s068


title: R1-6_d1_rep3

description:
QC: pass
s067


title: lamina_d1_rep1

description:
QC: pass
s070


title: R7_d1_rep1

description:
QC: pass
s065


title: R8_Rh6_d1_rep2

description:
QC: pass
s064


title: IRF9_IFNa2b_treated_Fibroblast

source_name: Fibroblast

value: Fibroblast


title: R7_d1_rep2

description:
QC: pass
s066


title: R8_Rh5_d1_rep1

description:
QC: pass
s061


title: R8_Rh5_d1_rep2

description:
QC: pass
s062


title: R7_Rh3_d1_rep1

description:
QC: suboptimal
s059


title: Kdm2_d1_rep1

description:
QC: pass
s057


title: Crz_d1_rep2

description:
QC: pass
s056

source_name: Crz


title: R7_Rh3_d1_rep2

description:
QC: suboptimal
s060


title: Crz_d1_rep1

description:
QC: pass
s055


title: MBON_bp1_d1_rep1

description:
QC: suboptimal
s185


title: Ilp2_d1_rep2

description:
QC: suboptimal
s054


title: Ilp2_d1_rep1

description:
QC: suboptimal
s053


title: Kdm2_d1_rep2

description:
QC: pass
s058


title: Dsk_d1_rep1

description:
QC: suboptimal
s051

source_name: Dsk


title: NPF_d1_rep1

description:
QC: pass
s049


title: Dm12_d1_rep2

description:
QC: pass
s046

value: INTACT


title: Dm12_d1_rep1

description:
QC: pass
s045


title: R8_Rh6_d1_rep1

description:
QC: pass
s063


title: R1-6_d1_rep1

description:
QC: pass
s043


title: NPF_d1_rep2

description:
QC: pass
s050


title: R1-6_d1_rep2

description:
QC: pass
s044


title: C2.C3_d1_rep2

description:
QC: pass
s042


title: C2.C3_d1_rep1

description:
QC: pass
s041


title: L1.L2_d2_rep1

description:
QC: pass
s039


title: L1.L2_d2_rep2

description:
QC: pass
s040


title: L1.L2_d1_rep2

description:
QC: pass
s038


title: L1.L2_d1_rep1

description:
QC: pass
s037


title: Lai_d1_rep2

description:
QC: pass
s036

source_name: Lai


title: Lai_d1_rep1

description:
QC: pass
s035


title: T1_d1_rep1

description:
QC: pass
s033


title: Lawf2_d1_rep2

description:
QC: pass
s032


title: Lawf2_d1_rep1

description:
QC: pass
s031


title: Lawf1_d1_rep2

description:
QC: pass
s030


title: Lawf1_d1_rep1

description:
QC: pass
s029


title: Tm1_d1_rep2

description:
QC: pass
s048


title: L4_d1_rep2

description:
QC: pass
s028


title: C3_d1_rep2

description:
QC: pass
s027


title: C3_d1_rep1

description:
QC: pass
s026


title: Dsk_d1_rep2

description:
QC: suboptimal
s052


title: Tm1_d1_rep1

description:
QC: pass
s047


title: C2_d1_rep1

description:
QC: pass
s024


title: L5_d1_rep2

description:
QC: pass
s023


title: PAM_4_d1_rep1

description:
QC: pass
s179


title: C2_d1_rep2

description:
QC: pass
s025


title: L5_d1_rep1

description:
QC: pass
s022


title: L3_d1_rep2

description:
QC: pass
s020


title: T1_d1_rep2

description:
QC: pass
s034


title: L4_d1_rep1

description:
QC: pass
s021


title: L3_d1_rep1

description:
QC: pass
s019


title: L2_d1_rep2

description:
QC: pass
s018


title: PAM_5_d1_rep1

description:
QC: suboptimal
s181


title: L1_d2_rep1

description:
QC: pass
s015


title: L1_d1_rep2

description:
QC: pass
s014


title: Tm9_d1_rep2

description:
QC: pass
s012


title: L1_d2_rep2

description:
QC: pass
s016


title: Tm9_d1_rep1

description:
QC: pass
