TROVE2 RNA-Seq in HepG2

General Information


RBP	TROVE2
Cell_Line	HepG2
Method	shRNA
Exp_Name	TROVE2-BGHLV16-HepG2
ENCODE_series_ID	ENCSR659HFE
Batch_ID	BGHLV16
Pool ID	Pool-141001
Local_Set_Name	set16
ENCODE_KD_Exp_ID	ENCSR946OFN
ENCODE_CN_Exp_ID	ENCSR689PHN
Rep1	TROVE2_BGHLV16_61
Rep2	TROVE2_BGHLV16_62
CN1	NT_BGHLV16_1
CN2	NT_BGHLV16_2
Rep1_qPCR	80.0
Rep2_qPCR	80.4
Rep1_WB	57.7
Rep2_WB	50.8
Antibody Cat#	A303-692A
Antibody Lot#	A303-692A
Antibody DCC ID	ENCAB703EAU
Status	Released
Project	ENCODE3
ID	425

Experiment Information (Status: Released)

	BGHLV16-61	BGHLV16-62
idx	229	230
TRCN#_or_BGC#	TRCN0000160593	TRCN0000160593
shRNA_or_gRNA_sequence	CGTTTCTTACTAGCTGTTGAT	CGTTTCTTACTAGCTGTTGAT
PAM
Name	TROVE2	TROVE2
Sample_ID	BGHLV16-61	BGHLV16-62
transduction_Date	7/31/2014	7/31/2014
days
RBP_name	TROVE2	TROVE2
qPCR_result	80.0	80.4
Ave_qPCR	80.2
RT-qPCR_primer-F	agcattggatgctgcttttt
RT-qPCR_primer-R	agaagcactgacatcaacagc
protein_conc	3655	3467
WB_result	57.7	50.8
Ave_WB	54.3
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	14.4	0
Rep2_TPM	14	0
Action
Library_start_date	9/23/2014	9/23/2014
repeat_library
Note
ID	2296	2297

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

	BGHLV16-61	BGHLV16-62
Sample_ID	BGHLV16-61	BGHLV16-62
Sample Name	TROVE2_BGHLV16_61	TROVE2_BGHLV16_62
Sample Name	TROVE2_BGHLV16_61	TROVE2_BGHLV16_62
RBP	TROVE2	TROVE2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	576	577

Library-Prep
Sequencing

Library-Prep Information

	BGHLV16-61	BGHLV16-62
Sample #
Sample Name	TROVE2-BGHLV16-61	TROVE2-BGHLV16-62
Sample_Name_Alias	TROVE2_BGHLV16_61	TROVE2_BGHLV16_62
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-23	2014-09-23
Lib_ID	Lib-140923	Lib-140923
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set1/A9.png	DNA_Library_LV16-17/set1/B9.png
RIN	9.6	9.3
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/G2.png	RNA_Library_LV16-17-18/set1/H2.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV16-61	BGHLV16-62
RBP	TROVE2	TROVE2
Batch_ID	BGHLV16	BGHLV16
WB_result	57.700	50.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2260	2261

Sequencing Information

	BGHLV16-61	BGHLV16-62
Sample_ID	BGHLV16-61	BGHLV16-62
Sample Name	TROVE2_BGHLV16_61	TROVE2_BGHLV16_62
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set16	set16
total_reads	29,550,000	32,430,000
total_aligned_reads	26,854,440	28,866,578
unique_aligned_reads	25,368,796	27,270,656
percent_uniqueAligned	0.85850	0.84091
correlation_replicates	0.994262	0.994262
spikein_reads	73,652	184,278
percent_spikeins	0.00249	0.00568
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	902	903

Data Submission Information

	BGHLV16-61	BGHLV16-61
ENCODE_alias	brenton-graveley:TROVE2_BGHLV16	brenton-graveley:TROVE2-BGHLV16-HepG2
ENCODE_accession	ENCSR946OFN	ENCSR659HFE
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV16-61	BGHLV16-61
Sample Name	TROVE2_BGHLV16_61	TROVE2_BGHLV16_61
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2856	7017

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_BGHLV16_61_ATCACG_L008_R1_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	902	HiSeq2000	100	paired-ended	1				NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE3	14302
TROVE2_BGHLV16_61_ATCACG_L008_R2_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	902	HiSeq2000	100	paired-ended	2				NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE3	14328
TROVE2_BGHLV16_61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	902					GRCh38	V40	TROVE2_BGHLV16_61_ATCACG_L008_R1_001.fastq.gz,TROVE2_BGHLV16_61_ATCACG_L008_R2_001.fastq.gz		ENCORE2	14354
TROVE2_BGHLV16_61_Signal.Unique.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	902					GRCh38	V40	TROVE2_BGHLV16_61/Aligned.sortedByCoord.out.bam		ENCORE2	14380
TROVE2_BGHLV16_61_Signal.Unique.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	902					GRCh38	V40	TROVE2_BGHLV16_61/Aligned.sortedByCoord.out.bam		ENCORE2	14406
TROVE2_BGHLV16_61_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	902					GRCh38	V40	TROVE2_BGHLV16_61/Aligned.sortedByCoord.out.bam		ENCORE2	14432
TROVE2_BGHLV16_61_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	902					GRCh38	V40	TROVE2_BGHLV16_61/Aligned.sortedByCoord.out.bam		ENCORE2	14458
TROVE2_BGHLV16_61_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	902					GRCh38	V40	TROVE2_BGHLV16_61_ATCACG_L008_R1_001.fastq.gz,TROVE2_BGHLV16_61_ATCACG_L008_R2_001.fastq.gz		ENCORE2	14484
TROVE2_BGHLV16_62_CGATGT_L008_R1_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	903	HiSeq2000	100	paired-ended	1				NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE3	14303
TROVE2_BGHLV16_62_CGATGT_L008_R2_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	903	HiSeq2000	100	paired-ended	2				NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE3	14329
TROVE2_BGHLV16_62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	903					GRCh38	V40	TROVE2_BGHLV16_62_CGATGT_L008_R1_001.fastq.gz,TROVE2_BGHLV16_62_CGATGT_L008_R2_001.fastq.gz		ENCORE2	14355
TROVE2_BGHLV16_62_Signal.Unique.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	903					GRCh38	V40	TROVE2_BGHLV16_62/Aligned.sortedByCoord.out.bam		ENCORE2	14381
TROVE2_BGHLV16_62_Signal.Unique.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	903					GRCh38	V40	TROVE2_BGHLV16_62/Aligned.sortedByCoord.out.bam		ENCORE2	14407
TROVE2_BGHLV16_62_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	903					GRCh38	V40	TROVE2_BGHLV16_62/Aligned.sortedByCoord.out.bam		ENCORE2	14433
TROVE2_BGHLV16_62_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	903					GRCh38	V40	TROVE2_BGHLV16_62/Aligned.sortedByCoord.out.bam		ENCORE2	14459
TROVE2_BGHLV16_62_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	903					GRCh38	V40	TROVE2_BGHLV16_62_CGATGT_L008_R1_001.fastq.gz,TROVE2_BGHLV16_62_CGATGT_L008_R2_001.fastq.gz		ENCORE2	14485