title: MPI-887_tissue

city: Regensburg

first: Christian

middle: W

last: Kohler

state: Bavaria

address: Am BioPark 9

department: Institute of Functional Genomics

country: Germany

institute: University of Regensburg

hyb_protocol: Affymetrix hybridization was carried on U133A GeneChips according to the manufacturer's recommendations. In brief, 15 microgram of Biotin-labelled and fragmented cRNA were mixed with 20x GeneChip Eukaryotic Hybridization Control (Affymetrix) and supplemented with B2 control oligonucletide, salmon sperm DNA, acetylated bovine serum albumin and hybridization buffer and water making up a total volume of 300 microliter

scan_protocol: After hybridization of night (16 hours, 45° C) the hybridization mixture was removed from the GeneChip and washing and staining of the GeneChips was performed in a fluidics station (Affymetrix). The detection of the Biotin-labeled cRNA was mediated by a streptavidin-phycoerythrin complex. The measurement of the fluorescence intensity was carried out in an Agilent scanner (GA2500)

data_processing: Probe level normalization was done using the calibration and variance stabilization method by Huber et al. (Bioinformatics 2002, PMID: 12169536). Probe-set summarization was performed using the median polish method on the normalised data (Irizarry et al. Nucleic Acids Research 2003, PMID: 12582260)

source_name: tumor

label_protocol: For Affymetrix GeneChip hybridization, 5 microgram of total RNA was employed to generate a double-stranded cDNA with the help of the INVITROGEN Superscript kit. After removal of small molecular components (Affymetrix Clean-up Module), Biotin-labelled cRNA was synthesized by application of the ENZO Labeling kit (T7 RNA polymerase). The concentration of the produced cRNA was determined photometrically (NanoDrop) and the size range of the labelled products was evaluated by BioAnalyzer (Agilent) measurement before and after fragmentation

extract_protocol: RNA was isolated using RNeasy Mini Kit (QIAGEN) and the concentration was determined photometrically (NanoDrop). The quality of the RNA was assessed based on the presence of the tht 18S and 28S tRNA by analysis of an aliquot in the Agilent BioAnalyzer (Agilent)

tag: category

value: absent

value: present


title: MPI-720_tissue

status: Public on Jul 23 2018

type: RNA

label: biotin

molecule: total RNA

organism: Homo sapiens


title: MPI-658_tissue


title: MPI-786_tissue


title: MPI-889_tissue


title: MPI-868_tissue


title: MPI-891_tissue


title: MPI-712_tissue


title: MPI-653_tissue


title: MPI-867_tissue


title: MPI-772_tissue


title: MPI-643_tissue


title: MPI-668_tissue


title: MPI-776_tissue


title: MPI-729_tissue


title: MPI-719_tissue


title: MPI-777_tissue


title: MPI-787_tissue


title: MPI-639_tissue


title: MPI-710_tissue


title: MPI-738_tissue


title: MPI-779_tissue


title: MPI-872_tissue


title: MPI-640_tissue


title: MPI-886_tissue


title: MPI-633_tissue


title: MPI-775_tissue


title: MPI-711_tissue


title: MPI-659_tissue


title: MPI-632_tissue


title: MPI-629_tissue


title: MPI-627_tissue


title: offspring oogenic germlines from mes-3 (M+P+); fem-2 hermaphrodites, rep2  (control)

type: SRA

city: Santa Cruz

first: Susan

last: Strome

state: CA

address: 1156 High St

department: MCD Biology

country: USA

institute: UC Santa Cruz

description: DESeq.diff.expression.mes3.malegerml.sperm.offspring.vs.controls.csv.gz

library_source: transcriptomic

data_processing:
TopHat2 was used to align the RNA-seq reads to the C. elegans genome (WS220) with default parameters.
HTSeq was used to obtain read counts per transcript.
Differentially expressed genes were determined with DESeq2 in R using HTSeq counts and a FDR < 0.05 as the significance cutoff.
RPKMs (Reads Per Kilobase of transcript, per Million mapped reads) were calculated by dividing HTseq counts by exonic transcript length (in kb) obtained from Wormbase and scaling the total read counts per sample to 1 million reads. If a gene had multiple transcript isoforms, the longest was chosen.
Genome_build: WS220
Supplementary_files_format_and_content: Text files for each sample with HTSeq counts per transcript (tab delimited), RPKM values per transcript averaged over replicates (comma delimited) and DESeq output for differential expression analysis performed (comma delimited). Gene identifiers are Gene Sequence Names as obtained from Wormbase version WS220.

organism: Caenorhabditis elegans

source_name: distal gonad arms of oogenic germlines cut at the late-pachytene gonad bend

growth_protocol:
C. elegans strains were maintained at 15°on OP50 bacteria as described (Brenner 1974).
see SAMPLES

extract_protocol:
Total RNA was purified using Trizol/chloroform extraction protocol.
Ribosomal RNA was depleted using an NEBNext rRNA Depletion kit (E6310), and libraries were prepared using an NEBNext Ultra RNA Library Prep Kit for Illumina (E7530).

treatment_protocol: L4 hermaphrodites or L4 males were transferred to new plates, and germlines were dissected from day 1 adults the next day. Mature sperm were collected from adult males cut in the middle.

tag: strain and genotype

tag: genotype of analyzed samples

value: mes-3/mes-3; fem-2/fem-2

tag: parents

value: mes-3/hT2-GFP; fem-2 feminized hermaphrodites x mes-3/hT2-GFP; fem-2 males

tag: xchromosome

value: autosome ratio:X:A=1:1 (XX hermaphrodites)


title: sperm from him-8 males, rep1 (control)

source_name: mature sperm

growth_protocol:
C. elegans strains were maintained at 20°on OP50 bacteria as described (Brenner 1974).
see SAMPLES

value: him-8 hermaphrodites

value: autosome ratio:X:A=0.5:1 (50% of sperm have an X; 50% lack an X)


title: sperm from him-8 males, rep3 (control)


title: offspring oogenic germlines from mes-3 (M+P-); fem-2 hermaphrodites, rep2

value: mes-3/hT2-GFP; fem-2 feminized hermaphrodites x mes-3; fem-2 males


title: sperm from him-8 males, rep2 (control)


title: offspring oogenic germlines from mes-3 (M+P-); fem-2 hermaphrodites, rep1


title: offspring oogenic germlines from mes-3 (M+P+); fem-2 hermaphrodites, rep1  (control)


title: male germlines from mes-3 males, rep1

source_name: distal gonad arms of spermatogenic germlines cut at the late-pachytene gonad bend

value: SS818 mes-3(bn35) /hT2-GFP

value: mes-3/hT2-GFP hermaphrodites x mes-3/hT2-GFP males

value: autosome ratio:X:A=0.5:1 (XO males)


title: oogenic germlines from fem-2 hermaphrodites, rep1

growth_protocol:
C. elegans strains were maintained at 15°on OP50 bacteria, and shifted to 20° at L4 stage for 24 hours before dissection.
see SAMPLES

value: fem-2/fem-2 hermaphrodites


title: oogenic germlines from wild-type N2 hermaphrodites, rep2

description:
DESeq.diff.expression.male.vs.oogen.germl.csv.gz
RPKM.male.oogen.germl.csv.gz

value: N2 wild-type

value: wild-type

value: N2 hermaphrodites


title: sperm from mes-3 males, rep2


title: oogenic germlines from wild-type N2 hermaphrodites, rep1


title: oogenic germlines from wild-type N2 hermaphrodites, rep3


title: male germlines from mes-3 males, rep3


title: MPI-604_tissue


title: male germlines from mes-3 males, rep2


title: oogenic germlines from fem-2 hermaphrodites, rep3


title: MPI-602_tissue


title: sperm from mes-3 males, rep1


title: sperm from mes-3 males, rep3


title: MPI-600_tissue


title: oogenic germlines from fem-2 hermaphrodites, rep2


title: male germlines from him-8, rep4 (also served as control for 'male germlines from mes-3 males')

description:
DESeq.diff.expression.male.vs.oogen.germl.csv.gz
DESeq.diff.expression.mes3.malegerml.sperm.offspring.vs.controls.csv.gz
RPKM.male.oogen.germl.csv.gz


title: MPI-603_tissue


title: male germlines from him-8, rep3 (also served as control for 'male germlines from mes-3 males')


title: male germlines from him-8, rep2 (also served as control for 'male germlines from mes-3 males')


title: male germlines from him-8, rep1 (also served as control for 'male germlines from mes-3 males')


title: male germlines from willd-type N2, rep1

value: N2 hermaphrodites X N2 males


title: male germlines from willd-type N2, rep2


title: Germlines from offspring of 'red-head' worms, rep1

data_processing:
TopHat2 was used to align the RNA-seq reads to the C. elegans transcriptome (WS220) with default parameters.
HTSeq was used to obtain read counts per transcript.
Differentially expressed genes were determined with DESeq2 in R using HTSeq counts and a FDR < 0.05 as the significance cutoff.
RPKMs (Reads Per Kilobase of transcript, per Million mapped reads) were calculated by dividing HTseq counts by exonic transcript length (in kb) obtained from Wormbase and scaling the total read counts per sample to 1 million reads. If a gene had multiple transcript isoforms, the longest was chosen.
Genome_build: WS220
Supplementary_files_format_and_content: Text files for each sample with HTSeq counts per transcript (tab delimited) and DESeq output for differential expression analysis performed (comma delimited). Gene identifiers are Gene Sequence Names as obtained from Wormbase version WS220.

growth_protocol: C. elegans strains were maintained at 24° on OP50 bacteria as described (Brenner 1974).

extract_protocol:
Total RNAs were purified using Trizol/chloroform extraction protocol.
Ribosomal RNA was depleted using an NEBNext rRNA Depletion kit (E6310), and libraries were prepared using an NEBNext Ultra RNA Library Prep Kit for Illumina (E7530).

treatment_protocol: Germlines were dissected from day 1 young adults.

tag: strain and genotype of analyzed germlines

value: Non-Mendelian 'red-head' hermaphrodites (germlines are genetically identical to HBR1280)


title: Germlines from 'red-head' worms (inherited only paternal chromosomes, Non-Mendelian inheritance), rep1

value: HBR1281 oxTi411[eft-3p::TdTomato::H2B::unc-54 3’UTR + Cbr-unc-119(+)] III; ddIs32[yfp::gpr-1(synthetic, CAI 1.0, artificial introns)] hermaphrodites x HBR1280 oxTi75[eft-3p::GFP::H2B::tbb-2 3’UTR + unc-18(+)] males


title: Germlines from offspring of 'red-head' worms, rep2


title: Germlines from 'red-head' worms (inherited only paternal chromosomes, Non-Mendelian inheritance), rep2

value: HBR1281 oxTi411[eft-3p::TdTomato::H2B::unc-54 3’UTR + Cbr-unc-119(+)] III; ddIs32[yfp::gpr-1(synthetic, CAI 1.0, artificial introns)] x HBR1280 oxTi75[eft-3p::GFP::H2B::tbb-2 3’UTR + unc-18(+)]


title: Control germlines from HBR1280 (inherited both maternal and paternal chromosomes, Mendelian inheritance), rep2

value: HBR1280 oxTi75[eft-3p::GFP::H2B::tbb-2 3’UTR + unc-18(+)] hermaphrodites


title: Control germlines from HBR1280 (inherited both maternal and paternal chromosomes, Mendelian inheritance), rep1


title: Sperm MNase-seq rep1

description: size-selection was performed during library construction to enrich for fragments from 100 ~ 250 bp

library_source: genomic

data_processing:
Paired-end MNase-seq reads were mapped to the C. elegans genome (Wormbase version WS220) using Bowtie with default settings.
To enrich for nucleosome protected DNA fragments, after mapping fragments with smaller than 140 bp were filtered out using bamtools 2.5.1.
Bedtools was used to scale the remaining mapped fragments bigger than 140 bp to 10 million autosomal fragments and to generate bedgraph files.
The UCSC genome browser tool bedGraphToBigWig was used to convert the bedgraph files to bigwig format.
Genome_build: WS220
Supplementary_files_format_and_content: bigWig format with mapped MNase fragments bigger than 140 bp.

