ATP5F1A RNA-Seq in HepG2

General Information


RBP	ATP5A1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	ATP5A1-BGHcLV29-HepG2
ENCODE_series_ID	ENCSR515NWM
Batch_ID	BGHcLV29
Pool ID	Pool-211117
Local_Set_Name	set50_H
ENCODE_KD_Exp_ID	ENCSR340ZLQ
ENCODE_CN_Exp_ID	ENCSR462MFN
Rep1	ATP5A1-BGHcLV29-9
Rep2	ATP5A1-BGHcLV29-10
CN1	NT-BGHcLV29-1
CN2	NT-BGHcLV29-2
Rep1_qPCR	76.8
Rep2_qPCR	74.4
Rep1_WB	82.5
Rep2_WB	82.0
Antibody Cat#	A304-939A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB205IOV
Status	Submitted
Project	ENCODE4
ID	847

Experiment Information (Status: Released)

	BGHcLV29-9	BGHcLV29-10
idx	840	841
TRCN#_or_BGC#	BGC#0000643	BGC#0000643
shRNA_or_gRNA_sequence	ATGGTATTGCCCGCGTACAT	ATGGTATTGCCCGCGTACAT
PAM	GGG	GGG
Name	ATP5A1_99	ATP5A1_99
Sample_ID	BGHcLV29-9	BGHcLV29-10
transduction_Date	7/20	7/20
days	D6	D6
RBP_name	ATP5A1	ATP5A1
qPCR_result	76.8	74.4
Ave_qPCR	75.6
RT-qPCR_primer-F	cgtgcgtctaactgagttgc
RT-qPCR_primer-R	tatccccttacacccgcata
protein_conc	0	3968
WB_result	82.5	82.0
Ave_WB	82.3
WB_DONE_date	7/29/21	JESS
MW	60kDa
IP	Rabbit / I
antibody_Cat#	A304-939A	LOT# 1
Antibody DCC ID	ENCAB205IOV
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/5/21	11/5/21
repeat_library
Note
ID	7015	7016

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ATP5A1	Product_ID: A304-939A Lot_ID: 1 Source: Bethyl Labs Target Name: ATP5A1-human

Experiment Status

	BGHcLV29-9	BGHcLV29-10
Sample_ID	BGHcLV29-9	BGHcLV29-10
Sample Name
Sample Name	ATP5A1-BGHcLV29-9	ATP5A1-BGHcLV29-10
RBP	ATP5A1	ATP5A1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	9977	9978

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV29-9	BGHcLV29-10
Sample #	5	6
Sample Name	ATP5A1-BGHcLV29-9	ATP5A1-BGHcLV29-10
Sample_Name_Alias
Index Well Position	E01	F01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-11-01	2021-11-01
Lib_ID	Lib-211101	Lib-211101
Tecan_Location
Tecan
Tecan_date
Size_bp	286	287
Peak_Molarity	46.40	38.00
libSampleQC_DNA_Well	DNA_Library_set50/set1/E1.png	DNA_Library_set50/set1/F1.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_set50/set1/E7.png	RNA_Library_set50/set1/F7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGHcLV29-9	BGHcLV29-10
RBP	ATP5A1	ATP5A1
Batch_ID	BGHcLV29	BGHcLV29
WB_result	82.500	82.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3092	3093

Sequencing Information

	BGHcLV29-9	BGHcLV29-10
Sample_ID	BGHcLV29-9	BGHcLV29-10
Sample Name	ATP5A1-BGHcLV29-9	ATP5A1-BGHcLV29-10
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_H	set50_H
total_reads	58,333,782	51,346,610
total_aligned_reads	51,402,028	46,865,022
unique_aligned_reads	48,469,544	44,190,220
percent_uniqueAligned	0.83090	0.86063
correlation_replicates	0.994998	0.994998
spikein_reads	11,750	12,458
percent_spikeins	0.00020	0.00024
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1875	1876

