title: 21 days differentiated Caco-2 cells incubated with L. brevis (W63) for 6 hours, biol rep 2

description: 21 days differentiated Caco-2 cells incubated with L. brevis (W63) for 6 hours, biological replicate 2

value: Caucasian colon adenocarcinoma


title: 21 days differentiated Caco-2 cells incubated with Frutafit TEX! (TEX) for 6 hours, biol rep 1

status: Public on Jul 19 2018

type: RNA

city: Wageningen

first: Nicole

last: de Wit

address: Bornse Weilanden 9

department: Food & Biobased Research

country: Netherlands

institute: Wageningen UR

description: 21 days differentiated Caco-2 cells incubated with Frutafit TEX! (TEX) for 6 hours, biological replicate 1

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm using the Affymetrix® Expression Console™ Software.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: 21 days differentiated Caco-2 cells

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: ATCC derived Caco-2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco-Invitrogen, Bleiswijk, The Netherlands) with 4.5 g/L glucose, 0.58 g/L glutamine, no pyruvate, supplemented with 10% heat inactivated FBS (Hyclone Perbio, Etten-Leur, The Netherlands) and used with passage numbers between 30 and 60. For transwell assays, 0.33x105 cells were grown on ThinCert transwells with 33.6 mm2 membranes and 0.4 μm pores in 24-well suspension culture plates. Cells were grown for 21 days at 5% CO2 and 37°C and apical (150 μl) and basolateral (700 μl) medium were replaced three times per week.

extract_protocol: Total RNA was prepared from the Caco-2 cells using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Glycerol stocks of Lactobacillus acidophilus W37 (W37), Lactobacillus brevis W63 (W63), and Lactobacillus casei W56 (W56) (Winclove, Amsterdam, The Netherlands) were produced from bacteria grown anaerobically overnight in MRS medium. Upon use, glycerol stocks were washed with PBS and resuspended in cells culture medium, brought to 37°C, to reach 10^7 CFU/mL. Inulin-type fructans and oligofructose were solubilized at 0.5 mg/mL in medium and filtered (0.2 m) to eliminate possible contaminations. The cell medium was replaced the day before the exposure experiments. Medium was removed from the apical and basal compartments and diluted samples were added in to the apical compartment while fresh DMEM+10%FBS medium was added to the basal compartment. In each experiment, the compound- and control samples were exposed to Caco-2 cells in triplicate and two or three independent exposure experiments were performed (= independent biological replicates). After 6h incubation, the Caco-2 cells were lysed with 300 μL TRIzol and the triplicates in each experiment were pooled for RNA isolation.

tag: Sex

value: male

tag: subjectid

value: TEX

tag: cell line

tag: cell line origin

tag: passage nr

tag: days of differentiation on transwells

tag: treatment


title: 21 days differentiated Caco-2 cells incubated with L. casei (W56) for 6 hours, biol rep 1

description: 21 days differentiated Caco-2 cells incubated with L. casei (W56) for 6 hours, biological replicate 1


title: 21 days differentiated Caco-2 cells incubated with L. brevis (W63) for 6 hours, biol rep 1

description: 21 days differentiated Caco-2 cells incubated with L. brevis (W63) for 6 hours, biological replicate 1


title: 21 days differentiated Caco-2 cells incubated with DMEM control medium probiotics (ctrl Pro) for 6 hours, biol rep 1

description: 21 days differentiated Caco-2 cells incubated with DMEM control medium probiotics (ctrl Pro) for 6 hours, biological replicate 1

value: Ctrl Pro


title: LE.085.BU_M

type: SRA

city: Leipzig

first: Edith

last: Willscher

address: Haertelstraße 16-18

country: Germany

institute: IZBI

description:
DESeq2_normalized_counts.txt
LE-085-BU_M

library_source: transcriptomic

data_processing:
Sequencing was performed according to the paired-end RNA sequencing protocols from Illumina on a HighSeq2000 with paired-end module (Illumina Inc). Seventy-six bps were sequenced, from each side of a fragment about 95-125 bp long and an average number 140 million reads per sample.
Paired-end reads were aligned to the human reference genome (hg19) using gsnap (version 2012-07-20) with default parameters. For each sample all reads overlapping a gene were assigned to the gene. Normalization was done based on the raw counts by library size using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: text file with DESeq2 normalized counts

source_name: skin

extract_protocol:
Biopsies of primary melanomas samples (n=57) and benign melanocytic nevi (n=23). Melanoma and nevus samples were snap frozen using liquid nitrogen and stored at -80oC until further processing. Laser-capture microdissection was performed as described earlier (Jäger et al., 2007). Total RNA was extracted from microdissected nevus and melanoma tissues using commercially available systems (RNeasy kit, Qiagen, Hilden, Germany). RNA quality was analyzed using an Agilent 2100 Bioanalyser (Agilent Technologies, Böblingen, Germany).
High-Throughput paired-end RNA sequencing library construction followed the standard Illumina mRNA library preparation protocol (www.illumina.com; Illumina Inc, San Diego, CA, U.S.A.), including poly-A mRNA isolation, fragmentation, and gel-based size selection.

tag: tissue

value: primary melanoma

tag: group

tag: melanoma on nevus

value: no

tag: braf mutation

value: mut

tag: nras mutation

value: wt


title: Mock_2: Mock replica 2

city: Madrid

first: Federico

last: Navarro-García

state: Madrid

address: Plaza de Ramón y Cajal

department: Microbiología y Parasitología

country: Spain

institute: Universidad Complutense de Madrid

data_processing:
Sequenced in an Illumina sequencing system HiSeq 2000 with a depth of 1.5 Gbp.
Quality analysis of libraries was performed with FastQC (Andrews, 2010). Prior to mapping reads to the reference database, all sequences were filtered to remove the first 10 bp of each read, the adaptor sequences, low quality sequences and reads with less than 30 bp using Cutadapt (Martin,2011).
Differentially expressed genes were determined with edgeR (Robinson et al. 2010) using as criteria fold change ≥2 and p-value<0.01. The heatmaps were done using Matrix2png interface platform (Pavlidis and Noble 2003).

organism: Arabidopsis thaliana

source_name: Mock replica 2

growth_protocol: Seeds were stratified for 3-5 days at 4°C and grown in growth chambers under long day conditions (16-h light/8-h dark photoperiod, 100 μmol·m-2·s-1) at 24°C.

extract_protocol:
Total RNA was extracted with RNeasy Plant Mini Kit (Qiagen) according to manufacturer´s instructions and then was frozen at -80°C until analyzed. The RNA concentration and integrity (RIN) were measured in a RNA nanochip (Bioanalyzer, Agilent Technologies 2100).
RNA-Seq libraries were generated using the TruSeq Stranded Total RNA Library Prep Kit (Illumina) .

treatment_protocol: Three types of samples were harvested: seedlings grown on ½ MS plates for 6 days under long day conditions before being transferred to (i) ½ MS (mock) or (ii) ½ MS supplemented with 10 µg·mL-1 of carbenicillin for 1 day (1 day Carbenicillin-treated plants); and (iii) seedlings grown on ½ MS plates supplemented with 10 µg·mL-1 of carbenicillin for 6 days under long day conditions before being transferred to  ½ MS supplemented with 10 µg·mL-1 of carbenicillin for 1 additional day (7 day Carbenicillin-treated plants).

tag: ecotype

value: root


title: Mock_1: Mock replica 1

source_name: Mock replica 1


title: FKH.007_M

description:
DESeq2_normalized_counts.txt
FKH-007_M

value: yes


title: KO.762.SW_M

description:
DESeq2_normalized_counts.txt
KO-762-SW_M


title: KO.1221_M

description:
DESeq2_normalized_counts.txt
KO-1221_M


title: LE.057.HK_M

description:
DESeq2_normalized_counts.txt
LE-057-HK_M


title: LE.051.WD_M

description:
DESeq2_normalized_counts.txt
LE-051-WD_M


title: LE.041.RL_M

description:
DESeq2_normalized_counts.txt
LE-041-RL_M


title: BO.025.SE_M

description:
DESeq2_normalized_counts.txt
BO-025-SE_M


title: LE.081.TR_M

description:
DESeq2_normalized_counts.txt
LE-081-TR_M


title: PH_M

description:
DESeq2_normalized_counts.txt
PH_M


title: RG_M

description:
DESeq2_normalized_counts.txt
RG_M


title: BE_M

description:
DESeq2_normalized_counts.txt
BE_M


title: BO.017.BU_M

description:
DESeq2_normalized_counts.txt
BO-017-BU_M


title: X3seBACS_BAC_plasmid_1

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

description:
plasmid DNA
BAC-STARR-seq library with DNA from three super-enhancer regions

library_source: genomic

data_processing:
Library strategy: DNA-Seq
Base-calling using default Illumina software by Edinburgh Genomics
Adapter contaminants trimmed using Skewer
Reads aligned to GRCh37/h19 genome using Bowtie2 (default parameters + “--very-sensitive”)
Only properly paired, concordantly aligning and uniquely mapping fragments
Read counts summed up per unique (chromosome,start-read1,end-read2) coordinate
Genome_build: hg19
Supplementary_files_format_and_content: tab-separated text file with read counts per coordinate

molecule: genomic DNA

source_name: BAC

growth_protocol: H9 human embryonic stem cells were cultured on Matrigel coated cell culture plates, using mTesR1 medium (Stem Cell Technology, 05850). Cells were routinely split (ratio 1:3-1:4) using 0.5mM EDTA (Invitrogen, 15575020). For transfection, single cells were obtained by Accutase treatment (Invitrogen, A1110501), in the presence of Rock inhibitor, Y-27632 (10uM, Cambridge bioscience, SM02-10). For conversion to the naive state, cells were split on irradiated MEFs on gelatin coated plates and media was changed to NHSM media, as described by Gafni et al. (Gafni et al., 2013), containing knockout DMEM (Invitrogen ), 20% knockout serum (Invitrogen), human insulin (Sigma, 12.5ug ml-1 final concentration), 20 ng ml-1 recombinant human LIF (Millipore), 8 ng ml-1 recombinant bFGF (Peprotech) and 1 ng ml-1 recombinant TGF-beta1 (Peprotech), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM beta-mercaptoethanol (Invitrogen), penicillin-streptomycin (Invitrogen) and small molecule inhibitors: PD0325901 (1uM, ERK1/2i, Axon Medchem); CHIR99021 (3uM, GSKbetai, Axon Medchem); SP600125 (10uM, JNKi, Abcam ab120065) and SB203580 (10 uM, p38i,Abcam ab120638) Y-27632 (5uM, ROCKi) and protein kinase C inhibitor G06983 (5 uM, PKCi, Abcam, ab144414). Cells were 1:10 passaged using TrypLETM (Invitrogen, 12604021) in the presence of Rock inhibitor and maintained for more than 10 passages in NHSM media prior to analysis. All cells were regularly karyotyped and checked for the presence of mycoplasm.

