CCAR1 RNA-Seq in K562

General Information


RBP	CCAR1
Cell_Line	K562
Method	shRNA
Exp_Name	CCAR1-BGKLV24-K562
ENCODE_series_ID	ENCSR051XWE
Batch_ID	BGKLV24
Pool ID	Pool-150615
Local_Set_Name	set24
ENCODE_KD_Exp_ID	ENCSR386YEV
ENCODE_CN_Exp_ID	ENCSR667PLJ
Rep1	CCAR1_BGKLV24_5_17598
Rep2	CCAR1_BGKLV24_6_17599
CN1	non-target_BGKLV24_1_17594
CN2	non-target_BGKLV24_2_17595
Rep1_qPCR	40.3
Rep2_qPCR	61.1
Rep1_WB	58.5
Rep2_WB	69.0
Antibody Cat#	A300-270A
Antibody Lot#	A300-270A
Antibody DCC ID	ENCAB369JZE
Status	Released
Project	ENCODE3
ID	556

Experiment Information (Status: Released)

	BGKLV24-5	BGKLV24-5	BGKLV24-6	BGKLV24-6
idx	342	0	343	0
TRCN#_or_BGC#	TRCN0000056005	TRCN0000056005	TRCN0000056005	TRCN0000056005
shRNA_or_gRNA_sequence	GCCCTAGTATGGAAGATTTAT	GCCCTAGTATGGAAGATTTAT	GCCCTAGTATGGAAGATTTAT	GCCCTAGTATGGAAGATTTAT
PAM
Name	CCAR1_05	CCAR1_05	CCAR1_05	CCAR1_05
Sample_ID	BGKLV24-5	BGKLV24-5	BGKLV24-6	BGKLV24-6
transduction_Date	2/27/2015	2/27/2015	2/27/2015	2/27/2015
days
RBP_name	CCAR1	CCAR1	CCAR1	CCAR1
qPCR_result	40.3	40.3	61.1	61.1
Ave_qPCR	50.7	50.7
RT-qPCR_primer-F	cagaggggatcaagtgccta	cagaggggatcaagtgccta
RT-qPCR_primer-R	gtgatcgctctcgctctctt	gtgatcgctctcgctctctt
protein_conc	3593	3593	3472	3472
WB_result	58.5	0	69.0	0
Ave_WB	63.7	0.0
WB_DONE_date	5/13/2015	6/13/2022
MW	133kDa	133kDa
IP	1		1
antibody_Cat#	A300-270A	A300-435A	A300-270A
Antibody DCC ID	ENCAB369JZE		ENCAB369JZE
submitted_to_DCC_date	8/6/2015
Rep1_TPM	59.4930894	0	0	0
Rep2_TPM	46.633399	0	0	0
Action
Library_start_date	5/22/2015		5/22/2015
repeat_library
Note
ID	387	389	388	390

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

	BGKLV24-5	BGKLV24-6
Sample_ID	BGKLV24-5	BGKLV24-6
Sample Name	CCAR1_BGKLV24_5_17598	CCAR1_BGKLV24_6_17599
Sample Name	CCAR1_BGKLV24_5_17598	CCAR1_BGKLV24_6_17599
RBP	CCAR1	CCAR1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	850	851

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-5	BGKLV24-6
Sample #
Sample Name	CCAR1-BGKLV24-5	CCAR1-BGKLV24-6
Sample_Name_Alias	CCAR1_BGKLV24_5_17598	CCAR1_BGKLV24_6_17599
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-22	2015-05-22
Lib_ID	Lib-150522	Lib-150522
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/F1.png	DNA_Library_LV21-24/set1/G1.png
RIN	9.9	8.9
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/H2.png	RNA_Library_LV20-22-24/set1/B1.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-5	BGKLV24-6
RBP	CCAR1	CCAR1
Batch_ID	BGKLV24	BGKLV24
WB_result	58.500	69.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2538	2539

