CCAR1 RNA-Seq in HepG2

General Information


RBP	CCAR1
Cell_Line	HepG2
Method	shRNA
Exp_Name	CCAR1-BGHLV20-HepG2
ENCODE_series_ID	ENCSR732LYQ
Batch_ID	BGHLV20
Pool ID	Pool-160425
Local_Set_Name	set20
ENCODE_KD_Exp_ID	ENCSR081IAO
ENCODE_CN_Exp_ID	ENCSR135LXL
Rep1	CCAR1_BGHLV20-5B
Rep2	CCAR1_BGHLV20-6B
CN1	NT_BGHLV20-1B
CN2	NT_BGHLV20-2B
Rep1_qPCR	52.2
Rep2_qPCR	55.1
Rep1_WB	64.4
Rep2_WB	57.7
Antibody Cat#	A300-270A
Antibody Lot#	A300-270A
Antibody DCC ID	ENCAB369JZE
Status	Released
Project	ENCODE3
ID	593

Experiment Information (Status: Released)

	BGHLV20-5	BGHLV20-6
idx	369	370
TRCN#_or_BGC#	TRCN0000056005	TRCN0000056005
shRNA_or_gRNA_sequence	GCCCTAGTATGGAAGATTTAT	GCCCTAGTATGGAAGATTTAT
PAM
Name	CCAR1_05	CCAR1_05
Sample_ID	BGHLV20-5	BGHLV20-6
transduction_Date	10/2/2014	10/2/2014
days
RBP_name	CCAR1	CCAR1
qPCR_result	52.2	55.1
Ave_qPCR	53.6
RT-qPCR_primer-F	cagaggggatcaagtgccta
RT-qPCR_primer-R	gtgatcgctctcgctctctt
protein_conc	5696	6111
WB_result	64.4	57.7
Ave_WB	61.1
WB_DONE_date	2/22/2016
MW	133kDa	wes
IP	1	1
antibody_Cat#	A300-270A	A300-270A
Antibody DCC ID	ENCAB369JZE
submitted_to_DCC_date	3/8/2016
Rep1_TPM	40.1	0
Rep2_TPM	29.3	0
Action
Library_start_date	3/10/2016	3/10/2016
repeat_library
Note
ID	2434	2435

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CCAR1	Product_ID: A300-270A Lot_ID: 1 Source: Bethyl Labs Target Name: CCAR1-human

Experiment Status

	BGHLV20-5	BGHLV20-6
Sample_ID	BGHLV20-5	BGHLV20-6
Sample Name	CCAR1_BGHLV20-5B	CCAR1_BGHLV20-6B
Sample Name	CCAR1_BGHLV20-5B	CCAR1_BGHLV20-6B
RBP	CCAR1	CCAR1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1211	1212

Library-Prep
Sequencing

Library-Prep Information

	BGHLV20-5	BGHLV20-6
Sample #
Sample Name	CCAR1-BGHLV20-5B	CCAR1-BGHLV20-6B
Sample_Name_Alias	CCAR1_BGHLV20-5B	CCAR1_BGHLV20-6B
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-10	2016-03-10
Lib_ID	Lib-160310	Lib-160310
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/A10.png	DNA_Library_LV33-34-25B-32/set2/A2.png
RIN	9.6	9.5
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/D11.png	RNA_Library_LV35_LV36/set1/E11.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV20-5	BGHLV20-6
RBP	CCAR1	CCAR1
Batch_ID	BGHLV20	BGHLV20
WB_result	64.400	57.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2888	2889

Sequencing Information

	BGHLV20-5	BGHLV20-6
Sample_ID	BGHLV20-5	BGHLV20-6
Sample Name	CCAR1_BGHLV20-5B	CCAR1_BGHLV20-6B
Pool ID	Pool-160425	Pool-160425
LocalServer_folder	set20	set20
total_reads	85,301,628	88,007,576
total_aligned_reads	65,796,896	67,460,240
unique_aligned_reads	61,425,794	63,050,504
percent_uniqueAligned	0.72010	0.71642
correlation_replicates	0.999111	0.999111
spikein_reads	165,792	176,302
percent_spikeins	0.00194	0.00200
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1537	1538