s011


title: Tm2_d1_rep2

description:
QC: pass
s010


title: Mi4_d1_rep1

description:
QC: pass
s007


title: Mi4_d1_rep2

description:
QC: pass
s008


title: L2_d1_rep1

description:
QC: pass
s017


title: L1_d1_rep1

description:
QC: pass
s013


title: Tm4_d1_rep1

description:
QC: pass
s005


title: Tm3_d1_rep2

description:
QC: pass
s004


title: Tm2_d1_rep1

description:
QC: pass
s009


title: FSPCre-PPARB KO tumor adjacent epithelium 1

city: Singapore

first: Eddie

middle: Han Pin

last: Tan

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

description:
Gene expression data from dissected tumor adjacent epithelium from mouse intestinal tumors
Tumor adjacentFSP-BKO2

hyb_protocol: 2 ug of cDNA were hybridized for 18hrs at 45C on GeneChip Mouse Gene 1.0ST Array under gentle agitation in genechip hybridization oven 640. Genechip fluidics station 450 was then used for the washing and staining of the chips.

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

data_processing: Partek genomic suite 6.0 was used to analyze samples by RMA.

label_protocol: Further sample processing of the RNA was carried out using GeneChip® WT Pico Kit

growth_protocol: Males 8-10 week-old FSPCre-PPARB -/- and PPARB flox/flox littermates were housed at 25 oC with regular light cycles of 12 light/12 dark hours.

extract_protocol: Tumor or adjacent epithelium were dissected from mouse tumor tissue sections

treatment_protocol: Mice are housed in cages of n=4, until they were 25 week-old or euthanized when total change in weight fell below 20% from starting weight.

value: FSPCre-PPARB -/-

tag: tissue source

value: Laser dissected tissue from sectioned tumors

value: Tumor adjacent epithelium


title: Wild type mechanical damage vs herbivore wounding 3

city: Turin

first: Cinzia

middle: Margherita

last: Bertea

state: To

address: via Quarello 11/A

department: Department of Life Sciences and Systems Biology

institute: University of Turin

description: WT mechanical damaged leaves (control) vs WT herbivore wounding leaves (treatment). Harvested  2 h after the treatments

hyb_protocol: Hybridization buffer (Agilent Gene Expression Hybridization Kit ) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (v 9.5.1.1)

data_processing: R package limma (v 3.4.4) was used for background subtraction and LOESS normalization.

organism: Arabidopsis thaliana

source_name: WT rosette leaves mechanical damaged

label_protocol: 500 ng of total RNA  were separately reverse-transcribed into double-strand cDNAs by the Moloney murine leukemia virus reverse transcriptase (MMLV-RT) and amplified for 2 h at 40°C using the Agilent Quick Amp Labelling Kit, two-color (Agilent Technologies). Subsequently, cDNAs were transcribed into antisense cRNA and labeled with either Cy3-CTP or Cy5-CTP fluorescent dyes for 2 h at 40°C following the manufacturer’s protocol. Cyanine-labeled cRNAs were purified using RNeasy Minikit (Qiagen). Purity and dye incorporation were assessed with the NanoDrop ND-1000 UV-VIS Spectrophotometer (Thermo Fisher Scientific) and the Agilent 2100 Bioanalyzer (Agilent Technologies).

