ATP5F1C RNA-Seq in K562

General Information


RBP	ATP5C1
Cell_Line	K562
Method	shRNA
Exp_Name	ATP5C1-BGKLV32-K562
ENCODE_series_ID	ENCSR945FQQ
Batch_ID	BGKLV32
Pool ID	Pool-160425
Local_Set_Name	set32
ENCODE_KD_Exp_ID	ENCSR231DXJ
ENCODE_CN_Exp_ID	ENCSR143COQ
Rep1	ATP5C1_BGKLV32-11
Rep2	ATP5C1_BGKLV32-12
CN1	NT_BGKLV32-1
CN2	NT_BGKLV32-2
Rep1_qPCR	81.6
Rep2_qPCR	84.6
Rep1_WB	59.1
Rep2_WB	61.3
Antibody Cat#	GTX114275
Antibody Lot#	GTX114275
Antibody DCC ID	ENCAB846GVR
Status	Released
Project	ENCODE3
ID	705

Experiment Information (Status: Released)

	BGKLV32-11	BGKLV32-12
idx	610	611
TRCN#_or_BGC#	TRCN0000043451	TRCN0000043451
shRNA_or_gRNA_sequence	GCTTCTGAGATGATTGACAAA	GCTTCTGAGATGATTGACAAA
PAM
Name	ATP5C1	ATP5C1
Sample_ID	BGKLV32-11	BGKLV32-12
transduction_Date	10/1/2015	10/1/2015
days
RBP_name	ATP5C1	ATP5C1
qPCR_result	81.6	84.6
Ave_qPCR	83.1
RT-qPCR_primer-F	agtgagcagagtgccaggat
RT-qPCR_primer-R	gggtacggttgaatgtcaatg
protein_conc	2914	2870
WB_result	59.1	61.3
Ave_WB	60.2
WB_DONE_date	11/9/2015
MW	33kDa
IP	1	1
antibody_Cat#	GTX114275	GTX114275
Antibody DCC ID	ENCAB846GVR	ENCAB846GVR
submitted_to_DCC_date	12/7/2015
Rep1_TPM	193.1828132	0
Rep2_TPM	140.945943	0
Action
Library_start_date	3/7/2016	3/7/2016
repeat_library
Note
ID	691	692

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ATP5C1	Product_ID: GTX114275 Lot_ID: 40156 Source: GeneTex Target Name: ATP5C1-human

Experiment Status

	BGKLV32-11	BGKLV32-12
Sample_ID	BGKLV32-11	BGKLV32-12
Sample Name	ATP5C1_BGKLV32-11	ATP5C1_BGKLV32-12
Sample Name	ATP5C1_BGKLV32-11	ATP5C1_BGKLV32-12
RBP	ATP5C1	ATP5C1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1159	1160

Library-Prep
Sequencing

Library-Prep Information

	BGKLV32-11	BGKLV32-12
Sample #
Sample Name	ATP5C1-BGKLV32-11	ATP5C1-BGKLV32-12
Sample_Name_Alias	ATP5C1_BGKLV32-11	ATP5C1_BGKLV32-12
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-07	2016-03-07
Lib_ID	Lib-160307	Lib-160307
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/A7.png	DNA_Library_LV33-34-25B-32/set1/B7.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/A12.png	RNA_Library_LV29-30-31-32/set1/B12.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV32-11	BGKLV32-12
RBP	ATP5C1	ATP5C1
Batch_ID	BGKLV32	BGKLV32
WB_result	59.100	61.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2844	2845

Sequencing Information

	BGKLV32-11	BGKLV32-12
Sample_ID	BGKLV32-11	BGKLV32-12
Sample Name	ATP5C1_BGKLV32-11	ATP5C1_BGKLV32-12
Pool ID	Pool-160425	Pool-160425
LocalServer_folder	set32	set32
total_reads	86,930,924	83,272,000
total_aligned_reads	71,243,516	70,520,032
unique_aligned_reads	64,956,636	64,387,052
percent_uniqueAligned	0.74722	0.77321
correlation_replicates	0.999073	0.999073
spikein_reads	354,324	351,664
percent_spikeins	0.00408	0.00422
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1493	1494

Data Submission Information

	BGKLV32-11	BGKLV32-11
ENCODE_alias	brenton-graveley:ATP5C1_BGKLV32	brenton-graveley:ATP5C1-BGKLV32-K562
ENCODE_accession	ENCSR231DXJ	ENCSR945FQQ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV32-11	BGKLV32-11
Sample Name	ATP5C1_BGKLV32-11	ATP5C1_BGKLV32-11
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-05-25	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3119	6597

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
ATP5C1_BGKLV32-11_GATCAG_L002_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1493	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21192
ATP5C1_BGKLV32-11_GATCAG_L002_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1493	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21222
ATP5C1_BGKLV32-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1493					GRCh38	V40	ATP5C1_BGKLV32-11_GATCAG_L002_001.R1.fastq.gz,ATP5C1_BGKLV32-11_GATCAG_L002_001.R2.fastq.gz		ENCORE2	21252
ATP5C1_BGKLV32-11_Signal.Unique.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1493					GRCh38	V40	ATP5C1_BGKLV32-11/Aligned.sortedByCoord.out.bam		ENCORE2	21282
ATP5C1_BGKLV32-11_Signal.Unique.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1493					GRCh38	V40	ATP5C1_BGKLV32-11/Aligned.sortedByCoord.out.bam		ENCORE2	21312
ATP5C1_BGKLV32-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1493					GRCh38	V40	ATP5C1_BGKLV32-11/Aligned.sortedByCoord.out.bam		ENCORE2	21342
ATP5C1_BGKLV32-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1493					GRCh38	V40	ATP5C1_BGKLV32-11/Aligned.sortedByCoord.out.bam		ENCORE2	21372
ATP5C1_BGKLV32-11_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1493					GRCh38	V40	ATP5C1_BGKLV32-11_GATCAG_L002_001.R1.fastq.gz,ATP5C1_BGKLV32-11_GATCAG_L002_001.R2.fastq.gz		ENCORE2	21402
ATP5C1_BGKLV32-12_TAGCTT_L002_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1494	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21193
ATP5C1_BGKLV32-12_TAGCTT_L002_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1494	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21223
ATP5C1_BGKLV32-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1494					GRCh38	V40	ATP5C1_BGKLV32-12_TAGCTT_L002_001.R1.fastq.gz,ATP5C1_BGKLV32-12_TAGCTT_L002_001.R2.fastq.gz		ENCORE2	21253
ATP5C1_BGKLV32-12_Signal.Unique.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1494					GRCh38	V40	ATP5C1_BGKLV32-12/Aligned.sortedByCoord.out.bam		ENCORE2	21283
ATP5C1_BGKLV32-12_Signal.Unique.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1494					GRCh38	V40	ATP5C1_BGKLV32-12/Aligned.sortedByCoord.out.bam		ENCORE2	21313
ATP5C1_BGKLV32-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1494					GRCh38	V40	ATP5C1_BGKLV32-12/Aligned.sortedByCoord.out.bam		ENCORE2	21343
ATP5C1_BGKLV32-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1494					GRCh38	V40	ATP5C1_BGKLV32-12/Aligned.sortedByCoord.out.bam		ENCORE2	21373
ATP5C1_BGKLV32-12_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1494					GRCh38	V40	ATP5C1_BGKLV32-12_TAGCTT_L002_001.R1.fastq.gz,ATP5C1_BGKLV32-12_TAGCTT_L002_001.R2.fastq.gz		ENCORE2	21403