molecule: genomic DNA

source_name: Mature sperm isolated from adult males

growth_protocol: CB1489 worms, which produce both hermaphrodites and males, were synchronously grown from starved L1s in S medium containing HB101 bacteria, shaking at 270 rpm at 20oC for ~62 hr. Day 1 adult males were separated from gravid hermaphrodites using 20- and 15-micron Nytex mesh: males were allowed to wiggle through the mesh; gravid hermaphrodites remained on top of the mesh. The packed males were evenly placed between two Plexiglass plates and pressed gently to squeeze sperm out. The collected sperm were filtered through 20-, 15-, 10-, and 5-micron Nytex mesh to eliminate contamination by non-sperm cells and spermatocytes.

extract_protocol:
DNA was extracted using phenol-chloroform. The degree of MNase digestion was assessed using agarose gel electrophoresis and an Agilent 2100 Bioanalyzer. DNA extracted from the mononucleosome-enriched digestions that were comparable between sperm and early embryos was used for library contruction.
Illumina sequencing libraries were constructed, using NEBNext Ultra DNA Library Prep Kit (NEB, E7370). During library construction, size selection was performed on adaptor-ligated DNA prior to amplification to remove fragments larger than 250 bp (40 μL of AMPure beads were used for 1st Bead Addition based on the manufacturers' instructions), and PCR-amplified DNA was purified using 1:1 AMPure XP beads, which removed fragments less than 100 bp.

treatment_protocol: 1-2 million sperm were digested with increasing amounts of MNase for 5 min at 37oC.

tag: strain and  genotype

tag: purity of sample

tag: mnase-digestion level

value: Heavily digested and mono-nucleosome enriched

tag: cross-linking

value: Sperm were fixed in 1% formaldehyde for 52 seconds.


title: Sperm input, rep2

description: Solubilized nucleosomes (histone-DNA complexes) were used as input.

data_processing:
Raw sequence reads from the Illumina HiSeq (50 bp single-end read sequencing for ChIP-seq) were mapped to the C. elegans genome (Wormbase version WS220) using Bowtie with default settings.
MACS2 was used to call peaks and to create bedgraph files with the following settings: -g ce --bdg --keep-dup=auto --broad --broad-cutoff=0.01 --nomodel --extsize=250.
Custom scripts were used to scale bedgraph files to 10 million total autosomal reads (to account for different X:A ratios of oocytes and embryo samples compared to sperm samples) and converted to bigwig using the bedGraphToBigWig UCSC Genome Browser tool.
Genome_build: WS220
Supplementary_files_format_and_content: bigWig containing scaled read coverage

growth_protocol: CB1489 worms, which produces both hermaphrodites and males, were synchronously grown from starved L1s in S medium containing HB101 E. coli, shaking at 270 rpm at 20oC for ~62 hr. Day 1 adult males were separated from gravid hermaphrodites using 20- and 15-micron Nytex mesh: males were allowed to wiggle through the mesh; gravid hermaphrodites remained on top of the mesh. The packed males were evenly placed between two Plexiglass plates and pressed gently to squeeze sperm out. The collected sperm were filtered through 20-, 15-, 10-, and 5-micron Nytex mesh to eliminate contamination by non-sperm cells and spermatocytes.

extract_protocol:
Sperm chromatin was crosslinked in 1% formaldehyde for 52 sec, digested with micrococcal nuclease, and sonicated with Covaris.
Libraries were prepared using MicroPlex Library Preparation kit v2 (Diagenode). Size selection was performed after library amplification using AMPure XP beads to enrich for 100-300 bp inserts.

tag: chip antibody

value: autosome ratio:X:A=0.5:1 (50% of sperm have an X, another 50% do not have an X)


title: Oocyte input, rep2

source_name: Ovulated but unfertilized oocytes collected from feminized worms

growth_protocol: Synchronized L1 larvae from CF512 were plated on 40-60 High Growth (HG) plates seeded with E. coli OP50 and grown for ~55 hr at 15oC until worms reached late L3 stage. Worms were then up-shifted to 25oC for 24-36 hr to feminize them. ~1 million feminized adults were washed from the plates, and densely packed worms were transferred to a 15 cm petri dish on ice. Worms were chopped with a razor blade for 5 min until oocytes were liberated. Oocytes and carcass fragments were poured over a 45-micron mesh. Oocytes passed through the mesh, while carcass fragments remained above the mesh. The flow-through was filtered through a 20-micron mesh to collect oocytes above the mesh, while smaller debris went through the mesh.

extract_protocol:
Oocyte chromatin was crosslinked in 2.2% formaldehyde for 5 min, sonicated with a tip sonicator, and digested with micrococcal nuclease.
Oocyte libraries were prepared with the NEBNext Ultra DNA library Prep Kit (NEB) following the manufacturers' instructions

value: autosome ratio:X:A=1:1


title: Early embryo MNase-seq rep2

source_name: Mixed stage early embryos

growth_protocol: Synchronized L1 worms were fed on HB101 bacteria for 52 hrs at 20 degree in S medium rotating at 270 rpm, then adult worms containing 5 or fewer embryos were treated with standard bleach solution to collect embryos contained in the uterus

treatment_protocol: Embryonic nuclei were isolated from early embryos using a dounce homogenizer and digested with increasing amounts of MNase at 37oC for 30 min.

value: N2 wild type

value: Embryos were cross-linked in 1.85% formaldehyde for 30 min


title: H3K4me3 oocyte ChIP, rep1

description: Solubilized nucleosomes (histone-DNA complexes) were pulled down with a specific antibody bound to magnetic beads. After reversing crosslinks, DNA was extracted using phenol-chloroform.

extract_protocol:
Oocyte chromatin was crosslinked in 2.2% formaldehyde for 5 min, sonicated with a tip sonicator, and digested with micrococcal nuclease.
Oocyte libraries were prepared with the NEBNext Ultra DNA library Prep Kit (NEB) following the manufacturers' instructions.


title: Sperm input, rep1


title: Early embryo MNase-seq rep1


title: H3K36me3 oocyte ChIP, rep1

value: H3K36me3 (Kimura MAB 13C9/CMA333, now marketed as Wako MABI0333 #300-95289)


title: Sperm MNase-seq rep2

growth_protocol: CB1489 worms, which produce both hermaphrodites and males, were synchronously grown from starved L1s in S medium containing HB101 bacteria shaking at 270 rpm at 20oC for ~62 hr. Day 1 adult males were separated from gravid hermaphrodites using 20- and 15-micron Nytex mesh: males were allowed to wiggle through the mesh; gravid hermaphrodites remained on top of the mesh. The packed males were evenly placed between two Plexiglass plates and pressed gently to squeeze sperm out. The collected sperm were filtered through 20-, 15-, 10-, and 5-micron Nytex mesh to eliminate contamination by non-sperm cells and spermatocytes.


title: H3K27me3 sperm ChIP, rep2

growth_protocol: CB1489 worms, which produce both hermaphrodites and males, were synchronously grown from starved L1s in S medium containing HB101 E. coli, shaking at 270 rpm at 20oC for ~62 hr. Day 1 adult males were separated from gravid hermaphrodites using 20- and 15-micron Nytex mesh: males were allowed to wiggle through the mesh; gravid hermaphrodites remained on top of the mesh. The packed males were evenly placed between two Plexiglass plates and pressed gently to squeeze sperm out. The collected sperm were filtered through 20-, 15-, 10-, and 5-micron Nytex mesh to eliminate contamination by non-sperm cells and spermatocytes.

value: H3K27me3 (Kimura MAB 1E7/CMA323, now marketed as Wako MABI0323 #309-95259)


title: H3K36me3 sperm ChIP, rep2


title: H3K36me3 sperm ChIP, rep1


title: H3K4me3 oocyte ChIP, rep2


title: H3K4me3 sperm ChIP, rep2


title: H3K36me3 oocyte ChIP, rep2


title: H3K27me3 oocyte ChIP, rep2


title: Early embryo input, rep2

growth_protocol: Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture at 20oC. Live embryos were cross-linked in M9 + 1.85% formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100 mM Tris-HCl pH 7.5 and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl). Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then sonicated 9 times on ice at the following settings: 30 sec; power output 3; 70% duty cycle. Cell debris was removed by centrifuging at 13,000 rpm for 15 minutes at 4ºC. The supernatant was filtered through a Millipore Ultrafree-MC 0.45 um filter unit (cat. UFC30HV0S) at 13,000 rpm, 4°C for 1 minute to remove lipids. Protein concentration was determined, and the extract was aliquoted and stored at -80ºC. For a detailed protocol see http://www.modencode.org/.
DNA was incubated with an End Repair Enzyme mix (NEB Klenow, T4 DNA polymerase and T4 PNK) to ensure blunt ends, then purified and incubated with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3' ends (a single A overhang for more efficient and directed ligation of the adaptors). After a second purification, the DNA fragments were ligated with single-end 'Homebrew' adaptors that contained an index sequence within. After ligation, the samples were purified twice using SPRI beads, allowing for a size selection step to get rid of excess adaptors. Samples were then amplified by PCR with single-end primers. Depending on the original fragmentation of DNA, samples were purified by SPRI or by separation and purification from an agarose gel.

value: autosome ratio:X:A=1:1 (vast majoriy XX hermaphrodites)


title: H3K4me3 sperm ChIP, rep1


title: H3K27me3 oocyte ChIP, rep1


title: H3K27me3 sperm ChIP, rep1


title: Early embryo input, rep1


title: H3K4me3 early embryo ChIP, rep2

description: 0.3-3 mg extract + 1% sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl). Antibody was added to each IP sample and incubated overnight at 4ºC. Immune complexes were incubated (2 hrs at 4ºC) with 50 ul of IgG dynabeads (Dyna), and washed 5 minutes with 1.5 mL of each of the following solutions: ChIP Buffer, ChIP Buffer + 1 M NaCl, ChIP Buffer + 500 mM NaCl, TEL Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and 2X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 uL elution buffer for 15 minutes at 65ºC. Samples were treated with RNAse for 30 minutes at 37ºC. Samples were treated with proteinase K at 55ºC for 1-2 hrs then transfer to 65ºC overnight to reverse crosslinks. DNA was cleaned up using Zymo kit. For a detailed protocol see http://www.modencode.org/.


title: Oocyte input, rep1


title: SJMMNORM015810_G1-14_OHCs_P7

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description: labeled outer hair cells with prestin-YFP

data_processing:
Basecalling was performed using Illumina Casava 1.7
FASTQ sequences adapter trimmed (curtadapt) and mapped to the mouse mm9 genome by a pipeline that serially  employs STAR and BWA
Mapped reads were counted with HTSEQ
Genome_build: mm9
Supplementary_files_format_and_content: count files are txt format files that contain raw read counts that map  to  transcripts for each defined gene.

organism: Mus musculus

source_name: mouse outer hair cells at P7

extract_protocol:
Total RNA was extracted from hand-picked cells using PicoPure RNA Isolation Kit (Thermo Fisher Scientific)
The total RNA was converted into cDNA and amplified using Ovation RNA-Seq System V2 (NuGEN). The amplified product was used for library construction using Ovation Rapid DR Multiplex System (NuGEN).