extract_protocol:
For chromatin immunoprecipitation, 2x10^7 H9 primed or naive hESC were harvested in 9 ml of medium and cross-linked by addition of 270 ul 37% Formaldehyde (Sigma, final concentration of 1%), for 10 min at room temperature under rotation. 1 ml of 1.25 M Glycine was added, cells were incubated on ice for 5 min and 3x washed with ice cold PBS. At this point, cross-linked cell pellets were snap-frozen and stored at -80ᴼC, or immediately processed for sonication. Prior to sonication, cells were resuspended in 1ml TE-I-NP40 (10mM TRIS-HCl pH 8, 1mM EDTA, 0.5% NP40, 1mM PMSF, 1x Protease inhibitor complex (PIC, Complete tablets, 04693116001, Roche)) incubated on ice for 5 min and centrifuged for 5 min at 2500 rpm at 4ᴼC in a refrigerated bench top centrifuge (Eppendorf). Supernatant was removed and nuclei were resuspended in 1 ml ice-cold lysis buffer (50mM TRIS-HCl pH 8, 10mM EDTA, 1% SDS, 1mM PMSF, 1x PIC) and transferred to a 15 ml Falcon tube for sonication, using a Diagenode Bioruptor Next Gen (40 cycles of 30” on, 30” off). After transfer to an Eppendorf tube and centrifugation for 10 min at 13200 rpm at 4ᴼC, chromatin solution was aliquoted and used for immunoprecipitation or snap-frozen and stored at -80ᴼC. A 20 µl sample was taken and served as a total input control. For immunoprecipitation, Protein Dynabeads G (10004D, Life Techology) were washed with PBS and incubated for 6 hours with 5 ug of antibody, at 4ᴼC on a rotating wheel. Antibodies used were: goat-anti-NANOG (AF1997, R&D Systems), rabbit-anti-OCT4 (AB19857, Abcam), rabbit-anti-H3K4me1 (AB8895, Abcam) and rabbit-anti-H3K27ac (AB4729, Abcam); as a control, respective IgG antibodies were used (rabbit-IgG: 10500C, Life Technology, goat-IgG: SC-2028, Santa Cruz Biotechnology). After washing with PBS, antibody-coupled beads were incubated with 200 ul chromatin solution, diluted to a final volume of 2 ml with dilution buffer (167mM NaCl, 16.7mM TRIS-HCl pH 8.1, 1.2mM EDTA, 0.01% SDS, 1.1% Triton-X100, 1mM PMSF, 1x PIC), overnight at 4ᴼC on a rotating wheel. Washing of beads was performed by incubation with ice-cold 1 ml of washing buffer, for 5 min, at 4ᴼC on a rotating wheel, followed by removal of supernatant using a magnetic stand, for each of the following: 2x with wash buffer 1 (10mM TRIS-HCl pH 7.6, 1mM EDTA, 0.1% SDS, 1% Triton-X100, 0.1% NaDeoxychloate), 2x with wash buffer 2 (10mM TRIS-HCl pH 7.6, 1mM EDTA, 0.1% SDS, 1% Triton-X100, 0.1% NaDeoxychloate, 150mM NaCl), 2x with wash buffer 3 (250mM LiCl, 0.5% NP40, 0.1% NaDeoxychloate), 1x with TE 1x with 0.2% TritonX-100 and 1x with TE 1x, after which beads were resuspended in 100ul TE1x. Immunoprecipitated chromatin and total input control were decross-linked, by addition of 3 ul of 10% SDS and 5 ul Proteinase K (20 ug/ul, Roche) and 10 ul RNAse A (50 ug/ul, Roche) to each tube and incubation overnight at 65°C on a shaking thermomixer block, 1400 rpm (Eppendorf). The next day, beads were briefly vortexed and supernatants were transferred to new tubes using the magnetic stand. 100ul of TE1x containing 500mM NaCl was added to the beads and briefly vortexed, after which the supernatant was added to the first fraction of collected supernatant. Following Phenol / chloroform extraction, DNA was precipitated using 1ul glycogen (20mg/ml), 1/10 vol NaOAc (3M) and 100% ice-cold Ethanol, at -20°C for 1 hour, followed by centrifugation at 13200 rpm for 1 hour at 4ᴼC. After a final wash with 70% ethanol, the DNA pellet was dried and resuspended in 50ul H2O. Concentration of ChIP DNA was determined by Qubit measurement following manufacturer’s instructions and sonication was assessed by gel-electrophoresis of total input DNA (target fragment size between 200 and 600 bp).
For ChIP-seq and ChIP-STARR-seq plasmid library generation, 10 ng of ChIP DNA was used as starting material. Using NEB Next ChIP-seq library preparation kit (E6200 or E6240, NEB), DNA was end-repaired, dA-tailed and adapter-ligated according to manufacturer’s instructions. After adapter ligation and purification using AMPure-XP beads (0.8x, Beckman Coulter) and elution into 30ul of 0.1xTE, 25 ul of the reaction product was used for ChIP-seq library preparation, by PCR amplification with Illumina index primers (7335 and 7500, NEB) using the NEB Next Q Hot start high fidelity master mix (M0543S, NEB) according to manufactures instructions (cycle conditions: 98ᴼC 30 sec, (98ᴼC 10 sec, 65ᴼC 75 sec) x15, 65ᴼC 5 min, 4ᴼC hold). After an additional round of AMPureXP bead purification, DNA was eluted in 0.1xTE without further size selection. Quality and quantity of the prepared ChIP-seq libraries was assessed on an Agilent Tapestation.   The remaining 5 ul of purified adapter ligated DNA were used for ChIP-STARR-seq plasmid library generation. Therefore, DNA was diluted to a total volume of 10 ul in 0.1xTE and used as an input in 8 x 50ul PCR reactions using Phusion Polymerase, High-fidelity buffer (M0530L, NEB) and primers 147 STARRseq libr FW (TAGAGCATGCACCGGACACTCTTTCCCTACACGACGCTCTTCCGATCT) and 148 STARRseq libr RV (GGCCGAATTCGTCGAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT) (Arnold et al., 2013), which prime on the adapter sequences and add a 5’and 3’ 15 nucleotide homology sequence to the reaction products which are used for Gibson assembly. After PCR amplification (cycle conditions: 98ᴼ 2 min, (98ᴼC 10 sec, 62ᴼC 30 sec, 72ᴼC 30 sec) x 15, 72ᴼC 5 min, 4ᴼC hold), PCR reactions were pooled, purified using AMPure XP beads (1.8x), eluted in 30 ul 0.1xTE and used for Gibson assembly. Therefore, 15 ug of the mammalian STARRseq plasmid (a kind gift of A.Stark) (Arnold et al., 2013) were digested with AgeI-HF and SalI-HF (NEB) for 8h at 37ᴼC, column purified (Nucleospin purification columns, 740609250, Machery-Nagel), eluted in 30 ul elution buffer and used as a vector in a Gibson reaction, using 2 ul of digested plasmid, 5 ul purified PCR product, 3 ul H20 and 10 ul of a home-made Gibson reaction (100mM Tris-HCl, 10mM MgCl2, 0.2 mM dNTP (each), 0.5U Phusion DNA polymerase (NEB), 0.16U 5’ T5 exonuclease (Epicentre), 2 Gibson reactions per library. After incubation at 50ᴼC for 1 hour, Gibson reaction were pooled and precipitated by addition of 1 ul Glycogen (20 ug/ul, Roche, 1090139300), 5 ul NaOAc (3M) and 125 ul ice-cold 100% ethanol, incubation at -20ᴼC for 1 hour and centrifugation for 1 hour at 13200 rpm at 4ᴼC, followed by a final wash in 70% ethanol. After air drying, DNA pellet was dissolved in 10 ul water and used for electroporation into electrocompetent MegaX DH10beta E.coli bacteria (Invitrogen), according to manufacturer’s instructions, using a Biorad pulser. A total of 5 electroporations per library were performed with each 2 ul of DNA. After recovery in 1 ml SOCS medium each, bacteria were grown for 1 hour at 37ᴼC in a bacterial shaker in the absence of antibiotics. Then, the remaining 5 ml of bacteria culture were incubated in a total volume of 2 liter of LB-media supplemented with Ampicillin and allowed to grow for 16 hours in a bacterial shaker at 37ᴼC. Plasmid DNA was isolated using a Qiagen Maxiprep kit according to manufacturer’s instructions and eluted in 500 ul 10mM Tris-HCl, pH 7.4. Concentration was determined by Nanodrop measurement. Plasmid DNA was amplified for sequencing by a nested PCR, using primers detecting the STARR-seq plasmid (160 STARR reporter specific primer for plasmid DNA fw, GGGCCAGCTGTTGGGGTG, and 153 STARR reporter specific primer 2 rv, CTTATCATGTCTGCTCGA*A*G*C, where * represent phosphorothioate bonds) and Illumina index primers.

tag: cell state

value: BAC

tag: chip target

value: None (BAC)


title: naive_Oct4_plasmid_2

description:
plasmid DNA
DNA-seq of ChIP-STARR-seq plasmid library constructed from OCT4 ChIP in naive hESCs

source_name: embryonic stem cells

value: Naive


title: primed_Oct4_plasmid_2

description:
plasmid DNA
DNA-seq of ChIP-STARR-seq plasmid library constructed from OCT4 ChIP in primed hESCs

value: Primed


title: naive_Input_ChIP_2

description: ChIP-seq total input control in naive hESCs

data_processing:
Base-calling using default Illumina software by Edinburgh Genomics
Genome_build: hg19

growth_protocol: H9 human embryonic stem cells were cultured on Matrigel coated cell culture plates, using mTesR1 medium (Stem Cell Technology, 05850). Cells were routinely split (ratio 1:3-1:4) using 0.5mM EDTA (Invitrogen, 15575020). For transfection, single cells were obtained by Accutase treatment (Invitrogen, A1110501), in the presence of Rock inhibitor, Y-27632 (10uM, Cambridge bioscience, SM02-10). For conversion to the naive state, cells were split on irradiated MEFs on gelatin coated plates and media was changed to NHSM media, as described by Gafni et al. (Gafni et al., 2013), containing knockout DMEM (Invitrogen ), 20% knockout serum (Invitrogen), human insulin (Sigma, 12.5ug ml-1 final concentration), 20 ng ml-1 recombinant human LIF (Millipore), 8 ng ml-1 recombinant bFGF (Peprotech) and 1 ng ml-1 recombinant TGF-beta1 (Peprotech), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM beta-mercaptoethanol (Invitrogen), penicillin-streptomycin (Invitrogen) and small molecule inhibitors: PD0325901 (1uM, ERK1/2i, Axon Medchem); CHIR99021 (3uM, GSKbetaetai, Axon Medchem); SP600125 (10uM, JNKi, Abcam ab120065) and SB203580 (10 uM, p38i,Abcam ab120638) Y-27632 (5uM, ROCKi) and protein kinase C inhibitor G06983 (5 uM, PKCi, Abcam, ab144414). Cells were 1:10 passaged using TrypLETM (Invitrogen, 12604021) in the presence of Rock inhibitor and maintained for more than 10 passages in NHSM media prior to analysis. All cells were regularly karyotyped and checked for the presence of mycoplasm.