growth_protocol: Arabidopsis plants (Col-0 and PDKO3) were grown as a single plant in plastic pots filled with soil. Growth chamber was set up at 23°C 16h in the light (160 μE m-2 s-1) and 8 in the dark for 22 days

extract_protocol: Total RNA extracted from rosette leaves using Agilent Plant RNA Isolation Mini kit including RNAse-free DNase (Qiagen) treatment

treatment_protocol: Mechanical damage: made by pattern wheel mimicking herbivore; Herbivore wounding: Spodoptera littoralis feeding

value: mechanical damaged

tag: age

value: day 22 (growth stage 3)

value: rosette leaves

tag: ecotype

value: Columbia 0

tag: genotype

value: WT

source_name: WT rosette leaves herbivore wounded

value: herbivore wounded


title: PPARB floxed tumor adjacent epithelium 3

description:
Gene expression data from dissected tumor adjacent epithelium from mouse intestinal tumors
Tumor adjacentFSP-BKO1

source_name: PPARB floxed tumor adjacent epithelium


title: Wild type mechanical damage vs herbivore wounding 1

description: WT mechanical damaged (control)  vs WT herbivore wounding leaves (treatment). Harvested 2 h after the treatments


title: PPARB floxed tumor adjacent epithelium 2

description:
Gene expression data from dissected tumor adjacent epithelium from mouse intestinal tumors
Tumor adjacentWT2

value: PPARB flox/flox


title: Atad3afl/fl rep2

first: Guoxiang

last: Jin

state: TX

address: 1515 Holcombe

department: Molecular&Cellular Oncology

institute: MD Anderson Cancer Center

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Genomestudio quantile normalization

label: Biotin

source_name: Mouse bone marrow

label_protocol: Biotin labeled cRNA was prepared using Ambion’s Illumina Total-Prep-96 RNA Amplification kit

extract_protocol: Total RNA was extracted by RNeasy Mini Kit

treatment_protocol: Day 12 after PolyIC induction

value: Bone marrow


title: Wild type mechanical damage vs herbivore wounding 2

description: WT mechanical damaged leaves (control) vs WT herbivore wounding leaves (treatment). Harvested 2 h after the treatments


title: FSPCre-PPARB KO tumor adjacent epithelium 2

description:
Gene expression data from dissected tumor adjacent epithelium from mouse intestinal tumors
Tumor adjacentFSP-BKO3


title: Atad3afl/fl rep1

description: replicate 1


title: PDKO3 mechanical damage vs herbivore wounding 2

description: PDKO3 mechanical damaged (control) vs PDKO3 herbivore wounding leaves (treatment). Harvested  2 h after the treatments

source_name: PDKO3 rosette leaves mechanical damaged

value: mutated in 3 genes encoding plasmodesmata

source_name: PDKO3 rosette leaves herbivore wounded

value: mutated in 3 plasmodesmata genes


title: FSPCre-PPARB KO tumor adjacent epithelium 3

description:
Gene expression data from dissected tumor adjacent epithelium from mouse intestinal tumors
Tumor adjacentWT3


title: Tm4_d1_rep2

description:
QC: pass
s006

value: head


title: Atad3afl/flMx1Cre rep1

description: replicate 1


title: Atad3afl/flMx1Cre rep2

description: replicate 2


title: Tm3_d1_rep1

description:
QC: pass
s003


title: FSPCre-PPARB KO tumor epithelium 1

description:
Gene expression data from dissected epithelium from mouse intestinal tumors
TumorFSP-BKO1

source_name: FSPCre-PPARB KO tumor epithelium

value: Tumor epithelium


title: FSPCre-PPARB KO tumor epithelium 3

description:
Gene expression data from dissected epithelium from mouse intestinal tumors
TumorFSP-BKO3


title: Mi1_d1_rep1

description:
QC: pass
s001


title: PDKO3 mechanical damage vs herbivore wounding 1

description: PDKO3 mechanical damaged (control) vs PDKO3  herbivore wounding leaves (treatment). Harvested  2 h after the treatments


title: FSPCre-PPARB KO tumor epithelium 2

description:
Gene expression data from dissected epithelium from mouse intestinal tumors
TumorFSP-BKO2