tag: genotype

value: prestin-YFPYFP/+ mice

tag: expression modification

value: Prestin-YFP KI


title: SJMMNORM015811_G1-Prestin-YFP_Ccl_OHC_m21_387

source_name: mouse mature outer hair cells


title: SJMMNORM015814_G1-Pvalb-Cre_Ai9_Ccl_IHC_m75_395

description: labeled inner hair cells with tdTomato

source_name: mouse mature inner hair cells

value: Pval-Cre+; Rosa26-CAG- loxP-stop-loxP-tdTomato+ mice

value: tdTomato OE


title: SJMMNORM015813_G1-Pvalb-Cre_Ai9_Ccl_IHC_m74_389

description: labeled inner hair cells with tdTomato


title: SJMMNORM015812_G1-Prestin-YFP_Ccl_OHC_f22_391


title: SJMMNORM015807_G1-Sample_254313_15_OHCs_P7


title: U2OS AS1 rep 2

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization within lumi package in R

source_name: U-2 OS

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

growth_protocol: U2OS cells were cultured in DMEM/F12 with 5% Horse serum, at 37oC, 5%CO2.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: lnc-miR100HG was knock down using Antisense aoligo or control oligo in U2OS cells,

tag: cell line

value: U-2 OS

tag: treatment

value: Antisense 1

value: lnc-miR100HG knockdown


title: SJMMNORM015809_G1-16_rHCs_P33

description: labeled converted hair cells with α9 AChR-EGFP and tdTomato

source_name: mouse converted hair cells

value: Fgfr3iCreER+; Atoh1-HA+; alpha9 AChR-EGFP+; Rosa26-CAG- loxP-stop-loxP-tdTomato+ mice

value: Atoh1-HA,  alpha9 AChR-EGFP, tdTomato OE in supporting cells


title: U2OS control rep 3

value: Control


title: U2OS AS1 rep 3


title: U2OS AS1 rep 1


title: SJMMNORM015806_G1-Sample_254311_13_rHCs_P33


title: U2OS control rep 1


title: U2OS control rep 2


title: T18 cluster rep3

city: Belvaux

first: Elisabeth

last: Letellier

address: 6, Avenue du Swing

department: Life Sciences Research Unit

country: Luxembourg

institute: University of Luxembourg

description: gene expression data from T18 sphere culture with miRNA cluster vector

hyb_protocol: 3.5 ug of labeled DNA + hybridization controls are injected into Affymetrix cartridge. Incubate with rotation at 60 rpm for 16 hr at 45°C then arrays are washed and scanned

scan_protocol: Arrays were scanned with the Affymetrix® GeneChip® Scanner 3000 following the protocol: GeneChip® Expression Wash, Stain and Scan For Cartridge Arrays P/N 702731 Rev. 4

data_processing: The data were imported, normalized and summarized to transcript cluster level using Partek GS software. We used GC RMA method with quantile normalization.

source_name: colorectal cancer T18 miRNA cluster sphere culture

label_protocol: In this procedure, the purified, sense-strand cDNA is fragmented by uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the unnatural dUTP residues and breaks the DNA strand. The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin. 5.5 μg of singlestranded cDNA is required for fragmentation and labeling

growth_protocol: Sphere cultures were maintained in serum-free medium containing growth factors

extract_protocol: Total RNA was extracted with Qiazol, using the miRNeasy extraction kit (Qiagen), following the user manual

treatment_protocol: Spheroid cultures were treated with lentiviral particles (specific miR-371~373 cluster and corresponding control particles from Biosettia) in the presence of polybrene and transduced cells were selected with Puromycin

tag: tissue

value: colorectal cancer

tag: vector

value: miR-371~373 vector (Biosettia)


title: PBMC genomic DNA ME/CFS 12

type: genomic

city: Fort Lauderdale

first: Lubov

last: Nathanson

state: Florida

address: 3321 College Ave.

department: INIM

institute: Nova Southeastern University

description: PBMC genomic DNA from ME/CFS subject 12

hyb_protocol: bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.

label: Cy3, Cy5

source_name: ME/CFS PBMC

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions

tag: gender

value: female

tag: subject id

value: ME/CFS subject 12

tag: disease state

value: Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)

tag: cell type

value: peripheral blood mononuclear cells (PBMC)


title: PBMC genomic DNA Healthy Control (HC) 5

description: PBMC genomic DNA from HC subject 5

source_name: HC PBMC

value: HC subject 5

value: Healthy Control (HC)


title: PBMC genomic DNA Healthy Control (HC) 12

description: PBMC genomic DNA from HC subject 12

value: HC subject 12


title: PBMC genomic DNA Healthy Control (HC) 7

description: PBMC genomic DNA from HC subject 7

value: HC subject 7


title: PBMC genomic DNA Healthy Control (HC) 10

description: PBMC genomic DNA from HC subject 10

value: HC subject 10


title: PBMC genomic DNA Healthy Control (HC) 3

description: PBMC genomic DNA from HC subject 3

value: HC subject 3


title: PBMC genomic DNA Healthy Control (HC) 8

description: PBMC genomic DNA from HC subject 8

value: HC subject 8


title: PBMC genomic DNA ME/CFS 11

description: PBMC genomic DNA from ME/CFS subject 11

value: ME/CFS subject 11


title: PBMC genomic DNA Healthy Control (HC) 11

description: PBMC genomic DNA from HC subject 11

value: HC subject 11


title: PBMC genomic DNA ME/CFS 4

description: PBMC genomic DNA from ME/CFS subject 4

value: ME/CFS subject 4


title: PBMC genomic DNA ME/CFS 8

description: PBMC genomic DNA from ME/CFS subject 8

value: ME/CFS subject 8


title: PBMC genomic DNA ME/CFS 6

description: PBMC genomic DNA from ME/CFS subject 6

value: ME/CFS subject 6


title: sRNA mop1-1 homozygous maize ears, (3-5 cm) rep 4

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description:
small RNA
Text containing distinct small RNAs with their raw abundance after removing the adapter sequences

data_processing:
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 18 and 31 nucleotides. small RNA reads were mapped to the maize genome (version AGPv2).
Genome_build: Maize Genome (version AGPv2)
Supplementary_files_format_and_content: Tag count file

organism: Zea mays

source_name: immature ears

extract_protocol: sRNA library constructed from immature ears (3-5 cm in length) of Maize mop1-1 homozygous mutant. the small RNA libraries were generated as described by Lu et al. (Methods 2007, 43:110), followed by sequencing with Illumina's SBS method. The adapter sequences were removed, and the abundance of each distinct small RNA was determined.

value: rdr2/mop1 homozygous mutant


title: PBMC genomic DNA ME/CFS 7

description: PBMC genomic DNA from ME/CFS subject 7

value: female

value: ME/CFS subject 7


title: PBMC genomic DNA ME/CFS 13

description: PBMC genomic DNA from ME/CFS subject 13

value: ME/CFS subject 13

value: Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)


title: PBMC genomic DNA ME/CFS 1

description: PBMC genomic DNA from ME/CFS subject 1

value: ME/CFS subject 1

value: peripheral blood mononuclear cells (PBMC)


title: PBMC genomic DNA ME/CFS 5

description: PBMC genomic DNA from ME/CFS subject 5

value: ME/CFS subject 5


title: PBMC genomic DNA Healthy Control (HC) 6

description: PBMC genomic DNA from HC subject 6

value: HC subject 6

value: Healthy Control (HC)


title: sRNA mop1-1 homozygous maize ears, (3-5 cm) rep 3


title: PBMC genomic DNA ME/CFS 2

description: PBMC genomic DNA from ME/CFS subject 2

value: ME/CFS subject 2


title: PBMC genomic DNA Healthy Control (HC) 4

description: PBMC genomic DNA from HC subject 4

value: HC subject 4


title: PBMC genomic DNA Healthy Control (HC) 2

description: PBMC genomic DNA from HC subject 2

value: HC subject 2


title: PBMC genomic DNA Healthy Control (HC) 9

description: PBMC genomic DNA from HC subject 9

value: HC subject 9


title: PBMC genomic DNA Healthy Control (HC) 1

description: PBMC genomic DNA from HC subject 1

value: HC subject 1


title: sRNA mop1-1 homozygous maize ears, (3-5 cm) rep 2


title: PBMC genomic DNA ME/CFS 9

description: PBMC genomic DNA from ME/CFS subject 9

value: ME/CFS subject 9


title: T18 cluster rep1

value: colorectal cancer

value: miR-371~373 vector (Biosettia)


title: sRNA mop1-1 homozygous maize ears, (3-5 cm) rep 1

value: rdr2/mop1 homozygous mutant


title: PBMC genomic DNA ME/CFS 10

description: PBMC genomic DNA from ME/CFS subject 10

value: female

value: ME/CFS subject 10


title: T18 cluster rep2


title: T18 ctrl rep3

description: gene expression data from T18 sphere culture with control vector

source_name: colorectal cancer T18 control sphere culture

value: Control vector (Biosettia)


title: PBMC genomic DNA ME/CFS 3

description: PBMC genomic DNA from ME/CFS subject 3

value: ME/CFS subject 3

value: Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)


title: SW620 cluster rep1

description: gene expression data from SW620 sphere culture with miRNA cluster vector

source_name: colorectal cancer SW620 miRNA cluster sphere culture

value: colorectal cancer lymph node metastasis


title: T18 ctrl rep1


title: SW620 cluster rep3


title: SW620 ctrl rep3

description: gene expression data from SW620 sphere culture with control vector

source_name: colorectal cancer SW620 control sphere culture


title: Run1865_132

city: Ann Arbor

first: Rajasree

last: Menon

state: Michigan

address: 4544E, MSRB2, Catherine Street, University of Michigan

department: Department of Computational  Medicine and Bioinformatics

institute: University of Michigan

data_processing:
The quality of the fastq files from the sequencer were first checked using FastQC (v0.11.4).
Sequence aligned using Star
Next, using the tools embedded in Picard tools (picard-tools-1.115) and the DropSeq analysis pipeline developed by the McCarroll lab (http://mccarrolllab.com/dropseq/), the fastq files were processed and the data matrix table containing the gene expression of the barcoded cells was generated. Individual cells were labeled with barcodes, and transcripts within each cell were tagged with distinct UMIs (Unique Molecular Identifiers) in order to determine absolute transcript abundance.
Genome_build: GRCh38
Supplementary_files_format_and_content: Data matrix table is in text format

source_name: Fetal kidney

extract_protocol:
All tissues were shipped overnight in Belzer’s solution at 4 degrees Celsius and were processed immediately upon arrival to the laboratory, as follows. One kidney was dissected in ice-cold PBS and finely minced in a petri dish on ice using razor blades. About 20 mg of tissue were added to 1 ml of cold active protease solution (PBS, 10 mg of Bacillus Licheniformis protease [Sigma, #P5380], 5 mM CaCl2, 20 U DNAse I [Roche, #4716728001]). The tissue was incubated in a 2 ml reaction tube for 15-20 min on a slow moving shaker (nutator) in a coldroom at 4°C with repeated trituration steps for 20 seconds every 5 minutes. Single cell dissociation was confirmed with a microscope. The dissociation was stopped with 1 ml ice cold PBS supplemented with 10% fetal bovine serum (FBS). Afterwards the cells were immediately pelleted at 300x g for 5 min at 4°C. Subsequently, the supernatant was discarded and cells were suspended in 2 ml PBS/10%FBS and pelleted again at 300x g for 5 min at 4°C. Then cells were suspended in PBS/0.01%BSA and pelleted again (300x g for 5 min at 4°C), suspended in 1 ml PBS/0.01%BSA, and passed through a 30 µM filter mesh (Miltenyi MACS smart strainer). Viability was then investigated with the Trypan-blue exclusion test and cell concentration was determined with a hemocytometer and adjusted to 200,000 cells/ml for Drop-seq.
Uniformly dispersed 1 nl-sized droplets were generated using self-built polydimethylsiloxane (PDMS) microfluidic co-flow devices on the basis of the AutoCAD design provided by the McCarroll group. The devices were treated with a water repellant solution (Aquapel) to create a hydrophobic channel surface. Drop-Seq runs followed closely the procedure published by Macosko et al. (Online Dropseq protocol v. 3.1 http://mccarrolllab.com/dropseq/). Barcoded beads (ChemGenes Corp., Wilmington, MA), suspended in lysis buffer, were co-flown with a single cell suspension and a droplet generation mineral oil (QX200, Bio-Rad Laboratories). Resulting droplets were collected in a 50 ml tube and immediately disrupted after adding 30 ml high-salt saline-sodium citrate buffer (6xSSC) and 1 ml perfluorooctanol. Subsequently, captured mRNA’s were reverse transcribed for 2 hours using 2,000 U of the Maxima H Minus Reverse Transcriptase (ThermoFisher) followed by an exonuclease treatment for 45 minutes to remove unextended primers. After two washing steps with 6xSSC buffer about 70,000 remaining beads (60% of input beads) were aliquoted (5,000 beads per 50 µl reaction) and PCR-amplified (5 cycles at 65˚C and 12 cycles at 67˚C annealing temperature). Aliquots of each PCR reaction were pooled and double-purified using 0.5x volume of Agencourt AMPure XP beads (# A63881, Beckman Coulter) and finally eluted in 10 µl EB buffer. Quality and quantity of the amplified cDNAs were analyzed on a BioAnalyzer High Sensitivity DNA Chip (Agilent Technologies, Santa Clara, CA). About 600 pg cDNA was fragmented and amplified (17 cycles) to generate a next-generation sequencing library by using the Nextera XT DNA sample preparation kit (Illumina).
The libraries were purified, quantified (Agilent High sensitivity DNA chip), and then sequenced (paired end 26x115 bases) on the Illumina HiSeq2500 platform. Custom primer (5’-GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC-3’) was used for the first sequence read to identify all different cell barcodes und unique molecular identifier (UMI) sequences.