extract_protocol:
For chromatin immunoprecipitation, 2x10^7 H9 primed or naive hESC were harvested in 9 ml of medium and cross-linked by addition of 270 ul 37% Formaldehyde (Sigma, final concentration of 1%), for 10 min at room temperature under rotation. 1 ml of 1.25 M Glycine was added, cells were incubated on ice for 5 min and 3x washed with ice cold PBS. At this point, cross-linked cell pellets were snap-frozen and stored at -80ᴼC, or immediately processed for sonication. Prior to sonication, cells were resuspended in 1ml TE-I-NP40 (10mM TRIS-HCl pH 8, 1mM EDTA, 0.5% NP40, 1mM PMSF, 1x Protease inhibitor complex (PIC, Complete tablets, 04693116001, Roche)) incubated on ice for 5 min and centrifuged for 5 min at 2500 rpm at 4ᴼC in a refrigerated bench top centrifuge (Eppendorf). Supernatant was removed and nuclei were resuspended in 1 ml ice-cold lysis buffer (50mM TRIS-HCl pH 8, 10mM EDTA, 1% SDS, 1mM PMSF, 1x PIC) and transferred to a 15 ml Falcon tube for sonication, using a Diagenode Bioruptor Next Gen (40 cycles of 30” on, 30” off). After transfer to an Eppendorf tube and centrifugation for 10 min at 13200 rpm at 4ᴼC, chromatin solution was aliquoted and used for immunoprecipitation or snap-frozen and stored at -80ᴼC. A 20 µl sample was taken and served as a total input control. For immunoprecipitation, Protein Dynabeads G (10004D, Life Techology) were washed with PBS and incubated for 6 hours with 5 ug of antibody, at 4ᴼC on a rotating wheel. Antibodies used were: goat-anti-NANOG (AF1997, R&D Systems), rabbit-anti-OCT4 (AB19857, Abcam), rabbit-anti-H3K4me1 (AB8895, Abcam) and rabbit-anti-H3K27ac (AB4729, Abcam); as a control, respective IgG antibodies were used (rabbit-IgG: 10500C, Life Technology, goat-IgG: SC-2028, Santa Cruz Biotechnology). After washing with PBS, antibody-coupled beads were incubated with 200 ul chromatin solution, diluted to a final volume of 2 ml with dilution buffer (167mM NaCl, 16.7mM TRIS-HCl pH 8.1, 1.2mM EDTA, 0.01% SDS, 1.1% Triton-X100, 1mM PMSF, 1x PIC), overnight at 4ᴼC on a rotating wheel. Washing of beads was performed by incubation with ice-cold 1 ml of washing buffer, for 5 min, at 4ᴼC on a rotating wheel, followed by removal of supernatant using a magnetic stand, for each of the following: 2x with wash buffer 1 (10mM TRIS-HCl pH 7.6, 1mM EDTA, 0.1% SDS, 1% Triton-X100, 0.1% NaDeoxychloate), 2x with wash buffer 2 (10mM TRIS-HCl pH 7.6, 1mM EDTA, 0.1% SDS, 1% Triton-X100, 0.1% NaDeoxychloate, 150mM NaCl), 2x with wash buffer 3 (250mM LiCl, 0.5% NP40, 0.1% NaDeoxychloate), 1x with TE 1x with 0.2% TritonX-100 and 1x with TE 1x, after which beads were resuspended in 100ul TE1x. Immunoprecipitated chromatin and total input control were decross-linked, by addition of 3 ul of 10% SDS and 5 ul Proteinase K (20 ug/ul, Roche) and 10 ul RNAse A (50 ug/ul, Roche) to each tube and incubation overnight at 65°C on a shaking thermomixer block, 1400 rpm (Eppendorf). The next day, beads were briefly vortexed and supernatants were transferred to new tubes using the magnetic stand. 100ul of TE1x containing 500mM NaCl was added to the beads and briefly vortexed, after which the supernatant was added to the first fraction of collected supernatant. Following Phenol / chloroform extraction, DNA was precipitated using 1ul glycogen (20mg/ml), 1/10 vol NaOAc (3M) and 100% ice-cold Ethanol, at -20°C for 1 hour, followed by centrifugation at 13200 rpm for 1 hour at 4ᴼC. After a final wash with 70% ethanol, the DNA pellet was dried and resuspended in 50ul H2O. Concentration of ChIP DNA was determined by Qubit measurement following manufacturer’s instructions and sonication was assessed by gel-electrophoresis of total input DNA (target fragment size between 200 and 600 bp).
For ChIP-seq library generation, 10 ng of ChIP DNA was used as starting material. Using NEB Next ChIP-seq library preparation kit (E6200 or E6240, NEB), DNA was end-repaired, dA-tailed and adapter-ligated according to manufacturer’s instructions. After adapter ligation and purification using AMPure-XP beads (0.8x, Beckman Coulter) and elution into 30ul of 0.1xTE, 25 ul of the reaction product was used for ChIP-seq library preparation, by PCR amplification with Illumina index primers (7335 and 7500, NEB) using the NEB Next Q Hot start high fidelity master mix (M0543S, NEB) according to manufactures instructions (cycle conditions: 98ᴼC 30 sec, (98ᴼC 10 sec, 65ᴼC 75 sec) x15, 65ᴼC 5 min, 4ᴼC hold). After an additional round of AMPureXP bead purification, DNA was eluted in 0.1xTE without further size selection. Quality and quantity of the prepared ChIP-seq libraries was assessed on an Agilent Tapestation.

value: Input


title: naive_Oct4_ChIP_2

description: ChIP-seq for OCT4 in naive hESCs


title: primed_Input_ChIP_2

description: ChIP-seq total input control in primed hESCs


title: NA_ACHN.2_Human_renal_cell_carcinoma_DS24471A[Dnase-seq]

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

country: USA

institute: Altius Institute / University of Washington

description:
Human_RCC_DNase-seq
ATCC:CRL-1611, cell line

data_processing:
Basecalling, RTA v1.13
Alignments to GRCh38, BWA v0.7.12
Read processing, Samtools v1.2
Read density, Bedops v2.4.15
Peak calling, Hotspot2 v2.1.1
Genome_build: hg19
Supplementary_files_format_and_content: Normalized density tracks, DHS peak calls as a .bed file

source_name: Human renal cell carcinoma cultures

growth_protocol: Macroscopically separate human kidney cortex and renal cell carcinoma was obtained with informed consent from patients undergoing nephrectomy for renal tumor cytoreduction. The tissue fragments were minced and digested with proteases (trypsin, collagenease) for 20 minutes at 37°C. The softened tissue fragments were placed in 10% RPMI + ITS+. After 3 days, the medium was refreshed after vigorous washing with PBS to remove glomerular cores that were partially attached. Tubular cells had an epithelioid morphology and proliferated rapidly. Renal carcinoma cells were vacuolated and grew slowly. Medium was refreshed every 3-4 days. When culture dishes were ~80% confluent,  cells were harvested for DNase-seq or RNA-seq which were performed per published protocols.

extract_protocol:
PEG precipitation and size fractionation of DNA
Low-input single-stranded library construction protocol as per PMIDs 23493070 & 26771485

treatment_protocol: Accutase disaggregated live single cell suspensions were permeabilized with NP40 and subjected to DNaseI treatment. The reaction was stopped by addition of EDTA and SDS. The cell extract was deproteinized (proteinase K) and RNA was digested (Rnase).

tag: patient age

tag: gender

value: Male

value: ATCC:CRL-1611, cell line


title: HIM13_Human_renal_cell_carcinoma_DS26692B[Dnase-seq]

value: Female


title: HIM13_Human_renal_cell_carcinoma_DS26693A[Dnase-seq]


title: NA_ACHN.1_Human_renal_cell_carcinoma_DS24547A[Dnase-seq]


title: HIM23_Human_kidney_tubule_DS41396[Dnase-seq]

source_name: Human kidney cortex tubule cultures


title: X3seBACS_BAC_ChIP_1

description: DNA-seq of BAC libraries for three super-enhancer loci


title: BO.019.WG_M

description:
DESeq2_normalized_counts.txt
BO-019-WG_M


title: HIM23_Human_kidney_tubule_DS41160[Dnase-seq]


title: primed_Oct4_ChIP_2

description: ChIP-seq for OCT4 in primed hESCs


title: HIM23_Human_renal_cell_carcinoma_DS40509[Dnase-seq]


title: FKH.027_M

description:
DESeq2_normalized_counts.txt
FKH-027_M


title: BO.013.NK_M

description:
DESeq2_normalized_counts.txt
BO-013-NK_M


title: HIM23_Human_renal_cell_carcinoma_DS40508[Dnase-seq]


title: BO.001.SH_2_M

description:
DESeq2_normalized_counts.txt
BO-001-SH_2_M


title: LH_M

description:
DESeq2_normalized_counts.txt
LH_M


title: BO.015.BW_M

description:
DESeq2_normalized_counts.txt
BO-015-BW_M


title: NA_7860.2_Human_renal_cell_carcinoma_DS37199[Dnase-seq]

description:
Human_RCC_DNase-seq
ATCC:CRL-1932, cell line

value: ATCC:CRL-1932, cell line


title: SH_M

description:
DESeq2_normalized_counts.txt
SH_M


title: HIM15_Human_kidney_tubule_DS37969[Dnase-seq]


title: HIM15_Human_kidney_tubule_DS37971[Dnase-seq]


title: FKH.011_M

description:
DESeq2_normalized_counts.txt
FKH-011_M


title: HIM15_Human_renal_cell_carcinoma_DS37974[Dnase-seq]


title: FKH.021_M

description:
DESeq2_normalized_counts.txt
FKH-021_M


title: HIM13_Human_kidney_tubule_DS27824[Dnase-seq]


title: HIM15_Human_renal_cell_carcinoma_DS37973[Dnase-seq]


title: LE.105.TF_M

description:
DESeq2_normalized_counts.txt
LE-105-TF_M


title: FKH.023_M

description:
DESeq2_normalized_counts.txt
FKH-023_M


title: NA_7860.1_Human_renal_cell_carcinoma_DS27192[Dnase-seq]


title: LE.045.WU_M

description:
DESeq2_normalized_counts.txt
LE-045-WU_M


title: LE.041.RL.042_N

description:
DESeq2_normalized_counts.txt
LE-041-RL-042_N

value: benign melanocytic nevi

tag: nevus type

value: dermal


title: X031_N

description:
DESeq2_normalized_counts.txt
031_N

value: compound


title: FKH.012_M

description:
DESeq2_normalized_counts.txt
FKH-012_M

value: primary melanoma

value: no


title: BO.015.BW.016_N

description:
DESeq2_normalized_counts.txt
BO-015-BW-016_N

value: mut

value: wt


title: BO.013.NK.014_N

description:
DESeq2_normalized_counts.txt
BO-013-NK-014_N


title: KS_M

description:
DESeq2_normalized_counts.txt
KS_M

value: yes


title: HIM23_Human_renal_cell_carcinoma_DS40496

data_processing:
Basecalling, RTA v1.13
Alignments to hg19, star v2.4.2a
Annotation, cufflinks v2.2.1, GENCODE v25
Subread, featureCounts v1.5.1
Genome_build: hg19
Supplementary_files_format_and_content: Total density tracks, Cufflinks FPKM expression levels per gene as a .txt file

extract_protocol:
Ambion mirVana RNA isolation kit
Illumina TruSeq Stranded Total RNA Library Prep Kit

treatment_protocol: Accutase disaggregated live single cell suspensions (500,000 - 1,000,000 cells) were stabilized in 1ml of RNALater and stored at 4°C till RNA extraction.


title: NA_7860_Human_renal_cell_carcinoma_DS34766

description:
Human_RCC_RNA-seq
ATCC:CRL-1932, cell line


title: HIM15_Human_renal_cell_carcinoma_rep2_DS37926


title: NA_ACHN_Human_renal_cell_carcinoma_DS37193

description:
Human_RCC_RNA-seq
ATCC:CRL-1611, cell line


title: HIM13_Human_kidney_tubule_DS26689[Dnase-seq]


title: BO.023.HS_M

description:
DESeq2_normalized_counts.txt
BO-023-HS_M


title: X010_N

description:
DESeq2_normalized_counts.txt
010_N


title: HIM15_Human_kidney_tubule_rep1_DS37923


title: HIM15_Human_kidney_tubule_rep2_DS37924


title: HIM13_Human_renal_cell_carcinoma_DS33395


title: UT-SCC-42B shScr 1

city: Helsinki

first: Outi

last: Monni

address: Haartmaninkatu 8

department: Department of Biomedicine

country: Finland

institute: University of Helsinki

description:
cell line from head and neck squamous cell carcinoma transduced with scramble shRNA
Henna_RNA_results_annotated_shPPFIA1_vs_shScr.xlsx
7_UT-SCC-42B_shScr_1_S7

data_processing:
Base-calling was done with Real-Time Analysis (RTA), RTA v2, (Illumina NextSeq 500).
Read quality was checked with FASTQC v0.11.3. Trimmomatic v0.36 was used in trimming the data, and qualimap v2.2 platform was used in analyzing the data.
MultiQC v0.8 tool was used in the data analysis. High quality reads were imported into STAR v2.5 for alignment into BAM files.
Genome_build: GRCh38
Supplementary_files_format_and_content: Differential expression analysis was performed by DESeq2 package R v3.2.3 and results underwent logarithmic transformation. Statistical test used was Wald. Processed data files in Excel (.xlsx) format contain log2 fold changes and p-values. Significantly differentially expressed genes were considered those with padj < 0,05 (Benjamini-Hochberg). Comparison between the two conditions shPPFIA1 and shScr has been evaluated with three different biological replicates per cell line (UT-SCC-42A, UT-SCC-42B, MDA-MB-231).

source_name: head and neck squamous cell carcinoma cell line

growth_protocol: UT-SCC-42A, UT-SCC-42B and MDA-MB-231 cell lines were grown on DMEM (Lonza) medium, and supplements 10% fetal bovine serum (FBS, Gibco), (100 U/ml) penicillin/streptomycin (Lonza), 2mM L-glutamin (Lonza) and 0,1 mM non essential amino acids (NEAA, Lonza) were added to the medium.