Data Submission Information

	BGHLV20-5
ENCODE_alias	brenton-graveley:CCAR1-BGHLV20-HepG2
ENCODE_accession	ENCSR732LYQ
object_type	gene_silencing_series
assay_type	knockdown followed by RNA-seq
Sample_ID	BGHLV20-5
Sample Name	CCAR1_BGHLV20-5B
Selected	Yes
Status	Released
Status_Date	2022-03-01
Project	ENCODE3

protocol_URL
ID	6609

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
CCAR1_BGHLV20-5B_GTGGCC_L005_001.R1.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1537	HiSeq2000	100	paired-ended	1				NT_BGHLV20-1B_GTCCGC_L004_001.R1.fastq.gz,NT_BGHLV20-2B_GTGAAA_L004_001.R1.fastq.gz	ENCODE3	15586
CCAR1_BGHLV20-5B_GTGGCC_L005_001.R2.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1537	HiSeq2000	100	paired-ended	2				NT_BGHLV20-1B_GTCCGC_L004_001.R2.fastq.gz,NT_BGHLV20-2B_GTGAAA_L004_001.R2.fastq.gz	ENCODE3	15628
CCAR1_BGHLV20-5B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1537					GRCh38	V40	CCAR1_BGHLV20-5B_GTGGCC_L005_001.R1.fastq.gz,CCAR1_BGHLV20-5B_GTGGCC_L005_001.R2.fastq.gz		ENCORE2	15670
CCAR1_BGHLV20-5B_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1537					GRCh38	V40	CCAR1_BGHLV20-5B/Aligned.sortedByCoord.out.bam		ENCORE2	15712
CCAR1_BGHLV20-5B_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1537					GRCh38	V40	CCAR1_BGHLV20-5B/Aligned.sortedByCoord.out.bam		ENCORE2	15754
CCAR1_BGHLV20-5B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1537					GRCh38	V40	CCAR1_BGHLV20-5B/Aligned.sortedByCoord.out.bam		ENCORE2	15796
CCAR1_BGHLV20-5B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1537					GRCh38	V40	CCAR1_BGHLV20-5B/Aligned.sortedByCoord.out.bam		ENCORE2	15838
CCAR1_BGHLV20-5B_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1537					GRCh38	V40	CCAR1_BGHLV20-5B_GTGGCC_L005_001.R1.fastq.gz,CCAR1_BGHLV20-5B_GTGGCC_L005_001.R2.fastq.gz		ENCORE2	15880
CCAR1_BGHLV20-6B_GTTTCG_L005_001.R1.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1538	HiSeq2000	100	paired-ended	1				NT_BGHLV20-1B_GTCCGC_L004_001.R1.fastq.gz,NT_BGHLV20-2B_GTGAAA_L004_001.R1.fastq.gz	ENCODE3	15587
CCAR1_BGHLV20-6B_GTTTCG_L005_001.R2.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1538	HiSeq2000	100	paired-ended	2				NT_BGHLV20-1B_GTCCGC_L004_001.R2.fastq.gz,NT_BGHLV20-2B_GTGAAA_L004_001.R2.fastq.gz	ENCODE3	15629
CCAR1_BGHLV20-6B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1538					GRCh38	V40	CCAR1_BGHLV20-6B_GTTTCG_L005_001.R1.fastq.gz,CCAR1_BGHLV20-6B_GTTTCG_L005_001.R2.fastq.gz		ENCORE2	15671
CCAR1_BGHLV20-6B_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1538					GRCh38	V40	CCAR1_BGHLV20-6B/Aligned.sortedByCoord.out.bam		ENCORE2	15713
CCAR1_BGHLV20-6B_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1538					GRCh38	V40	CCAR1_BGHLV20-6B/Aligned.sortedByCoord.out.bam		ENCORE2	15755
CCAR1_BGHLV20-6B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1538					GRCh38	V40	CCAR1_BGHLV20-6B/Aligned.sortedByCoord.out.bam		ENCORE2	15797
CCAR1_BGHLV20-6B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1538					GRCh38	V40	CCAR1_BGHLV20-6B/Aligned.sortedByCoord.out.bam		ENCORE2	15839
CCAR1_BGHLV20-6B_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1538					GRCh38	V40	CCAR1_BGHLV20-6B_GTTTCG_L005_001.R1.fastq.gz,CCAR1_BGHLV20-6B_GTTTCG_L005_001.R2.fastq.gz		ENCORE2	15881