tag: fetal age

value: 132 days

value: kidney


title: Run1865_87

value: 87 days


title: SW620 cluster rep2


title: SW620 ctrl rep1


title: IgG-immunoprecipitated RNA in day 6-primed T cells (replicate 2)

city: Guangzhou

first: Di

last: Huang

address: 107 Yanjiang West Road

country: China

institute: Sun-Yat-sen Memorial Hospital

description:
The mRNA and lncRNA profiles following immunoprecipitation with anti-IgG antibody in T cells primed by MDA-MB-231-lysate pulsed DCs for 6 days.
coprecipitated RNA

hyb_protocol: The labeled RNAs were mixed and hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC)

scan_protocol: Agilent Microarray Scanner (Agilent p/n G2565BA)

data_processing:
Quantile normalization across multiple arrays, log 2 transformation of expression levels, and images were analyzed with Agilent Feature Extraction Software
High quality expression values was selected for analysis, then differentially expressed genes were identified.

label_protocol: we label the RNAs with Cy3.

growth_protocol: T cells were isolated from peripheral blood of healthy donors and cultured in growth medium (RPMI-1640 with 10% human AB serum and IL-2 25 U/ml)

extract_protocol: RNA following immunoprecipitation with anti-p65, anti-IκBα and IgG antibodies was extracted from 2 replicates.

treatment_protocol: Mononuclear cells were obtained from peripheral blood of three HLA-A2+ healthy donors and cultured for 14 d in serum-free X-VIVO 20 medium (BioWhittaker, Walkersville, Maryland) with human GM-CSF (50 ng/ml; Peprotech) and IL-4 (20 ng/ml; Peprotech). Non-adherent DCs were enriched by depletion of contaminating T and B lymphocytes and pulsed for 20 h with lysates (200 μg protein/1 × 106 cells/ml) from MDA-MB-231 (HLA-A2+) that were lysed by 5 freeze/thaw cycles. T cells were incubated for 13 d in RPMI-1640 with 10% human AB serum (PromoCell) and IL-2 (25 U/ml; Peprotech) followed by incubation in the same medium with antigen-specific DCs (5:1) for 6 days. T cells were retrieved from the cocultures at day 6.

tag: donor

value: T cells

tag: rip antibody

value: control rabbit/mouse IgG (Cell Signaling Technology, Cat. No.2729/5415)


title: IκBα-immunoprecipitated RNA in day 6-primed T cells (replicate 1)

description:
The mRNA and lncRNA profiles following immunoprecipitation with anti-IκBαantibody in T cells primed by MDA-MB-231-lysate pulsed DCs for 6 days.
coprecipitated RNA

value: human IκBα (Cell Signaling Technology , Cat.No.#4814)


title: SW620 ctrl rep2


title: IκBα-immunoprecipitated RNA in day 6-primed T cells (replicate 2)


title: T-PLL_5

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

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

scan_protocol: The arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 with G7 update .

data_processing:
Images were analyzed using the Affymetrix Genotyping Console (SNP6.0 arrays) or the Affymetrix Chromosome Analysis Suite
[primary data description] CNV and LOH data from enriched T-PLL samples

source_name: Peripheral blood mononuclear cells

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was extracted from 1-2 x 10^7 enriched tumor cells per sample using the QIAamp DNA blood midi kit. DNA concentrations were measured with a Qubit Fluorometer 2.0. Quality assessment was performed with the Agilent Bioanalyzer 2100.

treatment_protocol: Gradient density centrifugation was followed by CD3+ enrichment using MACS (if CD4+ > 90%) or sorting of CD3+ and CD4+ tumor cells.

value: T-cell prolymphocytic leukemia

value: PBMCs

tag: cell type (sorted)

value: sorted CD3 pos CD4 pos T cells


title: p65-immunoprecipitated RNA in day 6-primed T cells (replicate 1)

description:
The mRNA and lncRNA profiles following immunoprecipitation with anti-p65antibody in T cells primed by MDA-MB-231-lysate pulsed DCs for 6 days.
coprecipitated RNA

value: human p65 (Cell Signaling Technology , Cat.No.8242)


title: T18 ctrl rep2

value: colorectal cancer


title: IVHSC_TP25

city: Beijing

first: Ji

last: Dong

address: Yiheyuan 5#

institute: Peking University

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Raw reads were first organized by specific cell barcode information attached in the read 2 of pair-ended reads. Second, unique molecular identifier (UMI) information were added into the corresponding read 1 which were then trimmed to remove template switch oligo (TSO) sequence and polyA tails. Subsequently, we also removed reads with adapter contaminants and low-quality bases (N>10%).
Third, the cleaned reads were aligned to the mm10 mouse transcriptome (UCSC) using Tophat (version 2.0.12) (Trapnell et al., 2009). Fourth, uniquely mapped reads were counted using htseq-count of the HTSeq package and grouped by cell-specific barcode (Anders et al., 2014). Based on UMI information, duplicated transcripts of each gene were removed. Finally, within a given cell, distinct UMIs of each gene were counted as the transcript number of that gene.
The expression levels TPM, where TPM (transcript-per-million) was calculated by the number of UMIs of each gene divided by all the number of UMIs of a given cell, then multiplying by 1,000,000.
Genome_build: mm10
Supplementary_files_format_and_content: txt files which include theTPM values of RefSeq genes.

molecule: polyA RNA

source_name: IVHSC

extract_protocol:
A modified STRT-seq protocol was applied for single-cell RNA-seq. Briefly, a single cell was picked into the lysis buffer by mouth pippete. The reverse transcription reaction was performed with 24 oligo (dT) primer anchored with the 8 bp cell specific barcode, and also with 8 bp unique molecular identifiers (UMIs).
After the first-strand reaction, the cDNA was amplified by 17 cycles. Then the amplified cDNA of the cells of the same fetal sample were pooled together to proceed the following steps. Biotinylated pre-indexed primer was used to amplify the PCR product by additional 4 cycles to introduce biotin tags to the 3’ end of the amplified cDNA. About 300 ng DNA was sheared to around 300 bp by Covaris S2 and the 3’ ternimal of the DNA was captured by Dynabeads® MyOne™ Streptavidin C1 beads (Thermo Fisher). RNA seq library was constructed using Kapa Hyper Prep Kit (Kapabiosystems) and subjected to 150 bp paired-end sequencing on illumina HiSeq 4000 platform (sequenced by Novogene).

value: HSC

tag: culture system

value: in vitro

tag: sample type

value: control HSCs and TGFB1-treated HSCs


title: IVHSC_TP24


title: IVHSC_TP26

value: control HSCs


title: T cells from donor 2 activated by breast tumor-specific DCs pulsed by MDA-MB-231 lysates for 6 days

description:
mRNA and lncRNA profiles
This sample was from donor 2 and cocultured with DCs pulsed by MDA-MB-231 lysates for 6 days.

hyb_protocol: The labeled RNAs were mixed and hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC).

scan_protocol: Slides were scanned with LuxScan 10K Microarray Scanner(CapitalBio, Beijing, China)

data_processing:
Quantile normalization across multiple arrays, log 2 transformation of expression levels, and images were analyzed with GenePix Pro 6.0 software(Axon Instruments, Foster City, CA, USA)
High quality expression values was selected for analysis, then differentially expressed genes were identified.

label_protocol: not provided

extract_protocol: Total RNA was extracted from 3 donors with 3 indicated treatments (5 x 10^6 cells for each sample) using the TRIzol Reagent (Cat#A33251, Thermo Fisher).

treatment_protocol: Mononuclear cells were obtained from peripheral blood of three HLA-A2+ healthy donors and cultured for 14 d in serum-free X-VIVO 20 medium (BioWhittaker, Walkersville, Maryland) with human GM-CSF (50 ng/ml; Peprotech) and IL-4 (20 ng/ml; Peprotech). Non-adherent DCs were enriched by depletion of contaminating T and B lymphocytes and pulsed for 20 h with lysates (200 μg protein/1 × 10^6 cells/ml) from MDA-MB-231 (HLA-A2+) that were lysed by 5 freeze/thaw cycles. T cells were incubated for 13 d in RPMI-1640 with 10% human AB serum (PromoCell) and IL-2 (25 U/ml; Peprotech) followed by incubation in the same medium with antigen-specific DCs (5:1) for 6 days. T cells were retrieved from the cocultures at day 0, day 1 and day6.


title: T-PLL_35

value: MACS  enriched CD3 pos T cells


title: T cells from donor 3 activated by breast tumor-specific DCs pulsed by MDA-MB-231 lysates for 1 day

description:
mRNA and lncRNA profiles
This sample was from donor 3 and cocultured with DCs pulsed by MDA-MB-231 lysates for 1 day.


title: IgG-immunoprecipitated RNA in day 6-primed T cells (replicate 1)


title: T cells from donor 1 activated by breast tumor-specific DCs pulsed by MDA-MB-231 lysates for 6 days

description:
mRNA and lncRNA profiles
This sample was from donor 1 and cocultured with DCs pulsed by MDA-MB-231 lysates for 6 days.


title: T-PLL_36


title: T cells from donor 3 without activation

description:
mRNA and lncRNA profiles
This sample was from donor 3 and untreated

source_name: T cells from donor 3 without activation


title: T cells from donor 2 without activation

description:
mRNA and lncRNA profiles
This sample was from donor 2 and untreated

source_name: T cells from donor 2 without activation


title: p65-immunoprecipitated RNA in day 6-primed T cells (replicate 2)


title: T-PLL_3


title: T cells from donor 1 activated by breast tumor-specific DCs pulsed by MDA-MB-231 lysates for 1 day

description:
mRNA and lncRNA profiles
This sample was from donor 1 and cocultured with DCs pulsed by MDA-MB-231 lysates for 1 day.


title: T cells from donor 1 without activation

description:
mRNA and lncRNA profiles
This sample was from donor 1 and untreated

source_name: T cells from donor 1 without activation


title: T cells from donor 2 activated by breast tumor-specific DCs pulsed by MDA-MB-231 lysates for 1 day

description:
mRNA and lncRNA profiles
This sample was from donor 2 and cocultured with DCs pulsed by MDA-MB-231 lysates for 1 day.


title: T-PLL_11


title: T-PLL_33


title: Patient2_Tumor6_Specimen31

status: Public on Jul 22 2018

city: Chiba

first: Hirokazu

last: Usui

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Department of Reproductive Medicine

country: Japan

institute: Graduate School of Medicine, Chiba University

hyb_protocol: DNA was amplified, fragmented and hybridized to each BeadChip arrays according to the manufacturer's instructions.

scan_protocol: The BeadChip array was scanned using the iScan (Illumina)

data_processing: Data were processed using GenomeStudio V2011.1

source_name: Ovarian teratoma

label_protocol: standard Illumina protocol

extract_protocol: Genomic DNA was extracted from MCT tissues using the Qiagen DNA Mini Kit.

value: female

value: ovarian teratoma

tag: devlopment stage

value: adult


title: T-PLL_7


title: Patient8_Tumor12_Specimen32


title: Patient2_Tumor4_Specimen30


title: Patient1_Tumor2_Specimen29


title: Patient14_Tumor20_Specimen21


title: T-PLL_38


title: T-PLL_34


title: Patient22_Tumor30_Specimen25


title: T cells from donor 3 activated by breast tumor-specific DCs pulsed by MDA-MB-231 lysates for 6 days

description:
mRNA and lncRNA profiles
This sample was from donor 3 and cocultured with DCs pulsed by MDA-MB-231 lysates for 6 days.