title: PDKO3 mechanical damage vs herbivore wounding 3


title: Wild type mechanical damage vs PDKO3 mechanical damage 1

description: WT mechanical damaged leaves (control)  vs PDKO3 mechanical damaged leaves (treatment). Harvested  2 h after the treatments


title: Wild type mechanical damage vs PDKO3 mechanical damage 2

description: WT mechanical damaged leaves  (control)  vs PDKO3 mechanical damaged leaves (treatment). Harvested  2 h after the treatments


title: PPARB floxed tumor epithelium 3

description:
Gene expression data from dissected epithelium from mouse intestinal tumors
TumorWT3

source_name: PPARB floxed tumor epithelium


title: PPARB floxed tumor adjacent epithelium 1

description:
Gene expression data from dissected tumor adjacent epithelium from mouse intestinal tumors
Tumor adjacentWT1


title: mock2_rep1

description:
QC: NA
c015

value: control

value: TAPIN


title: PPARB floxed tumor epithelium 2

description:
Gene expression data from dissected epithelium from mouse intestinal tumors
TumorWT2


title: no_driver_aGFP_beads_rep4

description:
QC: NA
c014


title: no_driver_aGFP_beads_rep3

description:
QC: NA
c013


title: PPARB floxed tumor epithelium 1

description:
Gene expression data from dissected epithelium from mouse intestinal tumors
TumorWT1


title: Tm1_d1_mock2_rep2

description:
QC: NA
c012

source_name: TAPIN control


title: Tm1_d1_mock2_rep1

description:
QC: NA
c011


title: Tm1_d1_mock1_rep2

description:
QC: NA
c010


title: Tm1_d1_mock1_rep1

description:
QC: NA
c009


title: mock2_rep2

description:
QC: NA
c016


title: Tm1_d1_input_rep2

description:
QC: NA
c006


title: Tm1_d1_capture1_rep1

description:
QC: NA
c007


title: Tm1_d1_input_rep1

description:
QC: NA
c005


title: no_driver_aGFP_beads_rep2

description:
QC: NA
c004

source_name: INTACT control

value: INTACT


title: L1L2_aFLAG_beads_rep2

description:
QC: NA
c002


title: no_driver_aGFP_beads_rep1

description:
QC: NA
c003


title: jaz10_8-3

city: Yokohama-Shi, Tsurumi Ku

first: Khurram

last: Bashir

state: Kanagawa

address: 1-7-22 Suehiro-cho

department: Center for Sustainable Resource Science

institute: RIKEN

description: Gene expression after treatment with 8

hyb_protocol: 600 ng of cRNAs  were hybridized to the microarray (GPL19830) at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer  (Agilent), and then dried immediately by brief centrifugation.

scan_protocol: The microarray was scanned by Agilent DNA Microarray Scanner G2505B and  raw data was extracted using Feature Extraction program ver 9.1.

data_processing: Quantile normalization was performed with log transformation and data was processed through one way ANOVA with Gene Spring. Futher Tuckey's HSD test with FDR was applied for individual combinations (Agilent Technology v14.9)

label_protocol: Total RNA (400 ng) was labeled with fluorescently-labeled Cy3, using a Quick Amp labeling kit (Agilent Technologies)

growth_protocol: A. thaliana ecotype Col-0 seeds were surface-sterilized in 5% sodium hypochlorite with 0.3% Tween20 and vernalized for 2–4 d at 4 °C. All seedlings were grown under a 16 h light (118 μmol·m−2·s−1; cool-white fluorescent light)/8 h dark cycle at 22 °C in a Biotron NC-220 growth chamber. WT and mutant seedlings were grown in 1/2 Murashige & Skoog (MS) liquid medium.

extract_protocol: Total RNA was isolated with an RNeasy Mini Kit

treatment_protocol: Six-d-old plants were incubated in autoclaved 1/2 MS liquid medium containing each filtered compound under a 16 h light /8 h dark cycle at 22°C in a Biotron NC-220 growth chamber. The plants were treated with or without ligands (3, ent6 or 8, 1 µM) for 8 h in the same growth chamber.

