title: seq-HK00013_H3K27me3_1E7_N2_Eemb_ChIP_Rep1

status: Public on Aug 10 2013

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: ChIP DNA; Antibody information listed below: official name: HK00013 H3K27me3:1E7:JL:1;target name: H3K27me3;host: Mouse;antigen: KQLATKAAR(me3-K)SAPATGGVKC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00013;short description: A protein G purified mouse monocloonal antibody agsinst H3K27me3.  Used for ChIP

data_processing:
ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM
Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]-o INT
Maximum number of gap opens [1]-e INT
Maximum number of gap extensions, -1 for k-difference mode (disallowing long gaps) [-1]-d INT
Disallow a long deletion within INT bp towards the 3?-end [16]-i INT
Disallow an indel within INT bp towards the ends [5]-l INT
Take the first INT subsequence as seed. If INT is larger than the query sequence, seeding will be disabled. For long reads, this option is typically ranged from 25 to 35 for ?-k 2?. [inf]-k INT
Maximum edit distance in the seed [2]-t INT
Number of threads (multi-threading mode) [1]-M INT
Mismatch penalty. BWA will not search for suboptimal hits with a score lower than (bestScore-misMsc). [3]-O INT
Gap open penalty [11]-E INT
Gap extension penalty [4]-R INT
Proceed with suboptimal alignments if there are no more than INT equally best hits. This option only affects paired-end mapping. Increasing this threshold helps to improve the pairing accuracy at the cost of speed, especially for short reads (~32bp).-c
Reverse query but not complement it, which is required for alignment in the color space.-N
Disable iterative search. All hits with no more than maxDiff differences will be found. This mode is much slower than the default.-q INT
Parameter for read trimming. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original read length. [0] bwa samse:Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.OPTIONS:-n INT
Maximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written. [3]  Processed data are obtained using following parameters: genome version is ce10

growth_protocol: Worm_embryo_growth_and_harvest_vSS5. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85% formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100 mM Tris-HCl pH 7.5 and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl). Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_vSS2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then sonicated 9 times on ice at the following settings: 30 sec; power output 3; 70% duty cycle. Cell debris was removed by centrifuging at 13,000 rpm for 15 minutes at 4ºC and taking the supernatant. Supernatants were filtered through Millipore Ultrafree-MC 0.45 ?m filter units (cat. UFC30HV0S) at 13,000 rpm, 4°C for 1 minute to remove lipids. Protein concentration was determined, and extracts were aliquoted and stored at -80ºC. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_vSS4. 0.3-3 mg extract + 1% sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl). Antibody was added to each IP sample and incubated overnight at 4ºC. Immune complexes were incubated (2 hrs at 4ºC) with 50 ?l of IgG dynabeads (Dyna), and washed 5 minutes with 1.5 mL of each of the following solutions: ChIP Buffer, ChIP Buffer + 1 M NaCl, ChIP Buffer + 500 mM NaCl, TEL Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and 2X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 ?L elution buffer for 15 minutes at 65ºC. Samples were treated with RNAse for 30 minutes at 37ºC. Samples were treated with proteinase K at 55ºC for 1-2 hrs then transfer to 65ºC overnight to reverse crosslinks. DNA was cleaned up using Zymo kit. For a detailed protocol see http://www.modencode.org/.
DNA for Library Prep is incubated with an End Repair Enzyme mix (NEB Klenow, T4 DNA polymerase and T4 PNK) to ensure blunt ends. It is then purified and incubated with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3? ends (a single A-overhang for more efficient and directed ligation of the adaptors). After a second purification, the DNA fragments is ligated with single-end ?Homebrew? adaptors which contain an index sequence within (Corbin Jones? lab). After ligation, the samples are purified TWICE using SPRI beads, allowing for a size selection step getting rid of excess adaptors. Samples are then amplified by PCR with single end primers. Depending on the original fragmentation of the DNA, samples can either be purified by SPRI or by separation and purification from an agarose gel.
Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.

tag: developmental stage

value: Early Embryo

value: wild type

tag: sex type

value: mixed Male and Hermaphrodite population


title: seq-WA30532379_H3K4me3_10001_N2_Eemb_Input_Rep1

type: SRA

description: input DNA

library_source: genomic

molecule: genomic DNA

organism: Caenorhabditis elegans

growth_protocol: Worm_embryo_growth_and_harvest_vSS4. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85% formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100 mM Tris-HCl pH 7.5 and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl). Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

tag: strain

tag: genotype


title: seq-WA30532379_H3K4me3_10001_N2_Eemb_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: WA305-34819 H3K4me3;target name: H3K4me3;host: Mouse;antigen: ART(me3-K)QTARKSTGC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: WA305-34819;short description: A protein G purified mouse monoclonal antibody to H3K3me3 (cat #305-34819) obtained from Waco. Used for ChIP.