title: Patient12_Tumor18_Specimen20


title: T-PLL_2


title: T-PLL_1


title: Patient23_Tumor31_Specimen38


title: Patient1_Tumor1_Specimen28


title: Patient17_Tumor24_Specimen22


title: Patient18_Tumor25_Specimen37


title: Patient20_Tumor28_Specimen24


title: Patient15_Tumor22_Specimen36


title: Patient7_Tumor11_Specimen19


title: T-PLL_10


title: T-PLL_4


title: R1_WT_ES_Dendra2

city: Cambridge

first: Charles

last: Li

state: MA

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

data_processing:
Reads were aligned to the mm9 mouse reference genome using Bowtie  version 1.2.2 with parameters  -p 4 --best -k 1 -m 1 --sam -l 40.
Genome_build: mm9
Supplementary_files_format_and_content: WIG files represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: Embryonic stem cell

growth_protocol: R1 mouse embryonic stem (ES) cells were cultured in serum-free 2i media (1:1 of DMEM/F-12 and Neurobasal media, supplemented with 1x N-2 supplement, 1x B-27 supplement, 100 U/ml PenStrep, 3 μg/ml AlbuMAX II, 1x MEM NEAA, 1mM Sodium pyruvate, 1mM L-glutamine (all from Thermo Fisher Scientific), 0.1 μM 2-Mercaptoethanol (Sigma- Aldrich), 1mM MEK inhibitor (PD0325910, Stemgent), 3mM GSK3β inhibitor (CHIR99021, Stemgent) and 100 U/ml LIF (Leukemia Inhibitory Factor, EMD Millipore) without feeder cells). Prior to cell culturing, all the flasks or petri dishes were incubated in 37°C for more than 5 hours with 5 μg/ml poly-L-ornithine (PLO, Sigma) in 1x PBS buffer, followed by 5 μg/ml Laminin (VWR) in 1x PBS buffer with >5 hours incubation in 37°C. The cells were grown in 37°C incubator maintaining 5% CO2 in a water-saturated atmosphere. Cell culture media were exchanged every 24 hours.

extract_protocol:
Cells were crosslinked on plates with 1% formaldehyde in media for 15 minutes at room temperature. 50 million cells were used per ChIP reaction. Whole cell extracts were sonicated on a QSonica Q700 tip sonicator to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.
Library construction was performed by the Whitehead Institute Genome Technology Core using the Swift Biosciences Accel-NGS 2S Plus DNA Library Kit according to manufacturer's protocol.

treatment_protocol: Prior to EpiLC differentiation induction, R1 ES cells were cultured in 2i media at least for two passages from frozen stocks. After washing with PBS and sieving with a 70μm cell strainer (Corning Falcon), ES cells were transferred to either 6-well plates for qRT-PCR or glass-bottom dishes for fluorescence imaging, in N2B27-based medium supplemented with 1% KOSR (Invitrogen) and 12 mg/ml bFGF (Peprotech). Dishes and plates were coated with 5 μg/mL Fibronectin.

value: Embryonic stem cell

tag: genotype

value: WT

tag: state

value: ES

tag: chip antibody

value: Dendra2 (Origene, TA180094, lot W003)


title: Patient8_Tumor12_Specimen33


title: R1_WT_ES_RPB1

tag: cell line


title: Patient13_Tumor19_Specimen35

tag: tissue


title: R1_WT_ES_H3K27ac


title: aorta_orch_XX_rep2

city: Lexington

first: Eric

middle: M

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

description: Gene expression data from the abdominal aorta of orchiectomized, XX male mice

hyb_protocol: Labeled samples were hybridized to Mouse Transcriptome1.0 Array (Affymetrix) using standard protocol

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 7G scanner

data_processing: The data were analyzed with Partek software using the Robust Multi-Array (RMA) algorithm with default analysis settings

source_name: abdominal aorta, orch, XX

label_protocol: 100ng total RNA was converted to fragmented biotinylated cDNA using the standard WT Plus protocol (Affymetrix)

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

tag: phenotypic sex

value: male

tag: sex chromosome complement

value: XX

tag: surgery

value: orchiectomy

tag: strain background

tag: rin


title: Patient6_Tumor10_Specimen18

tag: gender


title: aorta_orch_XX_rep4


title: aorta_orch_XX_rep1


title: R1_WT_ES_Input

tag: cell type


title: aorta_orch_XX_rep3


title: aorta_sham_XX_rep4

description: Gene expression data from the abdominal aorta of sham, XX male mice

source_name: abdominal aorta, sham, XX

value: sham


title: R1_DRHM_EpiLC_Dendra2

value: Dendra2-RPB1, Halo-MED19

value: EpiLC


title: Patient3_Tumor7_Specimen15


title: aorta_sham_XX_rep3


title: Patient5_Tumor9_Specimen17


title: R1_DRHM_EpiLC_H3K27ac


title: R1_DRHM_EpiLC_Input


title: Patient4_Tumor8_Specimen16


title: R1_WT_EpiLC_RPB1


title: R1_WT_EpiLC_Dendra2


title: aorta_sham_XX_rep2


title: aorta_sham_XX_rep1


title: R1_DRHM_EpiLC_RPB1


title: R1_WT_EpiLC_H3K27ac


title: Patient16_Tumor23_Specimen7


title: aorta_orch_XY_rep3

description: Gene expression data from the abdominal aorta of orchiectomized XY male mice

source_name: abdominal aorta, orch, XY

value: XY


title: aorta_orch_XY_rep4


title: aorta_sham_XY_rep5

description: Gene expression data from the abdominal aorta of sham, XY male mice

source_name: abdominal aorta, sham, XY


title: Patient21_Tumor29_Specimen11


title: Patient2_Tumor3_Specimen1


title: Patient2_Tumor5_Specimen14


title: R1_DRHM_ES_Dendra2


title: R1_DRHM_ES_RPB1


title: R1_DRHM_ES_H3K27ac


title: Patient19_Tumor26_Specimen8


title: Patient15_Tumor21_Specimen6


title: Patient10_Tumor15_Specimen3


title: Patient11_Tumor17_Specimen5


title: Patient20_Tumor27_Specimen9


title: Rich SMRT-Cappable-seq_RSII_control library

city: Ipswich

first: Bo

last: Yan

address: County Road

institute: New England Biolabs

description:
control_161222
Rich SMRT-Cappable-seq sequenced using RSII, control library

data_processing:
Customized scripts (https://github.com/elitaone/SMRT-cappable-seq) were used for trimming adaptor sequence
The trimmed reads were mapped to the E. coli genome using BLASR -clipping soft
The number of reads starting and ending at any position were counted using a customized script (https://github.com/elitaone/SMRT-cappable-seq)
Genome_build: NC_000913.3
Supplementary_files_format_and_content: tab-delimited text files include the number of reads at each TSS and TTS for each Sample

organism: Escherichia coli

source_name: MG1655_rich_PacBio RS II

growth_protocol: E. coli cells were grown under M9 minimal and Rich condition to logarithmic phase and harvested

extract_protocol: We used a customized library construction protocol for SMRT-Cappable-seq

treatment_protocol: The RNA was extracted using RNAeasy Midi Kit (Qiagen) with lysosome pretreatment

tag: strain

value: wild type

tag: growth phase

value: log phase

tag: growth media

value: rich condition


title: M9 SMRT-Cappable-seq_Sequel_replicate 2_enrich library

description:
180518_sample2
M9 SMRT-Cappable-seq sequenced using Sequel, replicate 2, enrich library

source_name: MG1655_minimal_PacBio Sequel

value: M9 minimal


title: aorta_sham_XY_rep1


title: aorta_sham_XY_rep4


title: Rich SMRT-Cappable-seq_RSII_enrich library

description:
enrich_161222
Rich SMRT-Cappable-seq sequenced using RSII, enrich library


title: M9 SMRT-Cappable-seq_Sequel_replicate 1_enrich library

description:
180518_sample1
M9 SMRT-Cappable-seq sequenced using Sequel, replicate 1, enrich library


title: aorta_sham_XY_rep3


title: R1_WT_EpiLC_Input


title: M9 SMRT-Cappable-seq_RSII_enrich library

description:
enrich_161020
M9 SMRT-Cappable-seq sequenced using RSII, enrich library

source_name: MG1655_minimal_PacBio RS II


title: M9 SMRT-Cappable-seq_RSII_control library

description:
control_161020
M9 SMRT-Cappable-seq sequenced using RSII, control library


title: aorta_sham_XY_rep2


title: Input_rep2

status: Public on Jul 21 2018

city: Philadelphia

first: Song-Jun

last: Xu

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Sequences were aligned using Bowtie v2.1.0  allowing for ≤2 mismatches to the reference in 50bp. Uniquely aligned reads were confirmed for H3K36me3 ChIP sequencing and used for subsequent analysis. Peak calling was performed using SICER with FDR < 0.05 as cutoff
For RNA-seq data,sequences were aligned using STAR-2.5.2a. Raw gene read counts with default parameters were used to compute fold changes and significance of expression differences using DESeq.Alternative splicing was quantified using the percent spliced in (PSI) metric using Multivariate Analysis of Transcript Splicing(rMATS, v3.2.4).
Bigwig files were generated using deepTools/bamCoverage --normalizeUsingRPKM
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: Nucleus Accumbens

extract_protocol:
Chromatin was clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  RNA was isolated from mouse nucleus accumbens for mRNA sequencing by following illumina RNA seq kit protocol.
Library was prepared following illumina protocol.
All RNA samples were pooled and sequenced in the same lane. All ChIP-seq were pooled and sequenced in the same lane.

value: NAc

tag: development stage

value: 6-8 weeks

tag: antibody


title: anti-H3K36me3, Abcam, ab9050 ChIP-s3eq_rep2

value: anti-H3K36me3, Abcam, ab9050


title: Input_rep1


title: anti-H3K36me3, Abcam, ab9050 ChIP-s3eq_rep1


title: Input_rep3


title: aorta_orch_XY_rep2


title: anti-H3K36me3, Abcam, ab9050 ChIP-seq_rep2


title: anti-H3K36me3, Abcam, ab9050 ChIP-seq_rep1


title: Patient20_Tumor28_Specimen23

value: female

value: ovarian teratoma

tag: devlopment stage

value: adult


title: T-PLL_8

tag: disease state

value: T-cell prolymphocytic leukemia

value: PBMCs

tag: cell type (sorted)

value: sorted CD3 pos CD4 pos T cells


title: Patient20_Tumor27_Specimen10


title: R1_DRHM_ES_Input

tag: cell line

value: Embryonic stem cell

tag: genotype

tag: state

value: ES

tag: chip antibody


title: Patient25_Tumor33_Specimen27

data_processing: Data were processed using GenomeStudio 2.0

tag: tissue


title: aorta_orch_XY_rep1

tag: phenotypic sex

value: male

tag: sex chromosome complement

tag: surgery

value: orchiectomy

tag: strain background


title: Patient10_Tumor16_Specimen4

tag: gender


title: Patient9_Tumor14_Specimen34


title: BY3

city: Hangzhou

first: Huizeng

last: Sun

state: Zhejiang

address: 866 Yuhangtang Road

department: College of Animal Sciences

institute: Zhejiang University

data_processing:
All the reads were demultiplexed according to their index sequences using CASAVA version 1.8 (Illumina)
The small RNAs sequencing reads with good quality were subjected to 3’ adaptor sequence trimming by sRNAbench.
The miRNA expression (CPM) were caculated by: miRNA reads number/total mapped reads per library*1000000
Genome_build: Baylor Btau 4.6.1
Supplementary_files_format_and_content: Tab-delimited text files include RPM values for each Sample

organism: Bos taurus

source_name: mammary gland

extract_protocol:
Total RNA was isolated from ~100 mg tissue using the mirVana miRNA Isolation Kit (Ambion® , Life Technologies, Carlsbad, CA, USA) following manufacturer’s protocol. The RNA concentration was determined using a Qubit 2.0 Fluorometer (Life Technologies). The quality of RNA was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA) with the RNA 6000 NanoLabchip Kit. RNA samples with the RNA integrity number (RIN) more than 7.0 were used for small RNA library construction and quantitative real-time PCR validation.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: diet

