EWSR1 RNA-Seq in K562

General Information


RBP	EWSR1
Cell_Line	K562
Method	shRNA
Exp_Name	EWSR1-BGKLV08-K562
ENCODE_series_ID	ENCSR911KXX
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR831YGP
ENCODE_CN_Exp_ID	ENCSR913CAE
Rep1	EWSR1-LV08-25
Rep2	EWSR1-LV08-26
CN1	Nontarget-LV08-1_00003527
CN2	nontarget-LV08-2_00003527
Rep1_qPCR	55.1
Rep2_qPCR	45.7
Rep1_WB	87.7
Rep2_WB	83.3
Antibody Cat#	A300-417A
Antibody Lot#	A300-417A
Antibody DCC ID	ENCAB366VTK
Status	Released
Project	ENCODE3
ID	289

Experiment Information (Status: Released)

	BGKLV08-25	BGKLV08-26
idx	26	27
TRCN#_or_BGC#	TRCN0000000036	TRCN0000000036
shRNA_or_gRNA_sequence	GACCGCCTATGCAACTTCTTA	GACCGCCTATGCAACTTCTTA
PAM
Name	EWSR1	EWSR1
Sample_ID	BGKLV08-25	BGKLV08-26
transduction_Date	4/4/2014	4/4/2014
days
RBP_name	EWSR1	EWSR1
qPCR_result	55.1	45.7
Ave_qPCR	50.4
RT-qPCR_primer-F	TCCTATGAAGACCCACCCAC
RT-qPCR_primer-R	TCCGAGCAAGGGAGACTTTA
protein_conc	2964	3246
WB_result	87.7	83.3
Ave_WB	85.5
WB_DONE_date	12/3/2015
MW	68kDa
IP	1	1
antibody_Cat#	A300-417A	A300-417A
Antibody DCC ID	ENCAB366VTK	ENCAB366VTK
submitted_to_DCC_date	12/7/2015
Rep1_TPM	33.5131306	0
Rep2_TPM	31.6840136	0
Action	Ready	Ready
Library_start_date	5/5/2014	5/5/2014
repeat_library
Note		2
ID	25	26

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EWSR1	Product_ID: A300-417A Lot_ID: 1 Source: Bethyl Labs Target Name: EWSR1-human

Experiment Status

	BGKLV08-25	BGKLV08-26
Sample_ID	BGKLV08-25	BGKLV08-26
Sample Name	EWSR1-LV08-25	EWSR1-LV08-26
Sample Name	EWSR1-LV08-25	EWSR1-LV08-26
RBP	EWSR1	EWSR1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	286	287

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-25	BGKLV08-26
Sample #
Sample Name	EWSR1-BGKLV08-25	EWSR1-BGKLV08-26
Sample_Name_Alias	EWSR1-LV08-25	EWSR1-LV08-26
Index Well Position	S22	S23
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/set2/G1.png	DNA_Library_LV08/set2/H1.png
RIN	9.2	9.3
libSample_RNA_Well	RNA_Library_LV08/set2/A2.png	RNA_Library_LV08/set2/B2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-25	BGKLV08-26
RBP	EWSR1	EWSR1
Batch_ID	BGKLV08	BGKLV08
WB_result	87.700	83.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1908	1909

Sequencing Information

	BGKLV08-25	BGKLV08-26
Sample_ID	BGKLV08-25	BGKLV08-26
Sample Name	EWSR1-LV08-25	EWSR1-LV08-26
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	50,430,000	34,400,000
total_aligned_reads	44,786,680	30,606,660
unique_aligned_reads	40,849,288	27,780,156
percent_uniqueAligned	0.81002	0.80756
correlation_replicates	0.998734	0.998734
spikein_reads	442,088	309,068
percent_spikeins	0.00877	0.00898
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	608	609

Data Submission Information

	BGKLV08-25	BGKLV08-25
ENCODE_alias	brenton-graveley:EWSR1-LV08	brenton-graveley:EWSR1-BGKLV08-K562
ENCODE_accession	ENCSR831YGP	ENCSR911KXX
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV08-25	BGKLV08-25
Sample Name	EWSR1-LV08-25	EWSR1-LV08-25
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2692	6701

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
EWSR1-LV08-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	608					GRCh38	V40	EWSR1-LV08-25_CGTACG_L003_R1_001.fastq.gz,EWSR1-LV08-25_CGTACG_L003_R2_001.fastq.gz		ENCORE2	11993
EWSR1-LV08-25_CGTACG_L003_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	608	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	12049
EWSR1-LV08-25_CGTACG_L003_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	608	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	12105
EWSR1-LV08-25_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	608					GRCh38	V40	EWSR1-LV08-25/Aligned.sortedByCoord.out.bam		ENCORE2	12161
EWSR1-LV08-25_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	608					GRCh38	V40	EWSR1-LV08-25/Aligned.sortedByCoord.out.bam		ENCORE2	12217
EWSR1-LV08-25_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	608					GRCh38	V40	EWSR1-LV08-25/Aligned.sortedByCoord.out.bam		ENCORE2	12273
EWSR1-LV08-25_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	608					GRCh38	V40	EWSR1-LV08-25/Aligned.sortedByCoord.out.bam		ENCORE2	12329
EWSR1-LV08-25_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	608					GRCh38	V40	EWSR1-LV08-25_CGTACG_L003_R1_001.fastq.gz,EWSR1-LV08-25_CGTACG_L003_R2_001.fastq.gz		ENCORE2	13328
EWSR1-LV08-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	609					GRCh38	V40	EWSR1-LV08-26_GAGTGG_L004_R1_001.fastq.gz,EWSR1-LV08-26_GAGTGG_L004_R2_001.fastq.gz		ENCORE2	11994
EWSR1-LV08-26_GAGTGG_L004_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	609	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	12050
EWSR1-LV08-26_GAGTGG_L004_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	609	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	12106
EWSR1-LV08-26_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	609					GRCh38	V40	EWSR1-LV08-26/Aligned.sortedByCoord.out.bam		ENCORE2	12162
EWSR1-LV08-26_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	609					GRCh38	V40	EWSR1-LV08-26/Aligned.sortedByCoord.out.bam		ENCORE2	12218
EWSR1-LV08-26_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	609					GRCh38	V40	EWSR1-LV08-26/Aligned.sortedByCoord.out.bam		ENCORE2	12274
EWSR1-LV08-26_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	609					GRCh38	V40	EWSR1-LV08-26/Aligned.sortedByCoord.out.bam		ENCORE2	12330
EWSR1-LV08-26_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	609					GRCh38	V40	EWSR1-LV08-26_GAGTGG_L004_R1_001.fastq.gz,EWSR1-LV08-26_GAGTGG_L004_R2_001.fastq.gz		ENCORE2	13329