extract_protocol:
Cells (300 000 cells/ml) were suspended in collagen I matrix (500µl) and plated in low adhesion plates (24-well plates from Corning for MDA-MB-231 cell line,poly-HEMA coated 24-well plates for HNSCC cell lines), and grown inside collagen I for five days. To extract the RNA, media was removed from the well and Trizol (Ambion, Life Technologies) was added on top of the collagen I and homogenised by precellys ceramic beads and homogenizator (Precellys). Briefly, RNA was isolated and purified using chloroform/isopropanol based method and purified with Qiagen RNeasy Mini kit, according to manufacturer's instructions (Qiagen).
1µg of total RNA was subjected to library synthesis. Libraries were prepared according to Illumina's instructions accompanied with RiboZero Complete Gold Human and NEBNext Directional RNA library kit. Library quality was checked by Bioanalyzer analysis (Agilent 2100). Library denaturation and dilution was made according to NextSeq500 system guide.

treatment_protocol: Briefly, cells were first transduced with different constructs to silence PPFIA1 (shPPFIA1 14,44,69, from Sigma-Aldrich), and three shScr transductions were used as a controls. Cells were selected with puromycin (1µM/µl). After selection cells were embedded into three dimensional collagen I and were grown for five days at +37˚C, 5%CO2. RNA was extracted from three-dimensional cell cultures.

tag: cell type

value: neck metastasis

tag: shRNA construct

value: ctrl/shScramble (plKO.1)


title: HIM15_Human_renal_cell_carcinoma_rep1_DS37925


title: HIM13_Human_kidney_tubule_DS33394


title: X1397_N

description:
DESeq2_normalized_counts.txt
1397_N


title: LE.105.TF.106_N

description:
DESeq2_normalized_counts.txt
LE-105-TF-106_N


title: LE.049.SDIII_M

description:
DESeq2_normalized_counts.txt
LE-049-SDIII_M


title: K562 Endpoint, Replicate 2

city: San Francsico

first: Max

last: Horlbeck

state: CA

address: 1700 4th Street

department: Cellular and Molecular Pharmacology

institute: UCSF

data_processing:
Base-calling and demultiplexing with bcl2fastq v2.17.1.14; --barcode-mismatches 1 --minimum-trimmed-read-length 5 --mask-short-adapter-reads 5 --use-bases-mask y19,y19,i6nn,y38 (for triple sequencing)
Each sgRNA (R1 and R2) or barcode pair (R3) was aligned to the expected library allowing 1 mismatch each using custom scripts (github.com/mhorlbeck/Gimap_tools, tripleseq_fastqgz_to_counts.py). For full triple sequencing analysis, an sgRNA pair was counted if both sgRNAs and barcodes mapped to the expected library and if sgRNA A and B each matched the correct barcode. Reads were summed across all lanes for a given sample. Counts from each of sgRNA, barcode, and triple sequencing for each sample were calculated, except for K562 T0 where only barcode sequencing was available.
sgRNA pair phenotypes for each cell line and screen replicate were calculated using custom scripts (gitub.com/mhorlbeck/GImap_tools, Gimap_analysis.py) comparing counts from T0 and endpoint samples. Phenotypes were normalized to the number of cell doublings measured over the course of the screen (K562 Rep1: 6.91, K562 Rep2: 7.61, Jurkat Rep1: 6.151474054, Jurkat Rep2: 6.44). Phenotypes from each sequencing analysis method were calculated along with averages between replicates.
Further analysis, including the computation of sgRNA- and gene-level epistasis scores, was performed using GImap_analysis.py and can be found at Mendeley (doi:10.17632/rdzk59n6j4.1).
Genome_build: hg19
Supplementary_files_format_and_content:
tab-delimited text containg summed read counts, phenotypes, and reference library table
For read_counts.txt, the 20 columns refer to the 2 K562 T0 samples analyzed just with barcode sequencing plus the 6 other samples analyzed with three different methods (barcode, sgRNA, and triple sequencing).
For phenotypes.txt, the 18 columns refer to 2 screens x 3 different ways to analyze the data x (2 replicates + replicate average).

source_name: K562 Endpoint

growth_protocol: A pool of lentiviral vectors each encoding two sgRNAs and matching barcode sequences were packaged in HEK293T cells and then transduced into K562 or Jurkat cells expressing dCas9-KRAB. Infected cells were selected with puromycin and passaged for 15-16 days. Cells were harvested for genomic DNA at T0 (day 5 post-infection for K562 and 6 for Jurkat) and at screen endpoint 10 days later.

extract_protocol:
Genomic DNA was harvested from all samples using the Machery-Nagel Blood XL kit. DNA was digested with Mfe1 overnight at 37C, then run on 0.8% agarose big gels to enrich for the lentiviral fragment expected to run at 2158bp. The Machery-Nagel gel extraction kit was to isolate DNA from gel for library construction.
The sgRNA- and barcode-encoding regions were then amplified by PCR using custom primers (see Key Resources table in the associated manuscript).
Amplified sequences were sequenced on an Illumina HiSeq 2500 or 4000 using custom sequencing primer sets (see Key Resources table in the associated manuscript).

tag: cell line

tag: timepoint

value: Endpoint

tag: replicate

tag: sequencing strategy

value: triple sequencing


title: BO.005.SA.006_N

description:
DESeq2_normalized_counts.txt
BO-005-SA-006_N

tag: tissue


title: BO.017.BU.018_N

description:
DESeq2_normalized_counts.txt
BO-017-BU-018_N

tag: group


title: HIM23_Human_kidney_tubule_DS40494


title: K562 Endpoint, Replicate 1


title: K562 T0, Replicate 2

value: barcode only


title: K562 T0, Replicate 1


title: LE.049.SDII_M

description:
DESeq2_normalized_counts.txt
LE-049-SDII_M

tag: melanoma on nevus


title: KO.1039_M

description:
DESeq2_normalized_counts.txt
KO-1039_M

tag: braf mutation


title: 293t_rich_6h

city: Seattle

first: Arvind

last: Subramaniam

address: 1100 Fairview Ave. N., MS #A3-020

institute: Fred Hutchinson Cancer Research Center

description:
monosome-bound RNA footprints
generated by MNase digestion and purified on a sucrose density gradient

data_processing:
bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using cutadapt v1.4.1 with the parameters --adapter=AAAAAAAAAA --minimum-length=13 --discard-untrimmed (see github repository http://github.com/rasilab/adarnell_2018 for code & detailed instructions)
Subtractive alignment to rRNA was performed using bowtie v1.1.1 with the parameters --seedlen=23 --threads=8 --sam (see github repository http://github.com/rasilab/adarnell_2018 for code & detailed instructions)
Alignment was performed to a the human transcriptome using rsem-calculate-expression (rsem v1.3.0) with the parameters --num-threads 8 --output-genome-bam --sort-bam-by-coordinate (see github repository http://github.com/rasilab/adarnell_2018 for code & detailed instructions)
Codon-specific and gene-specific ribosome density were calculated by running the R (v3.3.3) script calculate_codon_ribo_density_150overhang_20170807.R. Gene fold changes were then calculated using DESeq by running the R script calculate_gene_fold_change_20170615.R (see github repository http://github.com/rasilab/adarnell_2018 for code & detailed instructions)
Genome_build: hg38
Supplementary_files_format_and_content: for each sample, tab-delimited text file {title}.codon.ribo.density.tsv includes the normalized average ribosome density in a 150 nt window around each of the 61 sense codons
Supplementary_files_format_and_content: for each sample, tab-delimited text file {title}.cds.counts.tsv includes CDS counts for canonical transcripts (defined as follows :  only transcripts annotated as both CCDS in the APPRIS principal splice isoform database & of this subset, the transcript with the lowest CCDS number for each gene was selected to generate a unique set).

source_name: HEK293T cells, ATCC CRL-3216

growth_protocol: Adherent cells grown in DMEM +10% FBS + P/S at 37 degrees Celsius, 5% CO2. Grown to 75% confluency in two 15 cm. plates before beginning treatment.

extract_protocol:
Cells were flash frozen and lysed at 4 degrees Celsius in polysome lysis buffer containing 100 ug/mL cycloheximide. Monosome-bound mRNA footprints were prepared by MNase digestion, purified by sucrose density gradient fractionation, and recovered by acid phenol chloroform extraction. mRNA footprints were further purified by size selection on a 15% TBE urea polyacrylamide gel before library preparation. See methods section in associated manuscript for more details.
mRNA footprints were polyA-tailed and then reverse transcribed. RT products were purified on a 10% tbe urea polyacrylamide gel, circularized, subject to rRNA subtraction, and finally amplified by 6-12 cycles of PCR. After purification on a 10% TBE polyacrylamide gel, libraries were quantified by Agilent Tapestation. Multiplexed barcoded subsets of libraries were sequenced on an Illumina HiSeq 2500, using a Rapid Run protocol for 50 bp single end reads. See methods section in associated manuscript for more details.

treatment_protocol: Cells were washed in warm PBS before adding prewarmed treatment medium (see characteristics: treatment medium / treatment length)