Sequencing Information

	BGKLV24-5	BGKLV24-6
Sample_ID	BGKLV24-5	BGKLV24-6
Sample Name	CCAR1_BGKLV24_5_17598	CCAR1_BGKLV24_6_17599
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set24	set24
total_reads	39,900,000	29,940,000
total_aligned_reads	36,841,524	27,674,492
unique_aligned_reads	33,545,068	25,232,146
percent_uniqueAligned	0.84073	0.84276
correlation_replicates	0.997896	0.997896
spikein_reads	148,366	111,800
percent_spikeins	0.00372	0.00373
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1072	1073

Data Submission Information

	BGKLV24-5	BGKLV24-5
ENCODE_alias	brenton-graveley:CCAR1_BGKLV24	brenton-graveley:CCAR1-BGKLV24-K562
ENCODE_accession	ENCSR386YEV	ENCSR051XWE
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-5	BGKLV24-5
Sample Name	CCAR1_BGKLV24_5_17598	CCAR1_BGKLV24_5_17598
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2976	6610

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_BGKLV24_5_17598_CGTACG_L005_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1072	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE3	17184
CCAR1_BGKLV24_5_17598_CGTACG_L005_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1072	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE3	17220
CCAR1_BGKLV24_5_17598_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1072					GRCh38	V40	CCAR1_BGKLV24_5_17598_CGTACG_L005_R1_001.fastq.gz,CCAR1_BGKLV24_5_17598_CGTACG_L005_R2_001.fastq.gz		ENCORE2	17256
CCAR1_BGKLV24_5_17598_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1072					GRCh38	V40	CCAR1_BGKLV24_5_17598/Aligned.sortedByCoord.out.bam		ENCORE2	17292
CCAR1_BGKLV24_5_17598_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1072					GRCh38	V40	CCAR1_BGKLV24_5_17598/Aligned.sortedByCoord.out.bam		ENCORE2	17328
CCAR1_BGKLV24_5_17598_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1072					GRCh38	V40	CCAR1_BGKLV24_5_17598/Aligned.sortedByCoord.out.bam		ENCORE2	17364
CCAR1_BGKLV24_5_17598_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1072					GRCh38	V40	CCAR1_BGKLV24_5_17598/Aligned.sortedByCoord.out.bam		ENCORE2	17400
CCAR1_BGKLV24_5_17598_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1072					GRCh38	V40	CCAR1_BGKLV24_5_17598_CGTACG_L005_R1_001.fastq.gz,CCAR1_BGKLV24_5_17598_CGTACG_L005_R2_001.fastq.gz		ENCORE2	17436
CCAR1_BGKLV24_6_17599_GAGTGG_L005_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1073	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE3	17185
CCAR1_BGKLV24_6_17599_GAGTGG_L005_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1073	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE3	17221
CCAR1_BGKLV24_6_17599_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1073					GRCh38	V40	CCAR1_BGKLV24_6_17599_GAGTGG_L005_R1_001.fastq.gz,CCAR1_BGKLV24_6_17599_GAGTGG_L005_R2_001.fastq.gz		ENCORE2	17257
CCAR1_BGKLV24_6_17599_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1073					GRCh38	V40	CCAR1_BGKLV24_6_17599/Aligned.sortedByCoord.out.bam		ENCORE2	17293
CCAR1_BGKLV24_6_17599_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1073					GRCh38	V40	CCAR1_BGKLV24_6_17599/Aligned.sortedByCoord.out.bam		ENCORE2	17329
CCAR1_BGKLV24_6_17599_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1073					GRCh38	V40	CCAR1_BGKLV24_6_17599/Aligned.sortedByCoord.out.bam		ENCORE2	17365
CCAR1_BGKLV24_6_17599_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1073					GRCh38	V40	CCAR1_BGKLV24_6_17599/Aligned.sortedByCoord.out.bam		ENCORE2	17401
CCAR1_BGKLV24_6_17599_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1073					GRCh38	V40	CCAR1_BGKLV24_6_17599_GAGTGG_L005_R1_001.fastq.gz,CCAR1_BGKLV24_6_17599_GAGTGG_L005_R2_001.fastq.gz		ENCORE2	17437