value: corn stover

value: mammary gland


title: BY1


title: LY5

source_name: liver

value: liver


title: BY4


title: BM1

value: alfalfa hay


title: BD6

value: rice straw


title: LY6


title: LY1


title: BM5


title: LM6


title: BD5


title: BD3


title: BD1


title: LY2


title: BD4


title: BY5


title: LM5


title: BM3


title: LY3


title: BD2


title: BY2


title: LY4


title: BM4


title: BY6


title: Patient24_Tumor32_Specimen26


title: BM6


title: BM2


title: Patient9_Tumor13_Specimen2


title: Patient27_Tumor35_Specimen13


title: Patient26_Tumor34_Specimen12


title: LM2


title: LM4


title: LM3


title: KY2

source_name: jejunum epithelium

value: jejunum epithelium


title: KY1


title: KM4


title: KD6


title: LD2


title: KM5


title: LD4


title: KD1


title: KM3


title: LD5


title: LD1


title: LD3


title: KD3


title: KD2


title: KY5


title: KM2


title: KM1


title: KD5


title: KY3


title: KM6


title: LM1


title: KY4


title: LD6


title: KD4


title: IY6

source_name: duodenum epithelium

value: duodenum epithelium


title: IY5


title: IY3


title: KY6


title: IY1


title: IM6


title: IY2


title: IM5


title: IM2


title: ID5


title: ID6


title: IM4


title: ID2


title: ID4


title: SY2

source_name: rumen epithelium

value: rumen epithelium


title: SY3


title: SM4


title: SY5


title: SY1


title: ID1


title: SY6


title: SY4


title: SM2


title: SM3


title: SM5


title: SM1


title: IY4


title: IM3


title: IM1


title: ID3


title: SD5


title: SD3


title: SD1


title: SD2


title: SD4


title: SM6


title: RT_1

city: Buffalo

first: Mira

last: Edgerton

state: New York

address: 3435 Main St

department: Oral Biology

institute: University at Buffalo

description:
RTflow_v_37Static.RNAseqgene_exp.diff
37flow_v_RTflow.RNAseqgene_exp.diff

data_processing:
Base-calling was done using Illumina’s bcl2fastq version 2.17.1.14 using default parameters
Alignment was done using TopHat2 version 2.1.1 using default parameters
Filtering sequence quality assessment was done using FastQC version 0.11.5
Generation of normalized abundance measurements was done using Cufflinks version 2.2.1 using default parameters
Genome_build: SC5314
Supplementary_files_format_and_content: tab-delimited diff files generated using CuffDiff

organism: Candida albicans

source_name: 23 CFlow Biofilm

growth_protocol: Candida cells were grown on an ibidi ibitreat flow chamber for 24 h at 23°C or 37°C under flow (3.3 ml/min;0.8 dynes/cm2), or on an ibidi ibitreat 35mm µ-Dish at 37°C with gentle agitation (80 rpm on shaker).

extract_protocol:
The bottom of the slide or dish was cut with a razor blade, removed, and placed in 1 × PBS. The cells were removed by sonication (power cycle 4, 20% pulse rate for 1 m) and collected by centrifugation (2300 × g for 5 min). Cells were re-suspended in 1ml Trizol and vortexed (4 cycle, 6m/s) with 0.45µM glass beads using a FastPrep-24 5g Homogenizer (MP Biomedicals, Santa Ana, CA). 200µl of chloroform was added, mixed vigorously for 15 sec and kept for 2 min at room temperature. Lysed cells were centrifuged at 21000 × g for 10 min at 4°C to separate the upper clear aqueous layer and mixed with 0.5 volume of 100% ethanol. Total RNA was purified using RNAeasy minikit from Qiagen (Hilden, Germany). The RNA samples were stored at -80°C.
RNA libraries were prepared using the Illumina TruSeq RNA sample preparation kit.

tag: strain

tag: media

value: YPD

tag: flow;shear force

value: 3.3ml/min; 0.8 dynes/cm2

tag: growth surface

value: channel slide

tag: growth time


title: RT_3


title: Control_1

description:
37flow_v_37static.RNAseqgene_exp.diff
RTflow_v_37Static.RNAseqgene_exp.diff

source_name: 37 CStatic Biofilm

value: ibidi ibitreat u-Dish


title: 37_1

description:
37flow_v_37static.RNAseqgene_exp.diff
37flow_v_RTflow.RNAseqgene_exp.diff

source_name: 37 CFlow Biofilm

value: YPD (1% (w/v) yeast extract, 2 % (w/v) bacto peptone, and 2% (w/v) glucose)

value: ibidi ibitreat µ-Slide I0.8 channel slide


title: Cytoplasmic RNA-seq rep3

value: NAc

tag: development stage

value: 6-8 weeks


title: Cytoplasmic RNA-seq rep2


title: 37_3


title: Nuclear RNA-seq rep3


title: Cytoplasmic RNA-seq rep1


title: SD6


title: Nuclear RNA-seq rep2


title: Nuclear RNA-seq rep1


title: Control_2


title: Total RNA-seq_rep3


title: Total RNA-seq_rep1


title: Total RNA-seq_rep2


title: hippocampus_mock infected_rep7

city: Baltimore

first: Robert

last: Yolken

address: 600 N Wolfe st

department: Pediatrics

institute: Johns Hopkins

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Using the Affymetrix GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing:
Affymetrix CEL files were extracted with the Partek GS 6.6 platform and their data RMA and quantile-normalized to create log2 transcript signal values, which were summarized by Partek from exon to genes and used in subsequent ANOVA analysis.    Transcript annotation was subsequently updated.
MoGene-2_0-st.pgf
MoGene-2_0-st-v1.na33.2.mm10.transcript.csv

source_name: left or right hippocampus

label_protocol: The Affymetrix Ambion Expression WT kit was used as described in the manufacturer's manual.

growth_protocol: For infection the algae (SAG) was infected with the virus (ATCV1) for 6 hours prior oral administration to mice. For mock infection the same amount uninfected algae was used.

extract_protocol: Hippocampal total RNA was extracted using Qiagen miRNeasy kit. Total RNA was DNAse treated for 20 min at 37˚ͦC with TurboDNA-free™ (Ambion).

treatment_protocol: Mice at the age of 10-12 weeks were infeceted with SAG or SAG+ATCV by oral gavage. 6 months post infection mice were sacraficed and hippocampus was dissected.

tag: treatment

value: SAG


title: hippocampus_mock infected_rep8


title: hippocampus_mock infected_rep2


title: hippocampus_mock infected_rep5


title: hippocampus_infected_rep15


title: hippocampus_mock infected_rep6


title: hippocampus_mock infected_rep4


title: hippocampus_mock infected_rep1


title: hippocampus_infected_rep11


title: hippocampus_infected_rep16


title: knockout mouse #3 - stimulated

city: Toronto

first: Shannon

last: Dunn

state: ON

address: 30 Bond Street, Office Location: 209 Victoria Street, 5th floor, 516

department: Keenan Research Centre for Biomedical Research

country: Canada

institute: St. Michael's Hospital

description: KO biological replicate # 2 -stim

hyb_protocol: Mouse WG-6 v2.0 BeadChips were incubated at 58oC, with rotation speed 5 for 18 hours.

scan_protocol: BeadChips were scanned on the iScan (Illumina).

data_processing: Data files were quanitified in GenomeStudio v 2010.1 (Illumina). Quantile normalization was performed using GeneSpring v12.1 (Agilent).

source_name: CD4+ T cells

label_protocol: Illumina TotalPrep-96 Amplification kit (Ambion) was used as per manufacturer's protocol.

growth_protocol: T cells were cultured at 0.2 million cells per well in 96 well flat bottomed plates in complete media. Plates were pre-coated with anti-CD3 and anti-CD28

extract_protocol: Total RNA was isolated using Qiagen RNA easy kits

tag: activation conditions

value: activated with anti-CD3/anti-CD28 (1 µg/each)

value: mixed B6/129

tag: age

value: Young adult

tag: cell type

value: Naïve (CD62Lhi) CD4+ T cell


title: hippocampus_infected_rep9


title: hippocampus_infected_rep12


title: hippocampus_infected_rep14


title: hippocampus_infected_rep13


title: hippocampus_infected_rep6


title: hippocampus_infected_rep10


title: hippocampus_infected_rep8


title: knockout mouse #5 - stimulated

description: KO biological replicate #4 - stim


title: wildtype mouse #1/#2 sample pooled- unstimulated

description: WT biological replicate # 1-non-stim

value: frozen upon isolation


title: knockout mouse #1 - stimulated

description: KO biological replicate # 1 -stim


title: wildtype mouse #3 - stimulated

description: WT biological replicate # 2-stim


title: hippocampus_infected_rep4


title: hippocampus_infected_rep7


title: hippocampus_infected_rep5


title: wildtype mouse #5- non-stimulated

description: WT biological replicate # 4-non-stim


title: hippocampus_infected_rep3


title: hippocampus_infected_rep2


title: wildtype mouse #3 - non-stimulated

description: WT biological replicate # 2-non-stim


title: hippocampus_infected_rep1


title: knockout mouse #6 - non-stimulated

description: KO biological replicate #5-no stim


title: knockout mouse #6 - stimulated

description: KO biological replicate # 6-stim


title: knockout mouse #5 - non-stimulated

description: KO biological replicate #4-non-stim


title: knockout mouse #4 - non-stimulated

description: KO biological replicate # 3-non-stim


title: wildtype mouse #4 - stimulated

description: WT biological replicate # 3-stim


title: wildtype mouse #5 - stimulated

description: WT biological replicate # 4-stim


title: knockout mouse #1 - non-stimulated

description: KO biological replicate # 1-no stim


title: knockout mouse #3 - non-stimulated

description: KO biological replicate #2-non-stim


title: wildtype mouse #4 - non-stimulated

description: WT biological replicate # 3-non-stim


title: BT43N (Adjacent normal tissue to oligodendroglioma grade II)

city: Rupnagar

first: Javed

middle: N

last: Agrewala

state: Punjab

address: Indian Institute of Technology [IIT] Rupnagar-140001, Punjab, INDIA

department: Centre for Biomedical Engineering

country: India

institute: Indian Institute of Technology [IIT]

description: Human tissue

hyb_protocol: Hybridization was done for 16 hours at 45°C and 60 rpm using Affymetrix Hybridization Oven

scan_protocol: The gene chips were scanned using Affymetrix Gene chip scanner 3000 7G.

data_processing: The data was analyzed using GeneSpring software

label_protocol: Biotinlyated RNAs were prepared according to genechip 3' IVT  Express kit.

growth_protocol: Tissue is collected in RNALater solution.

extract_protocol: Total RNA was extracted from tumor tissue and normal tissue using an RNeasy kit (Qiagen, Limburg, Netherlands), according to the manufacturer's protocol. RNA purity and integrity was analyzed by BioAnalyser 2100 (Agilent Technologies, Santa Clara, CA).

treatment_protocol: No Treatment

tag: tissue


title: wildtype mouse #1/#2 sample pooled- stimulated

description: WT biological replicate # 1-stim


title: BT56N (Adjacent normal tissue to glioblastoma grade IV)

description: Human tissue


title: BT35N (Adjacent normal tissue to oligodendroglioma grade II)

description: Human tissue


title: S. cerevisiae CEN.PK122-2

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

description: S. cerevisiae was grown in in 2 L bioreactors (Applikon, Schiedam, The Netherlands) containing a 1.,4 L working volume. The cultures were constantly stirred at 800 rpm, sparged with 700 mL min-1 dried compressed air (Linde Gas Benelux, The Netherlands) and maintained at  30 ˚C for S. cerevisiae and  25 ˚C for S. kudriavzevii and S. eubayanus. The culture pH was kept at 5.0 during growth on glucose by automatic addition of 2M KOH. . Culture samples corresponding to ca. 240 mg of biomass wet weight were directly quenched in liquid nitrogen.