tag: tissue lineage

value: embryonic kidney

tag: treatment medium

value: DMEM + 10% dialyzed FBS

tag: treatment length

value: 6 hours

tag: genotype

value: wild type

tag: date experiment was sequenced

value: March 2017


title: LE.049.SDI_M

description:
DESeq2_normalized_counts.txt
LE-049-SDI_M

tag: nras mutation


title: FKH.008.010_N

description:
DESeq2_normalized_counts.txt
FKH-008-010_N

value: benign melanocytic nevi

tag: nevus type


title: 293t_leu_6h

value: DMEM + 10% dialyzed FBS −Leucine


title: KO.971_M

description:
DESeq2_normalized_counts.txt
KO-971_M

value: primary melanoma


title: MA.001.SH_M

description:
DESeq2_normalized_counts.txt
MA-001-SH_M

value: no


title: 293t_arg_6h

value: DMEM + 10% dialyzed FBS  −Arginine


title: BO.005.SA_M

description:
DESeq2_normalized_counts.txt
BO-005-SA_M

value: mut

value: wt


title: gcn2ko_rich_6h

source_name: HEK293T cells, ATCC CRL-3216, GCN2 KO

value: complete GCN2 knockout


title: gcn2ko_leu_6h


title: gcn2ko_arg_6h


title: LE.025.BI_M

description:
DESeq2_normalized_counts.txt
LE-025-BI_M


title: KO.1031_M

description:
DESeq2_normalized_counts.txt
KO-1031_M


title: KO.1347_M

description:
DESeq2_normalized_counts.txt
KO-1347_M


title: ragbq99l_leu_6h

source_name: HEK293T cells, ATCC CRL-3216 + AAVS1:Flag-RagB-Q99L


title: KO.1248_M

description:
DESeq2_normalized_counts.txt
KO-1248_M


title: ragbq99l_arg_6h


title: SM0_M

description:
DESeq2_normalized_counts.txt
SM0_M

value: yes


title: hrgfp_rich_6h

source_name: HEK293T cells, ATCC CRL-3216 + AAVS1:hrGFP


title: BO.009.BS_M

description:
DESeq2_normalized_counts.txt
BO-009-BS_M


title: SMIV_M

description:
DESeq2_normalized_counts.txt
SMIV_M


title: SMII_M

description:
DESeq2_normalized_counts.txt
SMII_M


title: SMIII_M

description:
DESeq2_normalized_counts.txt
SMIII_M


title: hrgfp_arg_6h


title: 293t_ragbq99l_rich_3h

value: 3 hours

value: March 2016


title: 293t_ragbq99l_arg_3h


title: hrgfp_leu_6h


title: 293t_ragbwt_rich_3h

source_name: HEK293T cells, ATCC CRL-3216 + AAVS1:Flag-RagB-WT


title: ragbq99l_rich_6h


title: 293t_ragbwt_leu_3h


title: BO.003.AW_M

description:
DESeq2_normalized_counts.txt
BO-003-AW_M


title: LE.037.RG_M

description:
DESeq2_normalized_counts.txt
LE-037-RG_M


title: 293t_ragbwt_arg_3h


title: LE.039.BE_M

description:
DESeq2_normalized_counts.txt
LE-039-BE_M


title: LE.117.RB_M

description:
DESeq2_normalized_counts.txt
LE-117-RB_M


title: RH_M

description:
DESeq2_normalized_counts.txt
RH_M


title: 293t_hrgfp_leutorin1_3h

value: DMEM + 10% dialyzed FBS −Leucine + 250 nM Torin1


title: 293t_hrgfp_rich_3h

value: embryonic kidney


title: 293t_ragbq99l_leu_3h


title: LE.129.NG_M

description:
DESeq2_normalized_counts.txt
LE-129-NG_M


title: KO.679_M

description:
DESeq2_normalized_counts.txt
KO-679_M


title: BO.011.WK_M

description:
DESeq2_normalized_counts.txt
BO-011-WK_M


title: SMI_M

description:
DESeq2_normalized_counts.txt
SMI_M


title: 293t_hrgfp_argtorin1_3h

value: DMEM + 10% dialyzed FBS  −Arginine + 250 nM Torin1


title: PS_M

description:
DESeq2_normalized_counts.txt
PS_M


title: 293t_hrgfp_leu_3h


title: FKH.027.028_N

description:
DESeq2_normalized_counts.txt
FKH-027-028_N

value: dermal


title: hela_rich_mono_3h

source_name: HeLa cells, ATCC CCL-2

value: HeLa

value: cervical adenocarcinoma

value: DMEM + 10% dialyzed FBS

value: wild type

value: August 2013


title: 293t_hrgfp_arg_3h


title: LE.021.TH.022_N

description:
DESeq2_normalized_counts.txt
LE-021-TH-022_N

value: benign melanocytic nevi

value: compound


title: X018_N

description:
DESeq2_normalized_counts.txt
018_N


title: LE.029.SE.030_N

description:
DESeq2_normalized_counts.txt
LE-029-SE-030_N

value: mut


title: hela_leu_mono_3h

value: DMEM + 10% dialyzed FBS −Leucine


title: hct116_rich_3h

source_name: HCT116 cells, NCI-60 panel

value: colorectal carcinoma

value: March 2017


title: hela_arg_mono_3h

value: DMEM + 10% dialyzed FBS  −Arginine

value: 3 hours


title: LE.019.WP.020_N

description:
DESeq2_normalized_counts.txt
LE-019-WP-020_N

value: wt


title: LE.037.RG.038_N

description:
DESeq2_normalized_counts.txt
LE-037-RG-038_N


title: hct116_leu_3h

description:
monosome-bound RNA footprints
generated by MNase digestion and purified on a sucrose density gradient


title: hct116_arg_3h


title: LE.061.TM.062_N

description:
DESeq2_normalized_counts.txt
LE-061-TM-062_N


title: 293t_rpC_rich_3h

value: embryonic kidney

value: October 2017


title: 293t_rpC_leu_3h


title: BO.001.SH.002_N

description:
DESeq2_normalized_counts.txt
BO-001-SH-002_N

value: dermal


title: LE.081.TR.082_N

description:
DESeq2_normalized_counts.txt
LE-081-TR-082_N


title: 293t_rpC_arg_3h

value: DMEM + 10% dialyzed FBS −Arginine


title: 293t_rpC_arg_6h

value: 6 hours


title: Mock_3: Mock replica 3

source_name: Mock replica 3

tag: ecotype

value: root


title: FKH.021.022_N

description:
DESeq2_normalized_counts.txt
FKH-021-022_N

source_name: skin


title: ED170306

city: Boston

first: Erin

middle: Elizabeth

last: Duffy

state: MA

address: 200 Longwood Ave, Goldenson 405

department: Neurobiology

institute: Harvard Medical School

description: 5 min s4U enriched rep 1

data_processing:
Adapters were trimmed using cutadapt 1.10
Sequencing reads were aligned using STAR (version 2.4.2a) to a joint index of the H. sapiens and S. pombe genomes (GRCh38 and sp2) and transcriptomes (NCBI and Ensembl Fungi v22; respective) or to the Mus musculus genome and transcriptome (GRCm38, NCBI).
s4U Chase-seq and MTS-TT-seq: BedGraphs were normalized using values that were calculated in edgeR based on counts from the S. pombe spike-ins
Genome coverage tracks were generated using STAR (version 2.4.2a)
Genome_build: GrCh38, GrCm38
Supplementary_files_format_and_content: bedGraph files for forward and reverse strands for each sample are separated

source_name: Immortalized K562s

growth_protocol: Immortalized K562s were cultured at 37 degrees C in high glucose RPMI media supplemented with 10% (v/v) fetal bovine serum, 1% (v/v) 2 mM L-glutamine, and 1% (v/v) penicilin/streptamycin. Mouse cortical neurons were isolated at E18 as previously described (Kaech et al. (2006) Nat. Protocols). About 2x10^6 cells were plated per 6-well dish.

extract_protocol:
All samples: Cells were resuspended in TRIzol reagent, flash frozen, and stored overnight at -80°C. Cell lysates were chloroform extracted once and total RNA purified by isopropanol precipitation. Contaminating DNA was digested with Turbo DNase. Samples were purified by phenol:chloroform extraction followed by a second isopropanol precipitation and resuspension in RNase-free water. 1-5 μg RNA in 9 μL RNase-free water was mixed with 1.5 μL 10x binding buffer (1 M NaCl, 100 mM HEPES pH 7.4, 10 mM EDTA, 0.5% Tween), and 3 μL DMF, added to MTS resin (10 μL aliquot), and incubated at room temperature in the dark for 2 h with rotation. Beads were captured on a magnetic rack and supernatant removed. Beads were incubated for 5 min with the following wash buffers: once with 100 μL 1x binding buffer, twice with 100 μL high salt wash buffer (1M NaCl, 100 mM Tris pH 7.4, 10 mM EDTA, 0,05% Tween), twice with 100 μL denaturing buffer (8 M guanidinium chloride), and three times with 100 μL buffer TE (10 mM Tris pH 7.4, 1 mM EDTA) at 55°C. RNA was eluted with 10 μL elution buffer (100 mM NaCl, 10 mM Tris pH 7.4, 1 mM EDTA, 10 mM DTT, and 100 pg fragmented total RNA from S. pombe), and incubated at room temperature in the dark for 15 min with rotation. Eluent was ethanol precipitated with 5-10 μg glycoblue, and RNA concentration was assayed by Bioanalyzer RNA 6000 Pico Kit (Agilent) according to the manufacturer’s instructions. For s4U Chase-Seq and TT-Seq: total RNA was sheared prior to s4U-RNA enrichment with MgCl2 at 94℃ for 4 min.
10 ng input and enriched RNA were used for rRNA-depleted library preparation. Sequencing libraries were constructed using the Clontech RNA Pico Input mammalian kit.

treatment_protocol: s4U Chase-Seq: Cultured cells at 50% confluence were labeled with 1 mM s4U for 2h, followed by chase with 20 mM uridine in fresh media. After 0.5h or 18h, cells were harvested in TRIzol. TT-Seq: Cultured cells at 80% confluence were labeled with 1 mM s4U for 5 min, followed by harvest in TRIzol. s4U DRB-Seq: Cells were treated wtih 500 μM DRB or DMSO for 3h. During the last 30, 20, or 10 min of DRB treatment for t=0, t=10, or t=20 min samples, respectively, 500 μM s4U was added to media. Cells were washed with PBS and media containing 500 μM s4U was added. Cells were harvested after 0, 10, or 20 min of media replacement.

value: Immortalized K562s

tag: experiment

value: MTS-TT-Seq

tag: s4u feed + chemical treatment

value: 5 min 1 mM s4U

tag: target molecule

value: biochemically enriched RNA


title: LE.117.RB.118_N

description:
DESeq2_normalized_counts.txt
LE-117-RB-118_N

value: benign melanocytic nevi

value: mut


title: LE.063.SP.064_N

description:
DESeq2_normalized_counts.txt
LE-063-SP-064_N


title: ED170305

description: 5 min s4U enriched rep 1


title: ED170304

description: no s4U enriched rep 2


title: ED170303

description: no s4U enriched rep 1


title: LE.047.LF.048_N

description:
DESeq2_normalized_counts.txt
LE-047-LF-048_N

value: compound


title: ED170302

description: RNA-Seq rep 2

value: total RNA


title: ED170301

description: RNA-Seq rep 1


title: ED161210

description: 18h chase enriched rep 2

value: s4U Chase-Seq

value: 2h 1 mM s4U, 18h 20 mM U


title: ED161208

description: 0.5h chase enriched rep 3

value: 2h 1 mM s4U, 0.5h 20 mM U


title: ED161209

description: 18h chase enriched rep 1


title: ED161201

description: RNA-Seq


title: ED161211

description: 18h chase enriched rep 3


title: ED161207

description: 0.5h chase enriched rep 2


title: ED161206

description: 0.5h chase enriched rep 1


title: ED161202

description: no s4U enriched rep 1


title: Dnmt1cKO_5

city: Madison

first: Chad

middle: Michael

last: Vezina

state: WI

address: 1656 Linden Drive

department: Comparative Biosciences

institute: University of Wisconsin-Madison

data_processing:
Basecalls/demuxxing performed using Illumina bcl2fastq, v2.17.1.14
Reads were filtered and trimmed for adapters and quality.
Expression estimates were calculated using RSEM v1.2.3 with alignments by bowtie v0.12.9
Genome_build: mm10
Supplementary_files_format_and_content: xlsx file with a table of Expected Counts expression estimates from the RSEM application

organism: Mus musculus

source_name: Bladder urothelium

growth_protocol: Embryos generated by timed matings

extract_protocol:
Bladder urothelium separated from stroma by trypsin digestion. Dissected tissues were placed directly into RLT Plus lysis buffer (Qiagen) for later processing. For each batch of harvest, dissected tissues from multiple embryos were pooled into one lysate. Total RNA was purified from the RLT Plus lysates using the RNeasy Plus Micro Kit (Qiagen) according to manufacturer’s instructions.
The following is an excerpt from Hou et al, Sci Rep. 2015; 5:9570, the manuscript that details the protocol employed. Poly-A-tailed mRNA is isolated from total RNA using oligo-dT beads. Purified mRNA is then fragmented with heat in fragmentation buffer. First strand cDNA is then synthesized using random hexamer oligos containing partial Illumina 3′ adaptor sequence. After RNA removal, a modified oligo containing partial Illumina's 5′ adaptor is then ligated to the 5′ of the single stranded cDNA. The library is then amplified by PCR using oligos that contain full Illumina adaptor sequences and our in-house index sequences.

tag: strain

value: Bladder urothelium

tag: age

value: Embryonic day 15.5

value: Bladder urothelium Dnmt1 knockout (Dnmt1cKO):Shhcre/+; Dnmt1flox/flox


title: Dnmt1cKO_4

tag: tissue


title: ED161203

description: no s4U enriched rep 2


title: OV-5-WT

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Signal intensities of probes were Quantile normalized (beadarray package in R/Bioconductor)

label: total RNA

source_name: OVCAR5 cell line

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

growth_protocol: HCT116 cell line was grown in DMEM media with 10% Fetal bovine serum and 1% Penicilline and Streptomycin and OVCAR5 and Colo205 cell lines were grown in RPMI1640 media with 10% Fetal bovine serum and 1% Penicilline and Streptomycinwith  at  37ºC under 5% CO2 condition

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instruction

treatment_protocol: HCT116, Colo205, OVCAR5 cells were either vehicle treated or Imetelstat treated for 2 weeks were used for preparing the total RNA and to perfrom gene expression array.

tag: cell line

tag: agent

value: Vehicle


title: Dnmt1cKO_3


title: COLO-WT

source_name: Colo205 cell line


title: PIP-RBPJ-1_rep2

city: Kyoto

first: Yulei

last: Wei

address: kyoto,tanakamonnzenncyo8-1, hyakumanbenn haitu 318

country: Japan

institute: Kyoto U

description: Gene expression after 24 hours treated cells

hyb_protocol: Hybridization was used the GeneChip® Hybridization, Wash and Stain Kit from Affymetrix following the manufacturer's instructions. 5.2 μg fragmented and labeled ss-DNA were mixed with Hybridization buffer and hybridization for 16h at 45℃.

scan_protocol: The Hyb-Wash-Scan mode was used,this section provides a summary of the operations for hybridization, wash, stain and imaging. The sepecific information are followed the Affymetrix® GeneChip® Command Console® User’s Guide (P/N 702569).

