title: 387_shALKBH1.1551_Rep2_Hypoxia

description: Hypoxia_ALKBH1_Knockdown_RNAseq_Processed.xlsx

data_processing:
FASTQ sequencing files were trimmed and then aligned to the hg19 human genome using the STAR aligner (Dobin et al., 2013).
Differential expression analysis was performed using CuffDiff (http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/).
ALKBH1 Knockdown in HYPOXIA: FASTQ sequencing reads were trimmed using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)  and transcript quantification was performed using Salmon in the quasi-mapping mode (Patro et al., 2017).
ALKBH1 Knockdown in HYPOXIA: Salmon “quant” files were converted using Tximport (https://bioconductor.org/packages/release/bioc/html/tximport.html) and differential expression analysis was performed using DESeq2 (Love et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: TPM Abundance values from Salmon and FPKM from CuffDiff are provided in Excel Tables

growth_protocol: 387 cells from a primary patient derived GBM tumor model were injected intracranially into a immunocompromised NSG mouse and allowed to grow into a tumor. Cells were dissociated and passaged in vitro. Cells were grown in 1% oxygen

extract_protocol:
Cells were collected and lysed in trizol. Cellular RNA was extracted using the Qiagen miRNeasy Mini Kit.
RNA was extracted with TRIzol (Invitrogen), Cellular RNA was extracted using the Qiagen miRNeasy Mini Kit (catalog number 217004) according to the manufacturers instructions.
Total RNA was prepared for sequencing using the Illumina TruSeq Stranded Total RNA Library Prep Kit according to the manufacturers instructions

value: Cells were treated with an shRNA targeting ALKBH1

tag: condition

value: Hypoxia


title: 387_shALKBH1.1008_Rep2_Hypoxia

status: Public on Nov 01 2018

type: SRA

city: San Diego

first: Jeremy

last: Rich

state: CA

address: 9500 Gilman Drive #0695

country: USA

institute: University of California, San Diego

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: Patient Derived Glioblastoma Stem Cell

tag: shRNA


title: 387_shALKBH1.1551_Rep1_Hypoxia


title: T8.12mo.F.Sp.3

city: Boston

first: Juhyun

last: Oh

address: 185 Cambridge Street

institute: Massachusetts General Hospital

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.3
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM12)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

organism: Mus musculus

source_name: Spleen

growth_protocol: 3 month old or 12 month old C57BL/6J mice from the Jackson Laboratory (Bar Harbor, ME) housed in facility at least one week before harvesting cells

extract_protocol:
Extractions follow ImmGen standard operating protocol (available on https://www.immgen.org/). Briefly, organs are harvested at 9am on day of sort, perterbed as little as possible during preparation, and 1000 cells are double sorted into TCL buffer (Qiagen, Hilden, Germany) containing 1% BME.
Libraries are constructed according to the standard protocol for Smart-seq2 (Picelli et al, 2013) at the Broad Techology Labs in Cambridge, MA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MC38 tumors were implanted subcutaneously and harvested for immune cell isolation at day 10 of tumor growth

tag: strain

tag: age

value: 12 month old

tag: sorting markers

tag: cell type

value: CD8+ T cells


title: rs.v1

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description:
RS_V1_S54_L008
processed data file: RS.vin.csv.gz

library_source: genomic

data_processing:
Basic read quality was verified using summaries produced by FastQC. The raw reads were trimmed and filtered using Trimmomatic. The reads for each MeDIP sample were mapped to the Rnor 6.0 rat genome using Bowtie2 with default parameter options. The mapped read files were then converted to sorted BAM files using SAMtools.
To identify DMRs, the reference genome was broken into 100 bp windows. Genomic windows with less than 40 mapped reads summed across all samples were removed prior to further analysis. The MEDIPS R package was then used to calculate differential coverage between control and exposure sample groups. The edgeR p-value was used to determine the relative difference between the two groups for each genomic window.
Windows with an edgeR p-value less than an arbitrarily selected threshold were considered DMRs. The DMR edges were extended until no genomic window with a p-value less than 0.1 remained within 1000 bp of the DMR.
CpG density and other information was then calculated for the DMR based on the reference genome.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

molecule: genomic DNA

organism: Rattus norvegicus

growth_protocol: Female and male rats of an outbred Hsd: Sprague Dawley SR®TM (Harlan) at about 70 and 100 days of age were fed ad lib with a standard rat diet and ad lib tap water for drinking. To obtain time-pregnant females, the female rats in proestrus were pair-mated with male rats. The sperm-positive (day 0) rats were monitored for diestrus and body weight. The gestating female rats treated were designated as the F0 generation. The offspring of the F0 generation rats were the F1. Non-littermate females and males aged 70-90 days from F1 generation of control or vinclozolin were bred to obtain F2 generation offspring. The F2 generation rats were similarly bred to obtain the F3 generation offspring. Individuals were maintained for 120 days and euthanized for sperm collection. The F1-F3 generation offspring were not themselves treated directly with vinclozolin. The control and vinclozolin lineage rats were housed in the same room with lighting, food and water.

extract_protocol:
Pregnant rats were euthanized when fetuses reached embryonic day 16 (E16) of gestation, and fetal gonads were collected for germ cell preparations. In addition, postnatal day 10 (P10) testes were obtained and used for spermatogonia cell isolation. At E16, sex was determined on the basis of gonadal morphology as previously described (30).  Germ cells were isolated exclusively from males.  Purified populations of male type T1 prospermatogonia (at E16) or postnatal day 10 (P10) spermatogonia were prepared using a mini StaPut gradient method as previously described (30, 43, 44). Briefly, fetal (E16) or postnatal (P10) testes were pooled and dissociated by incubation in 0.25% trypsin-EDTA (Sigma) with vigorous pipetting using a 1000 microliter pipette tip, and the resulting cell solution was filtered through 100 micron nylon mesh to yield a single cell suspension. This cell suspension was then loaded onto a 50 ml 2-4% bovine serum albumen (BSA) gradient prepared in KREBS buffer, and the cells were allowed to sediment at unit gravity at 4˚C for two hours as described (43, 44). The gradient was then fractionated and aliquots of the fractions were examined under phase optics to identify those enriched for the appropriate prospermatogonial or spermatogonial cell types on the basis of morphological characteristics. The enriched fractions were pooled to yield the final sample which was >85% pure for the desired male germ cell type in each case. The pooled samples were then stored at -80°C prior to processing for DNA preparations.  The epididymis was dissected free of connective tissue, a small cut made to the cauda and tissue placed in 5 ml of 1x PBS solution for up to 24 hours at 4°C.  The epididymal tissue was minced and the released sperm was centrifuged at 6,000 x g, then the supernant removed, and the pellet resuspended in NIM buffer, to be stored at -80O C until further use. One hundred µl of sperm suspension was sonicated, spun down at 6,000 g, the pellet washed with 1x PBS once, and then combined with 820 µL DNA extraction buffer and 80 µl 0.1M DTT. The sample was incubated at 65ºC for 15 minutes. Following this incubation 80 µl proteinase K (20 mg/ml) was added and the sample incubated at 55ºC for at least 2 hours under constant rotation. Then 300 µl of protein precipitation solution (Promega, A7953) was added, the sample mixed thoroughly and incubated for 15 min on ice. The sample was centrifuged at 14,000 rpm for 30 minutes at 4ºC. One ml of the supernatant was transferred to a 2 ml tube and 2 µl of glycoblue and 1 ml of cold 100 % isopropanol were added. The sample was mixed well by inverting the tube several times then left in -20ºC freezer for at least one hour. After precipitation the sample was centrifuged at 14,000 rpm for 20 min at 4ºC. The supernatant was taken off and discarded without disturbing the (blue) pellet. The pellet was washed with 70% cold ethanol by adding 500 µl of 70% ethanol to the pellet and returning the tube to the freezer for 20 minutes. After the incubation the tube was centrifuged for 10 min at 4ºC at 14,000 rpm and the supernatant discarded. The tube was spun again briefly to collect residual ethanol to bottom of tube and then as much liquid as possible was removed with gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 minutes). Pellet was then resuspended in 100 µl of nuclease free water.
Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed as follows: rat sperm DNA pools were generated using the appropriate amount of genomic DNA from each individual for 3 pools each of control and vinclozolin lineage animals. Genomic DNA was sonicated using the Covaris M220 the following way: the pooled genomic DNA was diluted to 130 μl with TE buffer into the appropriate Covaris tube. Covaris was set to 300 bp program and the program was run for each tube in the experiment. 10 μl of each sonicated DNA was run on 1.5% agarose gel to verify fragment size. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube and the volume measured. The sonicated DNA was then diluted with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) to 400 μl, heat-denatured for 10 min at 95˚C, then immediately cooled on ice for 10 min. Then 100 μl of 5X IP buffer and 5 μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4˚C.   The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) were pre-washed as follows: The beads were resuspended in the vial, then the appropriate volume (50 μl per sample) was transferred to a microfuge tube. The same volume of Washing Buffer (at least 1 mL 1XPBS with 0.1% BSA and 2mM EDTA) was added and the bead sample was resuspended. Tube was then placed into a magnetic rack for 1-2 minutes and the supernatant discarded. The tube was removed from the magnetic rack and the beads washed once. The washed beads were resuspended in the same volume of 1xIP buffer (50 mM sodium phosphate ph7.0, 700 mM NaCl, 0.25% TritonX-100) as the initial volume of beads. 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2h on a rotator at 4˚C.  After the incubation the bead-antibody-DNA complex was washed three times with 1X IP buffer as follows: The tube was placed into magnetic rack for 1-2 minutes and the supernatant discarded, then washed with 1xIP buffer 3 times. The washed bead-DNA solution is then resuspended in 250 μl digestion buffer with 3.5 μl Proteinase K (20mg/ml). The sample was then incubated for 2-3 hours on a rotator at 55˚ C and then 250 μl of buffered Phenol-Chloroform-Isoamylalcohol solution was added to the supe and the tube vortexed for 30 sec then centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250 μl chloroform were added to the supernatant from the previous step, vortexed for 30 sec and centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol were added and mixed well, then precipitated in -20˚C freezer for 1 hour to overnight.  The precipitate was centrifuged at 14,000rpm for 20min at 4˚C and the supernatant removed, while not disturbing the pellet. The pellet was washed with 500μl cold 70% ethanol in -20˚C freezer for 15 min. then centrifuged again at 14,000rpm for 5min at 4˚C and the supernatant discarded. The tube was spun again briefly to collect residual ethanol to bottom of tube and as much liquid as possible was removed with gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 minutes) then resuspended in 20μl H2O or TE. DNA concentration was measured in Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212).Histone chromatin immunoprecipitation with genomic DNA was performed as follows: rat sperm pools were generated using a total of 8 million sperm per pool for 3 pools of control and vinclozolin lineage animals. The control pools contained equal amounts of sperm for each of 3-4 individuals for a total of n=11 rats and the vinclozolin pools contained equal amounts of sperm for each of 3 individuals for a total of n=9 rats per exposure group. To remove any somatic cell contamination sperm samples from each animal were sonicated 10 seconds using a Sonic Dismembrator Model 300 (Thermo Scientific Fisher, USA) then centrifuged 4,000xg for 5 min at 4°C. The supernatant was discarded and the pellet resuspended and counted individually on a Neubauer counting chamber (Propper Manufacturing Co., Inc., New York, USA) prior to pooling. The sperm pools were reconstituted up to 1 ml with 1X PBS.

treatment_protocol: On days 8 through 14 of gestation, the F0 females were administered daily intraperitoneal injections of vinclozolin (100 mg/kg BW/day) or dimethyl sulfoxide (DMSO). Vinclozolin was obtained from Chem Service Inc. (West Chester, PA) and was injected in a 20 microliter DMSO vehicle.