tag: developmental stage

value: seedling

value: whole plant

value: Treated with 8


title: L1L2_aFLAG_beads_rep1

description:
QC: NA
c001


title: jaz10_8-2

description: Gene expression after treatment with 8


title: jaz10_3-3

description: Gene expression after treatment with 3

value: Treated with 3


title: jaz10_mock-3

description: Gene expression control conditions

value: mock treated


title: jaz10_8-1

description: Gene expression after treatment with 8


title: jaz10_3-1

description: Gene expression after treatment with 3


title: jaz9_8-1

description: Gene expression after treatment with 8


title: Tm1_d1_capture1_rep2

description:
QC: NA
c008


title: jaz10_mock-1

description: Gene expression control conditions


title: jaz10_mock-2

description: Gene expression control conditions


title: jaz10_3-2

description: Gene expression after treatment with 3


title: jaz9_8-2

description: Gene expression after treatment with 8


title: CHD3-KO_1

city: Oslo

first: Roza Berhanu

last: Lemma

address: Blindernveien 31

department: Department of Biosciences

country: Norway

institute: University of Oslo

description: Crisper-Cas9 generated cell lines

data_processing:
Basecalls were performed using RTA v2.7.7,  demultiplexing and conversion to FASTQ format was done using bcl2fastq v2.18.0.12.
Low quality reads and adaptors were trimmed/removed using Trimmomatic v0.36
Illumina spike-in PhiX were removed using BBMap v37.4
Cleaned reads were aligned to Homo sapiens GRCh38 ensembl release 90 using Tophat2 v2.1.1 with ‘--library-type fr-firststrand --no-mixed --no-novel-juncs' as parameters
Differential expression was calculated using cuffdiff in cufflinks suite v2.2.1 and viewed using the R package cummeRbund v2.16.
Genome_build: GRCh38 release 90
Supplementary_files_format_and_content: Replicate FPKM table from cummeRbund

growth_protocol: HAP1 cells were cultivated in IMDM (ThermoFisher Scientific) supplemented with 10% Fetal Bovine Serum and 1% Penicillin/Streptamycin

extract_protocol:
RNeasy Mini kit (Qiagen, 74104)
TruSeq stranded RNA library prep, poly(A) selection (Illumina)

