RAVER1 RNA-Seq in K562

General Information


RBP	RAVER1
Cell_Line	K562
Method	shRNA
Exp_Name	RAVER1-BGKLV08-K562
ENCODE_series_ID	ENCSR369IHW
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR904BCZ
ENCODE_CN_Exp_ID	ENCSR344XID
Rep1	RAVER1-LV08-41
Rep2	RAVER1-LV08-42
CN1	Nontarget-LV08-1_00003531
CN2	nontarget-LV08-2_00003531
Rep1_qPCR	71.5
Rep2_qPCR	76.9
Rep1_WB	79.3
Rep2_WB	75.8
Antibody Cat#	A303-939A
Antibody Lot#	A303-939A
Antibody DCC ID	ENCAB846NHA
Status	Released
Project	ENCODE3
ID	297

Experiment Information (Status: Released)

	BGKLV08-41	BGKLV08-42
idx	42	43
TRCN#_or_BGC#	TRCN0000074623	TRCN0000074623
shRNA_or_gRNA_sequence	GCCTCATTGCTCCTGTAATTT	GCCTCATTGCTCCTGTAATTT
PAM
Name	RAVER1	RAVER1
Sample_ID	BGKLV08-41	BGKLV08-42
transduction_Date	4/4/2014	4/4/2014
days
RBP_name	RAVER1	RAVER1
qPCR_result	71.5	76.9
Ave_qPCR	74.2
RT-qPCR_primer-F	GTCCGGAGAAGGGCTCCTG
RT-qPCR_primer-R	GGCAAAGCTGCGTTTCTG
protein_conc	3173	2569
WB_result	79.3	75.8
Ave_WB	77.6
WB_DONE_date
MW
IP	1	1
antibody_Cat#	A303-939A	A303-939A
Antibody DCC ID	ENCAB846NHA	ENCAB846NHA
submitted_to_DCC_date	5/4/2015
Rep1_TPM	15.9180868	0
Rep2_TPM	12.6616657	0
Action	Ready	Ready
Library_start_date	5/9/2014	5/9/2014
repeat_library
Note		3
ID	45	46

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RAVER1	Product_ID: A303-939A Lot_ID: 1 Source: Bethyl Labs Target Name: RAVER1-human

Experiment Status

	BGKLV08-41	BGKLV08-42
Sample_ID	BGKLV08-41	BGKLV08-42
Sample Name	RAVER1-LV08-41	RAVER1-LV08-42
Sample Name	RAVER1-LV08-41	RAVER1-LV08-42
RBP	RAVER1	RAVER1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	306	307

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-41	BGKLV08-42
Sample #
Sample Name	RAVER1-BGKLV08-41	RAVER1-BGKLV08-42
Sample_Name_Alias	RAVER1-LV08-41	RAVER1-LV08-42
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-08	2014-05-08
Lib_ID	Lib-140508	Lib-140508
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV08/set4/H1.png	DNA_Library_LV08/set4/A2.png
RIN	9.3	9.2
libSample_RNA_Well	RNA_Library_LV08/set3/A2.png	RNA_Library_LV08/set3/B2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-41	BGKLV08-42
RBP	RAVER1	RAVER1
Batch_ID	BGKLV08	BGKLV08
WB_result	79.300	75.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1926	1927

Sequencing Information

	BGKLV08-41	BGKLV08-42
Sample_ID	BGKLV08-41	BGKLV08-42
Sample Name	RAVER1-LV08-41	RAVER1-LV08-42
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	49,890,000	40,020,000
total_aligned_reads	44,636,840	35,808,676
unique_aligned_reads	40,783,564	32,829,862
percent_uniqueAligned	0.81747	0.82034
correlation_replicates	0.993869	0.993869
spikein_reads	422,506	355,344
percent_spikeins	0.00847	0.00888
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	626	627

Data Submission Information

	BGKLV08-41	BGKLV08-41
ENCODE_alias	brenton-graveley:RAVER1-LV08	brenton-graveley:RAVER1-BGKLV08-K562
ENCODE_accession	ENCSR904BCZ	ENCSR369IHW
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV08-41	BGKLV08-41
Sample Name	RAVER1-LV08-41	RAVER1-LV08-41
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2702	6888

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
RAVER1-LV08-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	626					GRCh38	V40	RAVER1-LV08-41_ATGTCA_L006_R1_001.fastq.gz,RAVER1-LV08-41_ATGTCA_L006_R2_001.fastq.gz		ENCORE2	12013
RAVER1-LV08-41_ATGTCA_L006_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	626	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003531_GATCAG_L005_R1_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	12069
RAVER1-LV08-41_ATGTCA_L006_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	626	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003531_GATCAG_L005_R2_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	12125
RAVER1-LV08-41_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	626					GRCh38	V40	RAVER1-LV08-41/Aligned.sortedByCoord.out.bam		ENCORE2	12181
RAVER1-LV08-41_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	626					GRCh38	V40	RAVER1-LV08-41/Aligned.sortedByCoord.out.bam		ENCORE2	12237
RAVER1-LV08-41_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	626					GRCh38	V40	RAVER1-LV08-41/Aligned.sortedByCoord.out.bam		ENCORE2	12293
RAVER1-LV08-41_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	626					GRCh38	V40	RAVER1-LV08-41/Aligned.sortedByCoord.out.bam		ENCORE2	12349
RAVER1-LV08-41_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	626					GRCh38	V40	RAVER1-LV08-41_ATGTCA_L006_R1_001.fastq.gz,RAVER1-LV08-41_ATGTCA_L006_R2_001.fastq.gz		ENCORE2	13348
RAVER1-LV08-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	627					GRCh38	V40	RAVER1-LV08-42_CCGTCC_L006_R1_001.fastq.gz,RAVER1-LV08-42_CCGTCC_L006_R2_001.fastq.gz		ENCORE2	12014
RAVER1-LV08-42_CCGTCC_L006_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	627	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003531_GATCAG_L005_R1_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	12070
RAVER1-LV08-42_CCGTCC_L006_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	627	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003531_GATCAG_L005_R2_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	12126
RAVER1-LV08-42_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	627					GRCh38	V40	RAVER1-LV08-42/Aligned.sortedByCoord.out.bam		ENCORE2	12182
RAVER1-LV08-42_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	627					GRCh38	V40	RAVER1-LV08-42/Aligned.sortedByCoord.out.bam		ENCORE2	12238
RAVER1-LV08-42_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	627					GRCh38	V40	RAVER1-LV08-42/Aligned.sortedByCoord.out.bam		ENCORE2	12294
RAVER1-LV08-42_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	627					GRCh38	V40	RAVER1-LV08-42/Aligned.sortedByCoord.out.bam		ENCORE2	12350
RAVER1-LV08-42_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	627					GRCh38	V40	RAVER1-LV08-42_CCGTCC_L006_R1_001.fastq.gz,RAVER1-LV08-42_CCGTCC_L006_R2_001.fastq.gz		ENCORE2	13349