tag: strain background

value: an outbred Hsd:Sprague Dawley

tag: lineage

value: vinclozolin

tag: development stage

value: RS

tag: tissue

value: sperm


title: 387_shALKBH1.1008_Rep1_Hypoxia


title: rs.v3

description:
RS_V3_S56_L008
processed data file: RS.vin.csv.gz


title: rs.v2

description:
RS_V2_S55_L008
processed data file: RS.vin.csv.gz


title: T8.12mo.F.Sp.2


title: 387_shCONT_Rep2_Hypoxia

value: Cells were treated with a non-targeting shRNA (shCONT)


title: T8.12mo.F.Sp.4


title: T8.12mo.F.Sp.1


title: rs.c1

description:
RS-C1_S20_L005
processed data file: RS.vin.csv.gz

value: control


title: rs.c2

description:
RS-C2_S21_L005
processed data file: RS.vin.csv.gz


title: FNP_TFAP2A_gg

city: Koeln

first: Milos

last: Nikolic

state: Nordrhein-Westfalen

address: Robert Koch Str. 21

country: Germany

institute: Center for Molecular Medicine Cologne

data_processing:
Library strategy: 4C-seq
Reads were assigned to samples based on the first 10 bases of the read. Subsequently, the primer sequence was removed from the read and the remaining sequence was trimmed to 36 bases. These 36 bases were aligned to the human (hg19) or chicken (gg3) reference genomes  using Bowtie 0.12.7.
The resulting mapped reads were analyzed with R3C-seq (Thongjuea et al., 2013) in order to generate RPM (reads per million) normalized bedgraph files for downstream visualization and analysis.
Genome_build: hg19; gg3

organism: Gallus gallus

source_name: FNP from stage HH24 chicken embryos

growth_protocol: WT hiPSC and BOFS hiPSC lines were grown in tissue culture plates coated with GelTrex (ThermoFisher Scientific, #1413301) using either mTeSRTM1 (STEMCELL Technologies, #05870) or StemMACS iPS-Brew XF medium (Miltenyl Biotec, #130-104-368). The medium of the cells was changed daily. hiPSC were differentiated into hNCC experiments as previously reported (Bajpai et al;2010). Briefly, hiPSCs were washed twice with PBS  and treated with 2mg/mL Collagenase solution (Life Technologies, #17104-019) in DMEM KO Medium to detach hiPSC colonies from the plate surface. 2mL of Collagenase solution was used for one well of a 6-well plate, followed with incubation period at 37C. After about one hour, collagenase solution was carefully aspirated and PBS was added to collect all the colonies into a 15mL falcon tube. Following another round of PBS washing, fresh pre-warmed hNCC Differentiation Medium  was added and resuspended to break big colonies into relatively smaller cell clumps. hiPSC clumps were then plated in petri dishes and kept at 37⁰C, which  after 2-3 days form floating Embryoid Bodies (EB) formation . Between day 6 and 9, EBs attached and gave rise to hNCC outgrowths. hNCC were collected at day 11 (d11hNCC) or expanded for two passages (p2hNCC) according to a recent protocol (Prescott et al; 2015). The hNCC differentiation medium was changed every 2-3 days. Chicken frontonasal prominences (FNP) were dissected from stage HH24 chicken embryos.

extract_protocol:
4C-seq assays were performed as previously described (Splinter et al., 2012; Stadhouders et al., 2013; Cruz-Molina et al., 2017) with slight modifications. Approximately 5-10 million hiPSC, hNCC or chicken FNP cells were crosslinked with 1% formaldehyde during 20 minutes and quenched with 0.125M glycine for 10 min. Cells were washed with PBS and resuspended in lysis buffer (50 mM Tris–HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% TX-100 and 1X protease inhibitors) during 10 min on ice.  Following centrifugation for 5 min at 650g (4 °C), nuclei were re-suspended in 0.5 ml of 1.2X restriction buffer with 0.3% SDS and incubated at 37 °C and 900 rpm for 1h. After that, Triton X-100 was added to a final concentration of 2% followed by 1h incubation at 37 °C and 900 rpm. Afterwards, chromatin was digested overnight at 37 °C and 900 rpm with 400 U of NlaIII (R0125L, NEB). NlaIII was inactivated by adding SDS to a final concentration of 1.6% and incubating the mixture for 20 min at 65 °C while shaking (900 rpm). The digested chromatin was transferred to 50-ml tubes and 6.125 ml of 1.15X ligation buffer (50 mM Tris-HCl pH 7.6, 10 mM MgCl2, 1 mM ATP, 1mM DTT) were added. Triton X-100 was also added to a final concentration of 1% and the resulting solution was incubated for 1 h at 37 °C while shaking gently. After that, digested chromatin was ligated with 100 U of T4 DNA ligase (15224-041, Life Technologies) for 8 h at 16 °C, followed by RNAse A treatment (300 μg, Peqlab) for 45 min at 37 °C. Subsequently, chromatin was de-crosslinked with 300 μg of Proteinase K (Peqlab) and overnight incubation at 65 °C. DNA was then purified by phenol/chloroform extraction followed by ethanol precipitation and re-suspension in 100 μl of water. At this step, the digestion and ligation efficiencies were evaluated by analysing a small fraction of the purified DNAs by agarose electrophoresis. The remaining DNA was digested with 50U of DpnII (R0543M, NEB) in 500 μl of 1x NEBuffer DpnII at 37 °C overnight. DNA samples were purified by phenol/chlorophorm extraction, followed by ethanol precipitation. Once purified, DNA samples were re-suspended in 500 μl of water and a second ligation was performed by adding 200 U of T4 DNA Ligase into a final volume of 14 ml 1X ligation buffer followed by overnight incubation at 16 °C. DNA samples were subjected to another round of phenol/chlorophorm extraction and ethanol precipitation, re-suspended in 100 μl of water and purified with a QIAgen PCR purification column (28104, QIAgen). The efficiencies of the second digestion and ligation were also evaluated by agarose electrophoresis.
4C samples were amplified by inverse PCR using primers located within different human (TFAP2A promoter, ENh480, Enh100) or chicken (3' TFAP2A) genomic regions and that included illumina adaptor sequences and short barcodes. The inverse PCRs were performed with the expand long template PCR system (11681842001, Roche) and 30 amplification cycles (94°C 2 min, 30x [94°C 10 sec, 60°C 1 min, 68°C 3 min], 68°C 5 min). The inverse PCR primers were designed as previously described (Stadhouders et al., 2013). Once amplified, 4C-seq libraries were sequenced on the HiSeq2500, generating reads of either 74 or 100 bp in length.

treatment_protocol: BOFS hiPSC were derived from fibroblasts isolated from a BOFS patient carrying a 88Mb de novo heterozygousinversion in chromosome 6.

tag: cell line

value: FNP

tag: genotype

value: WT

tag: treatment


title: pachy.v2

description:
Pachy_V2_S17_L008
processed data file: Pachy.vin.csv.gz

value: Pachy


title: T4.3mo.F.TI.3

source_name: Tumor

value: 3 month old

value: Conv. CD4+ T cells


title: pachy.v1

description:
Pachy_V1_S16_L008
processed data file: Pachy.vin.csv.gz


title: pachy.c3

description:
Pach-C3_S16_L004
processed data file: Pachy.vin.csv.gz


title: T4.3mo.F.Sp.4


title: rs.c3

description:
RS-C3_S22_L006
processed data file: RS.vin.csv.gz


title: pachy.c1

description:
Pach-C1_S14_L004
processed data file: Pachy.vin.csv.gz


title: p10.v3

description:
P10-V3_S14_L002
processed data file: P10.vin.csv.gz


title: p10.v2

description:
P10-V2_S13_L002
processed data file: P10.vin.csv.gz


title: p10.v1

description:
P10-V1_S12_L002
processed data file: P10.vin.csv.gz


title: T4.3mo.F.Sp.3


title: pachy.c2

description:
Pach-C2_S15_L004
processed data file: Pachy.vin.csv.gz


title: pachy.v3

description:
Pachy_V3_S1_L008
processed data file: Pachy.vin.csv.gz


title: cd11b+cd11c+.d35.r5

city: London

first: Damián

last: Perez-Mazliah

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Reads were adapter and quality trimmed using cutadapt v1.9.1 with the following non-default settings: “-a AGATCGGAAGAGC -A AGATCGGAAGAGC --minimum-length 30 -q 20,20”
Gene-level abundance estimates were generated from the trimmed reads using RSEM v1.2.31 running STAR v2.5.1b with default settings.  RSEM indices were built against the Mus musculus Ensembl release 89 transcriptome.
Genome_build: GRCm38
Supplementary_files_format_and_content: RSEM gene-level abundance estimates.

growth_protocol: Mice were housed at the BRF facilities of the MRC National Institute for Medical Research, Mill Hill, London

extract_protocol:
Total RNA was extracted using Ribopure kit (Ambion)
cDNA was generated from total RNA with the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA). Next-generation sequencing libraries were produced with the Ovation Ultralow System V2 (Nugen)

treatment_protocol: Spleen cells were dissected, surface stained with fluorescent probes/antibodies, and flow cytometry sorted directly into Tri reagent (Ambion) (1 vol sample/ 9 vol Tri reagent)