data_processing: The scanned images were captured and analyzed with Affymetrix geneAtlas imaging station  to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized with Expression Console(Affymetrix). Probe that at least 1 out of 2  samples flagged as Detected were maintained.

label: Biotin

source_name: Neural stem cell chemical treated for 24 hours, PIP-RBPJ-1

label_protocol: The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin. 5.5 μg of singlestranded DNA is required for fragmentation and labeling.

growth_protocol: The human H9 ES-derived neural stem cells were cultured by the protocal of the invitrogin.

extract_protocol: RNA was extracted by Qiagen Rneasy Mini Kit (154054839 ) following the manufacturer's instructions.

treatment_protocol: The human H9 ES-derived neural stem cells were cultured and treat with the PIP-RBPJ-1 2uM for 1 days. The cell treat with DMSO as negtive control.

tag: cell type

value: H9 ES-derived neural stem cells


title: Dnmt1cKO_2


title: COLO-GRN

value: Imetelstat


title: PIP-RBPJ-1_rep1


title: Dnmt1cKO_1


title: HCT116-GRN

source_name: HCT116 cell line


title: HCT116-WT


title: Control_2

value: Control:Shhcre/+; Dnmt1flox/+


title: DMSO_rep2

source_name: Neural stem cell chemical treated for 24 hours, DMSO

value: control


title: Cre neg_5

value: Cre negative litter mates


title: Cre neg_6


title: CK_3

city: Fuyang

first: Mi

last: NI

state: Anhui

address: No.100 Qinghe West Road

country: China

institute: Fuyang Normal Univ

data_processing:
The original image data is transferred into sequence data via base calling
We use BWA to map clean reads to genome reference and use Bowtie to gene reference.
Genes and isoforms expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization).
Genome_build: http://genome.jgi.doe.gov/Trias1/Trias1.download.html
Supplementary_files_format_and_content: FPKM calculated using RSEM, FPKM values represent counting fragments, not reads.

organism: Trichoderma asperellum

growth_protocol: The spore suspension of T. asperellum TJ01 was transferred to PD medium. After culturing at 28°C and 180 rpm for 24 h

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer’s instruction.
The mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates.

treatment_protocol: Culturing in Burk broth containing 0 μg/mL (control), 100 μg/mL, 500 μg/mL, or 1000 μg/mL dichlorvos at 28°C and 180 rpm for 24 h

tag: treated with

value: 0 μg/mL (control) dichlorvos at 28°C and 180 rpm for 24 h


title: DMSO_rep1

growth_protocol: The hu cultured by the protocal of the invitrogin.


title: CK_1


title: OV-5-GRN


title: Cre neg_3


title: Cre neg_2


title: Control_1


title: Cre neg_1


title: D10_3

source_name: Trichoderma_1000 μg/mL  dichlorvos

value: 1000 μg/mL dichlorvos at 28°C and 180 rpm for 24 h


title: Cre neg_7


title: c-Jun and c-Fos expressing vectors transduced, Replicate 3

city: London

first: Ander

last: Abarrategi

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: The Francis Crick Institute

description: 3HJF 3

hyb_protocol: The labeled, fragmented ssDNA was hybridized to the GeneChip Human Gene 2.0ST Array (Affymetrix, Santa Clara, CA) in a GeneChip Hybridization Oven 640 at 45ºC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software Genechip Command Console Software (AGCC)

data_processing: The intensity cell files were then imported, normalized for background correction (used RMA for normalization) with Genechip Expression Console Software

source_name: Human Bone Marrow_c-Jun and c-Fos expressing

label_protocol: Ambion WT Expression kit was used to prepare the cDNA, which was then labeled using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix, High Wycombe, UK).

growth_protocol: Cells were cultured in DMEM complemented with 10% FBS, Antibiotics and L-glutamine during 10 days after transduction and  before RNA extraction.

extract_protocol: RNA was extracted using Qiagen Rneasy kit.

treatment_protocol: c-DNA was cloned into pOTB7 plasmid, which carries Tomato gene as reporter fluorescent protein. Lentiviral particles were produced by transient calcium phosphate transfection of HEK-293 cells. hMPCs were transduced with those lentiviral particles. Tomato expression was assessed by flow cytometry and c-fos expression was confirmed via qPCR, western blot and immunofluorescence. Cells transduced with lentivirus coding only for fluorescent protein were used as controls. Three independent replicas are provided from each treatment: 3H 1, 3H 2, 3H 3 correspond to hMPCs transduced with control lentiviral particles. 3HF 1, 3HF 2 and 3HF 3 correspond to hMPCs tranduced with lentiviral particles designed for c-fos expression. 3HJ 1, 3HJ 2 and 3HJ 3 correspond to hMPCs tranduced with lentiviral particles designed for c-jun expression. 3HJF 1, 3HJF 2 and 3HJF 3 correspond to hMPCs tranduced with lentiviral particles designed for c-jun and c-fos expression.

value: Mesenchymal progenitor cells (MPCs)


title: Runx2 at 200 nM concentration

type: protein

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Proteins were diluted to 200 or 100 nM in a 175-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at room temperature. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Alexa-488-conjugated rabbit polyclonal antibody to His (Invitrogen) was diluted to 50 μg/ml in PBS / 2% milk and applied to a single-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

scan_protocol: Protein-bound microarrays were scanned to detect Alexa-488-conjugated antibody (488 nm ex, 522 nm em) using at least three different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots. Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices), bad spots were manually flagged and removed, and data from multiple Alexa 488 scans of the same slide were combined using masliner (MicroArray LINEar Regression) software.

data_processing:
To correct for any possible non-uniformities in protein binding, we adjusted the Alexa 488 signals according to their positions on the microarray. We calculated the median normalized intensity of the 15 x 15 block centered on each spot and divided the spot's signal by the ratio of the median within the block to the median over the entire chamber. Next, the Seed-and-wobble algorithm was applied to compute enrichment scores (E-scores) and median intensities for all possible 8-mers.
Enrichment scores (E-scores), median intensities, and z-scores for 8-mers

label: Alexa 488

molecule: protein

source_name: Human Runx2

label_protocol: Proteins were tagged with N-terminal GST by cloning. Protein-bound arrays were incubated with Alexa-488-conjugated rabbit polyclonal antibody to GST (Invitrogen).

growth_protocol: Gateway-compatible clones containing the full-length genes for Runx1, and Runx2 were purchased from GeneCopoeia and the genes were transferred into pDEST15 using the LR Clonase reaction (Life Technologies). This vector enables the production of N-terminally GST-tagged proteins. Cells were grown in LB broth to an OD600 of 0.4 to 0.6 and then expression was induced with IPTG at 30° to 37° C. Pelleted cells were frozen, stored at -20 C, and thawed cells were lysed with lysozyme.

extract_protocol: GST-tagged protein was purified from the soluble portion of the lysate using GST resin (GE Healthcare) according to manufacturer’s instructions.

tag: transcription factor

tag: protein concentration

value: Protein concentration:200nM


title: CK_2


title: c-Jun expressing vector transduced, Replicate 3

description: 3HJ 3

source_name: Human Bone Marrow_c-Jun expressing


title: D10_2


title: Runx1 at 200 nM concentration

source_name: Human Runx1


title: c-Jun expressing vector transduced, Replicate 2

description: 3HJ 2


title: c-Jun and c-Fos expressing vectors transduced, Replicate 1

description: 3HJF 1


title: D10_1


title: Cre neg_4

tag: genotype


title: Gabpa at 50 nM concentration

source_name: Human Gabpa

growth_protocol: Gateway-compatible clones containing the full-length genes for Ets1, Elk1, and Gabpa were purchased from GeneCopoeia and the genes were transferred into pDEST15 using the LR Clonase reaction (Life Technologies). This vector enables the production of N-terminally GST-tagged proteins. Cells were grown in LB broth to an OD600 of 0.4 to 0.6 and then expression was induced with IPTG at 30° to 37° C. Pelleted cells were frozen, stored at -20 C, and thawed cells were lysed with lysozyme.

value: Gabpa

value: Protein concentration:50nM


title: E2f4 at 200 nM concentration

source_name: Human E2f4

label_protocol: Proteins were tagged with GST by cloning. Protein-bound arrays were incubated with Alexa-488-conjugated rabbit polyclonal antibody to GST (Life Technologies, A11001).

growth_protocol: The Life Technologies Gateway cloning system was used to insert full length human E2f1, E2f3, and E2f4 genes into the pET-60 destination vector with a C-terminal GST tag. Cells were grown in LB culture to an OD600 of 0.4, then protein expression was induced with 1mM IPTG at 30°C for 2hrs (E2f1), or 20°C overnight (E2f4). Pelleted cells were frozen, then thawed cells were lysed in PBS lysis buffer for two hours at 4°C while gently rocking. The lysate was centrifuged, and the protein was recovered from the soluble lysate using a GE GSTrap FF GST tag affinity column according to manufacturer’s instructions.       This vector enables the production of N-terminally GST-tagged proteins. Cells were grown in LB broth to an OD600 of 0.4 to 0.6 and then expression was induced with IPTG at 30° to 37° C. Pelleted cells were frozen, stored at -20 C, and thawed cells were lysed with lysozyme.

extract_protocol: GST-tagged protein was purified from the soluble portion of the lysate using a GE GSTrap FF GST tag affinity column according to manufacturer’s instructions.


title: Elk1 at 200 nM concentration

source_name: Human Elk1


title: E2f3 at 200 nM concentration

source_name: Human E2f3


title: E2f1 at 200 nM concentration

source_name: Human E2f1


title: Ets1 at 70 nM concentration

source_name: Human Ets1

value: Protein concentration:70nM


title: D5_2

source_name: Trichoderma_500 μg/mL  dichlorvos

value: 500 μg/mL dichlorvos at 28°C and 180 rpm for 24 h


title: untreated LNCaP cells (miRNA)

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

description: miRNA expression data from untreated LNCaP cells

hyb_protocol: Labelled samples were hybridized to the Affymetrix GeneChip arrays as recommended by the manufacturer

scan_protocol: Arrays were scanned in a GeneChip scanner 3000 with G7 update

data_processing: HG-133Plus_2.0 CEL files were summarized using the MAS5.0 algorithm (Affymetrix GCOS v1.4)). The experimental samples was compared to the untreated sample using the comparison analysis algorithm (MAS5.0). miRNA_3.0 CEL files were summarized using  the Expression Console (Affymetrix) using the rma-dabg algorithm.

source_name: prostate carcinoma cell line LNCaP

label_protocol:
mRNA expression: total RNA samples (200 ng) were amplified and labeled with the Affymetrix ExpressKit protocol
miRNA expression: total RNA samples (600 ng) were labelled with the Flashtag Labeling Kit  (Affymetrix) as recommended by the manufacturer

growth_protocol: LNCaP cells were cultivated for 2 weeks in RPMI 1640 medium without phenol red indicator supplemented with 10% heat-inactivated FCS, L-Glutamin (1mM final concentration), Penicillin (100 U/ml) and Streptomycin (100 µg/ml).

extract_protocol: Extraction of total RNA was performed using miRNeasy Kit (Qiagen, Hilden, Germany) with a subsequent DNase digestion according to the manufacturer's instructions.

treatment_protocol: untreated

value: LNCaP

tag: treatment


title: D5_1


title: D5_3


title: c-Jun expressing vector transduced, Replicate 1

description: 3HJ 1


title: HSV1 infected, 6hpi, Replicate 2

city: Berkeley

first: David

middle: Trombley

last: McSwiggen

address: 470 Li Ka Shing Center

department: Molecular and Cell Biology

institute: University of California Berkeley

description:
RTDM003E
raw files mapped separately to hg19 and JQ673480 (HSV1 KOS), and processed separately within these two mappings

