ATP5F1A      CRISPR in K562      Control: NT-BGKcLV26

General Information
RBPATP5A1
Cell_LineK562
MethodCRISPR
Exp_NameATP5A1-BGKcLV26-K562
ENCODE_series_IDENCSR515DML
Batch_IDBGKcLV26
Pool IDPool-210908
Local_Set_Nameset48_K
ENCODE_KD_Exp_IDENCSR328DHD
ENCODE_CN_Exp_IDENCSR900GQL
Rep1ATP5A1-BGKcLV26-37
Rep2ATP5A1-BGKcLV26-38
CN1NT-BGKcLV26-1
CN2NT-BGKcLV26-2
Rep1_qPCR77.7
Rep2_qPCR92.0
Rep1_WB61.7
Rep2_WB72.2
Antibody Cat#A304-939A
Antibody Lot#LOT# 1
Antibody DCC IDENCAB205IOV
StatusReleased
ProjectENCODE4
ID794




Experiment Information (Status: Released)
BGKcLV26-37BGKcLV26-38
idx898899
TRCN#_or_BGC#BGC#0000643BGC#0000643
shRNA_or_gRNA_sequenceATGGTATTGCCCGCGTACATATGGTATTGCCCGCGTACAT
PAMGGGGGG
NameATP5A1_99ATP5A1_99
Sample_IDBGKcLV26-37BGKcLV26-38
transduction_Date3/30/213/30/21
daysDay 6Day 6
RBP_nameATP5A1ATP5A1
qPCR_result77.792.0
Ave_qPCR84.9
RT-qPCR_primer-Fcgtgcgtctaactgagttgc
RT-qPCR_primer-Rtatccccttacacccgcata
protein_conc48955552
WB_result61.772.2
Ave_WB66.9
WB_DONE_date4/22/21jess
MW60kDa
IPRabbit / I
antibody_Cat#A304-939ALOT# 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM292.40
Rep2_TPM299.70
ActionReadyReady
Library_start_date09/01/2109/01/21
repeat_library
Note
ID50305031




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
ATP5F1AProduct_ID: A304-939A
Lot_ID: 1
Source: Bethyl Labs
Target Name: ATP5F1A-human
ATP5A1-K562-CRISPR-A304-939A.png<br>Caption: Western blot following CRISPR against ATP5F1A in K562 whole cell lysate using ATP5F1A specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against ATP5F1A. ATP5F1A protein appears as the green arrow, GAPDH serves as a control and appears in red arrow.




Experiment Status
BGKcLV26-37BGKcLV26-38
Sample_IDBGKcLV26-37BGKcLV26-38
Sample Name
Sample NameATP5A1-BGKcLV26-37ATP5A1-BGKcLV26-38
RBPATP5A1ATP5A1
Cell_LineK562K562
Exp UID
StatusReleasedReleased
Status_date2021-11-192021-11-19
ProjectENCODE4ENCODE4
Note
ID97699770




Library-Prep Information
BGKcLV26-37BGKcLV26-38
Sample #2728
Sample NameATP5A1-BGKcLV26-37ATP5A1-BGKcLV26-38
Sample_Name_Alias
Index Well PositionC04D04
Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
LibPrep_date2021-07-222021-07-22
Lib_IDLib-210722Lib-210722
Tecan_Location
Tecan
Tecan_date
Size_bp293297
Peak_Molarity103.00122.00
libSampleQC_DNA_WellDNA_Library_set48-49/set1/C4.pngDNA_Library_set48-49/set1/D4.png
RIN9.79.8
libSample_RNA_WellRNA_Library_set48-49/set1/C4.pngRNA_Library_set48-49/set1/D4.png
SampleQC_methodTapeStationTapeStation
SampleQC_date2021-09-022021-09-02
Sample_IDBGKcLV26-37BGKcLV26-38
RBPATP5A1ATP5A1
Batch_IDBGKcLV26BGKcLV26
WB_result61.70072.200
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCODE4ENCODE4
ID15861587




Sequencing Information
BGKcLV26-37BGKcLV26-38
Sample_IDBGKcLV26-37BGKcLV26-38
Sample NameATP5A1-BGKcLV26-37ATP5A1-BGKcLV26-38
Pool IDPool-210908Pool-210908
LocalServer_folderset48_Kset48_K
total_reads102,696,89481,781,942
total_aligned_reads91,030,50273,635,208
unique_aligned_reads83,367,74867,353,306
percent_uniqueAligned0.811780.82357
correlation_replicates0.9989240.998924
spikein_reads38,72819,778
percent_spikeins0.000380.00024
original_ReadLength150150
QC_StatusSubmittedSubmitted
ID17631764