value: Spleen

value: MSP1-specific B cell

tag: phenotype

tag: days post-infection


title: p10.c3

description:
P10_C3_S43_L008
processed data file: P10.vin.csv.gz


title: cd11b+cd11c+.d35.r4


title: T4.3mo.F.Sp.1


title: p10.c2

description:
P10_C2_S42_L008
processed data file: P10.vin.csv.gz


title: T4.3mo.F.TI.1


title: T4.12mo.F.TI.4


title: e16.v4

description:
E16_V4_S40_L007
processed data file: E16.vin.csv.gz


title: p10.c1

description:
P10_C1_S41_L008
processed data file: P10.vin.csv.gz


title: cd11b+cd11c+.d35.r3


title: e16.v3

description:
E16_V3_S39_L007
processed data file: E16.vin.csv.gz


title: T4.12mo.F.TI.3


title: e16.v1

description:
E16_V1_S38_L007
processed data file: E16.vin.csv.gz


title: 387_shCONT_Rep1_Hypoxia

description: Hypoxia_ALKBH1_Knockdown_RNAseq_Processed.xlsx


title: e16.c3

description:
E16_C3_S34_L006
processed data file: E16.vin.csv.gz


title: T4.12mo.F.TI.2


title: e16.c2

description:
E16_C2_S33_L006
processed data file: E16.vin.csv.gz


title: cd11b+cd11c+.d35.r1


title: T4.12mo.F.TI.1


title: T4.12mo.F.Sp.4


title: cd11b-cd11c-.d35.r5


title: cauda.v1

description:
Cau-V1_S9_L002
processed data file: Cauda.vin.csv.gz

value: Cauda


title: cauda.v2

description:
Cau-V2_S10_L002
processed data file: Cauda.vin.csv.gz


title: cd11b+cd11c+.d35.r2


title: T4.12mo.F.Sp.3


title: cd11b-cd11c-.d35.r3


title: cauda.c3

description:
Cauda-C3_S34_L008
processed data file: Cauda.vin.csv.gz


title: cauda.c1

description:
Cauda-C1_S32_L008
processed data file: Cauda.vin.csv.gz


title: cauda.c2

description:
Cauda-C2_S33_L008
processed data file: Cauda.vin.csv.gz


title: cd11b-cd11c-.d35.r4


title: T4.12mo.F.Sp.2


title: e16.c1

description:
E16_C1_S32_L006
processed data file: E16.vin.csv.gz


title: cauda.v3

description:
Cau-V3_S11_L002
processed data file: Cauda.vin.csv.gz


title: caput.v3

description:
Caput_V3_S59_L008
processed data file: Caput.vin.csv.gz

value: Caput


title: caput.v2

description:
Caput_V2_S58_L008
processed data file: Caput.vin.csv.gz


title: T4.12mo.F.Sp.1

value: 12 month old


title: cd11b-cd11c-.d35.r1


title: caput.v1

description:
Caput_V1_S57_L008
processed data file: Caput.vin.csv.gz


title: caput.c3

description:
Caput-C3_S28_L007
processed data file: Caput.vin.csv.gz


title: DC.3mo.M.TI.1

value: Dendritic cells


title: cd11b-cd11c-.d35.r2


title: caput.c2

description:
Caput-C2_S27_L007
processed data file: Caput.vin.csv.gz

value: an outbred Hsd:Sprague Dawley


title: caput.c1

description:
Caput-C1_S26_L006
processed data file: Caput.vin.csv.gz


title: DC.3mo.F.TI.4


title: DC.3mo.F.TI.3


title: PM2

city: Geneva

first: Thilo

last: Kohler

address: 1, rue Michel Servet

department: Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva

data_processing:
The reads were mapped with the TopHat v.2 software to the Pseudomonas aeruginosa PA14 RefSeq genome NC_008463.1 for the PM samples, the Staphylococcus aureus Newman RefSeq genome NC_009641.1 for the SM samples and a merge of the two for the CC samples
The table of counts with the number of reads mapping to each gene feature of to the Pseudomonas aeruginosa PA14 RefSeq genome NC_008463.1 for the PM samples, the Staphylococcus aureus Newman RefSeq genome NC_009641.1 for the SM samples and a merge of the two for the CC samples was prepared with HTSeq v0.5.3p9
The differential expression analysis was performed with the statistical analysis R/Bioconductor package EdgeR v. 3.4.2.
The genes having a count above 1 count per million reads (cpm) in at least 3 samples were kept for the analysis. The differentially expressed genes tests were done with the exactTest() function using the exact negative binomial test.
Genome_build: PA14 RefSeq genome NC_008463.1 for the PM samples, the Staphylococcus aureus Newman RefSeq genome NC_009641.1 for the SM samples and a merge of the two for the CC samples
Supplementary_files_format_and_content: CPM

organism: Pseudomonas aeruginosa

source_name: P. aeruginosa monoculture replicate 2

growth_protocol: M14 medium

extract_protocol:
RNA was extracted after 3 h of co-culture
RNA were ribodepleted with the Ribo-Zero rRNA Removal kit (Bacteria) from Illumina (formely Epicentre) with 1300 ng as input material. Libraries were prepared with the Illumina TruSeq Stranded Total RNA kit according to manufacturer's specifications.
Ribo-depleted RNA-seq

treatment_protocol: RNA stabilized in Bacteria Protect reagent (Qiagen)

tag: strains

value: 3h monoculture in M14 medium


title: PM1

source_name: P. aeruginosa monoculture replicate 1


title: DC.3mo.F.TI.2


title: PM3

source_name: P. aeruginosa monoculture replicate 3


title: DC.3mo.F.Sp.4


title: DC.3mo.F.Sp.3


title: DMS114 resistant cell line number 3

type: genomic

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

country: Spain

institute: IDIBELL

description: resistance to treatment with FGFR1 tyrosine kinase inhibitors

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using HiScan SQ using standard recommended Illumina scanner setting

data_processing: Genome Studio V2011.2

label: Cy3, Cy5

source_name: SCLC cell line

label_protocol: Standard Illumina labelling protocol

growth_protocol: DMS114 cell line was grown under recommended conditions, and maintained at 37ºC in a humidified atmosphere of 5% CO2. To generate acquired resistance to the FGFR1 inhibitor, PD173074, sensitive DMS114 cells were cultured with a gradually increasing concentration of the drug for three/four months, to a final concentration of 1 μmol/L. Individual cells capable of proliferation were allowed to grow and were selected as pools of clones, transferred to separate plates and treated with 1 μmol/L of PD173074 thereafter.

extract_protocol: DNA extraction with Wizard DNA purification kit (Promega)

tag: clones


title: DC.3mo.M.Sp.1


title: DMS114 parental cell line

description: sensitive to treatment with FGFR1 tyrosine kinase inhibitors


title: DMS114 resistant cell line number 4


title: DC.12mo.M.TI.1


title: 7d A+T

type: RNA

city: Kyoto

first: Makoto

last: Ikeya

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

country: Japan

institute: Kyoto University

description: Gene expression data of induced chondrocyte derived from induced mesenchymal stromal cells (iMSCs)

hyb_protocol: Hybridisations were carried out with GeneChip® Hybridisation, Wash, and Stain Kit, with subsequent washing and staining of arrays on GeneChip® Fluid Station 450.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G

data_processing: Analysis was performed using GeneSpring 12.6.1 software. Data were normalized with the RMA16 algorithm.

label: biotin

source_name: FOP-iMSCs

label_protocol: 500ng of total RNA from samples were reversed transcribed according to the Ambion® WT Expression Kit Protocol. Synthesized cDNA was then Labeled with GeneChip® Terminal Labeling Kit.

growth_protocol: iMSCs were induced and maintained in a minimum essential medium alpha modification supplemented with 10% FBS, 5 ng/mL yFGF2 and 0.5% penicillin and streptomycin

extract_protocol: RNA was isolated with RNeasy mini kit (QIAGEN).

treatment_protocol: iMSCs were chondrogenic differentiated  for  7 days FOP-iMSCs with or without 100 ng/mL Activin-A, 100 nM TAK 165, 100 nM Lapatinib (selective EGFR/ERBB2 inhibitor) and 100 nM CP-724714 (selective ERBB2 inhibitor)

value: induced chondrocyte

value: Activin + TAK


title: DC.12mo.F.TI.3


title: DC.12mo.F.TI.2


title: DMS114 resistant cell line number 1


title: 7d A

value: Activin


title: TAM Treated NHMEC - repeat 3 - mAdbID:121323

city: Bethesda

first: Miriam

middle: Christine

last: Poirier

state: MD

address: 37 Convent Dr, MSC 4255, Bldg 37 Rm 4032 NIH

institute: National Cancer Institute, NIH

description: mAdb experiment ID: 121323

hyb_protocol: Affymetrix Hybridization Protocol Other: Residual DNA was removed by digestion with DNase I, and the total RNA quantity and purity were assessed by spectrophotometry (Agilent 2100 Bioanalyzer) and gel electrophoresis. cDNA was obtained using the SuperScript III First Strand-Synthesis System (Invitrogen). cDNAs were hybridized to the GeneChip Human Gene 1.0 ST Arrays (HuGene-1_0-st-v1 array; Affymetrix, Santa Clara, CA, USA).

scan_protocol: Affymetrix Scanning Protocol Other: The arrays were scanned by GeneChip Scanner (Affymetrix, Santa Clara,CA, USA).

data_processing:
Data Processing Protocol
Calculation Method: Arrays were normalized using Bioconductor Robust Multichip Average for intensity calculations.

source_name: TAM Treated NHMEC

label_protocol:
Sample Labeling Protocol
Other: cDNAs were fragmented and biotinylated.

extract_protocol:
RNase Easy Mini Kit
Other: For isolation of RNA, the cells were lysed with 1.0 mL of TRIzol Reagent (Invitrogen Life Technologies) and RNA was extracted using the RNase Easy Mini Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol:
Treatment type: compound
Agent: Tamoxifen (TAM)
Treatment dose: 10 µM
Treatment time: 48 hours
In-vitro treatment: Cells were exposed to 10 µM TAM for 48 hours.

value: Mammary

value: normal human mammary epithelial cells (NHMEC)


title: DC.12mo.M.Sp.1


title: Untreated NHMEC - repeat 4 - mAdbID:121324

description: mAdb experiment ID: 121324

source_name: Untreated NHMEC

treatment_protocol:
Treatment time: 48 hours
In-vitro treatment: Cells were exposed to DMSO for 48 hours.


title: 7d A+CP

value: Activin + CP-724714


title: 7d A+L

value: Activin + Lapatinib


title: TAM Treated NHMEC - repeat 4 - mAdbID:121325

description: mAdb experiment ID: 121325


title: 7d(-)

value: control


title: Untreated NHMEC - repeat 3 - mAdbID:121322

description: mAdb experiment ID: 121322


title: Untreated NHMEC - repeat 2 - mAdbID:121320

description: mAdb experiment ID: 121320


title: TAM Treated NHMEC - repeat 2 - mAdbID:121321

description: mAdb experiment ID: 121321


title: DC.12mo.F.Sp.4


title: InVivoNHEK_1.2mMCa+1μMCP-609,550_rep2

first: Ratklao

last: Siriwach

address: Sakyo-ku, Shogoin Kawahara-cho

department: Department of Drug Discovery Medicine

institute: Kyoto University Graduate School of Medicine

description: Gene expression after 72hr in 1.2mMCa+1μMCP-609,550-cultured NHEKs

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
75th percentile normalization in this study according to GeneSpring software from Agilent.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: NHEKs were seeded into 24-welled plated in concentration of 5x104 cells per well for 24 h. Growth factors were removed and cultured medium was changed to low calcium concentration (60 μM) medium for 2 days.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (QIAGEN, Germany) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: 10μM Oleoyl-L-α-lysophosphatidic acid  or 1μM CP-609,550 together with high calcium (final concentration 1.2 mM) were then added into the cell culture in the presence of 30 ng/ml IL-4. Cells were further incubated for 3 days at 37 ºC in a humidified incubator with 5% CO2.

value: normal human epidermal keratinocytes (NHEKs)

tag: stimulation condition


title: InVivoNHEK_1.2mMCa+1μMCP-609,550_rep3


title: InVivoNHEK_1.2mMCa+1μMCP-609,550_rep1


title: InVivoNHEK_1.2mMCa+10μMLPA_rep3

description: Gene expression after 72hr in 1.2mMCa+10μMLPA-cultured NHEKs


title: InVivoNHEK_1.2mMCa+10μMLPA_rep2


title: InVivoNHEK_1.2mMCa+10μMLPA_rep1


title: TAM Treated NHMEC - repeat 1 - mAdbID:121319

description: mAdb experiment ID: 121319


title: Untreated NHMEC - repeat 1 - mAdbID:121318

description: mAdb experiment ID: 121318


title: DC.12mo.F.Sp.3


title: Treg.3mo.F.TI.4

value: 3 month old

value: Regulatory T cells


title: Treg.3mo.F.TI.3


title: InVivoNHEK_1.2mMCa_rep3

description: Gene expression after 72hr in 1.2mMCa-cultured NHEKs


title: Untreated HESC - repeat 4 - mAdbID:119715

description: mAdb experiment ID: 119715

source_name: Untreated HESC

treatment_protocol:
Treatment time: 48 hours
In-vitro treatment: Cells were exposed to vehicle for 48 hours.

value: Endometrial tissue

value: human endometrial stromal cells (HESC)


title: Treg.3mo.F.TI.2


title: Treg.3mo.F.TI.1


title: InVivoNHEK_1.2mMCa_rep2


title: wild-type, biological rep2

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: 10 ug of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by Affymetrix GeneChip Command Console as CEL files. CHP files are generated by Affymetrix Expression Console. The data were analyzed with MAS 5.0 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Caenorhabditis elegans

source_name: wild-type worms on control(RNAi)

label_protocol: 200 ng total RNA converted to cRNA using Affymetrix GeneChip®3' IVT Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

growth_protocol: Wild-type and zip-3(gk3164) worms were synchronized by bleaching and raised in liquid culture.

extract_protocol: Total RNA was isolated using the RNA STAT reagent (Tel-Test Inc) according to the manufacturer's instructions.

