SMNDC1      shRNA in 293T      Batch: BG293LV05

Experiment Information (Status: Submitting)
BG293LV05-99BG293LV05-100
idx00
TRCN#_or_BGC#TRCN0000369078TRCN0000369078
shRNA_or_gRNA_sequenceCCGGGAAAGTGAAATGGCAACAATTCTCGAGAATTGTTGCCATTTCACTTTCTTTTTGCCGGGAAAGTGAAATGGCAACAATTCTCGAGAATTGTTGCCATTTCACTTTCTTTTTG
PAM
NameSMNDC1SMNDC1
Sample_IDBG293LV05-99BG293LV05-100
transduction_Date12/18/2312/18/23
daysD4D4
RBP_nameSMNDC1SMNDC1
qPCR_result59.257.8
Ave_qPCR58.5
RT-qPCR_primer-Ftgaaatggcaacaattcaaca
RT-qPCR_primer-Rtcacactctcaggtgaagcaa
protein_conc00
WB_result
Ave_WB
WB_DONE_date
MW
IP
antibody_Cat#
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM00
Rep2_TPM00
ActionReadyReady
Library_start_date
repeat_library
Note
ID1007110072




Western Blot
Western Blot info was not avaliable




Experiment Status
BG293LV05-99BG293LV05-100
Sample_IDBG293LV05-99BG293LV05-100
Sample Name
Sample NameSMNDC1-BG293LV05-99SMNDC1-BG293LV05-100
RBPSMNDC1SMNDC1
Cell_Line293T293T
Exp UID
StatusSubmittingSubmitting
Status_date2024-05-072024-05-07
ProjectENCORE2ENCORE2
Note
ID1287412875




Library-Prep Information
BG293LV05-99BG293LV05-100
Sample #4142
Sample NameSMNDC1-BG293LV05-99SMNDC1-BG293LV05-100
Sample_Name_Alias
Index Well PositionA12B12
Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
LibPrep_date2024-01-162024-01-16
Lib_IDLib-240116Lib-240116
Tecan_Location
Tecan
Tecan_date
Size_bp270272
Peak_Molarity62.3071.90
libSampleQC_DNA_WellDNA_Library_set69/set1/A6.pngDNA_Library_set69/set1/B6.png
RIN9.99.4
libSample_RNA_WellRNA_Library_set69/set1/C11.pngRNA_Library_set69/set1/D11.png
SampleQC_methodTapeStation_2022TapeStation_2022
SampleQC_date2024-01-192024-01-19
Sample_IDBG293LV05-99BG293LV05-100
RBPSMNDC1SMNDC1
Batch_IDBG293LV05BG293LV05
WB_result0.0000.000
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCORE2ENCORE2
ID42224223




Sequencing Information
BG293LV05-99BG293LV05-100
Sample_IDBG293LV05-99BG293LV05-100
Sample NameSMNDC1-BG293LV05-99SMNDC1-BG293LV05-100
Pool IDPool-240119Pool-240119
LocalServer_folderset69set69
total_reads20,355,21220,460,734
total_aligned_reads11,214,53516,749,994
unique_aligned_reads10,395,99815,599,760
percent_uniqueAligned0.510730.76242
correlation_replicates0.9895550.989555
spikein_reads9,8702,050
percent_spikeins0.000480.00010
original_ReadLength101101
QC_StatusSubmittingSubmitting
ID29412942




Data Submission Information
DCC submission information was not avaliable




File Information
file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
SMNDC1-BG293LV05-99_S173_L002_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set69/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2941NovaSeq6000100paired-ended1NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gzENCORE228524
SMNDC1-BG293LV05-99_S173_L002_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set69/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2941NovaSeq6000100paired-ended2NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gzENCORE228568
SMNDC1-BG293LV05-99_Aligned.sortedByCoord.out.bamENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2941GRCh38V40SMNDC1-BG293LV05-99_S173_L002_R1_001.filtered.trimmed.paired.fastq.gz,SMNDC1-BG293LV05-99_S173_L002_R2_001.filtered.trimmed.paired.fastq.gzENCORE228612
SMNDC1-BG293LV05-99_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2941GRCh38V40SMNDC1-BG293LV05-99/Aligned.sortedByCoord.out.bamENCORE228656
SMNDC1-BG293LV05-99_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2941GRCh38V40SMNDC1-BG293LV05-99/Aligned.sortedByCoord.out.bamENCORE228700
SMNDC1-BG293LV05-99_Signal.Unique.strand-.bwENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2941GRCh38V40SMNDC1-BG293LV05-99/Aligned.sortedByCoord.out.bamENCORE228744
SMNDC1-BG293LV05-99_Signal.Unique.strand+.bwENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2941GRCh38V40SMNDC1-BG293LV05-99/Aligned.sortedByCoord.out.bamENCORE228788
SMNDC1-BG293LV05-99_quant.sfENCODE_DATA/set69/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2941GRCh38V40SMNDC1-BG293LV05-99_S173_L002_R1_001.filtered.trimmed.paired.fastq.gz,SMNDC1-BG293LV05-99_S173_L002_R2_001.filtered.trimmed.paired.fastq.gzENCORE228832
SMNDC1-BG293LV05-100_S174_L002_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set69/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2942NovaSeq6000100paired-ended1NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gzENCORE228523
SMNDC1-BG293LV05-100_S174_L002_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set69/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2942NovaSeq6000100paired-ended2NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gzENCORE228567
SMNDC1-BG293LV05-100_Aligned.sortedByCoord.out.bamENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2942GRCh38V40SMNDC1-BG293LV05-100_S174_L002_R1_001.filtered.trimmed.paired.fastq.gz,SMNDC1-BG293LV05-100_S174_L002_R2_001.filtered.trimmed.paired.fastq.gzENCORE228611
SMNDC1-BG293LV05-100_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2942GRCh38V40SMNDC1-BG293LV05-100/Aligned.sortedByCoord.out.bamENCORE228655
SMNDC1-BG293LV05-100_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2942GRCh38V40SMNDC1-BG293LV05-100/Aligned.sortedByCoord.out.bamENCORE228699
SMNDC1-BG293LV05-100_Signal.Unique.strand-.bwENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2942GRCh38V40SMNDC1-BG293LV05-100/Aligned.sortedByCoord.out.bamENCORE228743
SMNDC1-BG293LV05-100_Signal.Unique.strand+.bwENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2942GRCh38V40SMNDC1-BG293LV05-100/Aligned.sortedByCoord.out.bamENCORE228787
SMNDC1-BG293LV05-100_quant.sfENCODE_DATA/set69/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2942GRCh38V40SMNDC1-BG293LV05-100_S174_L002_R1_001.filtered.trimmed.paired.fastq.gz,SMNDC1-BG293LV05-100_S174_L002_R2_001.filtered.trimmed.paired.fastq.gzENCORE228831