CCAR2 RNA-Seq in HepG2

General Information


RBP	CCAR2
Cell_Line	HepG2
Method	shRNA
Exp_Name	CCAR2-BGHLV18-HepG2
ENCODE_series_ID	ENCSR595RGO
Batch_ID	BGHLV18
Pool ID	Pool-141010
Local_Set_Name	set18
ENCODE_KD_Exp_ID	ENCSR237IWZ
ENCODE_CN_Exp_ID	ENCSR674KEK
Rep1	KIAA1967_BGHLV18_15
Rep2	KIAA1967_BGHLV18_16
CN1	NT_BGHLV18_1
CN2	NT_BGHLV18_2
Rep1_qPCR	70.7
Rep2_qPCR	73.5
Rep1_WB	91.7
Rep2_WB	90.9
Antibody Cat#	A303-942A
Antibody Lot#	A303-942A
Antibody DCC ID	ENCAB379QXE
Status	Released
Project	ENCODE3
ID	447

Experiment Information (Status: Released)

	BGHLV18-15	BGHLV18-16
idx	315	316
TRCN#_or_BGC#	TRCN0000053724	TRCN0000053724
shRNA_or_gRNA_sequence	GCATTGATTTGAGCGGCTGTA	GCATTGATTTGAGCGGCTGTA
PAM
Name	KIAA1967	KIAA1967
Sample_ID	BGHLV18-15	BGHLV18-16
transduction_Date	8/28/2014	8/28/2014
days
RBP_name	CCAR2	CCAR2
qPCR_result	70.7	73.5
Ave_qPCR	72.1
RT-qPCR_primer-F	gacccagaacatctgccagt
RT-qPCR_primer-R	aggtccaggtttccgaagag
protein_conc	4535	4799
WB_result	91.7	90.9
Ave_WB	91.3
WB_DONE_date	5/27/2015
MW	103kDa
IP	1	1
antibody_Cat#	A303-942A	A303-942A
Antibody DCC ID	ENCAB379QXE	ENCAB379QXE
submitted_to_DCC_date	8/6/2015
Rep1_TPM	10.5	0
Rep2_TPM	11.4	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	2380	2381

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CCAR2	Product_ID: A303-942A Lot_ID: 1 Source: Bethyl Labs Target Name: CCAR2-human

Experiment Status

	BGHLV18-15	BGHLV18-16
Sample_ID	BGHLV18-15	BGHLV18-16
Sample Name	KIAA1967_BGHLV18_15	KIAA1967_BGHLV18_16
Sample Name	KIAA1967_BGHLV18_15	KIAA1967_BGHLV18_16
RBP	CCAR2	CCAR2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	622	623

Library-Prep
Sequencing

Library-Prep Information

	BGHLV18-15	BGHLV18-16
Sample #
Sample Name	CCAR2-BGHLV18-15	CCAR2-BGHLV18-16
Sample_Name_Alias	KIAA1967_BGHLV18_15	KIAA1967_BGHLV18_16
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-02	2014-10-02
Lib_ID	Lib-141002	Lib-141002
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/A2.png	DNA_Library_LV18-19/set1/B2.png
RIN	9.6	9.2
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/G8.png	RNA_Library_LV16-17-18/set1/H8.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV18-15	BGHLV18-16
RBP	CCAR2	CCAR2
Batch_ID	BGHLV18	BGHLV18
WB_result	91.700	90.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2306	2307

Sequencing Information

	BGHLV18-15	BGHLV18-16
Sample_ID	BGHLV18-15	BGHLV18-16
Sample Name	KIAA1967_BGHLV18_15	KIAA1967_BGHLV18_16
Pool ID	Pool-141010	Pool-141010
LocalServer_folder	set18	set18
total_reads	34,690,000	45,560,000
total_aligned_reads	31,793,172	41,411,194
unique_aligned_reads	30,084,128	39,152,834
percent_uniqueAligned	0.86723	0.85937
correlation_replicates	0.997456	0.997456
spikein_reads	115,922	103,896
percent_spikeins	0.00334	0.00228
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	948	949

Data Submission Information

	BGHLV18-15	BGHLV18-15
ENCODE_alias	brenton-graveley:KIAA1967_BGHLV18	brenton-graveley:CCAR2-BGHLV18-HepG2
ENCODE_accession	ENCSR237IWZ	ENCSR595RGO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV18-15	BGHLV18-15
Sample Name	KIAA1967_BGHLV18_15	KIAA1967_BGHLV18_15
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2828	6611

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
KIAA1967_BGHLV18_15_GATCAG_L002_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	948	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14796
KIAA1967_BGHLV18_15_GATCAG_L002_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	948	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14834
KIAA1967_BGHLV18_15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	948					GRCh38	V40	KIAA1967_BGHLV18_15_GATCAG_L002_R1_001.fastq.gz,KIAA1967_BGHLV18_15_GATCAG_L002_R2_001.fastq.gz		ENCORE2	14872
KIAA1967_BGHLV18_15_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	948					GRCh38	V40	KIAA1967_BGHLV18_15/Aligned.sortedByCoord.out.bam		ENCORE2	14910
KIAA1967_BGHLV18_15_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	948					GRCh38	V40	KIAA1967_BGHLV18_15/Aligned.sortedByCoord.out.bam		ENCORE2	14948
KIAA1967_BGHLV18_15_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	948					GRCh38	V40	KIAA1967_BGHLV18_15/Aligned.sortedByCoord.out.bam		ENCORE2	14986
KIAA1967_BGHLV18_15_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	948					GRCh38	V40	KIAA1967_BGHLV18_15/Aligned.sortedByCoord.out.bam		ENCORE2	15024
KIAA1967_BGHLV18_15_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	948					GRCh38	V40	KIAA1967_BGHLV18_15_GATCAG_L002_R1_001.fastq.gz,KIAA1967_BGHLV18_15_GATCAG_L002_R2_001.fastq.gz		ENCORE2	15062
KIAA1967_BGHLV18_16_TAGCTT_L002_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	949	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14797
KIAA1967_BGHLV18_16_TAGCTT_L002_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	949	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14835
KIAA1967_BGHLV18_16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	949					GRCh38	V40	KIAA1967_BGHLV18_16_TAGCTT_L002_R1_001.fastq.gz,KIAA1967_BGHLV18_16_TAGCTT_L002_R2_001.fastq.gz		ENCORE2	14873
KIAA1967_BGHLV18_16_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	949					GRCh38	V40	KIAA1967_BGHLV18_16/Aligned.sortedByCoord.out.bam		ENCORE2	14911
KIAA1967_BGHLV18_16_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	949					GRCh38	V40	KIAA1967_BGHLV18_16/Aligned.sortedByCoord.out.bam		ENCORE2	14949
KIAA1967_BGHLV18_16_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	949					GRCh38	V40	KIAA1967_BGHLV18_16/Aligned.sortedByCoord.out.bam		ENCORE2	14987
KIAA1967_BGHLV18_16_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	949					GRCh38	V40	KIAA1967_BGHLV18_16/Aligned.sortedByCoord.out.bam		ENCORE2	15025
KIAA1967_BGHLV18_16_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	949					GRCh38	V40	KIAA1967_BGHLV18_16_TAGCTT_L002_R1_001.fastq.gz,KIAA1967_BGHLV18_16_TAGCTT_L002_R2_001.fastq.gz		ENCORE2	15063