treatment_protocol: Worms were fed control (RNAi)

value: whole organism

value: wild-type


title: Untreated HESC - repeat 3 - mAdbID:119713

description: mAdb experiment ID: 119713


title: wild-type, biological rep3


title: Treg.3mo.F.Sp.4


title: TAM Treated HESC - repeat 4 - mAdbID:119714

description: mAdb experiment ID: 119714

source_name: TAM Treated HESC


title: zip-3(gk3164), biological rep3

source_name: zip-3(gk3164) worms on control(RNAi)


title: InVivoNHEK_1.2mMCa_rep1


title: zip-3(gk3164), biological rep2


title: wild-type, biological rep1


title: zip-3(gk3164), biological rep1


title: Treg.3mo.F.Sp.3


title: TAM Treated HESC - repeat 3 - mAdbID:119712

description: mAdb experiment ID: 119712


title: Hep-Ethanol-24 hr-54

city: Philadelphia

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1020 Locust Street

department: Pathology, Anatomy and Cell Biology

institute: Thomas Jefferson University

description: SAMPLE 233

data_processing:
The data were normalized using the -ΔΔCt scheme. Expression values within samples were normalized using the median expression of 55 high performing genes (Ct_reaction - Ct_median_across_55_genes). Expression values within genes were scaled to the median using (Ct_median_across_all_samples - Ct_reaction)
Missing values were imputed using the k-nearest neighbors imputation after normalization

label: SYBR Green

source_name: Ethanol-24 hr

extract_protocol: Single hepatocytes extracted using laser capture microdissection were lysed and directly processed for reverse transcription followed by targeted pre-amplification. Pre-amplification of cDNA samples was performed for 22 cycles using TaqMan PreAmp Master Mix as per the manufacturer’s protocol. Primers for the 84 genes tested were custom designed. qPCR was performed on BioMark 96.96 Dynamic Array for 30 cycles.

treatment_protocol: Lieber-De Carli feeding protocol

value: Hepatocyte

value: liver

tag: diet

value: Ethanol

tag: time after partial hepatectomy

value: 24 hr


title: Hep-Ethanol-24 hr-53

description: SAMPLE 232


title: EmrR regulon replicate 3

city: Ribeirao Preto

first: Jose

middle: Freire

last: da Silva Neto

state: Sao Paulo SP

address: Av Bandeirantes 3900

department: Biologia Celular e Molecular e Bioagentes Patogenicos

country: Brazil

institute: Universidade de Sao Paulo

description:
WT Control x ∆emrR - rep3
Biological replicate 3 of 3

hyb_protocol: Pooled labeled cRNA samples were fragmented and hybridized to the C. violaceum microarray slides. After hybridization, slides were washed sequential according to the Agilent Two-Color Microarray-Based Exon Analysis Protocol, version 1.0 (Agilent Technologies)

scan_protocol: The slides were scanned with the G2505C Agilent DNA Microarray Scanner

data_processing: Data were extracted and normalized (LOWESS normalization) using the Agilent Feature Extraction software, version 10.5.

organism: Chromobacterium violaceum

source_name: C. violaceum WT untretaed

label_protocol: The fluorescence-labeled cRNA (complementary RNA) was generated of total RNA derived from each experimental condition using the Low Input Quick Amp WT Two-Color kit (Agilent Technologies)

growth_protocol: Bacteria were grown at 37 °C in LB medium until mid-log phase (OD600 of 0.8 to 1.0)

extract_protocol: Total RNA was extracted using Trizol reagent (Ambion) and purified with the illustra RNAspin Mini RNA Isolation Kit (GE Healthcare)

tag: strain

tag: growth

value: midlog phase LB

value: WT

source_name: C. violaceum ∆emrR untretaed

value: ∆emrR mutant (JF0769)

value: {delta}emrR


title: Hep-Ethanol-24 hr-52

description: SAMPLE 231

tag: cell type


title: Bub1b_R_-Dox_rep3

city: san francisco

first: Yen-Sin

last: Ang

state: CALIFORNIA

address: 1650 Owens Street

institute: Gladstone Institute, UCSF

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data was VST transformed, RSN normalized in R using LUMI package.

source_name: Embryonic Stem Cell

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

growth_protocol: rtTA-expressing ES cells Ainv15 were used for derivation of rescue clones and were maintained on primary mouse embryonic fibroblasts with DMEM media supplemented with 15% FBS, 100 mM MEM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 1 mM l-glutamine and 103 U ml-1 of LIF (Chemicon) and doxycycline (1ug/ml).

extract_protocol: Total 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.

treatment_protocol: Each rescue ES clone was grown in +Dox (1ug/ml) media; Dox withdrawal was performed for 5 days.

value: Embryonic stem cell line

tag: rescue clone

tag: condition

value: -Dox


title: TAM Treated HESC - repeat 1 - mAdbID:119708

description: mAdb experiment ID: 119708


title: Treg.3mo.F.Sp.1

source_name: Spleen

tag: age

tag: sorting markers


title: EmrR regulon replicate 1

description:
WT Control x ∆emrR - rep1
Biological replicate 1 of 3


title: Untreated HESC - repeat 2 - mAdbID:119711

description: mAdb experiment ID: 119711

tag: tissue


title: EmrR regulon replicate 2

description:
WT Control x ∆emrR - rep2
Biological replicate 2 of 3

tag: genotype


title: Hep-Ethanol-24 hr-51

description: SAMPLE 230


title: Treg.12mo.F.TI.4

source_name: Tumor

value: 12 month old


title: TAM Treated HESC - repeat 2 - mAdbID:119710

description: mAdb experiment ID: 119710


title: Bub1b_R_-Dox_rep2

tag: cell line


title: Bub1b_R_-Dox_rep1


title: Treg.3mo.F.Sp.2

value: 3 month old


title: EGFRvIII

city: San Francisco

first: Zhenyi

last: An

department: Neurology

institute: UCSF

description:
vIII_FPKM
ZA001D_VSC_S18_L005

data_processing:
TopHat  v2.0.14
Cufflinks
Cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: Glioblastoma

growth_protocol: DMEM:F12 with 20ng/ml EGF, 20ng/ml FGF, 1xB27 supplement and 1x Penicillin-Streptomycin

extract_protocol:
RNA was extracted using a ZYMO Research quick RNA miniprep kit (R1055)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Glioblastoma cell line

tag: genotype/variation

value: expressing EGFRvIII


title: EGFR+EGFRvIII

description:
EGFR+vIII_FPKM
ZA001E_ETV_SC_S19_L005

value: expressing EGFR+EGFRvIII


title: Bub1b_R_+Dox_rep3

value: +Dox


title: Hep-Ethanol-24 hr-50

description: SAMPLE 229


title: Untreated HESC - repeat 1 - mAdbID:119709

description: mAdb experiment ID: 119709

value: Endometrial tissue

value: human endometrial stromal cells (HESC)


title: Hep-Ethanol-24 hr-49

description: SAMPLE 228

value: Hepatocyte

value: liver


title: EGFR

description:
EGFR_FPKM
ZA001B_ESC_S16_L005

value: expressing EGFR


title: Treg.12mo.F.TI.3

value: Regulatory T cells


title: EGFR+EGFRvIII KRAS KO

description:
KRAS KO_FPKM
ZA001C_KSC_S17_L005

value: expressing EGFR+EGFRvIII KRAS KO


title: Treg.12mo.F.TI.2


title: Hep-Ethanol-24 hr-48

description: SAMPLE 227

value: Ethanol

value: 24 hr


title: Ppp2r1b_R_-Dox_rep2

value: Embryonic stem cell line


title: Bub1b_R_+Dox_rep2


title: Ctrl

description:
Parent_FPKM
ZA001F_PARENT_SC_S20_L005

value: control (parent)


title: Ppp2r1b_R_-Dox_rep3

value: -Dox


title: Ppp2r1b_R_-Dox_rep1


title: Bub1b_R_+Dox_rep1


title: Treg.12mo.F.TI.1

value: 12 month old


title: Treg.12mo.F.Sp.1


title: Treg.12mo.F.Sp.3


title: Treg.12mo.F.Sp.4


title: Treg.12mo.F.Sp.2


title: Hep-Ethanol-24 hr-47

description: SAMPLE 226


title: Hep-Ethanol-24 hr-45

description: SAMPLE 224


title: Hep-Ethanol-24 hr-46

description: SAMPLE 225


title: Hep-Ethanol-24 hr-44

description: SAMPLE 223


title: Hep-Ethanol-24 hr-43

description: SAMPLE 222


title: MF.3mo.F.TI.4

value: 3 month old

value: Macrophages


title: Hep-Ethanol-24 hr-42

description: SAMPLE 221


title: Hep-Ethanol-24 hr-41

description: SAMPLE 220


title: MF.3mo.F.TI.3


title: Ppp2r1b_R_+Dox_rep2


title: miR142 KO spleen biological replicate 2

city: St. Louis

first: Todd

middle: A.

last: Fehniger

state: MO

address: Department of Medicine, Oncology Division

department: Internal Medicine, Oncology Division

institute: Washington University

description: 21257 - SP_142KO_2

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module,2.5 ug of cDNA were hybridized into the GeneChip Hybridization Oven 640 for 18 hr at 45C on Gene 1.0 ST Array. GeneChip were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were analyzed using Expression Console software with Affymetrix default RMA Gene analysis settings.(Affymetrix, Inc).  Probe summarization (Robust Multichip Analysis, RMA), quality control analysis, and probe annotation were performed according to recommended guidelines (Expression Console Software, Affymetrix, Inc.).

source_name: miR142 KO spleen

label_protocol: Biotinylated cDNA were prepared according to the standard NuGen Ovation PicoSL WTA System V2 system from 500pg-50 ng total RNA

growth_protocol: 7-10 week old mice were sacrificed and tissues harvested.

extract_protocol: Trizol followed by phenol/chloroform extraction

treatment_protocol: NK cells were sorted (CD3- NK1.1+) from spleen and bone marrow of WT and miR-142 KO age/sex matched mice.

value: miR142 KO

value: spleen

value: NK cells


title: WT

first: Biao

last: Wang

address: 555 Mission Bay Blvd South

department: CVRI

institute: University of California, San Francisco

hyb_protocol: Using protocol provided for the manufacturer for mouse gene array 1.0.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Inguinal white adipose tissue

growth_protocol: Inguinal white adipose tissue was collected from ~8-week-old male wild-type and H4-TG mice housed at normal chow at room temperature.

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

tag: gender

value: Male

value: Inguinal white adipose


title: Hep-Ethanol-24 hr-40

description: SAMPLE 219

value: Hepatocyte

value: liver


title: H4-TG

label_protocol: Using protocol provided for the manufacturer for mouse gene array 1.0.


title: miR142 KO spleen biological replicate 1

description: 21256 - SP_142KO_1


title: Ppp2r1b_R_+Dox_rep1

value: +Dox


title: Ppm1g_R_+Dox_rep3


title: miR142 WT bone marrow biological replicate 3

description: 21259 - BM_WT_3

source_name: miR142 WT bone marrow

value: miR142 WT

value: bone marrow


title: Ppm1g_R_-Dox_rep2


title: MF.3mo.F.TI.1


title: Hep-Ethanol-24 hr-39

description: SAMPLE 218

value: Ethanol

value: 24 hr


title: Ppp2r1b_R_+Dox_rep3

value: Embryonic stem cell line


title: Ppm1g_R_-Dox_rep3

value: -Dox


title: miR142 WT spleen biological replicate 3

description: 21255 - SP_WT_3

source_name: miR142 WT spleen


title: MF.3mo.F.TI.2


title: Ppm1g_R_-Dox_rep1


title: Ppm1g_R_+Dox_rep2


title: Hep-Ethanol-24 hr-37

description: SAMPLE 216


title: MF.3mo.F.Sp.3


title: MF.3mo.F.Sp.4


title: miR142 WT bone marrow biological replicate 2

description: 21258 - BM_WT_2


title: Hep-Ethanol-24 hr-38

description: SAMPLE 217


title: MF.3mo.F.Sp.2


title: MF.3mo.F.Sp.1


title: miR142 KO bone marrow biological replicate 1

description: 21196 - BM_142KO_1

source_name: miR142 KO bone marrow


title: miR142 KO bone marrow biological replicate 2

description: 21197 - BM_142KO_2


title: Ppm1g_R_+Dox_rep1


title: Chek1_R_-Dox_rep3


title: miR142 KO bone marrow biological replicate 3

description: 21198 - BM_142KO_3


title: Hep-Ethanol-24 hr-34

description: SAMPLE 213


title: MF.12mo.F.TI.3

value: 12 month old


title: Hep-Ethanol-24 hr-33

description: SAMPLE 212


title: Hep-Ethanol-24 hr-36

description: SAMPLE 215


title: Hep-Ethanol-24 hr-32

description: SAMPLE 211


title: Chek1_R_-Dox_rep2


title: miR142 WT bone marrow biological replicate 1

description: 21193 - BM_WT_1


title: Chek1_R_+Dox_rep2


title: Hep-Ethanol-24 hr-35

description: SAMPLE 214


title: MF.12mo.F.TI.1


title: Chek1_R_-Dox_rep1


title: Hep-Ethanol-24 hr-31

description: SAMPLE 210


title: Chek1_R_+Dox_rep1


title: Chek1_R_+Dox_rep3


title: miR142 WT spleen biological replicate 2

description: 21188 - SP_WT_2


title: MF.12mo.F.TI.4


title: LNCaP shFOXA1 10d, LY 10uM 3d

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: SAMPLE 5

hyb_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.

