ASCC1 RNA-Seq in K562

General Information


RBP	ASCC1
Cell_Line	K562
Method	shRNA
Exp_Name	ASCC1-BGKLV08-K562
ENCODE_series_ID	ENCSR503GNR
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR253DCB
ENCODE_CN_Exp_ID	ENCSR913CAE
Rep1	ASCC1-LV08-5
Rep2	ASCC1-LV08-6
CN1	Nontarget-LV08-1_00003527
CN2	nontarget-LV08-2_00003527
Rep1_qPCR	78.5
Rep2_qPCR	79.8
Rep1_WB	64.2
Rep2_WB	71.9
Antibody Cat#	A303-871A
Antibody Lot#	A303-871A
Antibody DCC ID	ENCAB122UGS
Status	Released
Project	ENCODE3
ID	281

Experiment Information (Status: Released)

	BGKLV08-5	BGKLV08-6
idx	6	7
TRCN#_or_BGC#	TRCN0000136137	TRCN0000136137
shRNA_or_gRNA_sequence	GAATCATTTGATGGCCGAAAT	GAATCATTTGATGGCCGAAAT
PAM
Name	ASCC1	ASCC1
Sample_ID	BGKLV08-5	BGKLV08-6
transduction_Date	4/4/2014	4/4/2014
days
RBP_name	ASCC1	ASCC1
qPCR_result	78.5	79.8
Ave_qPCR	79.2
RT-qPCR_primer-F	gaaagaccccaatgctgaag
RT-qPCR_primer-R	cggccatcaaatgattctct
protein_conc	2627	2329
WB_result	64.2	71.9
Ave_WB	68.1
WB_DONE_date
MW
IP	1	1
antibody_Cat#	A303-871A	A303-871A
Antibody DCC ID	ENCAB122UGS	ENCAB122UGS
submitted_to_DCC_date	5/4/2015
Rep1_TPM	8.7928054	0
Rep2_TPM	12.0564379	0
Action	Ready	Ready
Library_start_date	5/5/2014	5/5/2014
repeat_library
Note		1
ID	5	6

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ASCC1	Product_ID: A303-871A Lot_ID: 1 Source: Bethyl Labs Target Name: ASCC1-human

Experiment Status

	BGKLV08-5	BGKLV08-6
Sample_ID	BGKLV08-5	BGKLV08-6
Sample Name	ASCC1-LV08-5	ASCC1-LV08-6
Sample Name	ASCC1-LV08-5	ASCC1-LV08-6
RBP	ASCC1	ASCC1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	270	271

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-5	BGKLV08-6
Sample #
Sample Name	ASCC1-BGKLV08-5	ASCC1-BGKLV08-6
Sample_Name_Alias	ASCC1-LV08-5	ASCC1-LV08-6
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-05	2014-05-05
Lib_ID	Lib-140505	Lib-140505
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV08/set1/F1.png	DNA_Library_LV08/set1/G1.png
RIN	9.3	9.3
libSample_RNA_Well	RNA_Library_LV08/set1/E1.png	RNA_Library_LV08/set1/F1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-5	BGKLV08-6
RBP	ASCC1	ASCC1
Batch_ID	BGKLV08	BGKLV08
WB_result	64.200	71.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1892	1893

Sequencing Information

	BGKLV08-5	BGKLV08-6
Sample_ID	BGKLV08-5	BGKLV08-6
Sample Name	ASCC1-LV08-5	ASCC1-LV08-6
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	47,150,000	46,030,000
total_aligned_reads	39,825,516	38,490,432
unique_aligned_reads	36,424,008	35,155,326
percent_uniqueAligned	0.77251	0.76375
correlation_replicates	0.998061	0.998061
spikein_reads	337,228	369,124
percent_spikeins	0.00715	0.00802
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	592	593

Data Submission Information

	BGKLV08-5	BGKLV08-5
ENCODE_alias	brenton-graveley:ASCC1-LV08	brenton-graveley:ASCC1-BGKLV08-K562
ENCODE_accession	ENCSR253DCB	ENCSR503GNR
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV08-5	BGKLV08-5
Sample Name	ASCC1-LV08-5	ASCC1-LV08-5
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2684	6595

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
ASCC1-LV08-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	592					GRCh38	V40	ASCC1-LV08-5_ACAGTG_L001_R1_001.fastq.gz,ASCC1-LV08-5_ACAGTG_L001_R2_001.fastq.gz		ENCORE2	11977
ASCC1-LV08-5_ACAGTG_L001_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	592	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12033
ASCC1-LV08-5_ACAGTG_L001_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	592	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12089
ASCC1-LV08-5_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	592					GRCh38	V40	ASCC1-LV08-5/Aligned.sortedByCoord.out.bam		ENCORE2	12145
ASCC1-LV08-5_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	592					GRCh38	V40	ASCC1-LV08-5/Aligned.sortedByCoord.out.bam		ENCORE2	12201
ASCC1-LV08-5_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	592					GRCh38	V40	ASCC1-LV08-5/Aligned.sortedByCoord.out.bam		ENCORE2	12257
ASCC1-LV08-5_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	592					GRCh38	V40	ASCC1-LV08-5/Aligned.sortedByCoord.out.bam		ENCORE2	12313
ASCC1-LV08-5_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	592					GRCh38	V40	ASCC1-LV08-5_ACAGTG_L001_R1_001.fastq.gz,ASCC1-LV08-5_ACAGTG_L001_R2_001.fastq.gz		ENCORE2	13312
ASCC1-LV08-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	593					GRCh38	V40	ASCC1-LV08-6_GCCAAT_L001_R1_001.fastq.gz,ASCC1-LV08-6_GCCAAT_L001_R2_001.fastq.gz		ENCORE2	11978
ASCC1-LV08-6_GCCAAT_L001_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	593	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12034
ASCC1-LV08-6_GCCAAT_L001_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	593	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12090
ASCC1-LV08-6_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	593					GRCh38	V40	ASCC1-LV08-6/Aligned.sortedByCoord.out.bam		ENCORE2	12146
ASCC1-LV08-6_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	593					GRCh38	V40	ASCC1-LV08-6/Aligned.sortedByCoord.out.bam		ENCORE2	12202
ASCC1-LV08-6_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	593					GRCh38	V40	ASCC1-LV08-6/Aligned.sortedByCoord.out.bam		ENCORE2	12258
ASCC1-LV08-6_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	593					GRCh38	V40	ASCC1-LV08-6/Aligned.sortedByCoord.out.bam		ENCORE2	12314
ASCC1-LV08-6_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	593					GRCh38	V40	ASCC1-LV08-6_GCCAAT_L001_R1_001.fastq.gz,ASCC1-LV08-6_GCCAAT_L001_R2_001.fastq.gz		ENCORE2	13313