EWSR1 RNA-Seq in HepG2

General Information


RBP	EWSR1
Cell_Line	HepG2
Method	shRNA
Exp_Name	EWSR1-BGHLV31-HepG2
ENCODE_series_ID	ENCSR604BHV
Batch_ID	BGHLV31
Pool ID	Pool-160229
Local_Set_Name	set31
ENCODE_KD_Exp_ID	ENCSR532ZPP
ENCODE_CN_Exp_ID	ENCSR538QOG
Rep1	EWSR1_BGHLV31-35
Rep2	EWSR1_BGHLV31-36
CN1	NT-BGHLV31-1
CN2	NT-BGHLV31-2
Rep1_qPCR	46.3
Rep2_qPCR	43.5
Rep1_WB	95.0
Rep2_WB	96.6
Antibody Cat#	A300-417A
Antibody Lot#	A300-417A
Antibody DCC ID	ENCAB366VTK
Status	Released
Project	ENCODE3
ID	696

Experiment Information (Status: Released)

	BGHLV31-35	BGHLV31-36
idx	783	784
TRCN#_or_BGC#	TRCN0000000034	TRCN0000000034
shRNA_or_gRNA_sequence	TGCATTGACTACCAGATTTAT	TGCATTGACTACCAGATTTAT
PAM
Name	EWSR1	EWSR1
Sample_ID	BGHLV31-35	BGHLV31-36
transduction_Date	9/24/2015	9/24/2015
days
RBP_name	EWSR1	EWSR1
qPCR_result	46.3	43.5
Ave_qPCR	44.9
RT-qPCR_primer-F	TCCTATGAAGACCCACCCAC
RT-qPCR_primer-R	TCCGAGCAAGGGAGACTTTA
protein_conc	3205	3909
WB_result	95.0	96.6
Ave_WB	95.8
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	3/8/2016
Rep1_TPM	33.3	0
Rep2_TPM	33.6	0
Action
Library_start_date	2/4/2016	2/4/2016
repeat_library
Note
ID	2872	2873

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

	BGHLV31-35	BGHLV31-36
Sample_ID	BGHLV31-35	BGHLV31-36
Sample Name	EWSR1_BGHLV31-35	EWSR1_BGHLV31-36
Sample Name	EWSR1_BGHLV31-35	EWSR1_BGHLV31-36
RBP	EWSR1	EWSR1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-07	2016-03-07
Project	ENCODE3	ENCODE3
Note
ID	1119	1120

Library-Prep
Sequencing

Library-Prep Information

	BGHLV31-35	BGHLV31-36
Sample #
Sample Name	EWSR1-BGHLV31-35	EWSR1-BGHLV31-36
Sample_Name_Alias	EWSR1_BGHLV31-35	EWSR1_BGHLV31-36
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-02-04	2016-02-04
Lib_ID	Lib-160204	Lib-160204
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV31-21B/set1/E6.png	DNA_Library_LV31-21B/set1/F6.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/E9.png	RNA_Library_LV29-30-31-32/set1/F9.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV31-35	BGHLV31-36
RBP	EWSR1	EWSR1
Batch_ID	BGHLV31	BGHLV31
WB_result	95.000	96.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2816	2817

Sequencing Information

	BGHLV31-35	BGHLV31-36
Sample_ID	BGHLV31-35	BGHLV31-36
Sample Name	EWSR1_BGHLV31-35	EWSR1_BGHLV31-36
Pool ID	Pool-160229	Pool-160229
LocalServer_folder	set31	set31
total_reads	59,760,342	55,365,512
total_aligned_reads	54,066,792	49,976,740
unique_aligned_reads	50,958,662	47,085,196
percent_uniqueAligned	0.85272	0.85044
correlation_replicates	0.997395	0.997395
spikein_reads	263,214	280,538
percent_spikeins	0.00440	0.00507
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1465	1466

Data Submission Information

	BGHLV31-35	BGHLV31-35
ENCODE_alias	brenton-graveley:EWSR1_BGHLV31	brenton-graveley:EWSR1-BGHLV31-HepG2
ENCODE_accession	ENCSR532ZPP	ENCSR604BHV
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV31-35	BGHLV31-35
Sample Name	EWSR1_BGHLV31-35	EWSR1_BGHLV31-35
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-07	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3092	6700

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_BGHLV31-35_CGTACG_L006_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1465	HiSeq2500	100	paired-ended	1				NT-BGHLV31-1_GATCAG_L005_001.R1.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20980
EWSR1_BGHLV31-35_CGTACG_L006_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1465	HiSeq2500	100	paired-ended	2				NT-BGHLV31-1_GATCAG_L005_001.R2.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	21006
EWSR1_BGHLV31-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1465					GRCh38	V40	EWSR1_BGHLV31-35_CGTACG_L006_001.R1.fastq.gz,EWSR1_BGHLV31-35_CGTACG_L006_001.R2.fastq.gz		ENCORE2	21040
EWSR1_BGHLV31-35_Signal.Unique.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1465					GRCh38	V40	EWSR1_BGHLV31-35/Aligned.sortedByCoord.out.bam		ENCORE2	21066
EWSR1_BGHLV31-35_Signal.Unique.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1465					GRCh38	V40	EWSR1_BGHLV31-35/Aligned.sortedByCoord.out.bam		ENCORE2	21092
EWSR1_BGHLV31-35_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1465					GRCh38	V40	EWSR1_BGHLV31-35/Aligned.sortedByCoord.out.bam		ENCORE2	21118
EWSR1_BGHLV31-35_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1465					GRCh38	V40	EWSR1_BGHLV31-35/Aligned.sortedByCoord.out.bam		ENCORE2	21144
EWSR1_BGHLV31-35_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1465					GRCh38	V40	EWSR1_BGHLV31-35_CGTACG_L006_001.R1.fastq.gz,EWSR1_BGHLV31-35_CGTACG_L006_001.R2.fastq.gz		ENCORE2	21170
EWSR1_BGHLV31-36_GAGTGG_L006_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1466	HiSeq2500	100	paired-ended	1				NT-BGHLV31-1_GATCAG_L005_001.R1.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20981
EWSR1_BGHLV31-36_GAGTGG_L006_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1466	HiSeq2500	100	paired-ended	2				NT-BGHLV31-1_GATCAG_L005_001.R2.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	21007
EWSR1_BGHLV31-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1466					GRCh38	V40	EWSR1_BGHLV31-36_GAGTGG_L006_001.R1.fastq.gz,EWSR1_BGHLV31-36_GAGTGG_L006_001.R2.fastq.gz		ENCORE2	21041
EWSR1_BGHLV31-36_Signal.Unique.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1466					GRCh38	V40	EWSR1_BGHLV31-36/Aligned.sortedByCoord.out.bam		ENCORE2	21067
EWSR1_BGHLV31-36_Signal.Unique.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1466					GRCh38	V40	EWSR1_BGHLV31-36/Aligned.sortedByCoord.out.bam		ENCORE2	21093
EWSR1_BGHLV31-36_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1466					GRCh38	V40	EWSR1_BGHLV31-36/Aligned.sortedByCoord.out.bam		ENCORE2	21119
EWSR1_BGHLV31-36_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1466					GRCh38	V40	EWSR1_BGHLV31-36/Aligned.sortedByCoord.out.bam		ENCORE2	21145
EWSR1_BGHLV31-36_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1466					GRCh38	V40	EWSR1_BGHLV31-36_GAGTGG_L006_001.R1.fastq.gz,EWSR1_BGHLV31-36_GAGTGG_L006_001.R2.fastq.gz		ENCORE2	21171