data_processing: The data were processed and normalised using Illumina GenomeStudio

source_name: ATCC

growth_protocol: Cells were maintained in RPMI supplemented with 10% FBS and 1% PS.

extract_protocol: Total RNA were extracted using Trizol according to manufacturer's instructions. The quantity and quality of the isolated RNAs was determined using ND-1000 Spectrophotometer.

treatment_protocol: LNCaP cells were infected with pLenti-cmv-puro-TGFBR2 lentivirus followed by puromycin selection to establish LNRII stable cell line. LNRII cells were then treated with 5ng/ml TGFB3 ligand or vehicle control for 3 days before being harvested. LNCaP cells were infected with shCtr or shFOXA1 lentivirus, and followed by puromycin selection 48h post infection. Cells were then treated with 10uM LY2157299 or vehicle control for 3 days before being harvested.

value: LNCaP

tag: treatment

value: WT


title: MF.12mo.F.Sp.4

first: Juhyun

last: Oh

institute: Massachusetts General Hospital

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.3
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM12)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

extract_protocol:
Extractions follow ImmGen standard operating protocol (available on https://www.immgen.org/). Briefly, organs are harvested at 9am on day of sort, perterbed as little as possible during preparation, and 1000 cells are double sorted into TCL buffer (Qiagen, Hilden, Germany) containing 1% BME.
Libraries are constructed according to the standard protocol for Smart-seq2 (Picelli et al, 2013) at the Broad Techology Labs in Cambridge, MA
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Macrophages


title: miR142 KO spleen biological replicate 3

description: 21192 - SP_142KO_3

value: miR142 KO

value: spleen


title: LNCaP shCtr 10d

description: SAMPLE 3

scan_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.

value: shCtrl


title: Hep-Ethanol-24 hr-30

description: SAMPLE 209


title: MF.12mo.F.Sp.3


title: MF.12mo.F.TI.2


title: Hep-Ethanol-24 hr-29

description: SAMPLE 208


title: miR142 WT spleen biological replicate 1

description: 21187 - SP_WT_1

value: NK cells


title: Hep-Ethanol-24 hr-28

description: SAMPLE 207

value: Hepatocyte


title: MF.12mo.F.Sp.2


title: MF.12mo.F.Sp.1


title: LNCaP shFOXA1 10d

description: SAMPLE 4

label_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.


title: Ulcerative colitis ascending colon subject 20

first: Tony

last: Segal

address: 5 University Street

department: Medicine

institute: UCL

description:
200536980043_L
included in the non normalised data but not the normalised data as there was discordant expression of genes which should not be present in the site of biopsy allocated and therefore did not meet our quality control standard

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed using Illumina Genome Studio software

source_name: Colonic pinch biopsy

label_protocol: 250 ng of total RNA was amplified and purified using the Illumina TotalPrep-96 RNA amplification kit

extract_protocol: 67 Biopsies (∼25 mg/biopsy) were lysed in 300 μL RNeasy Fibrous Tissue kit (Qiagen) RLT buffer and 0.14 M β-mercaptoethanol (β-ME) (Sigma-Aldrich, St Louis, MO) and then homogenized by centrifugation at 10,000 g through a Qiashredder column (Qiagen). Protein was removed by incubation for 10 minutes at 55°C with 10 μL Proteinase K (20 mg/mL) (>600 mAU/mL) (Qiagen). Total RNA was extracted on RNeasy Mini spin columns and DNA was removed with RNase free DNase digestion (Qiagen).

treatment_protocol: Healthy controls (HC) were recruited from individuals undergoing colonoscopy, matched for gender and age (+/- 5 years) (Table 1).  Biopsies collected during routine colonoscopies and were performed on UC patients undergoing surveillance that had clinically quiescent disease for a minimum of three months prior to the procedure and upon inspection had macroscopically normal colonic mucosa. Paired endoscopic pinch biopsies (Olympus biopsy-forceps, FB-24U-1) were obtained from macroscopically normal mucosa of the ascending colon and rectum.

value: F

value: Ascending colon

tag: diagnosis

value: Healthy control=NA Ulcerative colitis=E Extent of disease:1=proctitis 2=left sided disease 3=pancolitis:E2

tag: patient id


title: CD11b(AdTGFb1, Exp3) (DC 956)

city: Hannover

first: David

middle: S.

last: DeLuca

address: Carl-Neuberg-Str 1

department: Biomedical Research in End-stage and Obstructive Lung Disease Hannover

institute: Hannover Medical School

description:
N0309
AdTGFß1

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version 2.16.0.10 (Illumina).
The FASTQ files were adapter and quality trimmed using Trim Galore! (version 0.4.1) with default settings as described in the User Guide except for the setting of the quality cutoff (-q/--quality) which was set to a Phred score of 15. Trim Galore! used Cutadapt (version 1.9.1) as subroutine.Quality control of FASTQ files was performed by FastQC (version 0.11.4) before and after trimming.After sequencing, BCL files were de-multiplexed and converted to FASTQ files (GATC).
After trimming, FASTQ files were mapped against a reference genome with the splice-aware aligner STAR (version 2.5.0c) to generate BAM files. The BAM files were built in a 2-pass Mapping (--twopassMode Basic) and were finally sorted (--outSAMtype BAM SortedByCoordinate). All other setting have been left as default as described in the manual. The genome index files were created by STAR with default settings using Mus musculus sequence and annotation data (UCSC, build mm9) available on illumina’s iGenome site (http://support.illumina.com/sequencing/sequencing_software/igenome.html).
Read counts per gene were calculated using htseq-count with the UCSC GTF for mm9
Normalization and differential expression analysis were performed with DESeq2
Genome_build: UCSC mm9
Supplementary_files_format_and_content: cd11b_expression.data.txt provides the raw read counts as produced by htseq-count

source_name: CD11b DCs

growth_protocol: WT mice (C57BL/6J) were purchased from Charles River (Sulzfeld, Germany). Animals were kept under individually ventilated cages (IVC) conditions with free access to food and water, unless otherwise stated, and were used for experiments at 8 to 12 weeks of age. All animal experiments were approved by the Lower Saxony State Office for Consumer Protection and Food Safety.

extract_protocol:
RNeasy Micro-Kit from Qiagen
500 ng of total RNA per sample were utilized as input for mRNA enrichment procedure with ‘NEBNext® Poly(A) mRNA Magnetic Isolation Module’ (E7490L; New England Biolabs) followed by stranded cDNA library generation using ‘NEBNext® Ultra Directional RNA Library Prep Kit for Illumina’ (E7420L; New England Biolabs). All steps were performed as recommended in user manualE7420 (Version 6.0_08-2015; NEB) except that all reactions were downscaled to 2/3 of initial volumes. Furthermore, one additional purification step was introduced at the end of the standard procedure, using of 1x ‘Agencourt® AMPure® XP Beads’ (#A63881; Beckman Coulter, Inc.). cDNA libraries were barcoded by single indexing approach, using ‘NEBNext Multiplex Oligos for Illumina – Set 1’ (Index Primer 1 – 12). All generated cDNA libraries were amplified by 10 cycles of final pcr.

treatment_protocol: Replication-deficient adenoviral vectors without gene insertion (empty control vector, AdCL), or vector containing the biologically active form of the porcine TGF-β1 gene were prepared as previously detailed ( Sime PJ, 1997). WT mice were anesthetized with an intraperitoneal injection of xylazine (3 mg/kg body weight; Bayer, Leverkusen, Germany) and ketamine (75 mg/kg; Albrecht, Aulendorf, Germany), and were then subjected to intratracheal aspiration of 108 plaque-forming units of respective AdTGF-β1 or empty control (AdCL) vectors.

value: CD11b DCs

value: Wildtype


title: Hep-Ethanol-24 hr-25

description: SAMPLE 204

value: liver

tag: diet

value: Ethanol

value: 24 hr


title: Hep-Ethanol-24 hr-26

description: SAMPLE 205

tag: time after partial hepatectomy


title: Hep-Ethanol-24 hr-27

description: SAMPLE 206


title: LNRII control 3d

description: SAMPLE 1

value: LNRII

value: control


title: Hep-Ethanol-24 hr-24

description: SAMPLE 203


title: CD11b(AdTGFb1, Exp3) (DC 955)

description:
N0308
AdTGFß1

tag: strain


title: sFB-protein-iPS.3

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

description: To export to gene expression data based on unique probe id, we use Illumina BeadStudio software.

hyb_protocol: Labeled, amplified material (1,500 ng per array) was hybridized to a ver. 2 of the Illumina MouseRef-8 BeadChip (24K) according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA). Array signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the BeadChip manual.

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions.

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using log2 transformatoin.

source_name: induced pluripotent stem cell of mouse

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina’s recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina® TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using RiboGreen were measured (Quant-iTTM RiboGreen® RNA assay kit; Invitrogen-Molecular Probes, ON, Canada) by the Victor3 spectrophotometer (PerkinElmer, CT) and cRNA quality was checked on a 1% agarose gel.