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced paired mates were mapped on hg19 genome build using Bowtie2 with the following parameters: --no-unal --local --very-sensitive-local --no-discordant --no-mixed --contain --overlap --dovetail --phred33 –I 10 –X 2000. Sequenced paired mates were mapped on JQ673480 (HSV1 strain KOS) genome build using Bowtie2 and the following parameters: --no-unal --no-discordant --no-mixed --contain --overlap --dovetail --phred33.
From the length distribution of sequenced reads, we performed in silico size selection for short reads (under 100 bp) and for 180 - 250 bp reads (mono-nucleosome sized fragments).
DeepTools (bamCoverage) was used to generate bigwig files for the corresponding fragment size using the following parameters: -bs 1 -ignoreDuplicates --minFragmentLength 20 --maxFragmentLength 100 ; or -bs 1 -ignoreDuplicates --minFragmentLength 180 --maxFragmentLength 250
The resulting bigwig file was used to generate the genome browser shot in IGV, and the TSS plots using Deeptools (computeMatrix functions).
Genome_build: hg19 and JQ673480 (HSV1 KOS)
Supplementary_files_format_and_content:
bigwig files for all reads, and for reads under 100 bp and 180-250 bp generated using Deeptools; The headers for all the .length files are 'Raw Read Counts' and 'Fragment Length'.

organism:
Homo sapiens
Human alphaherpesvirus 1 strain KOS

source_name: HSV1 infected, 6hpi

growth_protocol: Human U2OS cells (female osteosarcoma) were cultured at 37°C and 5% CO2 in 1 g/L glucose DMEM supplemented with 10% Fetal Bovine Serum and 10 U/mL Penicillin-Streptomycin, and we subcultivated at a ratio of 1:3 – 1:6 every two to four days.

extract_protocol:
ATAC-seq experiments were performed as previously described (Buenrostro et al., 2013).
Libraries were processed using Nextera DNA Librarpy Prep Kit

treatment_protocol: 100,000 cells were seeded into 6-well plates and infected with an MOI of 1 and incubated for the specified amount of time, in the presence of 300 µg/mL PAA if applicable.

tag: cell line source

value: Human Osteosarcoma, Female, 15 yr old

tag: infected with

value: HSV1 strain KOS

tag: time point


title: HSV1 infected with PAA, 6hpi, Replicate 2

description:
RTDM003F
raw files mapped separately to hg19 and JQ673480 (HSV1 KOS), and processed separately within these two mappings

source_name: HSV1 infected with PAA, 6hpi


title: 293t_hrgfp_richtorin1_3h

source_name: HEK293T cells, ATCC CRL-3216 + AAVS1:hrGFP

tag: tissue lineage

value: embryonic kidney

tag: treatment medium

value: DMEM + 10% dialyzed FBS + 250 nM Torin1

tag: treatment length

value: 3 hours

tag: date experiment was sequenced

value: March 2016


title: HSV1 infected, 4hpi, Replicate 2

description:
RTDM003D
raw files mapped separately to hg19 and JQ673480 (HSV1 KOS), and processed separately within these two mappings

source_name: HSV1 infected, 4hpi


title: HSV1 infected, 2hpi, Replicate 2

description:
RTDM003C
raw files mapped separately to hg19 and JQ673480 (HSV1 KOS), and processed separately within these two mappings

source_name: HSV1 infected, 2hpi


title: D1_2

source_name: Trichoderma_100 μg/mL  dichlorvos

tag: strain

value: 100 μg/mL  dichlorvos at 28°C and 180 rpm for 24 h


title: D1_1


title: LNCaP cells cultivated in charcoal-stripped FCS (miRNA)

description: miRNA expression data from NE-like LNCaP cells

treatment_protocol: FCS was replaced by charcoal-stripped FCS (Sigma Aldrich, Hamburg, Germany) and LNCaP cells were cultivated for 14 days in androgen-free medium where medium was replaced every 72 h.

value: charcoal-stripped FCS


title: HSV1 infected with PAA, 6hpi, Replicate 1

description:
RTDM002F
raw files mapped separately to hg19 and JQ673480 (HSV1 KOS), and processed separately within these two mappings


title: 1_25 second 6hr

first: Tae-Kang

last: Kim

department: Dermatology

data_processing: The data were normalised using Illumina GenomeStudio version 2011.1

source_name: keratocytes_1,25(OH)2D3  for 6hrs

growth_protocol: Grown in KGM medium supplemented with KGF (Lonza) on collagen-coated plates

extract_protocol: RNA extraction was performed using Absolutely RNA Miniprep Kit (Stratagen).

treatment_protocol: 100nM compounds or vehicle were treated in growing media for 6hr and 24 hr

tag: subject

value: African American donors

tag: tissue

value: Neonatal foreskins

value: neonatal human epidermal keratinocytes

tag: passage

value: passage 3

value: 1,25(OH)2D3  for 6hrs


title: EtOH_control second 6hr

source_name: keratocytes_0.1% ethanol (control) for 6hrs

tag: cell type

value: 0.1% ethanol (control) for 6hrs


title: HSV1 infected, 2hpi, Replicate 1

description:
RTDM002C
raw files mapped separately to hg19 and JQ673480 (HSV1 KOS), and processed separately within these two mappings

tag: cell line


title: HSV1 infected, 4hpi, Replicate 1

description:
RTDM002D
raw files mapped separately to hg19 and JQ673480 (HSV1 KOS), and processed separately within these two mappings


title: HSV1 infected, 6hpi, Replicate 1

description:
RTDM002E
raw files mapped separately to hg19 and JQ673480 (HSV1 KOS), and processed separately within these two mappings


title: EtOH_control first 6hr

value: passage 2

tag: treated with


title: 20_23 second 6hr

source_name: keratocytes_20,23(OH)2D3 for 6hrs


title: U2OS Uninfected, Replicate 1

description:
RTDM002A
raw files mapped separately to hg19 and JQ673480 (HSV1 KOS), and processed separately within these two mappings

source_name: U2OS Uninfected


title: 1_25 24hr

source_name: keratocytes_1,25(OH)2D3  for 24hrs


title: 1_25 first 6hr


title: 20_23 first 6hr


title: U2OS Uninfected, Replicate 2

description:
RTDM003A
raw files mapped separately to hg19 and JQ673480 (HSV1 KOS), and processed separately within these two mappings


title: HSV1 infected with PAA, 6hpi, pooled replicates

description:
RTDM_pooled_F
raw files mapped separately to hg19 and JQ673480 (HSV1 KOS), and processed separately within these two mappings


title: EtOH_control 24hr

source_name: keratocytes_0.1% ethanol (control) for 24hrs

value: 0.1% ethanol (control) for 24hrs


title: 20_23 24hr

source_name: keratocytes_20,23(OH)2D3 for 24hrs


title: HSV1 infected, 4hpi, pooled replicates

description:
RTDM_pooled_D
raw files mapped separately to hg19 and JQ673480 (HSV1 KOS), and processed separately within these two mappings

source_name: HSV1 infected, 4hpi, pooled replicates


title: HSV1 infected, 2hpi, pooled replicates

description:
RTDM_pooled_C
raw files mapped separately to hg19 and JQ673480 (HSV1 KOS), and processed separately within these two mappings

source_name: HSV1 infected, 2hpi, pooled replicates


title: FPS17: serB_A4_F1_I0_R1

city: La Jolla

first: Adam

middle: M

last: Feist

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California, San Diego

data_processing:
Sequenced reads were mapped onto CP009273.1 reference genome sequence using bowtie2 v.2.3.4.1 with parameters -X 1000 -N 1 -p 20 -3 3 -1 <R1_files> -2 <R2_files> -x <index>.
The SAM output file of bowtie2 was converted to BAM and sorted using samtools version 1.8
Expression levels of each gene in units transcripts per million (TPM) were computed from fragment counts normalized per kilobase of feature length per million mapped fragments (FPKM) using the R (v.3.5.0) package DESeq2 in Bioconductor.
Differentially expressed genes were identified using the R package DESeq2 in Bioconductor. Gene expression fold changes were considered significant if the log2(fold change) was greater than 1 and the calculated p-value was smaller that 0.05.
Genome_build: CP009273.1
Supplementary_files_format_and_content: A single .csv file containing all TPM values in a matrix table for all genes in each sample is provided.

organism: Escherichia coli BW25113

source_name: Adapted - serB knockout, Experiment4, Flask1, Population

growth_protocol: All samples were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 2 g/L D-glucose and 50 mg/L Kanamycin A (with the exception of wild type which was grown in the absence of antibiotics) .

extract_protocol:
Total RNA was isolated and purified using Qiagen’s RNeasy minikit column according to the manufacturer’s specifications. The total RNA quality was checked with the Agilent Bioanalyzer RNA 600 nano kit. Ribosomal RNA (rRNA) was removed utilizing Ribo-Zero rRNA removal kit (Epicentre) for Gram-negative bacteria.
The KAPA RNA HyperPrep kit (Kapa Biosystems) was used for generation of paired-end, strand-specific RNA sequencing libraries. The final pool of libraries was subjected to a 1x SPRI bead size selection to further remove unincorporated PCR primers.
RNAsequencing libraries were run on an Illumina NextSeq 550 machine using a NextSeq 500/550 Mid Output v2 kit (150 cycles).

treatment_protocol: The cell cultures were treated with RNAprotect reagent (Qiagen).

tag: carbon source

value: D-glucose

tag: genotype/variation

value: serB knockout


title: FPS18: serB_A4_F1_I0_R2


title: U2OS Uninfected, pooled replicates

description:
RTDM_pooled_A
raw files mapped separately to hg19 and JQ673480 (HSV1 KOS), and processed separately within these two mappings

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced paired mates were mapped on hg19 genome build using Bowtie2 with the following parameters: --no-unal --local --very-sensitive-local --no-discordant --no-mixed --contain --overlap --dovetail --phred33 –I 10 –X 2000. Sequenced paired mates were mapped on JQ673480 (HSV1 strain KOS) genome build using Bowtie2 and the following parameters: --no-unal --no-discordant --no-mixed --contain --overlap --dovetail --phred33.
From the length distribution of sequenced reads, we performed in silico size selection for short reads (under 100 bp) and for 180 - 250 bp reads (mono-nucleosome sized fragments).
DeepTools (bamCoverage) was used to generate bigwig files for the corresponding fragment size using the following parameters: -bs 1 -ignoreDuplicates --minFragmentLength 20 --maxFragmentLength 100 ; or -bs 1 -ignoreDuplicates --minFragmentLength 180 --maxFragmentLength 250
The resulting bigwig file was used to generate the genome browser shot in IGV, and the TSS plots using Deeptools (computeMatrix functions).
Genome_build: hg19 and JQ673480 (HSV1 KOS)
Supplementary_files_format_and_content:
bigwig files for all reads, and for reads under 100 bp and 180-250 bp generated using Deeptools; The headers for all the .length files are 'Raw Read Counts' and 'Fragment Length'.   .

source_name: U2OS Uninfected, pooled replicates

value: Human Osteosarcoma, Female, 15 yr old


title: TFK-1 with miR-145, replicate 1

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description:
TFK_1_145_1
TFK-1 cells were transfected using RNAiMAX for miR-145 mimics.

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000.