title: seq-HK00013_H3K27me3_1E7_N2_Eemb_Input_Rep2

description: input DNA


title: seq-HK00013_H3K27me3_1E7_N2_Eemb_ChIP_Rep2


title: seq-HK00013_H3K27me3_1E7_N2_Eemb_Input_Rep1

description: input DNA


title: seq-WA30532379_H3K4me3_10001_N2_Eemb_ChIP_Rep2


title: seq-WA30532379_H3K4me3_10001_N2_Eemb_Input_Rep2

description: input DNA


title: seq-ab8895_H3K4me1_733246_N2_Eemb_ChIP_Rep1

status: Public on Aug 28 2013

description: ChIP DNA; Antibody information listed below: official name: ab8895 H3K4me1:733246;target name: H3K4me1;host: Rabbit;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab8895;short description: A rabbit affinity purified antibody to H3K4me1 from Abcam (ab8895 lot #733246). Used for ChIP.

value: mixed Male and Hermaphrodite


title: seq-ab8895_H3K4me1_733246_N2_Eemb_Input_Rep2

description: input DNA


title: seq-ab8895_H3K4me1_733246_N2_Eemb_ChIP_Rep2


title: H3118 control, biological rep2

status: Public on Apr 21 2014

type: RNA

city: Gainesville

first: Lizi

last: Wu

state: FL

address: 2033 Mowry Road

country: USA

institute: University of Florida

description: Gene expression data from fusion positive salivary gland tumor cells, control

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner

data_processing: The data were normalized using MAS5 normalization approach with Affymetrix GCOS software.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: human mucoepidermoid carcinoma cell line derived from parotid, luciferase shRNA control

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

growth_protocol: Cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% inactivated fetal bovine serum at 37°C under 5% CO2.

extract_protocol: RNA was isolated with the Trizol Reagent (Invitrogen) and purified by the Qiagen Rneasy Column with in column DNase digestion

treatment_protocol: Cells were infected with retroviruses twice on two consecutive dates. Infected cells were subjected to FACS sorting for GFP+ cells 72 hours after 1st infection and  total RNA were isolated.

tag: cell line

value: fusion-positive H3118 MEC cells

tag: genotype/variataion

value: luciferase shRNA control


title: HSY MAML2 knock-down, biological rep1

status: Public on Oct 30 2015

description: Gene expression data from fusion negative salivary gland tumor cells, MAML2 knock down

source_name: human parotid adenocarcinoma cell line, MAML2 knock-down

value: fusion-negative HSY parotid adenocarcinoma cells

value: MAML2 knock-down


title: H3118 CRTC1-MAML2/MAML2 knock-down, biological rep2

description: Gene expression data from fusion positive salivary gland tumor cells, CRTC1-MAML2 knock down

source_name: human mucoepidermoid carcinoma cell line derived from parotid, CRTC1-MAML2/MAML2 knock-down

value: CRTC1-MAML2/MAML2 knock-down


title: H3118 CRTC1-MAML2/MAML2 knock-down, biological rep1

description: Gene expression data from fusion positive salivary gland tumor cells, CRTC1-MAML2/MAML2 knock down


title: H3118 control, biological rep1


title: HSY control, biological rep2

description: Gene expression data from fusion negative salivary gland tumor cells, control

source_name: human parotid adenocarcinoma cell line, luciferase shRNA control


title: seq-WA30634849_H3K27ac_8002_N2_Eemb_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: WA306-34849 H3K27ac;target name: H3K27ac;host: Mouse;antigen: 19 end of N amino acids of homo sapiens histone H3.1;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: WA306-34849;short description: A protein G purified mouse monoclonal antibody to H3K27ac (cat #306-34849) obtained from Wako. Used for ChIP.


title: HSY MAML2 knock-down, biological rep2


title: HSY control, biological rep1


title: 4d red light grown hmr-22 seedlings/replicate 1

status: Public on Jun 01 2014

city: Riverside

first: Meng

last: Chen

state: CA

address: 2150 Batchelor Hall, 900 University Ave.

institute: University of California, Riverside

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: GeneSpring GX 12.1 to RMA normalize and correct background on all the data

organism: Arabidopsis thaliana

source_name: whole seedling (root, hypocotyl, cotyledon)

label_protocol: standard Affymetrix procedures

growth_protocol: Wild-type (Col-0) and hmr mutant seeds were surface-sterilized and plated on half-strength Murashige and Skoog (MS) growth medium without sucrose. The seeds were stratified in the dark at 4ºC for 4 d. Seedlings were grown in constant red light (Rc, 10μmol/m2/s) at 21°C for 4 d.

