EIF1      CRISPR in K562      Control: NT-BGKcLV42-1,NT-BGKcLV42-2

General Information
RBPEIF1
Cell_LineK562
MethodCRISPR
Exp_NameEIF1-BGKcLV42-K562
ENCODE_series_ID
Batch_IDBGKcLV42
Pool IDPool-240715
Local_Set_Nameset73
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1EIF1-BGKcLV42-29
Rep2EIF1-BGKcLV42-30
CN1NT-BGKcLV42-1
CN2NT-BGKcLV42-2
Rep1_qPCR46.8
Rep2_qPCR59.7
Rep1_WB89.8
Rep2_WB96.0
Antibody Cat#12496S
Antibody Lot#lot # 1
Antibody DCC ID
StatusSubmitted
ProjectENCORE2
ID1538




Experiment Information (Status: Submitting)
BGKcLV42-29BGKcLV42-30
idx00
TRCN#_or_BGC#BGC#0001131BGC#0001131
shRNA_or_gRNA_sequenceTGACTGAACTCACCTCTACGTGACTGAACTCACCTCTACG
PAMAGGAGG
NameEIF1_83EIF1_83
Sample_IDBGKcLV42-29BGKcLV42-30
transduction_Date4/23/244/23/24
daysD6D6
RBP_nameEIF1EIF1
qPCR_result46.859.7
Ave_qPCR53.2
RT-qPCR_primer-Fagggatcgctgatgattacg
RT-qPCR_primer-Rtctccatattccggatgctc
protein_conc35703233
WB_result89.896.0
Ave_WB92.9
WB_DONE_date5/2/24
MW13kd
IP
antibody_Cat#12496Slot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM00
Rep2_TPM00
ActionReadyReady
Library_start_date
repeat_library
Note
ID57915792




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
EIF1Product_ID: 12496S
Lot_ID: 1
Source: Cell Signaling Technology
Target Name: EIF1-human
EIF1-HEPG2-CRISPR-12496S.png<br>Caption: Western blot following CRISPR against EIF1 in HepG2 whole cell lysate using EIF1 specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against EIF1. EIF1 protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.
CST_12496S_1_EIF1.png<br>Caption: IP-WB analysis of 12496S whole cell lysate using the EIF1 specific antibody, 12496S. Lanes 1 and 2 are 2.5% of five million whole cell lysate input and 50% of IP enrichment, respectively, using a normal IgG antibody. Lane 3 is 50% of IP enrichment from five million whole cell lysate using the EIF1-specific antibody, 12496S. The same antibody was used to detect protein levels via Western blot. This antibody passes preliminary validation and will be further pursued for secondary validation. *NOTE* Protein sizes are taken from Genecards.org and are only estimates based on sequence. Actual protein size may differ based on protein characteristics and electrophoresis method used.
EIF1-K562-CRISPR-12496S.png<br>Caption: Western blot following CRISPR against EIF1 in K562 whole cell lysate using EIF1 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against EIF1. EIF1 protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.




Experiment Status
BGKcLV42-29BGKcLV42-30
Sample_IDBGKcLV42-29BGKcLV42-30
Sample Name
Sample NameEIF1-BGKcLV42-29EIF1-BGKcLV42-30
RBPEIF1EIF1
Cell_LineK562K562
Exp UID
StatusSubmittingSubmitting
Status_date2025-02-132025-02-13
ProjectENCORE2ENCORE2
Note
ID1307013071




Library-Prep Information
BGKcLV42-29BGKcLV42-30
Sample #2728
Sample NameEIF1-BGKcLV42-29EIF1-BGKcLV42-30
Sample_Name_Alias
Index Well PositionC04D04
Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
LibPrep_date2024-06-212024-06-21
Lib_IDLib-240621Lib-240621
Tecan_Location
Tecan
Tecan_date
Size_bp303291
Peak_Molarity113.0095.10
libSampleQC_DNA_WellDNA_Library_set73/set1/C4.pngDNA_Library_set73/set1/D4.png
RIN10.010.0
libSample_RNA_WellRNA_Library_set73/set1/C4.pngRNA_Library_set73/set1/D4.png
SampleQC_methodTapeStation_2022TapeStation_2022
SampleQC_date2024-07-152024-07-15
Sample_IDBGKcLV42-29BGKcLV42-30
RBPEIF1EIF1
Batch_IDBGKcLV42BGKcLV42
WB_result89.80096.000
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCORE2ENCORE2
ID42964297