extract_protocol: Total RNA was isolated from tissues with TRIzol (Life Technologies, NY) reagent according to the manufacturer’s protocol. RNA quality and integrity were confirmed by electrophoresis on agarose gel stained with ethidium bromide

value: induced pluripotent stem cell


title: FVB-sFB.3

source_name: mouse embryonic stem cell

value: embryonic stem cell


title: sFB-protein-iPS.1


title: LNRII TGFB3 5ng/ml 3d

description: SAMPLE 2

value: WT


title: FVB-sFB.2


title: sFB-protein-iPS.4


title: FVB-sFB.1


title: C57-mES.4


title: Hep-Ethanol-24 hr-23

description: SAMPLE 202

source_name: Ethanol-24 hr


title: Ulcerative colitis ascending colon subject 19

value: Healthy control=NA Ulcerative colitis=E Extent of disease:1=proctitis 2=left sided disease 3=pancolitis:E1


title: Ulcerative colitis ascending colon subject 18

value: M


title: CD11b(AdCL, Exp3) (DC 949)

description:
N0306
Control

value: Control


title: CD11b(AdTGFb1, Exp3) (DC 954)

description:
N0307
AdTGFß1


title: Ulcerative colitis ascending colon subject 17


title: Hep-Ethanol-24 hr-22

description: SAMPLE 201

value: Hepatocyte


title: CD11b(AdCL, Exp3) (DC 944)

description:
N0305
Control


title: sFB-protein-iPS.2


title: Hep-Ethanol-24 hr-21

description: SAMPLE 200


title: CD11b(AdCL, Exp3) (DC 943)

description:
N0304
Control


title: CD11b(AdTGFb1, Exp1) (DC 54)

description:
N0303
AdTGFß1


title: Hep-Ethanol-24 hr-20

description: SAMPLE 199


title: CD11b(AdTGFb1, Exp1) (DC 52)

description:
N0302
AdTGFß1


title: C57-mES.3


title: CD11b(AdTGFb1, Exp1) (DC 14)

description:
N0301
AdTGFß1


title: Hep-Ethanol-24 hr-19

description: SAMPLE 198


title: Ulcerative colitis ascending colon subject 8

value: F

value: Healthy control=NA Ulcerative colitis=E Extent of disease:1=proctitis 2=left sided disease 3=pancolitis:E3


title: Ulcerative colitis ascending colon subject 12

value: Ascending colon


title: Hep-Ethanol-24 hr-18

description: SAMPLE 197


title: Ulcerative colitis ascending colon subject 14


title: CD11b(AdCL, Exp1) (DC 9)

description:
N0300
Control

value: CD11b DCs


title: Hep-Ethanol-24 hr-17

description: SAMPLE 196


title: Ulcerative colitis ascending colon subject 3

value: Healthy control=NA Ulcerative colitis=E Extent of disease:1=proctitis 2=left sided disease 3=pancolitis:E2


title: CD11b(AdCL, Exp1) (DC 8)

description:
N0299
Control

value: Wildtype


title: Hep-Ethanol-24 hr-16

description: SAMPLE 195

value: liver

value: Ethanol


title: C57-mES.1


title: Hep-Ethanol-24 hr-15

description: SAMPLE 194

value: 24 hr


title: Ulcerative colitis rectum subject 18

description:
200616460066_J
included in the non normalised data but not the normalised data as there was discordant expression of genes which should not be present in the site of biopsy allocated and therefore did not meet our quality control standard

value: Rectum


title: C57-mES.2


title: CD11b(AdCL, Exp1) (DC 7)

description:
N0298
Control


title: Ulcerative colitis ascending colon subject 7


title: GFPoct4.4


title: input DNA_R2

city: Taipei

first: Ya-Ping

last: Yen

address: 128 Academia Road, Section 2, Nankang

department: Institute of molecular biology

country: Taiwan

institute: Academia Sinica

data_processing:
Reads were trimmed by PEAT
Aligned to the mm10 genome using Bowtie2
All alignments were extended downstream to span an exact 150 bp-long region. Extensions that exceeded the ends of chromosomes were clipped.
The extended alignments were input into the genomecov functionality supported in the bedtools suite to generate read coverage profiles at a base-pair resolution. The coverage for each chromosomal position was normalized according to the mappable read count. Each sample was averaged and binned to reveal major trends.
MACS 1.4 to call peaks in each ChIP-seq sample with the corresponding input library and then overlapping peaks were merged using MAnorm to reveal loci with a significant change between two samples.
Genome_build: mm10
Supplementary_files_format_and_content: peaks_bed.txt

source_name: motor neurons

growth_protocol: ESCs were cultured and differentiated into spinal MNs, as previously described (Wichterle et al., 2002; Wichterle et al., 2009)

extract_protocol:
Dissociated motor neurons were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27me3 antibody
Libraries were prepared according to Illumina's instructions accompanying the KAPA TruSeq DNA library prep kit (KK8201). Briefly, DNA was end-repaired by using End Repair Mix (ERP). After adapter ligation DNA was PCR amplified with Illumina primers for 12 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: ES-derived motor neurons

tag: passages

tag: chip antibody


title: input DNA_R1

tag: cell type


title: Ulcerative colitis ascending colon subject 2


title: Hep-Ethanol-24 hr-14

description: SAMPLE 193


title: Meg3 KD_H3K27me3_ChIP-Seq_R2

value: Meg3 KD

value: H3K27me3 (Abcam,  ab6002)


title: Ulcerative colitis rectum subject 11

description:
200616460040_I
included in the non normalised data but not the normalised data as there was discordant expression of genes which should not be present in the site of biopsy allocated and therefore did not meet our quality control standard


title: Meg3 KD_H3K27me3_ChIP-Seq_R1


title: Hep-Ethanol-24 hr-12

description: SAMPLE 191


title: GFPoct4.3

value: embryonic stem cell


title: Hep-Ethanol-24 hr-13

description: SAMPLE 192


title: Ctrl_H3K27me3_ChIP-Seq_R2

value: wildtype


title: GFPoct4.1


title: GFPoct4.2


title: E14-mES.4


title: Ulcerative colitis rectum subject 19

value: Healthy control=NA Ulcerative colitis=E Extent of disease:1=proctitis 2=left sided disease 3=pancolitis:E1


title: Hep-Ethanol-24 hr-10

description: SAMPLE 189

value: Hepatocyte


title: Ulcerative colitis ascending colon subject 1

value: M


title: Ctrl_H3K27me3_ChIP-Seq_R1


title: Ulcerative colitis ascending colon subject 4


title: Hep-Ethanol-24 hr-11

description: SAMPLE 190


title: FVB-sFB.4


title: Ulcerative colitis rectum subject 14

value: F


title: Neonatal7

city: Gainesville

first: Jacquelyn

middle: Mary

last: Walejko

state: FL

department: Pharmacodynamics

institute: University of Florida

description: Gene expression in heart tissue at day 1 of life

hyb_protocol: 600 ng of Cy3-labeled cRNA was fragmented and mixed with hybridization buffer using the Agilent gene expression hybridization kit (5188-5242, Santa Clara, CA, USA). These were applied to a sheep 8 X 15 K array slide (Agilent 019921) and hybridized at 65°C for 17 h at 10 rpm. Following hybridization, the arrays were washed, dried, and stabilized according to manufacturer’s instructions.

scan_protocol: Slides were scanned immediately after washing on an Agilent Microarray Scanner (G2505B, Santa Clara, CA, USA) using one color scan setting at the Interdisciplinary Center for Biotechnology Research at the University of Florida.

data_processing: The scanned images were analyzed with Agilent Feature extraction 9.1 software using default parameters. Features flagged as Feature Nonuniform outliers were excluded from further analysis.

organism: Ovis aries

source_name: Left ventricle cardiac tissue, Animal 1767A

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng of DNase-treated RNA using Agilent Quick Amp Kit (5190-0442, Santa Clara, CA, USA) and purified with Qiagen Rneasy kit (Valencia, CA, USA). Dye incorporation and cRNA yield were determined with the NanoDrop ND-1000 spectrophotometer (ThermoFisher, Wilmington, DE, USA).

extract_protocol: Left ventricular cardiac tissue samples (~200 mg from 7 fetuses and 7 newborns) were homogenized and messenger RNA (mRNA) was extracted with Trizol and purified with on-column DNase digestion (Qiagen RNeasy Plus Kits, Germantown, MD, USA). RNA concentration was determined using a Nanodrop-1000 Spectrophotometer (ThermoFisher, Wilmington, DE, USA) and RNA integrity was determined on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Heart tissue was collected from the left venricle on the day of birth (newborn group) or at gestational day 142 (fetal group) and immediately frozen in liquid nitrogen. Samples were stored at -80 °C until mRNA extraction.

value: Day 1

tag: Sex

value: Female


title: scRNAseq of cells from the preoptic region of a pool of three male mice: Replicate 3

city: Boston

last: Moffitt

state: MA

address: 200 Longwood Ave

department: Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital

description: Processed data are contained with the matrix.mtx file and correspond to all cell names that end with -6

data_processing:
Construction of fastq files using cellranger (v2.0.0) mkfastq command
Alignment of files to reference genome using cellranger (v2.0.0) count
Aggregation of multiple samples using cellranger (v2.0.0) aggr
Genome_build: mm10-1.2.0
Supplementary_files_format_and_content: matrix.mtx contains the aggreggated counts from all samples
barcodes.tsv contains the name associated with each cell for all samples. The order is the same as the order of entries in matrix.mtx
genes.tsv contains the name associated with each measured gene. The order is the same as the order of entries in matrix.mtx

molecule: polyA RNA

source_name: Preoptic region of the hypothalamus

growth_protocol: Mice were between 60 and 70 PND

extract_protocol:
The preoptic region of the hypothalamus was dissected from freshly prepared brains, dissociated into individual cells via protease treatement, FACS sorted to enrich live cells, and then prepared using the 10X Chromium protocols.
Libraries were constructed following the instructions of the 10xGenomics Chromium platform

treatment_protocol: Mice were housed individually for 3 days prior to sampling

value: brain

tag: brain region

value: Preoptic region of the hypothalamus

value: male


title: Hep-Ethanol-24 hr-8

description: SAMPLE 187

value: liver

value: Ethanol


title: Hep-Ethanol-24 hr-9

description: SAMPLE 188

value: 24 hr


title: Neonatal5

source_name: Left ventricle cardiac tissue, Animal 5562C

tag: age


title: Ulcerative colitis rectum subject 15

city: London

tag: tissue

value: Rectum

value: Healthy control=NA Ulcerative colitis=E Extent of disease:1=proctitis 2=left sided disease 3=pancolitis:E2


title: Neonatal6

source_name: Left ventricle cardiac tissue, Animal 1462

value: Male


title: E14-mES.3

value: embryonic stem cell


title: Neonatal4

source_name: Left ventricle cardiac tissue, Animal 5562A


title: scRNAseq of cells from the preoptic region of a pool of three male mice: Replicate 2

description: Processed data are contained with the matrix.mtx file and correspond to all cell names that end with -5


title: E14-mES.2


title: E14-mES.1


title: scRNAseq of cells from the preoptic region of a pool of three male mice: Replicate 1

description: Processed data are contained with the matrix.mtx file and correspond to all cell names that end with -4


title: Neonatal3

source_name: Left ventricle cardiac tissue, Animal 1477


title: Neonatal2

source_name: Left ventricle cardiac tissue, Animal 5562B


title: Ulcerative colitis rectum subject 9

value: Healthy control=NA Ulcerative colitis=E Extent of disease:1=proctitis 2=left sided disease 3=pancolitis:E3


title: Ulcerative colitis rectum subject 13


title: Hep-Ethanol-24 hr-5

description: SAMPLE 184


title: scRNAseq of cells from the preoptic region of a pool of three female mice: Replicate 2

description: Processed data are contained with the matrix.mtx file and correspond to all cell names that end with -2

value: female


title: Hep-Ethanol-24 hr-7

description: SAMPLE 186

value: Hepatocyte


title: scRNAseq of cells from the preoptic region of a pool of three female mice: Replicate 1

description: Processed data are contained with the matrix.mtx file and correspond to all cell names that end with -1


title: Hep-Ethanol-24 hr-4

description: SAMPLE 183


title: Neonatal1

source_name: Left ventricle cardiac tissue, Animal 1767B


title: Ulcerative colitis rectum subject 7


title: Hep-Ethanol-24 hr-3

description: SAMPLE 182


title: Hep-Ethanol-24 hr-6

description: SAMPLE 185


title: Hep-Ethanol-24 hr-2

description: SAMPLE 181


title: Ulcerative colitis rectum subject 10

value: M


title: Hep-Ethanol-0 hr-55

description: SAMPLE 179

source_name: Ethanol-0 hr

value: 0 hr


title: Ulcerative colitis rectum subject 8

value: F


title: Hep-Ethanol-24 hr-1

description: SAMPLE 180


title: Hep-Ethanol-0 hr-53

description: SAMPLE 177


title: Hep-Ethanol-0 hr-54

description: SAMPLE 178


title: Hep-Ethanol-0 hr-52

description: SAMPLE 176


title: Hep-Ethanol-0 hr-51

description: SAMPLE 175


title: Fetal5

description: Gene expression in heart tissue at gestational age 142

source_name: Left ventricle cardiac tissue, Animal 1355A

value: Gestational day 142


title: Fetal6

source_name: Left ventricle cardiac tissue, Animal 1237B

value: Female


title: Ulcerative colitis rectum subject 6

source_name: Colonic pinch biopsy


title: Fetal4

source_name: Left ventricle cardiac tissue, Animal 1562


title: Ulcerative colitis rectum subject 2


title: Healthy control ascending subject 18

value: Ascending colon

value: Healthy control=NA Ulcerative colitis=E Extent of disease:1=proctitis 2=left sided disease 3=pancolitis:NA


title: Healthy control ascending subject 17


title: Ulcerative colitis rectum subject 4

value: Healthy control=NA Ulcerative colitis=E Extent of disease:1=proctitis 2=left sided disease 3=pancolitis:E1


title: SC10_rep2

city: Nashville

first: B Bishal

last: Paudel

state: TN

address: 2220 Pierce Ave PRB447

department: Biochemistry

institute: Vanderbilt University

data_processing:
mRNA enrichment and  cDNA library preparation were done with Illumina Tru-Seq stranded mRNA sample prep kit.
Sequencing  was done at Paired-End 75 bp on the Illumina HiSeq 3000.
Reads were aligned to the GRCh38  human reference genome using HISAT2
gene counts were obtained  using featureCounts
All downstream analyses were performed in R (https:  //www.r-project.org) using the Bioconductor framework (https://www.bioconductor.org).
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts for each sample obtained by featureCounts in R

source_name: Skin

growth_protocol: Single-cell-derived isogenic subclones were isolated from parental SK-MEL-5 cells in drug-free conditions by limiting dilution, and examined for drug sensitivity before frozen for further analyses. Three subclones (SC10, SC07, SC01) were selected for transcriptomic analysis based on their initial response to BRAF-inhibitors, PLX-4720.