extract_protocol: Total RNA was extracted using SpectrumTM Plant Total RNA Kit (Sigma)

tag: ecotype


title: 4d red light grown hmr-5 seedlings/replicate 1


title: 4d red light grown hmr-22 seedlings/replicate 2


title: 4d red light grown hmr-5 seedlings/replicate 3


title: 4d red light grown WT(Col-0) seedlings/replicate 3

value: Wild-type


title: 4d red light grown hmr-22 seedlings/replicate 3


title: 4d red light grown WT(Col-0) seedlings/replicate 1


title: 4d red light grown WT(Col-0) seedlings/replicate 2


title: 4d red light grown hmr-5 seedlings/replicate 2


title: seq-WA30634849_H3K27ac_8002_N2_Eemb_ChIP_Rep1


title: seq-ab8898_H3K9me3_339901_N2_Eemb_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: AB8898 H3K9ME3:339901;target name: H3K9me3;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1-100 of human histone H3 tri methylated at K9.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: AB8898;short description: An affinity purified rabbit polyclonal antibody to H3K9me3 (lot# 339901) obtained from Abcam. Used for ChIP.


title: seq-ab8898_H3K9me3_339901_N2_Eemb_Input_Rep2

description: input DNA


title: seq-ab8895_H3K4me1_733246_N2_Eemb_Input_Rep1

description: input DNA


title: seq-WA30634849_H3K27ac_8002_N2_Eemb_Input_Rep2

description: input DNA


title: seq-WA30634849_H3K27ac_8002_N2_Eemb_Input_Rep1

description: input DNA


title: seq-ab8898_H3K9me3_339901_N2_Eemb_ChIP_Rep1


title: seq-ab8898_H3K9me3_339901_N2_Eemb_Input_Rep1

description: input DNA


title: seq-SDQ3520_LIN61_N2_L3_Input_Rep2

status: Public on Jul 26 2013

description: Input DNA

data_processing: to be updated

growth_protocol: Worm_L3_growth_and_harvest_vPK1. About 2-7 million of worms are bleached and then hatched in M9 for 24-42 hrs. About 100 embryos are seeded onto the plate to test for contamination and hatching efficiency. Remaining hatched L1 larvae are inoculated in a proper volume of liquid culture. Next day when larvae reach the L3 stage they are cleaned by M9 washes and sucrose gradient and collected by freezing in liquid nitrogen. Just before collection DIC pictures are taken and about 50ul of worms are stained for DAPI to assess the stage.

extract_protocol:
Worms are frozen, ground, crosslinked for 20 minutes in EGS, and for an additional 10 minutes in EGS plus formaldehyde. Later, washed pellets are resuspended in FA buffer and subjected to sonication in Bioruptor (20-30 pulses of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP.
Worm_chromatin_immunoprecipitation_vIL2. Appropriate amount of extract is incubated overnight with a proper amount of antibody (exceptional antibodies due to better results are incubated 2hrs). Afterwards, 40ul of equilibrated magnetic beads (either protein A or G, depending on antibody) are added and incubated for 2 hrs. Later, washes with FA, 500mM-salt FA, 1M salt FA, TEL, and TE buffer are performed and DNA is eluted in elution buffer (1% SDS in TE with 250 mM NaCl) ? two times with 57 ?l volume each, at 65°C. Samples are treated with RNAse, proteinase K and then crosslinks are reversed overnight at 65°C. DNA is purified on Qiagen PCR purification columns, tested by q-PCR for ChIP quality, and stored at -20°C for future applications.
ChIP or input DNA is blunt ended, A-tailed, ligated to adaptors, amplified by PCR, then size selected using AMPure beads.  The protocol uses the Illuimina TruSeq DNA Sample Prep Kit.
Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.

value: L3 Larva


title: seq-SDQ3520_LIN61_N2_L3_Input_Rep1

description: Input DNA


title: seq-SDQ3520_LIN61_N2_L3_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: LIN-61 SDQ3520;target name: LIN-61;host: Rabbit;antigen: VGYAEKYNLELVPPDEFKGTFRWDEYLEKESAETLPLDLFKPMPSQERLDKFKVGLRLEAADMCENQFICPATVKSVHGRLINVNFDGWDEEFDELYDVD;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ3520;short description: An Affinity purified Rabbit Polyclonal antibody to LIN-61 obtained from SDI (LIN-61 SDQ3520);input DNA


title: seq-SDQ3520_LIN61_N2_L3_ChIP_Rep2


title: seq-NA_N2_MXemb_3_A_EE1432

status: Public on Sep 21 2010

city: Chapel Hill

first: Everett

last: Zhou

state: NC

address: 1000 Manning Dr.