Data Submission Information

	BGHcLV29-9	BGHcLV29-9	BGHcLV29-9	BGHcLV29-9	BGHcLV29-9	BGHcLV29-9	BGHcLV29-10	BGHcLV29-10	BGHcLV29-10	BGHcLV29-10
ENCODE_alias	brenton-graveley:ATP5A1-BGHcLV29	brenton-graveley:ATP5A1-BGHcLV29-9	brenton-graveley:L-ATP5A1-BGHcLV29-9	brenton-graveley:ATP5A1-BGHcLV29-9_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ATP5A1-BGHcLV29-9_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ATP5A1-BGHcLV29-HepG2	brenton-graveley:ATP5A1-BGHcLV29-10	brenton-graveley:L-ATP5A1-BGHcLV29-10	brenton-graveley:ATP5A1-BGHcLV29-10_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ATP5A1-BGHcLV29-10_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR340ZLQ	ENCBS822FZF	ENCLB851YYJ	ENCFF005OHQ	ENCFF703RED	ENCSR515NWM	ENCBS266VSE	ENCLB203ISS	ENCFF562ROW	ENCFF014TIQ
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV29-9	BGHcLV29-9	BGHcLV29-9	BGHcLV29-9	BGHcLV29-9	BGHcLV29-9	BGHcLV29-10	BGHcLV29-10	BGHcLV29-10	BGHcLV29-10
Sample Name	ATP5A1-BGHcLV29-9	ATP5A1-BGHcLV29-9	ATP5A1-BGHcLV29-9	ATP5A1-BGHcLV29-9	ATP5A1-BGHcLV29-9	ATP5A1-BGHcLV29-9	ATP5A1-BGHcLV29-10	ATP5A1-BGHcLV29-10	ATP5A1-BGHcLV29-10	ATP5A1-BGHcLV29-10
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV50H_biosample_protocol	LV50H_library_protocol				LV50H_biosample_protocol	LV50H_library_protocol
protocol_URL		ATP5A1-BGHcLV29-9.pdf	L-ATP5A1-BGHcLV29-9.pdf				ATP5A1-BGHcLV29-10.pdf	L-ATP5A1-BGHcLV29-10.pdf
ID	5845	5883	5955	6027	6099	6168	5884	5956	6028	6100

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
ATP5A1-BGHcLV29-9_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1875	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5764
ATP5A1-BGHcLV29-9_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1875	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5806
ATP5A1-BGHcLV29-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1875					GRCh38	V40	ATP5A1-BGHcLV29-9_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz,ATP5A1-BGHcLV29-9_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18929
ATP5A1-BGHcLV29-9_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1875					GRCh38	V40	ATP5A1-BGHcLV29-9/Aligned.sortedByCoord.out.bam		ENCORE2	18987
ATP5A1-BGHcLV29-9_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1875					GRCh38	V40	ATP5A1-BGHcLV29-9/Aligned.sortedByCoord.out.bam		ENCORE2	19033
ATP5A1-BGHcLV29-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1875					GRCh38	V40	ATP5A1-BGHcLV29-9/Aligned.sortedByCoord.out.bam		ENCORE2	19079
ATP5A1-BGHcLV29-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1875					GRCh38	V40	ATP5A1-BGHcLV29-9/Aligned.sortedByCoord.out.bam		ENCORE2	19125
ATP5A1-BGHcLV29-9_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1875					GRCh38	V40	ATP5A1-BGHcLV29-9_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz,ATP5A1-BGHcLV29-9_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19171
ATP5A1-BGHcLV29-10_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1876	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5763
ATP5A1-BGHcLV29-10_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1876	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5805
ATP5A1-BGHcLV29-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1876					GRCh38	V40	ATP5A1-BGHcLV29-10_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz,ATP5A1-BGHcLV29-10_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18928
ATP5A1-BGHcLV29-10_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1876					GRCh38	V40	ATP5A1-BGHcLV29-10/Aligned.sortedByCoord.out.bam		ENCORE2	18986
ATP5A1-BGHcLV29-10_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1876					GRCh38	V40	ATP5A1-BGHcLV29-10/Aligned.sortedByCoord.out.bam		ENCORE2	19032
ATP5A1-BGHcLV29-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1876					GRCh38	V40	ATP5A1-BGHcLV29-10/Aligned.sortedByCoord.out.bam		ENCORE2	19078
ATP5A1-BGHcLV29-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1876					GRCh38	V40	ATP5A1-BGHcLV29-10/Aligned.sortedByCoord.out.bam		ENCORE2	19124
ATP5A1-BGHcLV29-10_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1876					GRCh38	V40	ATP5A1-BGHcLV29-10_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz,ATP5A1-BGHcLV29-10_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19170