Data Submission Information
BGKcLV26-37BGKcLV26-37BGKcLV26-37BGKcLV26-37BGKcLV26-37BGKcLV26-37BGKcLV26-38BGKcLV26-38BGKcLV26-38BGKcLV26-38
ENCODE_aliasbrenton-graveley:ATP5A1-BGKcLV26brenton-graveley:ATP5A1-BGKcLV26-37brenton-graveley:L-ATP5A1-BGKcLV26-37brenton-graveley:ATP5A1-BGKcLV26-37_S33_L003_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:ATP5A1-BGKcLV26-37_S33_L003_R2_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:ATP5A1-BGKcLV26-K562brenton-graveley:ATP5A1-BGKcLV26-38brenton-graveley:L-ATP5A1-BGKcLV26-38brenton-graveley:ATP5A1-BGKcLV26-38_S34_L003_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:ATP5A1-BGKcLV26-38_S34_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accessionENCSR328DHDENCBS311PCGENCLB708XMBENCFF418NUWENCFF819WDBENCSR515DMLENCBS492EVYENCLB244JAMENCFF424WZGENCFF859ACN
object_typeexperimentbiosamplelibraryfile_fastq1file_fastq2gene_silencing_seriesbiosamplelibraryfile_fastq1file_fastq2
assay_typeknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seq
Sample_IDBGKcLV26-37BGKcLV26-37BGKcLV26-37BGKcLV26-37BGKcLV26-37BGKcLV26-37BGKcLV26-38BGKcLV26-38BGKcLV26-38BGKcLV26-38
Sample NameATP5A1-BGKcLV26-37ATP5A1-BGKcLV26-37ATP5A1-BGKcLV26-37ATP5A1-BGKcLV26-37ATP5A1-BGKcLV26-37ATP5A1-BGKcLV26-37ATP5A1-BGKcLV26-38ATP5A1-BGKcLV26-38ATP5A1-BGKcLV26-38ATP5A1-BGKcLV26-38
SelectedYesNoYesYesYesYesNoYesYesYes
StatusReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleased
Status_Date2021-11-192021-11-192021-11-192021-11-192021-11-192022-03-022021-11-192021-11-192021-11-192021-11-19
ProjectENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4
LV48K_library_protocolLV48K_library_protocol
protocol_URLL-ATP5A1-BGKcLV26-37.pdfL-ATP5A1-BGKcLV26-38.pdf
ID3459355236863820395470953553368738213955




File Information
file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
ATP5A1-BGKcLV26-37_S33_L003_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set48_K/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab1763NovaSeq6000100paired-ended1NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gzENCODE43856
ATP5A1-BGKcLV26-37_S33_L003_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set48_K/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab1763NovaSeq6000100paired-ended2NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gzENCODE43906
ATP5A1-BGKcLV26-37_Aligned.sortedByCoord.out.bamENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab1763GRCh38V40ATP5A1-BGKcLV26-37_S33_L003_R1_001.filtered.trimmed.paired.fastq.gz,ATP5A1-BGKcLV26-37_S33_L003_R2_001.filtered.trimmed.paired.fastq.gzENCORE225543
ATP5A1-BGKcLV26-37_quant.sfENCODE_DATA/set48_K/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab1763GRCh38V40ATP5A1-BGKcLV26-37_S33_L003_R1_001.filtered.trimmed.paired.fastq.gz,ATP5A1-BGKcLV26-37_S33_L003_R2_001.filtered.trimmed.paired.fastq.gzENCORE225593
ATP5A1-BGKcLV26-37_Signal.Unique.strand+.bwENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1763GRCh38V40ATP5A1-BGKcLV26-37/Aligned.sortedByCoord.out.bamENCORE226559
ATP5A1-BGKcLV26-37_Signal.Unique.strand-.bwENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1763GRCh38V40ATP5A1-BGKcLV26-37/Aligned.sortedByCoord.out.bamENCORE226609
ATP5A1-BGKcLV26-37_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1763GRCh38V40ATP5A1-BGKcLV26-37/Aligned.sortedByCoord.out.bamENCORE226659
ATP5A1-BGKcLV26-37_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1763GRCh38V40ATP5A1-BGKcLV26-37/Aligned.sortedByCoord.out.bamENCORE226709
ATP5A1-BGKcLV26-38_S34_L003_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set48_K/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab1764NovaSeq6000100paired-ended1NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gzENCODE43857
ATP5A1-BGKcLV26-38_S34_L003_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set48_K/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab1764NovaSeq6000100paired-ended2NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gzENCODE43907
ATP5A1-BGKcLV26-38_Aligned.sortedByCoord.out.bamENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab1764GRCh38V40ATP5A1-BGKcLV26-38_S34_L003_R1_001.filtered.trimmed.paired.fastq.gz,ATP5A1-BGKcLV26-38_S34_L003_R2_001.filtered.trimmed.paired.fastq.gzENCORE225544
ATP5A1-BGKcLV26-38_quant.sfENCODE_DATA/set48_K/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab1764GRCh38V40ATP5A1-BGKcLV26-38_S34_L003_R1_001.filtered.trimmed.paired.fastq.gz,ATP5A1-BGKcLV26-38_S34_L003_R2_001.filtered.trimmed.paired.fastq.gzENCORE225594
ATP5A1-BGKcLV26-38_Signal.Unique.strand+.bwENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1764GRCh38V40ATP5A1-BGKcLV26-38/Aligned.sortedByCoord.out.bamENCORE226560
ATP5A1-BGKcLV26-38_Signal.Unique.strand-.bwENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1764GRCh38V40ATP5A1-BGKcLV26-38/Aligned.sortedByCoord.out.bamENCORE226610
ATP5A1-BGKcLV26-38_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1764GRCh38V40ATP5A1-BGKcLV26-38/Aligned.sortedByCoord.out.bamENCORE226660
ATP5A1-BGKcLV26-38_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1764GRCh38V40ATP5A1-BGKcLV26-38/Aligned.sortedByCoord.out.bamENCORE226710