CCAR2 RNA-Seq in K562

General Information


RBP	CCAR2
Cell_Line	K562
Method	shRNA
Exp_Name	CCAR2-BGKLV25-K562
ENCODE_series_ID	ENCSR158YIO
Batch_ID	BGKLV25
Pool ID	Pool-151101
Local_Set_Name	set25
ENCODE_KD_Exp_ID	ENCSR984CLJ
ENCODE_CN_Exp_ID	ENCSR620PUP
Rep1	KIAA1967_BGKLV25-29
Rep2	KIAA1967_BGKLV25-30
CN1	NT_BGKLV25-1
CN2	NT_BGKLV25-2
Rep1_qPCR	72.9
Rep2_qPCR	74.8
Rep1_WB	69.6
Rep2_WB	66.1
Antibody Cat#	A303-942A
Antibody Lot#	A303-942A
Antibody DCC ID	ENCAB379QXE
Status	Released
Project	ENCODE3
ID	618

Experiment Information (Status: Released)

	BGKLV25-29	BGKLV25-29	BGKLV25-29	BGKLV25-29	BGKLV25-29	BGKLV25-30	BGKLV25-30	BGKLV25-30	BGKLV25-30	BGKLV25-30
idx	430	432	432	432	432	431	433	433	433	433
TRCN#_or_BGC#	TRCN0000053724	TRCN0000053724	TRCN0000053724	TRCN0000053724	TRCN0000053724	TRCN0000053724	TRCN0000053724	TRCN0000053724	TRCN0000053724	TRCN0000053724
shRNA_or_gRNA_sequence	GCATTGATTTGAGCGGCTGTA	GCATTGATTTGAGCGGCTGTA	GCATTGATTTGAGCGGCTGTA	GCATTGATTTGAGCGGCTGTA	GCATTGATTTGAGCGGCTGTA	GCATTGATTTGAGCGGCTGTA	GCATTGATTTGAGCGGCTGTA	GCATTGATTTGAGCGGCTGTA	GCATTGATTTGAGCGGCTGTA	GCATTGATTTGAGCGGCTGTA
PAM
Name	KIAA1967/DBC1	KIAA1967/DBC1	CCAR2/DBC1	CCAR2/DBC1	CCAR2/DBC1	KIAA1967/DBC1	KIAA1967/DBC1	KIAA1967/DBC1	KIAA1967/DBC1	KIAA1967/DBC1
Sample_ID	BGKLV25-29	BGKLV25-29	BGKLV25-29	BGKLV25-29	BGKLV25-29	BGKLV25-30	BGKLV25-30	BGKLV25-30	BGKLV25-30	BGKLV25-30
transduction_Date	3/17/2015	3/17/2015	3/17/2015	3/17/2015	3/17/2015	3/17/2015	3/17/2015	3/17/2015	3/17/2015	3/17/2015
days
RBP_name	CCAR2	CCAR2	CCAR2	CCAR2	CCAR2	CCAR2	CCAR2	CCAR2	CCAR2	CCAR2
qPCR_result	72.9	72.9	72.9	72.9	72.9	74.8	74.8	74.8	74.8	74.8
Ave_qPCR	73.8	73.8	73.8	73.8	73.8
RT-qPCR_primer-F	gacccagaacatctgccagt	gacccagaacatctgccagt	gacccagaacatctgccagt	gacccagaacatctgccagt	gacccagaacatctgccagt
RT-qPCR_primer-R	aggtccaggtttccgaagag	aggtccaggtttccgaagag	aggtccaggtttccgaagag	aggtccaggtttccgaagag	aggtccaggtttccgaagag
protein_conc	3473	3473	3473	3473	3473	3970	3970	3970	3970	3970
WB_result	69.6	52.1	65.2683977	77.093	58	66.1	64.9	71.7	75.8	50
Ave_WB	67.8	58.5	68.5	76.4	54.0
WB_DONE_date	5/27/2015	2/16/2016	8/20/2019	5/19/2022	7/5/2022		WES	WES
MW	103kDa	103kDa	103kDa	103kDa	103kDa
IP	1					1	FU'S
antibody_Cat#	A303-942A	#200093	RN117PW	A300-432A	A300-433A	A303-942A	#200093	lot# 001	lot# 2	lot# 2
Antibody DCC ID	ENCAB379QXE		ENCAB703CVO	ENCAB189SUY	ENCAB429NEH	lot #1
submitted_to_DCC_date	8/6/2015			8/16/22	8/16/22
Rep1_TPM	28.3902385	28.3902385	0	0	0	0	0	0	0	0
Rep2_TPM	22.457747	22.457747	0	0	0	0	0	0	0	0
Action
Library_start_date	6/23/2015					6/23/2015
repeat_library
Note
ID	495	497	499	501	503	496	498	500	502	504

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
CCAR2	Product_ID: RN117PW Lot_ID: 1 Source: MBLI Target Name: CCAR2-human
CCAR2	Product_ID: A300-432A Lot_ID: 2 Source: Bethyl Labs Target Name: CCAR2-human
CCAR2	Product_ID: A300-433A Lot_ID: 2 Source: Bethyl Labs Target Name: CCAR2-human