data_processing:
RNA-Seq reads were aligned to S. eubayanus CBS12357T, S. kudriavzevii CR85 and S. cerevisiae CEN.PK113-7D reference using STAR version 2.5.3a in 2Pass mode
resulted sequence alignment map file (SAM) were filtered on ambigious alignments and sorted with samtools to sorted binary alignement file (BAM)
The sorted BAM file was processed with htseq-count from the HTSeq framework version 0.9.1 with -m union and -stranded reverse to calculate the transcript counts
The raw transcript counts were normalized on fragments per kilobase million (FPKM) by applying rpkm module from edgeR package
Genome_build: S. eubayanus CBS12357 from Baker et al. for sample 1 and 2; S. kudriavzevii CR85 from Boonekamp et al. for samples 3 and 4; S. cerevisiae CEN.PK113-7D from Salazar et al. for samples 5 and 6
Supplementary_files_format_and_content: Comma delimited file, normalized transcript counts

organism: Saccharomyces cerevisiae

source_name: cultures

growth_protocol: S. eubayanus, S. kudriavzevii and S. cerevisiae batch cultures were grown  in bioreactors performed in independent duplicate. SMG was supplemented with 0.,2 g L -1 antifoam Emulsion C (Sigma-Aldrich, St. Louis, MO). The reactors were inoculated at OD660 0.,3 with cells resuspended in demineralized water, which were obtained from exponential growing shake flask cultures growing at the same temperature and medium as was used in the bioreactors. Cultures were performed in 2 L bioreactors (Applikon, Schiedam, The Netherlands) containing a 1.,4 L working volume. The cultures were constantly stirred at 800 rpm, sparged with 700 mL min-1 dried compressed air (Linde Gas Benelux, The Netherlands) and maintained at  30 ˚C for S. cerevisiae and  25 ˚C for S. kudriavzevii and S. eubayanus. The culture pH was kept at 5.0 during growth on glucose by automatic addition of 2M KOH. (SM) containing 3.0 g L-1 KH2PO4, 5.0 g L-1 (NH4)2SO4, 0.5 g L-1 MgSO4, 7 H2O, 1 mL L-1 trace element solution, and 1 mL L-1 vitamin solution. The pH was set to 6 with 2 M KOH prior to autoclaving at 120 °C for 20 min. Vitamin solutions (Verduyn et al. 1992) were sterilized by filtration and added to the sterile medium. Concentrated sugar solutions were autoclaved at 110 °C for 20 min and added to the sterile flasks to give a final concentration of 20 g L-1 carbon source (glucose (SMG), maltose (SMM)

extract_protocol:
The resulting ice pellet was gently thawed on ice and spun down at 4700 x g for 5 min at 0 o C. Pellets were then resuspended in 1.2 mL of ice-cold AE buffer (50 mM sodium acetate and 10 mM EDTA, pH 5.0), followed by addition of 1.2 mL of acid phenol/chloroform/isoamyl alcohol mix and 0.12 mL 10 % sodium dodecyl sulfate. The resulting mix was vortexed for 30 s and incubated for 5 min at 65 °C. After homogenizing for 30 sec by vortexing, 800 µL aliquots were distributed in RNase-free screw-cap tubes (Tai et al. 2005). After centrifugation (15 min at 10,000 x g), the aqueous phase was transferred to a new tube containing 0.4 mL of acid phenol/chloroform. The mix was vortexed for 30 seconds, centrifuged (15 min at 10,000 x g) and the aqueous phase was again transferred to a new tube. RNA was then ethanol precipitated and re-suspended in RNAse-free water. Prior to cDNA synthesis, purity, concentration and integrity of the RNA in the samples was assessed with the Nanodrop (Thermo Fisher Scientific), Qubit (Thermo Fisher Scientific) and Tapestation 220 with RNA Screen Tape (Agilent Technologies), respectively, according the manufacturers’ recommendations.
cDNA libraries were prepared using the TruSeq RNA V2 kit (Illumina)and sequenced on HISeq 2500 (Illumina) at Novogene (HK) Company Ltd (Hong Kong, China).

treatment_protocol: S. eubayanus CBS 12357T , S. kudriavzevii and S. cerevisiae Culture samples corresponding to ca. 240 mg of biomass wet weight were directly quenched in liquid nitrogen.

tag: carbon source

value: Glucose


title: S. cerevisiae CEN.PK122-1


title: SEM_siMLL/AF4_TP2

city: Rotterdam

first: Patricia

last: Garrido Castro

address: Wytemaweg 80

department: Dept. Pediatrics

institute: Erasmus MC - Sophia Children's Hospital

description:
SAMPLE 7
MLL/AF4 knock-down at TP2

hyb_protocol: standard Illumina hyb protocol

scan_protocol: standard Illumina scan protocol

data_processing:
Data was processed using Genome Studio (Illumina), using quantile normalization and background subtraction
Quantile normalized and log-transformed (corresponds to log naturalis scale). Samples were filtered for detection p-values<0.2, and non-expressed samples (NaN, negative log-values) removed.

source_name: B-cell precursor ALL cell line SEM

label_protocol: standard Illumina labelling

growth_protocol: SEM cell line was cultured at standard conditions; antibiotica-free RPMI-1640 medium supplemented 10% FCS and 1% Glutamine.

extract_protocol: RNA was extracted using the QIAGEN RNeasyMini Kit, using the manufacturer's protocol. RNA quality was confirmed by Agilent Bioanalyser

treatment_protocol: SEM cells were serially transfected with siRNAs using electroporation, three times at at two day intervals for up to 3 times, representing a siRNA treatment time course of 6 days. Material was harvested for analyses immediately prior to the subsequent electroporation and at the final time point, two days after the 3rd electroporation, corresponding to a sustained MLL/AF4 knock-down period of 2 (TP1), 4 (TP2) and 6 (TP3) days, respectively.

tag: cell line

value: MLL/AF4-positive B-cell precursor ALL cell line SEM

tag: knockdown

tag: time point (tp)

tag: knockdown period

value: 4 days


title: BT32D (Gliosarcoma grade IV tumor tissue)

description: Human tissue

source_name: Gliosarcoma grade IV tumor tissue

value: Gliosarcoma grade IV tumor tissue


title: BT56D (Glioblastoma grade IV tumor tissue)

description: Human tissue

source_name: Glioblastoma grade IV tumor tissue

value: Glioblastoma grade IV tumor tissue


title: knockout mouse #4 - stimulated

description: KO biological replicate #3-stim


title: BT43D (Oligodendroglioma grade II tumor tissue)

description: Human tissue

source_name: Oligodendroglioma grade II tumor tissue

value: Oligodendroglioma grade II tumor tissue


title: BT35D (Oligodendroglioma grade II tumor tissue)

description: Human tissue


title: BT24D (Low grade astrocytoma grade II tumor tissue)

description: Human tissue


title: BT25N (Adjacent normal tissue to rhabdoid tumor grade IV)

description: Human tissue


title: BT25D (Rhabdoid tumor grade IV tumor tissue)

description: Human tissue

source_name: Rhabdoid tumor grade IV tumor tissue

value: Rhabdoid tumor grade IV tumor tissue


title: BT32N (Adjacent normal tissue to gliosarcoma grade IV)

description: Human tissue


title: SEM_siCtrl_TP2

description:
SAMPLE 5
control siRNA at TP2

value: siCtrl


title: SEM_siMLL/AF4_TP1

description:
SAMPLE 6
MLL/AF4 knock-down at TP1

value: 2 days


title: SEM_siCtrl_TP1

description:
SAMPLE 3
control siRNA at TP1


title: KO_HepG2_1_1

city: S. Giovanni Rotondo (FG)

first: Tommaso

last: Mazza

address: Viale Cappuccini, 1

department: Bioinformatics

country: Italy

institute: IRCCS Casa Sollievo della Sofferenza

description: RIN: 9.60

data_processing:
Reads trimming performed using Trimmomatic
Residual adapter removed using cutadapt
Reads aligned with TopHat 2
Reads were RPKM-normalized
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample ...

source_name: HepG2 - immortalized cell line

growth_protocol: HepG2 cell line was purchased from ATCC and cultured in DMEM (1X) supplemented with 10% fetal bovine serum (FBS), with 1% penicillin/streptomycin.

extract_protocol:
Total RNA was reverse transcribed using the Quantitect Transcription kit (Qiagen), according to the manufacturer's instructions
Indexed libraries were prepared from purified RNA with the TruSeq Total Stranded RNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions. Libraries were quantified using the Agilent 2100 Bioanalyzer (Agilent Technologies). Index-tagged samples were equimolar and the overall concentration was 2 nM. The pooled samples were subject to cluster generation and sequenced using an Illumina HiSeq 2500 System (Illumina) in a 2x100 paired-end format at a final concentration of 8 pmol.

treatment_protocol: After plating, HepG2 an cells were transduced with retroviral macroH2A-specific shRNA cassettes as described (Kong R et al., Nucleic Acid Res, 2014; PMID: 24071584), and selected with 2 μg/ml puromycin.

value: Hepatocellular Carcinoma

value: Liver

value: 15-year-old Caucasian American male


title: KO_HepG2_1_2

description: RIN: 8.90


title: S. eubayanus CBS12357-2

description: S. eubayanus CBS 12357T was grown in in 2 L bioreactors (Applikon, Schiedam, The Netherlands) containing a 1.,4 L working volume. The cultures were constantly stirred at 800 rpm, sparged with 700 mL min-1 dried compressed air (Linde Gas Benelux, The Netherlands) and maintained at  30 ˚C for S. cerevisiae and  25 ˚C for S. kudriavzevii and S. eubayanus. The culture pH was kept at 5.0 during growth on glucose by automatic addition of 2M KOH. . Culture samples corresponding to ca. 240 mg of biomass wet weight were directly quenched in liquid nitrogen.

organism: Saccharomyces eubayanus


title: S. kudriavzevii CR85-2

description: S. kudriavzevii CR85 was grown in in 2 L bioreactors (Applikon, Schiedam, The Netherlands) containing a 1.,4 L working volume. The cultures were constantly stirred at 800 rpm, sparged with 700 mL min-1 dried compressed air (Linde Gas Benelux, The Netherlands) and maintained at  30 ˚C for S. cerevisiae and  25 ˚C for S. kudriavzevii and S. eubayanus. The culture pH was kept at 5.0 during growth on glucose by automatic addition of 2M KOH. . Culture samples corresponding to ca. 240 mg of biomass wet weight were directly quenched in liquid nitrogen.

organism: Saccharomyces kudriavzevii


title: BT24N (Adjacent normal tissue to low grade astrocytoma grade II)

description: Human tissue


title: U87 siBCL3, TMZ rep 3

city: Chicago

first: Bakhtiar

last: Yamini

address: 900 E 57th St

department: Department of Surgery

institute: University of Chicago

description: SAMPLE 12

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

source_name: U87 siBCL3_TMZ

growth_protocol: Human glioma cell line U87 grown in complete DMEM medium supplemented with 10% FBS and 1%PS

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

treatment_protocol: The U87 cells was transfected with siRNA targeting BCL3 (dharmacon) or control siRNA, and followed by temozolomide treatment (100uM) for 24 hr before RNA extraction.

value: Human glioma cell line

tag: transfected with

value: siRNA targeting BCL3

tag: treated with

value: 100uM temozolomide (TMZ) for 24 hr


title: U87 siCtrl, TMZ rep 1

description: SAMPLE 4

source_name: U87 siCtrl_TMZ

value: control siRNA


title: U87 siCtrl, TMZ rep 3

description: SAMPLE 6


title: U87 siCtrl, DMSO rep 3

description: SAMPLE 3

source_name: U87 siCtrl_DMSO

value: DMSO


title: GFP_HepG2_1

description: RIN: 9.10


title: GFP_HepG2_3

description: RIN: 9.70


title: U87 siBCL3, DMSO rep 2

description: SAMPLE 8

source_name: U87 siBCL3_DMSO


title: U87 siCtrl, TMZ rep 2

description: SAMPLE 5


title: U87 siCtrl, DMSO rep 2

description: SAMPLE 2


title: U87 siBCL3, TMZ rep 2

description: SAMPLE 11


title: U87 siBCL3, DMSO rep 3

description: SAMPLE 9


title: U87 siBCL3, DMSO rep 1

description: SAMPLE 7


title: AAMLEX3

status: Public on Jul 20 2018

city: Shanghai

first: zhongzhong

last: ji

state: Shanghai China

address: Huashan Rd. 1940, build 3.  Shanghai,

institute: SJTU CHINA

data_processing:
Raw reads were first cleaned by removing adaptor sequences, low quality sequences (Sanger base quality < 20), and reads with unknown nucleotides larger than 10%. The TopHat-Cufflinks- Cuffmerge-Cuffdiff pipeline was used to analyze the clean data with default parameters .
The clean reads were mapped to the human GRCh38  reference genome using TopHat v2.0.13 . Cufflinks v2.2.0 was used to construct, identify, and estimate the abundance from TopHat alignment results. The parameter Fragment Per Kilobase of transcript per Million fragments mapped (FPKM) was used to quantify the abundance of assembled transcripts.
Cufflinks results for all samples were used to merge the assemblies by Cuffmerge v1.0.0 . Cuffdiff v2.2.0 was used to re-estimate the abundance of transcripts. Expression levels were measured using the FPKM method, and the distribution of gene expression was analyzed. Statistical comparison of the DEGs between two groups of samples was also performed using Cuffdiff v2.2.0.
To assess the significance of differential gene expression, the threshold of q-value was set at 0.05, and the absolute value of log2 ratios (fold change between two groups of samples) at 1.
Genome_build: ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz
Supplementary_files_format_and_content: tab-delimited file with RPKM values for all Sample

growth_protocol: Pca cell line were cultured in Dulbecco’s modified Eagle’s medium (Gibco, USA) containing 10% fetal bovine serum and 80U/ml penicillin and streptomycin.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen, USA)  according to the manufacturer's instructions, and was then treated with RNase-free DNase I (TaKaRa, China) to remove genomic DNA contamination.
Sequencing libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer's recommendations, and index codes were added to attribute sequences to each sample.