extract_protocol:
Total RNA was extracted using Trizol extraction method as described.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Untreated expression of three subclones

tag: mutation

value: BRAF-mutated

value: Melanoma


title: SC07_rep3

tag: cell line


title: SC10_rep1


title: Fetal1

source_name: Left ventricle cardiac tissue, Animal 1237A


title: Healthy control ascending subject 12

description:
200536980043_F
included in the non normalised data but not the normalised data as the minimum detection value for our quality control was not met


title: SC07_rep2


title: Ulcerative colitis rectum subject 1

value: Rectum


title: Fetal2

source_name: Left ventricle cardiac tissue, Animal 1481


title: Healthy control ascending subject 14


title: Fetal3

source_name: Left ventricle cardiac tissue, Animal 1355B


title: Ulcerative colitis rectum subject 3

value: Healthy control=NA Ulcerative colitis=E Extent of disease:1=proctitis 2=left sided disease 3=pancolitis:E2


title: Healthy control ascending subject 16


title: Hep-Ethanol-0 hr-50

description: SAMPLE 174

value: liver

value: Ethanol


title: SC07_rep1


title: Hep-Ethanol-0 hr-49

description: SAMPLE 173


title: SC01_rep2


title: SC01_rep1


title: Hep-Ethanol-0 hr-48

description: SAMPLE 172


title: SC10_rep3


title: SC01_rep3


title: Hep-Ethanol-0 hr-47

description: SAMPLE 171


title: Hep-Ethanol-0 hr-46

description: SAMPLE 170


title: Hep-Ethanol-0 hr-45

description: SAMPLE 169


title: SZ-ABX-2-pgVAT

city: Dallas

first: Li

last: Li

state: TX

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center

data_processing:
The paired-end clean reads were aligned to the reference genome using STAR and each gene reads numbers were count by HTseq.
Differential expression gene (DEG) analysis was performed by DEseq2 package in which gene length and dispersion bias was corrected.
The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate (FDR).
Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: SUB_readcount.csv: raw_counts_scWAT
Supplementary_files_format_and_content: EP_readcount.csv: raw_counts_pgVAT

source_name: pgVAT

extract_protocol:
Total RNA from fat tissue were extract by RNeasy Mini Kit (Qiagen) according to manufacturer’s recommendations and validated by the Agilent 2100 Bioanalyzer.
Sequencing libraries were generated using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, USA).
150 bp paired-end reads were sequenced on Illumina Hiseq Xten platform in CapitalBio technology corporation (Beijng).

value: pgVAT

tag: group

value: SZ-ABX


title: SZ-ABX-1-pgVAT


title: SZ-ABX-3-pgVAT


title: ABX-3-pgVAT

value: ABX


title: ABX-2-pgVAT


title: Healthy control ascending subject 13

tag: gender


title: Hep-Ethanol-0 hr-44

description: SAMPLE 168

value: Hepatocyte


title: ABX-1-pgVAT


title: Hep-Ethanol-0 hr-42

description: SAMPLE 166

value: 0 hr


title: Healthy control ascending subject 10

value: M


title: Hep-Ethanol-0 hr-43

description: SAMPLE 167


title: Healthy control ascending subject 9


title: Hep-Ethanol-0 hr-40

description: SAMPLE 164


title: Hep-Ethanol-0 hr-39

description: SAMPLE 163


title: SEPT9_v3_rep_C

city: Bronx

first: Cristina

last: Montagna

address: 1301 Morris Park Avenue

institute: Albert Einstein College of Medicine

description:
SEPT9 upregulation
Sample_jz12

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie
Read count data were analyzed using DESeq
Detection of differentially expressed genes was perfformed using DESeq using the MCF7 control cells as reference
text file contaiing normalized read counts for each isoform relative to the SEPT9 over expressing clones was generated by DESeq
Genome_build: hg19
Supplementary_files_format_and_content: text file genetad by DESeq containing the normalized count matrix

growth_protocol: All cell lines were grown in DMEM supplemented with 8% fetal bovine serum and incubated in 5% CO2/37°C

extract_protocol:
MCF7_SEPT9_v1, MCF7_SEPT9_v2, and MCF7_SEPT9_v3-overexpressing cell lines and the MCF7 control cells (MCF7_C) were placed in culture simultaneously and split to establish three biological replicates; the plates were taken from culture when they reached 70% confluence.  The cells were then lysed directly on the plate with Qiazol lysis reagent (Qiagen, Valencia, CA) and placed at -80°C until all samples were ready for RNA extraction.  Total RNA was isolated using the miRNeasy kit (Qiagen, Valencia, CA) and assessed using an Agilent Bioanalyzer. All RNA had an RNA integrity number (RIN) score of 10.
The mRNA was randomly fragmented using the RNA fragmentation kit from Ambion. First-strand cDNA synthesis was performed using random primers and SuperScriptII reverse-transcriptase (Invitrogen, Carlsbad CA). This was followed by second-strand cDNA synthesis using DNA Polymerase I and RNase H (Invitrogen, Carlsbad CA). The Illumina adaptor was ligated to the ends of the double-stranded cDNA fragments and a 200bp size-selection of the final product was performed by gel-excision, following the Illumina-recommended protocol. Template molecules of 200bp cDNA with the adaptor attached were enriched by PCR to create the final library.

treatment_protocol: MCF7 clones overexpressing GFP chimera SEPT9_v1, SEPT9_v2, and SEPT9_v3 isoforms were previously described (PMID:21831286).  FACS enrichment of GFP positive clones was performed using live MCF7 clones. About 5x106 cells were trypsinized, washed in 2ml of 0.5%BSA in PBS, re-suspended in 0.5ml of 0.5%BSA in PBS, and then filtered using a 40μm cell strainer (Falcon Corning, Corning NY). GFP negative cells were used as a control and to set the threshold of true positive intensities. FACS was performed using the BD FACSAria II (BD Biosciences, San Jose, CA) equipped with a 100μm nozzle and a pressure of 20psi at 4°C. Cells were sorted in 5ml of complete media and immediately plated overnight to allow recovery.

tag: treatment

value: Stably expressing CMV_SEPT9_v3

value: Breast cancer


title: SEPT9_v2_rep_C

description:
SEPT9 upregulation
Sample_jz11

value: Stably expressing CMV_SEPT9_v2


title: Healthy control ascending subject 11

value: F

value: Ascending colon

tag: diagnosis

value: Healthy control=NA Ulcerative colitis=E Extent of disease:1=proctitis 2=left sided disease 3=pancolitis:NA


title: Healthy control ascending subject 7

tag: patient id


title: SEPT9_v1_rep_C

description:
SEPT9 upregulation
Sample_jz10

value: Stably expressing CMV_SEPT9_v1


title: Healthy control ascending subject 15


title: Ctrl-2-pgVAT

value: Ctrl


title: Hep-Ethanol-0 hr-41

last: Vadigepalli

institute: Thomas Jefferson University

description: SAMPLE 165

data_processing:
The data were normalized using the -ΔΔCt scheme. Expression values within samples were normalized using the median expression of 55 high performing genes (Ct_reaction - Ct_median_across_55_genes). Expression values within genes were scaled to the median using (Ct_median_across_all_samples - Ct_reaction)
Missing values were imputed using the k-nearest neighbors imputation after normalization

extract_protocol: Single hepatocytes extracted using laser capture microdissection were lysed and directly processed for reverse transcription followed by targeted pre-amplification. Pre-amplification of cDNA samples was performed for 22 cycles using TaqMan PreAmp Master Mix as per the manufacturer’s protocol. Primers for the 84 genes tested were custom designed. qPCR was performed on BioMark 96.96 Dynamic Array for 30 cycles.

tag: diet


title: Healthy control ascending subject 6


title: Ctrl-1-pgVAT


title: Hep-Ethanol-0 hr-38

description: SAMPLE 162

tag: time after partial hepatectomy


title: Healthy control ascending subject 3


title: Healthy control ascending subject 4


title: SZ-ABX-6-scWAT

source_name: scWAT

tag: strain

value: scWAT


title: SEPT9_v3_rep_B

description:
SEPT9 upregulation
Sample_jz8


title: Hep-Ethanol-0 hr-37

description: SAMPLE 161

value: liver


title: Ctrl-3-pgVAT


title: Healthy control rectum subject 16

value: Rectum


title: Healthy control ascending subject 2


title: SZ-ABX-5-scWAT


title: Healthy control rectum subject 17


title: Hep-Ethanol-0 hr-36

description: SAMPLE 160

value: Ethanol


title: Healthy control rectum subject 15


title: Healthy control rectum subject 10

description:
200616460040_A
included in the non normalised data but not the normalised data as the minimum detection value for our quality control was not met


title: Hep-Ethanol-0 hr-35

description: SAMPLE 159


title: SEPT9_v2_rep_B

description:
SEPT9 upregulation
Sample_jz7


title: Healthy control rectum subject 13


title: Healthy control rectum subject 14


title: SZ-ABX-3-scWAT

value: SZ-ABX


title: SZ-ABX-4-scWAT


title: Wt_rep_C

description:
no SEPR9 upregulation
Sample_jz9


title: SZ-ABX-2-scWAT


title: Wt_rep_B

description:
no SEPR9 upregulation
Sample_jz5


title: SEPT9_v3_rep_A

description:
SEPT9 upregulation
Sample_jz4


title: Hep-Ethanol-0 hr-33

description: SAMPLE 157


title: Hep-Ethanol-0 hr-32

description: SAMPLE 156


title: SZ-ABX-1-scWAT


title: Hep-Ethanol-0 hr-34

description: SAMPLE 158


title: Healthy control rectum subject 12


title: ABX-5-scWAT

value: ABX


title: SEPT9_v2_rep_A

description:
SEPT9 upregulation
Sample_jz3


title: Hep-Ethanol-0 hr-31

description: SAMPLE 155

value: Hepatocyte


title: SEPT9_v1_rep_A

description:
SEPT9 upregulation
Sample_jz2


title: SEPT9_v1_rep_B

description:
SEPT9 upregulation
Sample_jz6


title: Hep-Ethanol-0 hr-29

description: SAMPLE 153

value: 0 hr


title: Hep-Ethanol-0 hr-30

description: SAMPLE 154


title: Healthy control rectum subject 11


title: ABX-2-scWAT


title: 387_Normoxia_N6mA_DIPseq

city: San Diego

first: Jeremy

last: Rich

address: 9500 Gilman Drive #0695

institute: University of California, San Diego

description: N6-mA DIP-seq from patient derived glioblastoma cell specimens

data_processing:
Library strategy: DIP-seq
FASTQ files were trimmed with Trim Galore and aligned to the hg19 genome using BWA (for ChIPseq) or Bowtie2 (for N6mA DIPseq) as described in the methods.
SAM files were sorted and duplicates were removed using PicardTools as described in the methods
Bigwigs were generated from BAM files using DeepTools
Peaks were called using the EPIC implementation of the SICER algorithm as described in the methods. For differential peak calling, the Non-targeting shRNA file was used as the input, as described in the methods.
See methods section in manuscript for complete data processing details for ChIP, DIP, and Bisulfite sequencing analysis
Genome_build: hg19
Supplementary_files_format_and_content: BIGWIG and BED files

source_name: Patient Derived Glioblastoma Stem Cell

growth_protocol:
Cells from a primary patient derived GBM tumor model were injected intracranially into a immunocompromised NSG mouse and allowed to grow into a tumor. Cells were dissociated and passaged in vitro.
Cells were grown in neurobasal media supplemented with sodium pyruvate, B27, glutamax, EGF/FGF, and penicillin/streptomycin as described in more detail in the methods. Cells were treated with the indicated shRNA.

