ATP5F1C RNA-Seq in HepG2

General Information


RBP	ATP5C1
Cell_Line	HepG2
Method	shRNA
Exp_Name	ATP5C1-BGHLV30-HepG2
ENCODE_series_ID	ENCSR405FAO
Batch_ID	BGHLV30
Pool ID	Pool-151215C
Local_Set_Name	set30
ENCODE_KD_Exp_ID	ENCSR713OLV
ENCODE_CN_Exp_ID	ENCSR067GHD
Rep1	ATP5C1_BGHLV30-13
Rep2	ATP5C1_BGHLV30-14
CN1	NT_BGHLV30-1
CN2	NT_BGHLV30-2
Rep1_qPCR	94.2
Rep2_qPCR	91.1
Rep1_WB	49.5
Rep2_WB	57.2
Antibody Cat#	GTX114275
Antibody Lot#	GTX114275
Antibody DCC ID	ENCAB846GVR
Status	Released
Project	ENCODE3
ID	677

Experiment Information (Status: Released)

	BGHLV30-13	BGHLV30-14
idx	697	698
TRCN#_or_BGC#	TRCN0000043451	TRCN0000043451
shRNA_or_gRNA_sequence	GCTTCTGAGATGATTGACAAA	GCTTCTGAGATGATTGACAAA
PAM
Name	ATP5C1	ATP5C1
Sample_ID	BGHLV30-13	BGHLV30-14
transduction_Date	8/25/2015	8/25/2015
days
RBP_name	ATP5C1	ATP5C1
qPCR_result	94.2	91.1
Ave_qPCR	92.7
RT-qPCR_primer-F	agtgagcagagtgccaggat
RT-qPCR_primer-R	gggtacggttgaatgtcaatg
protein_conc	3930	4375
WB_result	49.5	57.2
Ave_WB	53.3
WB_DONE_date	9/22/2015
MW	33kDa
IP	1	1
antibody_Cat#	GTX114275	GTX114275
Antibody DCC ID	ENCAB846GVR	ENCAB846GVR
submitted_to_DCC_date	12/7/2015
Rep1_TPM	75.6	0
Rep2_TPM	63.8	0
Action
Library_start_date	11/5/2015	11/5/2015
repeat_library
Note	x	x
ID	2788	2789

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

	BGHLV30-13	BGHLV30-14
Sample_ID	BGHLV30-13	BGHLV30-14
Sample Name	ATP5C1_BGHLV30-13	ATP5C1_BGHLV30-14
Sample Name	ATP5C1_BGHLV30-13	ATP5C1_BGHLV30-14
RBP	ATP5C1	ATP5C1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-04	2016-03-04
Project	ENCODE3	ENCODE3
Note
ID	1044	1045

Library-Prep
Sequencing

Library-Prep Information

	BGHLV30-13	BGHLV30-14
Sample #
Sample Name	ATP5C1-BGHLV30-13	ATP5C1-BGHLV30-14
Sample_Name_Alias	ATP5C1_BGHLV30-13	ATP5C1_BGHLV30-14
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-05	2015-11-05
Lib_ID	Lib-151105	Lib-151105
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/E9.png	DNA_Library_LV28-29-30/set1/F9.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/E4.png	RNA_Library_LV29-30-31-32/set1/F4.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV30-13	BGHLV30-14
RBP	ATP5C1	ATP5C1
Batch_ID	BGHLV30	BGHLV30
WB_result	49.500	57.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2736	2737

Sequencing Information

	BGHLV30-13	BGHLV30-14
Sample_ID	BGHLV30-13	BGHLV30-14
Sample Name	ATP5C1_BGHLV30-13	ATP5C1_BGHLV30-14
Pool ID	Pool-151215C	Pool-151215C
LocalServer_folder	set30	set30
total_reads	137,689,604	83,886,562
total_aligned_reads	114,575,572	69,866,452
unique_aligned_reads	107,753,000	65,732,026
percent_uniqueAligned	0.78258	0.78358
correlation_replicates	0.999719	0.999719
spikein_reads	375,194	204,064
percent_spikeins	0.00272	0.00243
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1362	1363

Data Submission Information

	BGHLV30-13	BGHLV30-13
ENCODE_alias	brenton-graveley:ATP5C1_BGHLV30	brenton-graveley:ATP5C1-BGHLV30-HepG2
ENCODE_accession	ENCSR713OLV	ENCSR405FAO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV30-13	BGHLV30-13
Sample Name	ATP5C1_BGHLV30-13	ATP5C1_BGHLV30-13
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3071	6596

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_BGHLV30-13_CGTACG_L008_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1362	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20700
ATP5C1_BGHLV30-13_CGTACG_L008_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1362	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20734
ATP5C1_BGHLV30-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1362					GRCh38	V40	ATP5C1_BGHLV30-13_CGTACG_L008_001.R1.fastq.gz,ATP5C1_BGHLV30-13_CGTACG_L008_001.R2.fastq.gz		ENCORE2	20768
ATP5C1_BGHLV30-13_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1362					GRCh38	V40	ATP5C1_BGHLV30-13/Aligned.sortedByCoord.out.bam		ENCORE2	20802
ATP5C1_BGHLV30-13_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1362					GRCh38	V40	ATP5C1_BGHLV30-13/Aligned.sortedByCoord.out.bam		ENCORE2	20836
ATP5C1_BGHLV30-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1362					GRCh38	V40	ATP5C1_BGHLV30-13/Aligned.sortedByCoord.out.bam		ENCORE2	20870
ATP5C1_BGHLV30-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1362					GRCh38	V40	ATP5C1_BGHLV30-13/Aligned.sortedByCoord.out.bam		ENCORE2	20904
ATP5C1_BGHLV30-13_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1362					GRCh38	V40	ATP5C1_BGHLV30-13_CGTACG_L008_001.R1.fastq.gz,ATP5C1_BGHLV30-13_CGTACG_L008_001.R2.fastq.gz		ENCORE2	20938
ATP5C1_BGHLV30-14_GAGTGG_L008_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1363	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20701
ATP5C1_BGHLV30-14_GAGTGG_L008_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1363	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20735
ATP5C1_BGHLV30-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1363					GRCh38	V40	ATP5C1_BGHLV30-14_GAGTGG_L008_001.R1.fastq.gz,ATP5C1_BGHLV30-14_GAGTGG_L008_001.R2.fastq.gz		ENCORE2	20769
ATP5C1_BGHLV30-14_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1363					GRCh38	V40	ATP5C1_BGHLV30-14/Aligned.sortedByCoord.out.bam		ENCORE2	20803
ATP5C1_BGHLV30-14_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1363					GRCh38	V40	ATP5C1_BGHLV30-14/Aligned.sortedByCoord.out.bam		ENCORE2	20837
ATP5C1_BGHLV30-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1363					GRCh38	V40	ATP5C1_BGHLV30-14/Aligned.sortedByCoord.out.bam		ENCORE2	20871
ATP5C1_BGHLV30-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1363					GRCh38	V40	ATP5C1_BGHLV30-14/Aligned.sortedByCoord.out.bam		ENCORE2	20905
ATP5C1_BGHLV30-14_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1363					GRCh38	V40	ATP5C1_BGHLV30-14_GAGTGG_L008_001.R1.fastq.gz,ATP5C1_BGHLV30-14_GAGTGG_L008_001.R2.fastq.gz		ENCORE2	20939