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SRPRA RNA-Seq in HepG2



SRPRA      CRISPR in HepG2      Control:

General Information
RBPSRPRA
Cell_LineHepG2
MethodCRISPR
Exp_NameSRPRA-BGHcLV36-HepG2
ENCODE_series_ID
Batch_IDBGHcLV36
Pool IDPool-230130
Local_Set_Nameset55
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1SRPRA-BGHcLV36-39
Rep2SRPRA-BGHcLV36-40
CN1NT-BGHcLV36-1
CN2NT-BGHcLV36-2
Rep1_qPCR43.2
Rep2_qPCR40.8
Rep1_WB68.0
Rep2_WB56.0
Antibody Cat#A305-141A
Antibody Lot#lot # 1
Antibody DCC ID
StatusSubmitted
ProjectENCORE2
ID1045




Experiment Information (Status: Submitting)
BGHcLV36-39BGHcLV36-40
idx11701171
TRCN#_or_BGC#BGC#0001056BGC#0001056
shRNA_or_gRNA_sequenceAATCAACGCGTTAACGGGTCAATCAACGCGTTAACGGGTC
PAMCGGCGG
NameSRPRA_100SRPRA_100
Sample_IDBGHcLV36-39BGHcLV36-40
transduction_Date8/2/228/2/22
daysD6D6
RBP_nameSRPRASRPRA
qPCR_result43.240.8
Ave_qPCR42.0
RT-qPCR_primer-Fgcacagagatccaacagcaa
RT-qPCR_primer-Rtcttcatggtagtgggagca
protein_conc48525629
WB_result68.056.0
Ave_WB62.0
WB_DONE_date8/10/22
MW70kd
IP
antibody_Cat#A305-141Alot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM00
Rep2_TPM00
ActionReadyReady
Library_start_date
repeat_library
Note
ID73517352




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
SRPRAProduct_ID: A305-141A
Lot_ID: 1
Source: Bethyl Labs
Target Name: SRPRA-human
SRPRA-hepg2-CRISPR-A305-141A.png<br>Caption: Western blot following CRISPR against SRPRA in HepG2 whole cell lysate using SRPRA specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against SRPRA. SRPRA protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.
SRPRA-K562-CRISPR-A305-141A.png<br>Caption: Western blot following CRISPR against SRPRA in K562 whole cell lysate using SRPRA specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against SRPRA. SRPRA protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.




Experiment Status
BGHcLV36-39BGHcLV36-40
Sample_IDBGHcLV36-39BGHcLV36-40
Sample Name
Sample NameSRPRA-BGHcLV36-39SRPRA-BGHcLV36-40
RBPSRPRASRPRA
Cell_LineHepG2HepG2
Exp UID
StatusSubmittingSubmitting
Status_date2023-04-142023-04-14
ProjectENCORE2ENCORE2
Note
ID1095210953




Library-Prep Information
BGHcLV36-39BGHcLV36-40
Sample #1112
Sample NameSRPRA-BGHcLV36-39SRPRA-BGHcLV36-40
Sample_Name_Alias
Index Well PositionC02D02
Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
LibPrep_date2023-01-132023-01-13
Lib_IDLib-230113Lib-230113
Tecan_Location
Tecan
Tecan_date
Size_bp304296
Peak_Molarity50.1048.20
libSampleQC_DNA_WellDNA_Library_set54-56/set1/C2.pngDNA_Library_set54-56/set1/D2.png
RIN9.89.9
libSample_RNA_WellRNA_Library_set54-56/set1/C2.pngRNA_Library_set54-56/set1/D2.png
SampleQC_methodTapeStation_2022TapeStation_2022
SampleQC_date2023-01-272023-01-27
Sample_IDBGHcLV36-39BGHcLV36-40
RBPSRPRASRPRA
Batch_IDBGHcLV36BGHcLV36
WB_result68.00056.000
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCORE2ENCORE2
ID33823383




Sequencing Information
BGHcLV36-39BGHcLV36-40
Sample_IDBGHcLV36-39BGHcLV36-40
Sample NameSRPRA-BGHcLV36-39SRPRA-BGHcLV36-40
Pool IDPool-230130Pool-230130
LocalServer_folderset55set55
total_reads43,233,85948,855,146
total_aligned_reads38,026,89944,850,800
unique_aligned_reads36,030,40942,496,575
percent_uniqueAligned0.833380.86985
correlation_replicates0.9989990.998999
spikein_reads4,9665,242
percent_spikeins0.000110.00011
original_ReadLength101101
QC_StatusSubmittingSubmitting
ID22552256




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
SRPRA-BGHcLV36-39_S11_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set55/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2255NovaSeq6000100paired-ended1NT-BGHcLV36-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gzENCORE28410
SRPRA-BGHcLV36-39_S11_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set55/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2255NovaSeq6000100paired-ended2NT-BGHcLV36-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE28460
SRPRA-BGHcLV36-39_Aligned.sortedByCoord.out.bamENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2255GRCh38V40SRPRA-BGHcLV36-39_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRPRA-BGHcLV36-39_S11_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE225651
SRPRA-BGHcLV36-39_Signal.Unique.strand+.bwENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2255GRCh38V40SRPRA-BGHcLV36-39/Aligned.sortedByCoord.out.bamENCORE225701
SRPRA-BGHcLV36-39_Signal.Unique.strand-.bwENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2255GRCh38V40SRPRA-BGHcLV36-39/Aligned.sortedByCoord.out.bamENCORE225751
SRPRA-BGHcLV36-39_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2255GRCh38V40SRPRA-BGHcLV36-39/Aligned.sortedByCoord.out.bamENCORE225801
SRPRA-BGHcLV36-39_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2255GRCh38V40SRPRA-BGHcLV36-39/Aligned.sortedByCoord.out.bamENCORE225851
SRPRA-BGHcLV36-39_quant.sfENCODE_DATA/set55/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2255GRCh38V40SRPRA-BGHcLV36-39_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRPRA-BGHcLV36-39_S11_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE225901
SRPRA-BGHcLV36-40_S12_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set55/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2256NovaSeq6000100paired-ended1NT-BGHcLV36-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gzENCORE28411
SRPRA-BGHcLV36-40_S12_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set55/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2256NovaSeq6000100paired-ended2NT-BGHcLV36-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE28461
SRPRA-BGHcLV36-40_Aligned.sortedByCoord.out.bamENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2256GRCh38V40SRPRA-BGHcLV36-40_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRPRA-BGHcLV36-40_S12_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE225652
SRPRA-BGHcLV36-40_Signal.Unique.strand+.bwENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2256GRCh38V40SRPRA-BGHcLV36-40/Aligned.sortedByCoord.out.bamENCORE225702
SRPRA-BGHcLV36-40_Signal.Unique.strand-.bwENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2256GRCh38V40SRPRA-BGHcLV36-40/Aligned.sortedByCoord.out.bamENCORE225752
SRPRA-BGHcLV36-40_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2256GRCh38V40SRPRA-BGHcLV36-40/Aligned.sortedByCoord.out.bamENCORE225802
SRPRA-BGHcLV36-40_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2256GRCh38V40SRPRA-BGHcLV36-40/Aligned.sortedByCoord.out.bamENCORE225852
SRPRA-BGHcLV36-40_quant.sfENCODE_DATA/set55/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2256GRCh38V40SRPRA-BGHcLV36-40_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRPRA-BGHcLV36-40_S12_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE225902