institute: UNC

description: This is input dataset for EE1432

data_processing: pipeline v.1.3, Data received between Feb 9 - May 30, 2009

source_name: Caenorhabditis elegans_N2_MXemb

growth_protocol: Worm_embryo_growth_and_harvest_v5. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol: Worm_chromatin_immunoprecipitation_vKI2. Antibody was incubated with protein A/G beads at 4 oC for at least 1 hr to prepare antibody-beads complex. For each reaction, 0.5-2 mg of protein extract was taken and sarkosyl was added to 1% final concentration. The extract was precleared by incubating with protein A/G beads for 30 min at 4 oC. Before immunoprecipitation, 10% of extract was taken and treated with RNase. The extract was mixed with the antibody-beads complex and incubated overnight at 4C. After washing beads, immune complexes were eluted from beads twice with 150uL elution buffer (1% SDS in TE with 250 mM NaCl) for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit. For a detailed protocol see http://www.modencode.org/. || Solexa_Library_Prep_vKI1. DNA was incubated with End Repair Enzyme mix (Epicentre, Madison) to ensure blunt ends and then with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3\` ends. The DNA fragments were ligated with single-end adaptor (Illumina) and then amplified by PCR with single end primers. The amplicon was loaded into an agarose gel, and size-selected DNA was recovered from the gel.

treatment_protocol: Worm_embryo_extraction_v3. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4?C and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C. For a detailed protocol see http://www.modencode.org/.

tag: Stage

value: MXemb

tag: chip antibody


title: seq-SDQ3891_LEM2_N2_MXemb_1_A_EE8_KI021

description:
Missing KI21 in UNC DB
input_experiment: seq-NA_N2_MXemb_3_A_EE1432

data_processing:
alignment: BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/.  The input is fastq and the output is sam file.
peak_calling: ChIP-Seq MACS Peak-calling:JL:1. Peak calls were determined by using Model-based Analysis of ChIP-Seq (MACS) software. MACS was supplied with the following parameters: tagSize = 25 mfold = 10,30 genomeSize = 90000000 bandwidth = 300 pvalue = 1e-5 Input = sam file Output = bed file
pipeline v.1.3, Data received between Feb 9 - May 30, 2009

extract_protocol: Worm_chromatin_immunoprecipitation_vKI3. Antibody was incubated with protein A/G beads at 4 oC for at least 1 hr and then washed by extraction buffer. For each reaction, 0.5-2 mg of protein extract was taken and sarkosyl was added to 1% final concentration. Before immunoprecipitation, 10% of extract was taken. The extract was mixed with the antibody-beads complex and incubated overnight at 4C. After washing beads, immune complexes were eluted from beads twice with 150uL elution buffer (1% SDS in TE with 250 mM NaCl) for 15minutes at 65C. Samples were treated with RNase A at room temperature for ? 1 hr then proteinase K at 55C for ? 1 hr. Samples were transferred to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit. For a detailed protocol see http://www.modencode.org/. || Solexa_Library_Prep_vKI1. DNA was incubated with End Repair Enzyme mix (Epicentre, Madison) to ensure blunt ends and then with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3\` ends. The DNA fragments were ligated with single-end adaptor (Illumina) and then amplified by PCR with single end primers. The amplicon was loaded into an agarose gel, and size-selected DNA was recovered from the gel.

treatment_protocol: Worm_embryo_extraction_v2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4?C and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C. For a detailed protocol see http://www.modencode.org/.

tag: antibody manufacturer

value: SDI

tag: antibody catalog #


title: SFMBT1 knock-down, biological rep1

status: Public on Jan 28 2013

description:
SFMBT1-1
Gene expression data.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner.

data_processing: The data were normalized using the MAS5 normalization approach with Affymetrix GCOS software.

organism: Mus musculus

source_name: mouse C2C12 cells, shSFMBT1

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

growth_protocol: Cells were grown in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 20% inactivated fetal bovine serum at 37°C under 5% CO2. The stable cells were selected and maintained with 2 ug/ml of puromycin.

extract_protocol: RNA was isolated with the Trizol Reagent (Invitrogen) and purified by the Qiagen Column with in-column DNase digestion.

treatment_protocol: shluc C2C12 (control), and shSFMBT1 C2C12 knock down.

tag: cell type

value: myoblasts

tag: shRNA


title: SFMBT1 knock-down, biological rep2

description:
SFMBT1-2
Gene expression data.


title: Vector control, biological rep1

description:
Control-1
Gene expression data.

source_name: mouse C2C12 cells, scramble shRNA control

value: shLuc


title: Vector control, biological rep2

description:
Control-2
Gene expression data.