Sequencing Information
BGKcLV42-29BGKcLV42-30
Sample_IDBGKcLV42-29BGKcLV42-30
Sample NameEIF1-BGKcLV42-29EIF1-BGKcLV42-30
Pool IDPool-240715Pool-240715
LocalServer_folderset73set73
total_reads43,960,89441,638,920
total_aligned_reads39,329,32138,206,585
unique_aligned_reads36,278,14435,255,708
percent_uniqueAligned0.825240.84670
correlation_replicates0.9972310.997231
spikein_reads3,4121,398
percent_spikeins0.000080.00003
original_ReadLength101101
QC_StatusSubmittingSubmitting
ID31633164




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
EIF1-BGKcLV42-29_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set73/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab3163NovaSeq6000100paired-ended1NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gzENCORE230362
EIF1-BGKcLV42-29_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set73/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab3163NovaSeq6000100paired-ended2NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE230452
EIF1-BGKcLV42-29_Aligned.sortedByCoord.out.bamENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab3163GRCh38V40EIF1-BGKcLV42-29_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF1-BGKcLV42-29_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE231294
EIF1-BGKcLV42-29_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab3163GRCh38V40EIF1-BGKcLV42-29_Aligned.sortedByCoord.out.bamENCORE231384
EIF1-BGKcLV42-29_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab3163GRCh38V40EIF1-BGKcLV42-29_Aligned.sortedByCoord.out.bamENCORE231474
EIF1-BGKcLV42-29_Signal.Unique.strand-.bwENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab3163GRCh38V40EIF1-BGKcLV42-29_Aligned.sortedByCoord.out.bamENCORE231564
EIF1-BGKcLV42-29_Signal.Unique.strand+.bwENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab3163GRCh38V40EIF1-BGKcLV42-29_Aligned.sortedByCoord.out.bamENCORE231654
EIF1-BGKcLV42-29_quant.sfENCODE_DATA/set73/salmon_ENCORE2_file_linkstranscript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab3163GRCh38V40EIF1-BGKcLV42-29_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF1-BGKcLV42-29_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE231744
EIF1-BGKcLV42-30_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set73/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab3164NovaSeq6000100paired-ended1NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gzENCORE230363
EIF1-BGKcLV42-30_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set73/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab3164NovaSeq6000100paired-ended2NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE230453
EIF1-BGKcLV42-30_Aligned.sortedByCoord.out.bamENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab3164GRCh38V40EIF1-BGKcLV42-30_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF1-BGKcLV42-30_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE231295
EIF1-BGKcLV42-30_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab3164GRCh38V40EIF1-BGKcLV42-30_Aligned.sortedByCoord.out.bamENCORE231385
EIF1-BGKcLV42-30_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab3164GRCh38V40EIF1-BGKcLV42-30_Aligned.sortedByCoord.out.bamENCORE231475
EIF1-BGKcLV42-30_Signal.Unique.strand-.bwENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab3164GRCh38V40EIF1-BGKcLV42-30_Aligned.sortedByCoord.out.bamENCORE231565
EIF1-BGKcLV42-30_Signal.Unique.strand+.bwENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab3164GRCh38V40EIF1-BGKcLV42-30_Aligned.sortedByCoord.out.bamENCORE231655
EIF1-BGKcLV42-30_quant.sfENCODE_DATA/set73/salmon_ENCORE2_file_linkstranscript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab3164GRCh38V40EIF1-BGKcLV42-30_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF1-BGKcLV42-30_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE231745