Experiment Status

	BGKLV25-29	BGKLV25-30
Sample_ID	BGKLV25-29	BGKLV25-30
Sample Name	KIAA1967_BGKLV25-29	KIAA1967_BGKLV25-30
Sample Name	KIAA1967_BGKLV25-29	KIAA1967_BGKLV25-30
RBP	CCAR2	CCAR2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-12-08	2015-12-08
Project	ENCODE3	ENCODE3
Note
ID	914	915

Library-Prep
Sequencing

Library-Prep Information

	BGKLV25-29	BGKLV25-30
Sample #
Sample Name	CCAR2-BGKLV25-29	CCAR2-BGKLV25-30
Sample_Name_Alias	KIAA1967_BGKLV25-29	KIAA1967_BGKLV25-30
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-23	2015-06-23
Lib_ID	Lib-150623	Lib-150623
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/E2.png	DNA_Library_LV24-25-26/set1/F2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/G10.png	RNA_Library_LV22-23-25/set1/H10.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV25-29	BGKLV25-30
RBP	CCAR2	CCAR2
Batch_ID	BGKLV25	BGKLV25
WB_result	69.600	66.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2606	2607

Sequencing Information

	BGKLV25-29	BGKLV25-30
Sample_ID	BGKLV25-29	BGKLV25-30
Sample Name	KIAA1967_BGKLV25-29	KIAA1967_BGKLV25-30
Pool ID	Pool-151101	Pool-151101
LocalServer_folder	set25	set25
total_reads	138,370,032	85,701,704
total_aligned_reads	140,761,612	85,877,114
unique_aligned_reads	128,435,714	78,640,698
percent_uniqueAligned	0.92820	0.91761
correlation_replicates	0.998448	0.998448
spikein_reads	742,026	398,706
percent_spikeins	0.00536	0.00465
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1248	1249

Data Submission Information

	BGKLV25-29	BGKLV25-29
ENCODE_alias	brenton-graveley:KIAA1967_BGKLV25	brenton-graveley:CCAR2-BGKLV25-K562
ENCODE_accession	ENCSR984CLJ	ENCSR158YIO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV25-29	BGKLV25-29
Sample Name	KIAA1967_BGKLV25-29	KIAA1967_BGKLV25-29
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3006	6612

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_BGKLV25-29_CGTACG_L006_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1248	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19574
KIAA1967_BGKLV25-29_CGTACG_L006_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1248	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19610
KIAA1967_BGKLV25-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1248					GRCh38	V40	KIAA1967_BGKLV25-29_CGTACG_L006_001.R1.fastq.gz,KIAA1967_BGKLV25-29_CGTACG_L006_001.R2.fastq.gz		ENCORE2	19646
KIAA1967_BGKLV25-29_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1248					GRCh38	V40	KIAA1967_BGKLV25-29/Aligned.sortedByCoord.out.bam		ENCORE2	19682
KIAA1967_BGKLV25-29_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1248					GRCh38	V40	KIAA1967_BGKLV25-29/Aligned.sortedByCoord.out.bam		ENCORE2	19718
KIAA1967_BGKLV25-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1248					GRCh38	V40	KIAA1967_BGKLV25-29/Aligned.sortedByCoord.out.bam		ENCORE2	19754
KIAA1967_BGKLV25-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1248					GRCh38	V40	KIAA1967_BGKLV25-29/Aligned.sortedByCoord.out.bam		ENCORE2	19790
KIAA1967_BGKLV25-29_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1248					GRCh38	V40	KIAA1967_BGKLV25-29_CGTACG_L006_001.R1.fastq.gz,KIAA1967_BGKLV25-29_CGTACG_L006_001.R2.fastq.gz		ENCORE2	19980
KIAA1967_BGKLV25-30_GAGTGG_L006_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1249	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19575
KIAA1967_BGKLV25-30_GAGTGG_L006_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1249	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19611
KIAA1967_BGKLV25-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1249					GRCh38	V40	KIAA1967_BGKLV25-30_GAGTGG_L006_001.R1.fastq.gz,KIAA1967_BGKLV25-30_GAGTGG_L006_001.R2.fastq.gz		ENCORE2	19647
KIAA1967_BGKLV25-30_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1249					GRCh38	V40	KIAA1967_BGKLV25-30/Aligned.sortedByCoord.out.bam		ENCORE2	19683
KIAA1967_BGKLV25-30_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1249					GRCh38	V40	KIAA1967_BGKLV25-30/Aligned.sortedByCoord.out.bam		ENCORE2	19719
KIAA1967_BGKLV25-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1249					GRCh38	V40	KIAA1967_BGKLV25-30/Aligned.sortedByCoord.out.bam		ENCORE2	19755
KIAA1967_BGKLV25-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1249					GRCh38	V40	KIAA1967_BGKLV25-30/Aligned.sortedByCoord.out.bam		ENCORE2	19791
KIAA1967_BGKLV25-30_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1249					GRCh38	V40	KIAA1967_BGKLV25-30_GAGTGG_L006_001.R1.fastq.gz,KIAA1967_BGKLV25-30_GAGTGG_L006_001.R2.fastq.gz		ENCORE2	19981