TROVE2 RNA-Seq in K562

General Information


RBP	TROVE2
Cell_Line	K562
Method	shRNA
Exp_Name	TROVE2-BGKLV19-K562
ENCODE_series_ID	ENCSR383KLQ
Batch_ID	BGKLV19
Pool ID	Pool-151201
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR060KRD
ENCODE_CN_Exp_ID	ENCSR092WKG
Rep1	TROVE2_BGKLV19-57B_rpt
Rep2	TROVE2_BGKLV19-58B_rpt
CN1	NT_BGKLV19-1B_repeat
CN2	NT_BGKLV19-2B_repeat
Rep1_qPCR	94.1
Rep2_qPCR	90.3
Rep1_WB	82.7
Rep2_WB	87.4
Antibody Cat#	A303-692A
Antibody Lot#	A303-692A
Antibody DCC ID	ENCAB703EAU
Status	Released
Project	ENCODE3
ID	592

Experiment Information (Status: NotSatisfied)

	BGKLV19-57	BGKLV19-58
idx	264	265
TRCN#_or_BGC#	TRCN0000160593	TRCN0000160593
shRNA_or_gRNA_sequence	CGTTTCTTACTAGCTGTTGAT	CGTTTCTTACTAGCTGTTGAT
PAM
Name	TROVE2	TROVE2
Sample_ID	BGKLV19-57	BGKLV19-58
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	TROVE2	TROVE2
qPCR_result	94.1	90.3
Ave_qPCR	92.2
RT-qPCR_primer-F	agcattggatgctgcttttt
RT-qPCR_primer-R	agaagcactgacatcaacagc
protein_conc	2759	3145
WB_result	82.7	87.4
Ave_WB	85.1
WB_DONE_date	1/5/2015
MW	61kDa
IP	1	1
antibody_Cat#	A303-692A	A303-692A
Antibody DCC ID	ENCAB703EAU	ENCAB703EAU
submitted_to_DCC_date	4/2/2015
Rep1_TPM	11.5244938	0
Rep2_TPM	8.19820335	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	291	292

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
TROVE2	Product_ID: A303-692A Lot_ID: 1 Source: Bethyl Labs Target Name: TROVE2-human

Experiment Status

	BGKLV19-57	BGKLV19-57	BGKLV19-58	BGKLV19-58
Sample_ID	BGKLV19-57	BGKLV19-57	BGKLV19-58	BGKLV19-58
Sample Name	TROVE2_BGKLV19_57B	TROVE2_BGKLV19-57B_rpt	TROVE2_BGKLV19_58B	TROVE2_BGKLV19-58B_rpt
Sample Name	TROVE2_BGKLV19_57B	TROVE2_BGKLV19-57B_rpt	TROVE2_BGKLV19_58B	TROVE2_BGKLV19-58B_rpt
RBP	TROVE2	TROVE2	TROVE2	TROVE2
Cell_Line	K562	K562	K562	K562
Exp UID
Status	NotSatisfied	Released	NotSatisfied	Released
Status_date	2014-12-11	2016-01-16	2014-12-11	2016-01-16
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE3
Note	Bad Correlation between replicates		Bad Correlation between replicates
ID	20	938	21	939

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-57	BGKLV19-57	BGKLV19-58	BGKLV19-58
Sample #
Sample Name	TROVE2-BGKLV19-57B	TROVE2-BGKLV19-57C	TROVE2-BGKLV19-58B	TROVE2-BGKLV19-58C
Sample_Name_Alias	TROVE2_BGKLV19_57B	TROVE2_BGKLV19-57B_rpt	TROVE2_BGKLV19_58B	TROVE2_BGKLV19-58B_rpt
Index Well Position	S18	S22	S19	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-03	2015-09-28	2014-10-03	2015-09-28
Lib_ID	Lib-141003	Lib-150928	Lib-141003	Lib-150928
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/A12.png	DNA_Library_LV27/set2/E1.png	DNA_Library_LV18-19/set1/B12.png	DNA_Library_LV35/set1/A5.png
RIN	9.6	9.6	9.5	9.5
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/E6.png	RNA_Library_LV19-21-24/set1/E6.png	RNA_Library_LV19-21-24/set1/F6.png	RNA_Library_LV19-21-24/set1/F6.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-57	BGKLV19-57	BGKLV19-58	BGKLV19-58
RBP	TROVE2	TROVE2	TROVE2	TROVE2
Batch_ID	BGKLV19	BGKLV19	BGKLV19	BGKLV19
WB_result	82.700	82.700	87.400	87.400
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	C	B	C
Lib_Status	SendToSequence	SendToSequence	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE3
ID	2388	2652	2389	2653