treatment_protocol: No treatment

value: Male Chronic Myelogenous Leukemia (CML) cell line derived from KBM-7

tag: cell line

value: CHD3 knock out cell line


title: SENP1-KO_3

description: Crisper-Cas9 generated cell lines

value: SENP1 knock out cell line


title: CHD3-KO_3

description: Crisper-Cas9 generated cell lines


title: jaz9_8-3

description: Gene expression after treatment with 8


title: jaz9_3-3

description: Gene expression after treatment with 3


title: SENP1-KO_2

description: Crisper-Cas9 generated cell lines


title: jaz9_mock-3

description: Gene expression control conditions


title: SENP1-KO_1

description: Crisper-Cas9 generated cell lines


title: jaz9_3-2

description: Gene expression after treatment with 3


title: ctrl_3

description: Crisper-Cas9 generated cell lines

value: control cell line


title: CHD3-KO_2

description: Crisper-Cas9 generated cell lines


title: jaz9_mock-1

description: Gene expression control conditions


title: jaz9_mock-2

description: Gene expression control conditions


title: jaz9_3-1

description: Gene expression after treatment with 3


title: ctrl_1

description: Crisper-Cas9 generated cell lines


title: ctrl_2

description: Crisper-Cas9 generated cell lines


title: WT 8-3

description: Gene expression after treatment with 8

source_name: WT 8

value: WT


title: WT 8-1

description: Gene expression after treatment with 8


title: WT 6-2

description: Gene expression after treatment with 6

source_name: WT 6

value: Treated with 6


title: CHD3-KO_atac_2

description:
Crisper-Cas9 generated cell lines
CHD3-KO_atac_2

data_processing:
Low quality reads and adaptors were removed using TrimGalore v0.3.3
Illumina spike-in PhiX were removed using BBMap v37.4
clean reads in fastq format were aligned to the human genome build hg19 using bwa mem v0.7.5a with default parameters
reads with mapq<20, improperly aligned reads and reads aligning to mitochondrial chromosome were filtered using SAMtools v0.1.19
peak calling was performed using MACS2 v2.1.0 with “--broad-cutoff 0.1 -f 'AUTO' -g hs -m 5 50 --bw 150 --fix-bimodal --extsize 100 -q 0.01” as parameters
resulting peaks were refined using the bdgcmp function of MACS2 v2.1.0 with the 'ppois' method
bedGraph files containing refined peaks were converted to bigWig format using the tool, bedGraphToBigWig v4 and visualized in the UCSC genome browser
Genome_build: hg19
Supplementary_files_format_and_content: tracks (peaks) in bigWig file format

source_name: Male Chronic Myelogenous Leukemia (CML) cell line derived from KBM-7

extract_protocol: Illumina Nextera Library prep kit (FC-121-1030)

value: CHD3 knock out


title: CHD3-KO_atac_3

description:
Crisper-Cas9 generated cell lines
CHD3-KO_atac_3


title: SENP1-KO_atac_3

description:
Crisper-Cas9 generated cell lines
SENP1-KO_atac_3

value: SENP1 knock out


title: WT 6-3

description: Gene expression after treatment with 6


title: gDNA-atac_2


title: SENP1-KO_atac_2

description:
Crisper-Cas9 generated cell lines
SENP1-KO_atac_2


title: WT 8-2

description: Gene expression after treatment with 8


title: gDNA-atac_1


title: gDNA-atac_3


title: WT 6-1

description: Gene expression after treatment with 6


title: CHD3-KO_atac_1

description:
Crisper-Cas9 generated cell lines
CHD3-KO_atac_1


title: WT mock-3

description: Gene expression control conditions

source_name: WT mock


title: WT 3-1

description: Gene expression after treatment with 3

source_name: WT 3


title: ctrl_atac_3


title: WT 3-3

description: Gene expression after treatment with 3


title: WT mock-1

description: Gene expression control conditions


title: WT 3-2

description: Gene expression after treatment with 3


title: ctrl_atac_1


title: WT mock-2

description: Gene expression control conditions


title: SENP1-KO_atac_1

description:
Crisper-Cas9 generated cell lines
SENP1-KO_atac_1


title: YPD_IL01_AER_R1 [RNA-Seq_3strains]

status: Public on Aug 04 2018

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

institute: University of Wisconsin

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
YPD_IL01_AER_R1

data_processing:
Alignment to  reference genome S288C R64-1-1 using BWA mem
Counts generated using HTSeq
RPKM Calculated
Genome_build: S288C R64-1-1
Supplementary_files_format_and_content: rpkm

source_name: Gasch Lab/ GLBRC

growth_protocol: Yeast grown in shaker flasks in aerobic conditions or in an anaerobi chamber

extract_protocol:
RNA extraction by hot acid-phenol extraction
Illumina TruSeq stranded library prep

treatment_protocol: Alcohol added to each culture for denoted times, if indicated

tag: agent

value: YPD

tag: strain


title: ctrl_atac_2

tag: genotype/variation

value: control


title: Butanol_IL01_ANAE_R2 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Butanol_IL01_ANAE_R2

value: Butanol


title: Butanol_Y7568_ANAE_R1 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Butanol_Y7568_ANAE_R1


title: Butanol_IL01_ANAE_R1 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Butanol_IL01_ANAE_R1


title: Ethanol_IL01_ANAE_R1 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Ethanol_IL01_ANAE_R1

value: Ethanol