treatment_protocol: Pca cells were treated with 5uM Amlexanox (TargetMol, USA), or DMSO for 7 days

value: prostate cancer (PCa) cell line

value: Amlexanox for 7 days


title: U87 siCtrl, DMSO rep 1

description: SAMPLE 1


title: SEM_MOCK_TP1

description:
SAMPLE 1
pulse control at TP1

value: MLL/AF4-positive B-cell precursor ALL cell line SEM

value: pulse control


title: AAMLEX2


title: SEM_siMLL/AF4_TP3

description:
SAMPLE 8
MLL/AF4 knock-down at TP3

value: 6 days


title: S. eubayanus CBS12357-1

value: Glucose

tag: strain


title: S. kudriavzevii CR85-1


title: AAMLEX1


title: ADMS03

value: DMSO for 7 days


title: ADMS01


title: ADMS02


title: SEM_siCtrl_TP3

description:
SAMPLE 4
control siRNA at TP3

value: siCtrl


title: SEM_MOCK_TP2

description:
SAMPLE 2
pulse control at TP2

value: 4 days


title: proliferated_neuroblastoma_OT_replicate4

city: Vandoeuvre-lès-Nancy

first: Sebastien

last: Hergalant

address: Faculté de Médecine. 9 avenue de la forêt de Haye

country: France

institute: INSERM

description:
14b-OT-p
Gene expression of proliferated neuroblastoma cells transfected with OT chimeric proteins.

hyb_protocol: 2.5 ug of Cy3-labelled and Cy5-labelled cRNA (specific activity >6.0 pmol Cy3/ug or Cy5/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55µL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 µL of 2x GEx Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Mouse GE Microarray 4x44K for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Arrays were washed and scanned on the G2505C Agilent scanner.

data_processing: Quantification was using the Agilent Feature Extraction software.

label_protocol: Cyanine-3 (Cy3) or Cyanine-5 (Cy5) labeled cRNA were prepared from 0.2 ug RNA using the Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: For proliferation studies, cells were cultured in a medium containing 90% DMEM with 4.5 g/L glucose (Gibco, supplemented with sodium pyruvate) and 10% FCS at 37 °C in an atmosphere of air (95%) and carbon dioxide (5%). For differentiation studies, 1 day before the initiation of differentiation, cells were trypsinized gently and replated in cultured dishes at a density of 4-8 x 10^4 per 60-mm Petri dish. The differentiation medium contained 2.5% FCS and 1.25% DMSO (Sigma) in DMEM with 4.5 g/L glucose.

extract_protocol: RNA was extracted from Proliferated Control (WT-p ; n=4), Proliferated TO (TO-p ; n=4), Proliferated OT (OT-p ; n=4), Differentiated Control (WT-d ; n=4), Differentiated TO (TO-d ; n=4) and Differentiated OT cells (OT-d ; n=4) using the RNeasy Mini Kit (Qiagen #74104) and the concentration was measured by NanoDrop (Thermo Scientific, Wilmington, DE, USA). Its quality was controlled by 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). Genomic DNA was extracted following the phenol-chloroform method.

treatment_protocol: Chimeric proteins were produced by the fusion of either N-terminal (TO) or C-terminal (OT) of transcoblamin (TCN2) to oleosin. Expressed TO fusion protein has high binding affinity toward Cbl whereas OT fusion protein has no detectable Cbl binding activity.

value: Neuroblastoma

tag: tissue origination

value: brain

tag: medium

value: proliferation

tag: chimeric protein

value: fusion of C-terminal (OT) of transcoblamin (TCN2) to oleosin


title: SP_3

city: Los Angeles

first: Richard

middle: Sungho

last: Ahn

address: 611 Charles E. Young Drive East, UCLA, Boyer Hall, 510C

department: Microbiology, Immunology, and Molecular Genetics

institute: University of California Los Angeles

data_processing:
Read quality was checked using FastQC v. 0.11.4
Reads with adapter contamination were trimmed using Trimmomatic v. 0.32
Reads aligned using STAR vs. 2.4.2a
FPKMs and differential expression tests calculated using the Cufflinks Suite v. 2.2.1.
Gene annotations obtained from RefSeq
Genome_build: hg19
Supplementary_files_format_and_content: TXT file containing a matrix of FPKM values for all samples.

source_name: Scalp psoriatic skin

extract_protocol:
RNA was extracted from one 4-mm punch biopsy specimen for bulk RNA sequencing with the Qiagen Allprep DNA/RNA mini kit.
Samples that passed quality control underwent library preparation using the Ovation RNA-Seq System V2 protocol (Nugen) or the Ribozero (Illumina) kits.

value: skin

tag: disease state

value: scalp psoriasis


title: CP_4

source_name: Conventional psoriatic skin

value: psoriasis


title: SP_2


title: SP_1


title: SP_4


title: proliferated_neuroblastoma_TO_replicate3

description:
7-TO-p
Gene expression of proliferated neuroblastoma cells transfected with TO chimeric proteins.

value: fusion of N-terminal (TO) of transcoblamin (TCN2) to oleosin


title: proliferated_neuroblastoma_WT_replicate3

description:
1-WT-p
Gene expression of proliferated neuroblastoma cells.


title: differentiated_neuroblastoma_OT_replicate3

description:
16-OT-d
Gene expression of differentiated neuroblastoma cells transfected with OT chimeric proteins.

value: differentiation


title: proliferated_neuroblastoma_TO_replicate2

description:
7b-TO-p
Gene expression of proliferated neuroblastoma cells transfected with TO chimeric proteins.


title: differentiated_neuroblastoma_TO_replicate4

description:
11b-TO-d
Gene expression of differentiated neuroblastoma cells transfected with TO chimeric proteins.


title: differentiated_neuroblastoma_WT_replicate2

description:
6b-WT-d
Gene expression of differentiated neuroblastoma cells.


title: differentiated_neuroblastoma_TO_replicate1

description:
11-TO-d
Gene expression of differentiated neuroblastoma cells transfected with TO chimeric proteins.


title: proliferated_neuroblastoma_TO_replicate4

description:
9-TO-p
Gene expression of proliferated neuroblastoma cells transfected with TO chimeric proteins.


title: differentiated_neuroblastoma_OT_replicate2

description:
18-OT-d
Gene expression of differentiated neuroblastoma cells transfected with OT chimeric proteins.


title: proliferated_neuroblastoma_WT_replicate4

description:
3-WT-p
Gene expression of proliferated neuroblastoma cells.


title: differentiated_neuroblastoma_TO_replicate3

description:
10-TO-d
Gene expression of differentiated neuroblastoma cells transfected with TO chimeric proteins.


title: differentiated_neuroblastoma_OT_replicate4

description:
18b-OT-d
Gene expression of differentiated neuroblastoma cells transfected with OT chimeric proteins.


title: differentiated_neuroblastoma_OT_replicate1

description:
17-OT-d
Gene expression of differentiated neuroblastoma cells transfected with OT chimeric proteins.


title: proliferated_neuroblastoma_WT_replicate2

description:
2-WT-p
Gene expression of proliferated neuroblastoma cells.


title: differentiated_neuroblastoma_WT_replicate3

description:
4-WT-d
Gene expression of differentiated neuroblastoma cells.


title: differentiated_neuroblastoma_TO_replicate2

description:
20-TO-d
Gene expression of differentiated neuroblastoma cells transfected with TO chimeric proteins.


title: differentiated_neuroblastoma_WT_replicate1

description:
19-WT-d
Gene expression of differentiated neuroblastoma cells.


title: CP_1


title: CP_2


title: C43

source_name: Control skin

value: healthy control


title: C45


title: C44


title: CP_3


title: C40


title: C39


title: C41


title: C38


title: C37


title: HF_2

source_name: Palmoplantar psoriatic skin

value: palmoplantar psoriasis


title: C35


title: proliferated_neuroblastoma_OT_replicate1

description:
15-OT-p
Gene expression of proliferated neuroblastoma cells transfected with OT chimeric proteins.


title: proliferated_neuroblastoma_TO_replicate1

description:
8-TO-p
Gene expression of proliferated neuroblastoma cells transfected with TO chimeric proteins.


title: proliferated_neuroblastoma_OT_replicate3

description:
13-OT-p
Gene expression of proliferated neuroblastoma cells transfected with OT chimeric proteins.


title: differentiated_neuroblastoma_WT_replicate4

description:
6-WT-d
Gene expression of differentiated neuroblastoma cells.


title: proliferated_neuroblastoma_WT_replicate1

description:
1b-WT-p
Gene expression of proliferated neuroblastoma cells.


title: proliferated_neuroblastoma_OT_replicate2

description:
14-OT-p
Gene expression of proliferated neuroblastoma cells transfected with OT chimeric proteins.


title: HF_1


title: U87 siBCL3, TMZ rep 1

description: SAMPLE 10

value: Human glioma cell line

value: siRNA targeting BCL3

value: 100uM temozolomide (TMZ) for 24 hr


title: RWPE1-BAC-RARG-EGFP_DMSO_IgG_R2

first: Mark

middle: D

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

description: RARg.basal.bw

data_processing:
Sequenced reads were trimmed for adaptor sequences, and alignment was performed using Rsubread
peaks were called from aligned reads using CSAW
Genome_build: hg19
Supplementary_files_format_and_content: Peaks (enriched regions over IgG) are supplied in bigWig format

source_name: non-malignant prostate cell line infected with BAC-RARG-EGFP

growth_protocol: Cells were maintained in Keratinocyte Serum Free Medium supplemented with EGF and Bovine Pituitary Extract, with G418 for selection.

extract_protocol:
DNA was extracted after IP using Omega Cycle Pure Kit
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Exponentially growing cells were treated with 10nM CD437 or DMSO vehicle, and samples were crosslinked and harvested after 2 hours of exposure.

tag: gender

value: male

value: non-malignant prostate epithelial cell

tag: ip

value: IgG

tag: treatment

value: DMSO

tag: treatment time


title: RWPE1-BAC-RARG-EGFP_DMSO_GFP_R3

description: RARg.basal.bw

tag: cell type

value: GFP


title: RWPE1-BAC-RARG-EGFP_CD437_GFP_R2


title: RWPE1-BAC-RARG-EGFP_CD437_input_R3

value: input


title: RWPE1-BAC-RARG-EGFP_DMSO_IgG_R3

description: RARg.basal.bw


title: RWPE1-BAC-RARG-EGFP_DMSO_IgG_R1

description: RARg.basal.bw


title: RWPE1-BAC-RARG-EGFP_CD437_IgG_R2


title: RWPE1-BAC-RARG-EGFP_DMSO_input_R3

description: RARg.basal.bw


title: RWPE1-BAC-RARG-EGFP_CD437_input_R2


title: RWPE1-BAC-RARG-EGFP_CD437_GFP_R3


title: RWPE1-BAC-RARG-EGFP_DMSO_GFP_R2

description: RARg.basal.bw


title: RWPE1-BAC-RARG-EGFP_CD437_IgG_R1


title: RWPE1-BAC-RARG-EGFP_CD437_input_R1


title: RWPE1-BAC-RARG-EGFP_DMSO_input_R2

description: RARg.basal.bw


title: RWPE1-BAC-RARG-EGFP_CD437_GFP_R1


title: RWPE1-BAC-RARG-EGFP_CD437_IgG_R3


title: RWPE1-BAC-RARG-EGFP_DMSO_GFP_R1

description: RARg.basal.bw


title: RWPE1-BAC-RARG-EGFP_DMSO_input_R1

description: RARg.basal.bw