Sequencing Information

	BGKLV19-57	BGKLV19-57	BGKLV19-58	BGKLV19-58
Sample_ID	BGKLV19-57	BGKLV19-57	BGKLV19-58	BGKLV19-58
Sample Name	TROVE2_BGKLV19_57B	TROVE2_BGKLV19-57B_rpt	TROVE2_BGKLV19_58B	TROVE2_BGKLV19-58B_rpt
Pool ID	Pool-141015	Pool-151201	Pool-141015	Pool-151201
LocalServer_folder	set19	set19	set19	set19
total_reads	55,300,000	69,292,192	38,210,000	99,262,862
total_aligned_reads	44,690,550	64,670,530	35,814,102	93,192,382
unique_aligned_reads	41,465,960	58,996,556	32,781,102	84,901,454
percent_uniqueAligned	0.74984	0.85142	0.85792	0.85532
correlation_replicates	0.565195	0.999356	0.565195	0.999356
spikein_reads	506,542	663,082	125,512	942,010
percent_spikeins	0.00916	0.00957	0.00328	0.00949
original_ReadLength	100	101	100	101
QC_Status	BadCorrelation	Submitted	BadCorrelation	Submitted
ID	1030	1294	1031	1295

Data Submission Information

	BGKLV19-57	BGKLV19-57
ENCODE_alias	brenton-graveley:TROVE2_BGKLV19-B_rpt	brenton-graveley:TROVE2-BGKLV19-K562
ENCODE_accession	ENCSR060KRD	ENCSR383KLQ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-57	BGKLV19-57
Sample Name	TROVE2_BGKLV19-57B_rpt	TROVE2_BGKLV19-57B_rpt
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-01-14	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3037	7018

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
TROVE2_BGKLV19-57B_rpt_1.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1294	HiSeq2000	100	paired-ended	1				NT_BGKLV19-1B_repeat_1.fastq.gz,NT_BGKLV19-2B_repeat_1.fastq.gz	ENCODE3	15269
TROVE2_BGKLV19-57B_rpt_2.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1294	HiSeq2000	100	paired-ended	2				NT_BGKLV19-1B_repeat_1.fastq.gz,NT_BGKLV19-2B_repeat_1.fastq.gz	ENCODE3	15275
TROVE2_BGKLV19-57B_rpt_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1294					GRCh38	V40	TROVE2_BGKLV19-57B_rpt_1.fastq.gz,TROVE2_BGKLV19-57B_rpt_2.fastq.gz		ENCORE2	15277
TROVE2_BGKLV19-57B_rpt_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1294					GRCh38	V40	TROVE2_BGKLV19-57B_rpt/Aligned.sortedByCoord.out.bam		ENCORE2	15333
TROVE2_BGKLV19-57B_rpt_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1294					GRCh38	V40	TROVE2_BGKLV19-57B_rpt/Aligned.sortedByCoord.out.bam		ENCORE2	15391
TROVE2_BGKLV19-57B_rpt_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1294					GRCh38	V40	TROVE2_BGKLV19-57B_rpt/Aligned.sortedByCoord.out.bam		ENCORE2	15449
TROVE2_BGKLV19-57B_rpt_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1294					GRCh38	V40	TROVE2_BGKLV19-57B_rpt/Aligned.sortedByCoord.out.bam		ENCORE2	15507
TROVE2_BGKLV19-57B_rpt_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1294					GRCh38	V40	TROVE2_BGKLV19-57B_rpt_1.fastq.gz,TROVE2_BGKLV19-57B_rpt_2.fastq.gz		ENCORE2	16404
TROVE2_BGKLV19-58B_rpt_1.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1295	HiSeq2000	100	paired-ended	1				NT_BGKLV19-1B_repeat_1.fastq.gz,NT_BGKLV19-2B_repeat_1.fastq.gz	ENCODE3	15270
TROVE2_BGKLV19-58B_rpt_2.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1295	HiSeq2000	100	paired-ended	2				NT_BGKLV19-1B_repeat_1.fastq.gz,NT_BGKLV19-2B_repeat_1.fastq.gz	ENCODE3	15276
TROVE2_BGKLV19-58B_rpt_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1295					GRCh38	V40	TROVE2_BGKLV19-58B_rpt_1.fastq.gz,TROVE2_BGKLV19-58B_rpt_2.fastq.gz		ENCORE2	15278
TROVE2_BGKLV19-58B_rpt_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1295					GRCh38	V40	TROVE2_BGKLV19-58B_rpt/Aligned.sortedByCoord.out.bam		ENCORE2	15334
TROVE2_BGKLV19-58B_rpt_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1295					GRCh38	V40	TROVE2_BGKLV19-58B_rpt/Aligned.sortedByCoord.out.bam		ENCORE2	15392
TROVE2_BGKLV19-58B_rpt_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1295					GRCh38	V40	TROVE2_BGKLV19-58B_rpt/Aligned.sortedByCoord.out.bam		ENCORE2	15450
TROVE2_BGKLV19-58B_rpt_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1295					GRCh38	V40	TROVE2_BGKLV19-58B_rpt/Aligned.sortedByCoord.out.bam		ENCORE2	15508
TROVE2_BGKLV19-58B_rpt_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1295					GRCh38	V40	TROVE2_BGKLV19-58B_rpt_1.fastq.gz,TROVE2_BGKLV19-58B_rpt_2.fastq.gz		ENCORE2	16405