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of human HTA-2_0-type from Affymetrix. A Custom CDF Version 20 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary.

source_name: miR-145 mimic-transfected bile duct carcinoma cells TFK-1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: TFK-1 were maintained in RPMI-1640 medium. Media was supplemented with 10% fetal calf serum and 1% Penicillin-streptomycin (100 IU/ml and 100 g/ml, respectively).

extract_protocol: Total RNA of cell lines was isolated using TRIzol Reagent (Invitrogen, Life Technologies, Carlsbad, CA) according to the manufacturer's instructions.

treatment_protocol: TFK-1 cells were transfected using RNAiMAX for miRNA mimics or Lipofectamine 2000 transfection reagent for plasmid DNA (Life Technologies) according to the manufacturer's instructions.

value: bile duct carcinoma cell line

tag: treatment

value: miR-145-5p mimic


title: envzM3600

city: Hefei

first: Zhi

last: Liang

address: No.96, JinZhai Road

department: School of Life Sciences

institute: University of Science & Technology of C

description: Mutation

data_processing:
Sequencing reads were mapped to the E. coli genome with bowtie2
Read counts per gene determined using HTseq count before normalized using DESeq2
PCA analysis was performed using the top 500 genes with the most variations.
Supplementary_files_format_and_content: The txt file includes the gene expression profiles of all the samples. The xlsx file contains the PC1 and PC2 values of all the samples.

organism: Escherichia coli

growth_protocol: Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) at 37°C overnight. A single colony was diluted in 2.5ml LB medium containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) and was shaken at 250 rpm and 37°C overnight.

extract_protocol:
After exposed under the red light with a specific ON/OFF frequency for 10 hours, 1ml bacterial culture was sampled and the bacterial cells were collected at 4 °C. The total RNA of E. coli was extracted using RNAprep pure Cell/Bacteria Kit (TIANGEN, DP430) and preserved at -80 °C.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In the 15 ml centrifuge tube (Corning, 430791), the overnight culture was diluted to 2ml in fresh LB medium containing Ampicillin (50 ng/μl), Chloramphenicol (170 ng/μl) and IPTG (0.5mM) to reach OD600 = 0.01. The LED tube was screwed into the centrifuge tube and connected with the control box. Then the power of the control box was turned on and the LED frequency input was generated. At last, the 15 ml centrifuge tube with LED tube was put into the Thermomixer comfort (Eppendorf) and shaken at 650 rpm and 37°C for 10 hours.

tag: plasmid

value: pLCenvZM, pPCB (mutation)

tag: input signal frequency


title: TFK-1 with miR-145, replicate 2

description:
TFK_1_145_2
TFK-1 cells were transfected using RNAiMAX for miR-145 mimics.


title: Uhordei_infectedMaizeSeedling_20hpi_R3

city: Regensburg

first: Urs

last: Lahrmann

address: Am Biopark 9

department: Project Group Personalized Tumor Therapy

institute: Fraunhofer ITEM

hyb_protocol: Samples for Microarray analyses were processed with Gene Expression Hybridization Kit, Gene Expression Wash Buffer Kit (Agilent) and the RNeasy Mini Kit (Qiagen) according to the manufacturers’ instructions.

scan_protocol: Total-RNA was used as input for reverse transcription.Microarrays were performed on 8x15k microarrays (Agilent) and scanned using the following parameters: profile: AgilentHD_GX_1Color,Slide ID: AutoDetect, Channels: G, Scan region: Agilent HD (61 x 21,6mm), resolution: 2µm, Tiff: 20bit, RPMT: 100%, GPMT: 100%, XDS: no XDR. The image was processed in Agilent Feature Extraction and data analysis was performed using Partek® Genomics Suite Software (Partek Inc.).

data_processing: Changes in U. hordei gene expression in planta (at 20 hpi, 40 hpi, 3 dpi and 6 dpi) were calculated relative to U. hordei yeast-like cells grown in axenic culture.

organism: Ustilago hordei

source_name: U. hordei infected maize seedling at 20 hpi

label_protocol: Samples for Microarray analyses were processed with the One Color Quick Amp Labeling kit, One Color Spike-In Kit, (Agilent)

growth_protocol: Ustilago hordei (4857-4 Mat-1 and 4857-5 Mat-2) cultures were incubated in YEPSlight (0.4% yeast extract, 0.4% peptone, and 2% saccharose) liquid medium at 22°C with 200 rpm shaking. Susceptible barley cultivar (Golden Promise) was grown in a greenhouse at 70% relative humidity, at 22°C during the day and the night; with a light/dark regime of 15/9 hrs and 100 Watt m-2 supplemental light when the sunlight influx intensity was less than 150 Watt m-2.

extract_protocol: Total RNA was isolated from axenic culture and U. hordei-infected barley plants (at 20 hpi, 40 hpi, 3 dpi and 6 dpi). The third leaf of the infected barley plant was collected by cutting 1 cm below the injection needle sites and approximately 3 cm of the leaf was taken for RNA extraction. For 20 hpi time point the melted latex was used to collect penetrated fungal materials. Samples were then frozen in liquid nitrogen and grinded by using a mortar and pestle under constant liquid nitrogen cooling conditions. The total RNA was isolated from the fine powder using the TRIzol® extraction method (Invitrogen; Karlsruhe, Germany) according to the manufacturer’s instructions. Total RNA was then cleaned with Turbo DNA-Free™ Kit (Ambion/Applied Biosystems; Darmstadt, Germany) to remove any DNA contamination according to the manufacturer’s instructions.

treatment_protocol: For virulence assay, both wild type and mutant strains of U. hordei were grown in YEPSlight liquid medium at 22°C and 200 rpm shaking to get an OD600 of 0.6-0.8. The cells were then centrifuged at 3500 rpm for 10 min at RT and resuspended in sterile water supplemented with 0.1% Tween-20 to get the OD600 of 3.0. Then U. hordei suspension was injected into the center of the leaf whirl of 10 to 12-day-old barley seedlings (three-leaf stage) with a syringe with needle. All infection assays were performed in three biological replicates with at least 16 plants.

tag: growth condition

value: in planta

tag: dpi

value: at 20 hpi on maize


title: HSV1 infected, 6hpi, pooled replicates

description:
RTDM_pooled_E
raw files mapped separately to hg19 and JQ673480 (HSV1 KOS), and processed separately within these two mappings

source_name: HSV1 infected, 6hpi, pooled replicates

tag: cell line source

tag: infected with

value: HSV1 strain KOS

tag: time point


title: TFK-1 with Allstar, replicate 1

description:
TFK_1_Allstar_1
TFK-1 cells were transfected using RNAiMAX for AllStars control.

source_name: AllStars control-transfected bile duct carcinoma cells TFK-1

value: AllStars control


title: Spneumoniae_ gls24B_50_rep_2

city: Majadahonda

first: Antonio

middle: J.

last: Martin-Galiano

address: Ctra. Majadahonda-Pozuelo, km 2.2

department: Bacterial genetics

institute: Instituto de Salud Carlos III

description: RNA extracted from S. pneumoniae R6 gls24B deletion mutant

hyb_protocol: 250 ng of labelled cDNA were used for hybridization. Arrays were hybridized at 65ºC for 40 hours.

scan_protocol: Scanning was done on a Roche MS200 scanner

data_processing: Raw data were extracted and normalized using Agilent Feature extraction 11.5.1.1 software. The median expression of every probeset was obtained, scaled to log2 and normalized by quantile using Bioconductor.

organism: Streptococcus pneumoniae R6

source_name: Bacteria

label_protocol: 25 ng of RNA were used to obtain cDNA with WTA2 from Sigma. This cDNA was labelled with Cy3 with ULS kit following Agilent's instructions

growth_protocol: Bacteria were grown in THYE  + either 500 or 50 microg/mL BSA until OD620=0.25

extract_protocol: RNA was extracted with Mini Rneasy columns from Quiagen and treated with DNAse I

treatment_protocol: No additional treatment was applied

value: gls24B deletion mutant

tag: phase

value: Exponential growth

tag: medium

value: THYE + 50 microg/mL BSA


title: TFK-1 with miR-145, replicate 3

description:
TFK_1_145_3
TFK-1 cells were transfected using RNAiMAX for miR-145 mimics.


title: Uhordei_infectedBarleySeedling_6dpi_R2

source_name: U. hordei infected barley seedling at 6 dpi

value: at 6 dpi on barley


title: Spneumoniae_ gls24B_500_rep_2

value: THYE + 500 microg/mL BSA


title: Uhordei_infectedMaizeSeedling_20hpi_R1


title: Uhordei_infectedBarleySeedling_6dpi_R3


title: FPS15: thrA_A2_F1_I0_R1

source_name: Adapted - thrA knockout, Experiment2, Flask1, Population

value: thrA knockout


title: TFK-1 with Allstar, replicate 2

description:
TFK_1_Allstar_2
TFK-1 cells were transfected using RNAiMAX for AllStars control.


title: Uhordei_infectedBarleySeedling_3dpi_R3

source_name: U. hordei infected barley seedling at 3 dpi

value: at 3 dpi on barley


title: envzM1800

description: Mutation

tag: strain


title: FPS16: thrA_A2_F1_I0_R2

value: D-glucose


title: Spneumoniae_ R6_50_rep_2

description: RNA extracted from S. pneumoniae R6

value: wild type


title: Spneumoniae_ gls24B_50_rep_1


title: Spneumoniae_ R6_50_rep_1

description: RNA extracted from S. pneumoniae R6


title: envzM2400

description: Mutation


title: FPS14: ptsI_A3_F1_I0_R2

source_name: Adapted - ptsI knockout, Experiment3, Flask1, Population

value: ptsI knockout


title: envzM1200

description: Mutation


title: FPS13: ptsI_A3_F1_I0_R1


title: TFK-1 with Allstar, replicate 3

description:
TFK_1_Allstar_3
TFK-1 cells were transfected using RNAiMAX for AllStars control.

value: bile duct carcinoma cell line


title: envzM900

description: Mutation


title: Uhordei_infectedMaizeSeedling_20hpi_R2


title: FPS12: ptsI_A1_F5_I1_R2

source_name: Adapted - ptsI knockout, Experiment1, Flask5, Clone


title: KO rep 3

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description:
All_genes_NormalizedReadsPerKb.txt
Genes_up_with_KO_NormalizedReadsPerKb.txt
Genes_down_with_KO_NormalizedReadsPerKb.txt

data_processing:
Aligment to mm9 using STAR (Dobin et al. 2013)
Exon reads quantified using iRNA-seq pipeline (Madsen et al. 2015)
Differential gene expression identified using DESeq2 (Love et al. 2014)
For calling differentially expressed genes, a FDR < 0.01 and threshold of minimum 10 reads per kb on average for the given condition were used
Genome_build: mm9
Supplementary_files_format_and_content: txt-file with normalized reads for each gene (reads per kb)

molecule: polyA RNA

source_name: Brown adipose tissue

growth_protocol: Mice were housed at room temperature

extract_protocol:
RNA extraction was completed using TRI reagent
Polyadenylated RNA was isolated from 1 μg of total RNA by incubation with oligo-dT beads and prepared according to the manufacturer’s instructions (TruSeq 2, Illumina)

value: knockout of CRLS1

tag: age

value: 20 weeks

tag: housing temperature

value: Room temperature


title: KO rep 4


title: KO rep 5


title: Uhordei_infectedBarleySeedling_6dpi_R1

value: in planta


title: FPS11: ptsI_A1_F5_I1_R1


title: Uhordei_infectedBarleySeedling_3dpi_R2


title: Uhordei_infectedBarleySeedling_3dpi_R1


title: KO rep 2


title: FPS6: serB_A1_F5_I1_R2

source_name: Adapted - serB knockout, Experiment1, Flask5, Clone

value: serB knockout


title: Uhordei_infectedBarleySeedling_40hpi_R3

source_name: U. hordei infected barley seedling at 40 hpi

value: at 40 hpi on barley


title: FPS5: serB_A1_F5_I1_R1


title: envzM600

description: Mutation

value: pLCenvZM, pPCB (mutation)


title: envz3600

description: Wildtype

value: pLCenvZ, pPCB (wild type)


title: envz1800

description: Wildtype


title: KO rep 1


title: WT rep 4

value: wild-type


title: FPS4: thrA_A1_F5_I1_R2

source_name: Adapted - thrA knockout, Experiment1, Flask5, Clone


title: Spneumoniae_ gls24B_500_rep_1

value: gls24B deletion mutant

value: Exponential growth


title: FPS3: thrA_A1_F5_I1_R1

value: thrA knockout


title: envz1200

description: Wildtype


title: WT rep 3


title: envz2400

description: Wildtype


title: Spneumoniae_ R6_500_rep_1

description: RNA extracted from S. pneumoniae R6

value: THYE + 500 microg/mL BSA


title: WT rep 5


title: Uhordei_infectedBarleySeedling_40hpi_R2


title: c-Jun and c-Fos expressing vectors transduced, Replicate 2

description: 3HJF 2

source_name: Human Bone Marrow_c-Jun and c-Fos expressing

tag: cell type

value: Mesenchymal progenitor cells (MPCs)


title: WT rep 1


title: Uhordei_infectedBarleySeedling_40hpi_R1


title: Spneumoniae_ R6_500_rep_2

description: RNA extracted from S. pneumoniae R6

value: wild type


title: FPS2: wt_R2

source_name: wild type

value: D-glucose


title: envz900

description: Wildtype


title: WT rep 2


title: Uhordei_infectedBarleySeedling_20hpi_R3

source_name: U. hordei infected barley seedling at 20 hpi

value: at 20 hpi on barley