extract_protocol:
DNA extraction protocol is described in the method section
For ChIP-seq and N6-mA DIPseq, NEB NEBNext® Ultra™ DNA Library Prep Kit

treatment_protocol:
For N6mA DIPseq, Rabbit polyclonal antibody to N6-mA (Synaptic Systems, Cat#202-003) was used.
For H3K9me3 ChIPseq, rabbit polyclonal antibody to Histone H3K9me3 (Abcam,Cat#ab8898) was used
For H3K27me3 ChIPseq, rabbit polyclonal antibody to Histone H3K27me3 , (Active Motif, Cat#39155) was used
For H3K4me3 ChIPseq, rabbit polyclonal antibody to Histone H3K4me3 (Abcam,Cat#8580)
For ALKBH1 ChIPseq, rabit polyclonal antibody to ALKBH1 (Abcam, Cat#ab126596) was used
Chromatin Immunoprecipitation (ChIP) was performed as previously described. Briefly, formaldehyde-fixed cells were lysed and sheared (Branson S220) on wet ice. The sheared chromatin was cleared and incubated overnight at 4  C with 5  mg H3K9me3 antibody (Abcam, ab8898), H3K27me3 (active motif, 39155), or H3K4me3 (Abcam) respectively. Antibody-chromatin complexes were immunoprecipitated with protein G magnetic Dynal beads (Life Technologies), washed, eluted, reverse crosslinked, and treated with RNAse A followed by proteinase K. ChIP DNA was purified using Ampure XP beads (Beckmann Coulter) and then used to prepare sequencing libraries by NEB NEBNext   Ultra    DNA Library Prep Kit for Illumina for sequencing.
For N6mA DIPsequencing, briefly, genomic DNA from patient-derived glioblastoma stem cell models was purified with a DNeasy kit (QIAGEN, 69504). For each sample, 5   g DNA was sonicated to 200   300 bp with Bioruptor. Then, adaptors were ligated to genomic DNA fragments following the Illumina protocol. The ligated DNA fragments were denatured at 95 degree for 5 minutes. Then, the single-stranded DNA fragments were immunoprecipitated with N6-mA antibodies (5   g for each reaction, 202-003, Synaptic Systems) overnight at 4  C. N6-mA enriched DNA fragments were purified according to the Active Motif hMeDIP protocol. IP DNA and input DNA were PCR amplified with NEBNext indexing primers, and were then subjected to multiplexed library construction and sequencing with Illumina HiSeq sequencing

tag: cell treatment

value: Cells were grown in 20% oxygen


title: Wt_rep_A

description:
no SEPR9 upregulation
Sample_jz1


title: ABX-3-scWAT


title: Ctrl-6-scWAT


title: 387_Normoxia_Input_for_N6mA_DIPseq


title: Hep-Ethanol-0 hr-28

first: Rajanikanth

description: SAMPLE 152


title: Hep-Ethanol-0 hr-27

description: SAMPLE 151


title: Healthy control rectum subject 9

value: M


title: scRNAseq of cells from the preoptic region of a pool of three female mice: Replicate 3

first: Jeffrey

description: Processed data are contained with the matrix.mtx file and correspond to all cell names that end with -3

source_name: Preoptic region of the hypothalamus

value: brain

value: Preoptic region of the hypothalamus

value: female


title: ABX-4-scWAT


title: 387_Hypoxia_Input_for_N6mA_DIPseq

value: Cells were grown in 1% oxygen


title: 387_Hypoxia_N6mA_DIPseq


title: Ctrl-5-scWAT


title: Hep-Ethanol-0 hr-25

description: SAMPLE 149


title: T387_shALKBH1.1551_N6mA_DIPseq

value: Cells were treated with an shRNA targeting ALKBH1 (shALKBH1.1551)


title: Healthy control rectum subject 7

value: F

value: Healthy control=NA Ulcerative colitis=E Extent of disease:1=proctitis 2=left sided disease 3=pancolitis:NA


title: Healthy control rectum subject 8


title: Healthy control rectum subject 4


title: Ctrl-4-scWAT

value: scWAT

value: Ctrl


title: Hep-Ethanol-0 hr-23

description: SAMPLE 147

value: liver


title: ABX-1-scWAT


title: Healthy control rectum subject 5

value: Rectum


title: Ctrl-3-scWAT


title: T387_shALKBH1.1008_N6mA_DIPseq

value: Cells were treated with an shRNA targeting ALKBH1 (shALKBH1.1008)


title: Healthy control rectum subject 3


title: Hep-Ethanol-0 hr-26

description: SAMPLE 150

value: Ethanol


title: Hep-Ethanol-0 hr-22

description: SAMPLE 146

value: Hepatocyte


title: Ctrl-2-scWAT


title: H9.2_lt-NES

city: Aachen

first: Qiong

last: Lin

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

hyb_protocol: Whole-Genome Gene Expression Direct Hybridization standard Illumina protocol

scan_protocol: Direct Hyb

data_processing: The data were pre-processed and normalised using quantile normalisation with illuminaio and limma in R.

source_name: R346: lt-NES

label_protocol: Ambion/LifeTechnologies Illumina TotalPrep-96 RNA Amplification Kit

growth_protocol: Adult human peripheral blood cells are cultured using a published protocol (van den Akker et al., 2010). Neonatal human cord blood cells are cultured in DMEM/F12 medium supplemented with FCS, SCF, TPO, Flt-3 ligand, and IL-6. All the iNSCs are cultured in N2B27 medium supplemented with CHIR99021, purmorphamine, A83-01, and human LIF. All the smNPCs are cultured as described previously (Reinhardt et al., 2013) and all the lt-NES are cultured as described previously ((Koch et al., 2009).

extract_protocol: Total RNA was isolated from cell cultures using RNeasy mini kit (Qiagen)

treatment_protocol: Cells are washed by DPBS before collection

tag: subject status

value: healthy

value: hPSC-derived long-term neuroepithelium stem cell (lt-NES) line


title: Healthy control rectum subject 2


title: T387_shCONT_N6mA_DIPseq

value: Cells were treated with a non-targeting shRNA (shCONT)


title: Hep-Ethanol-0 hr-24

city: Philadelphia

description: SAMPLE 148

tag: cell type

value: 0 hr


title: Hep-Ethanol-0 hr-21

description: SAMPLE 145


title: Ctrl-1-scWAT


title: T387_Input_for_N6mA_DIPseq

value: No Treatment


title: CB-iNSC_116f-s2

source_name: R343: CB-iNSC

value: female

value: neonatal

value: brain

value: neonatal cord blood cell-derived iNSC (CB-iNSC) line


title: GSC23plus_N6mA_DIPseq


title: Hep-Ethanol-0 hr-19

description: SAMPLE 143


title: Hep-Ethanol-0 hr-20

description: SAMPLE 144


title: H9.2_smNPC

source_name: R333: smNPC

value: hPSC-derived small molecule-induced neural progenitor cell (smNPC) line


title: CB-iNSC_120m-s5

source_name: R341: CB-iNSC

value: male


title: GSC23_Input_for_N6mA_DIPseq


title: vivo15hr_rep2

city: Irvine

first: Ali

last: Mortazavi

address: 2300 E biological science 3

institute: University of California Irvine

data_processing:
Unstranded, paired-end 43 bp RNA-seq reads for each worm were mapped to the S. feltiae transcriptome downloaded from WormBase ParaSite (WS263) using Bowtie 1.0.0 with the following options: -X 1500 -a -m 200 --S -- seedlen 25 -n 2 --offrate 1 -p 64 -v 3  (Langmead et al. 2009). After Bowtie, gene expression was quantified with RSEM with the following options: rsem-calculate-expression -- bam -- paired-end. Gene expression for S. carpocapsae were performed as previously described (Lu et al. 2017) and reported in Transcripts Per Million (TPM). We used counts for differential gene expression analysis.
The Transcript per million (TPM) generated by rsem-calculate-expression for S. feltiae samples were normalized according to groups using the R package limma (Ritchie et al., 2015) because samples were collected, processed and sequenced in different batches. Samples were batched corrected between 3 and 9 hours in vitro to 6 hours in vitro, 3,6,9,12,15 in vivo with edgeR package removebatcheffects with log2 of TPM matrix.
Genome_build: S_felt_v1

organism: Steinernema feltiae

source_name: activated in a live waxworm

growth_protocol: As described in Serra L., Chang D., Macchietto M., Williams K., Murad R., Lu D., *Dillman A.R., & *Mortazavi A. 2018. Adapting the Smart-seq2 protocol for robust single worm RNA-seq. Bio-protocol 8(4): e2729.

extract_protocol:
as described in Serra L., Chang D., Macchietto M., Williams K., Murad R., Lu D., *Dillman A.R., & *Mortazavi A. 2018. Adapting the Smart-seq2 protocol for robust single worm RNA-seq. Bio-protocol 8(4): e2729.
as described in Serra L., Chang D., Macchietto M., Williams K., Murad R., Lu D., *Dillman A.R., & *Mortazavi A. 2018. Adapting the Smart-seq2 protocol for robust single worm RNA-seq. Bio-protocol 8(4): e2729.
PolyA RNA  unstranded, paired-end, read_length= 43 bp

value: SN

tag: genotype

value: wildtype

tag: developmental stage

value: Infective Juvenile (IJ)

value: in vivo activated

tag: time point

value: whole body


title: I3_smNPC

source_name: R336: smNPC

tag: age

tag: tissue


title: T387plus_N6mA_DIPseq


title: CB-iNSC_117m-s5

source_name: R339: CB-iNSC


title: Hep-Ethanol-0 hr-18

address: 1020 Locust Street

description: SAMPLE 142

source_name: Ethanol-0 hr

value: Hepatocyte

value: liver

value: Ethanol


title: vivo12hr_rep3


title: Hep-Ethanol-0 hr-17

description: SAMPLE 141


title: vivo15hr_rep1


title: vivo15hr_rep3


title: cw2386inputforN6mA_DIPseq

description: N6-mA DIP-seq from patient derived glioblastoma specimens

growth_protocol:
Cells from a primary patient derived GBM tumor
Cells were grown in neurobasal media supplemented with sodium pyruvate, B27, glutamax, EGF/FGF, and penicillin/streptomycin as described in more detail in the methods. Cells were treated with the indicated shRNA.

tag: antibody


title: Hep-Ethanol-0 hr-16

description: SAMPLE 140