TRIP6 RNA-Seq in K562

General Information


RBP	TRIP6
Cell_Line	K562
Method	shRNA
Exp_Name	TRIP6-BGKLV29-K562
ENCODE_series_ID	ENCSR468XCA
Batch_ID	BGKLV29
Pool ID	Pool-151215C
Local_Set_Name	set29
ENCODE_KD_Exp_ID	ENCSR152IWT
ENCODE_CN_Exp_ID	ENCSR032YMP
Rep1	TRIP6_BGKLV29-63
Rep2	TRIP6_BGKLV29-64
CN1	NT_BGKLV29-1
CN2	NT_BGKLV29-2
Rep1_qPCR	59.9
Rep2_qPCR	71.8
Rep1_WB	71.3
Rep2_WB	73.0
Antibody Cat#	A300-865A
Antibody Lot#	A300-865A
Antibody DCC ID	ENCAB323MCR
Status	Released
Project	ENCODE3
ID	668

Experiment Information (Status: Released)

	BGKLV29-63	BGKLV29-64
idx	598	599
TRCN#_or_BGC#	TRCN0000061440	TRCN0000061440
shRNA_or_gRNA_sequence	GTGAGAATTGTTGCTCTGGAT	GTGAGAATTGTTGCTCTGGAT
PAM
Name	TRIP6_40	TRIP6_40
Sample_ID	BGKLV29-63	BGKLV29-64
transduction_Date	8/11/2015	8/11/2015
days
RBP_name	TRIP6	TRIP6
qPCR_result	59.9	71.8
Ave_qPCR	65.9
RT-qPCR_primer-F	agccaggtcaggaggagact	agccaggtcaggaggagact
RT-qPCR_primer-R	ccacactcctcgcacttgta	ccacactcctcgcacttgta
protein_conc	3591	3706
WB_result	71.3	73.0
Ave_WB	72.1
WB_DONE_date	9/9/2015
MW	50kDa
IP	1	1
antibody_Cat#	A300-865A	A300-865A
Antibody DCC ID	ENCAB323MCR	ENCAB323MCR
submitted_to_DCC_date	3/8/2016
Rep1_TPM	20.4865048	0
Rep2_TPM	17.4877213	0
Action
Library_start_date	11/2/2015	11/2/2015
repeat_library
Note	x	x
ID	679	680

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
TRIP6	Product_ID: A300-865A Lot_ID: 1 Source: Bethyl Labs Target Name: TRIP6-human

Experiment Status

	BGKLV29-63	BGKLV29-64
Sample_ID	BGKLV29-63	BGKLV29-64
Sample Name	TRIP6_BGKLV29-63	TRIP6_BGKLV29-64
Sample Name	TRIP6_BGKLV29-63	TRIP6_BGKLV29-64
RBP	TRIP6	TRIP6
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	1040	1041

Library-Prep
Sequencing

Library-Prep Information

	BGKLV29-63	BGKLV29-64
Sample #
Sample Name	TRIP6-BGKLV29-63	TRIP6-BGKLV29-64
Sample_Name_Alias	TRIP6_BGKLV29-63	TRIP6_BGKLV29-64
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-02	2015-11-02
Lib_ID	Lib-151102	Lib-151102
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/C8.png	DNA_Library_LV28-29-30/set1/D8.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/G3.png	RNA_Library_LV29-30-31-32/set1/H3.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV29-63	BGKLV29-64
RBP	TRIP6	TRIP6
Batch_ID	BGKLV29	BGKLV29
WB_result	71.300	73.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2724	2725

Sequencing Information

	BGKLV29-63	BGKLV29-64
Sample_ID	BGKLV29-63	BGKLV29-64
Sample Name	TRIP6_BGKLV29-63	TRIP6_BGKLV29-64
Pool ID	Pool-151215C	Pool-151215C
LocalServer_folder	set29	set29
total_reads	93,401,366	66,249,364
total_aligned_reads	81,519,898	58,785,068
unique_aligned_reads	74,555,962	53,782,858
percent_uniqueAligned	0.79823	0.81182
correlation_replicates	0.997902	0.997902
spikein_reads	368,960	268,844
percent_spikeins	0.00395	0.00406
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1358	1359

Data Submission Information

	BGKLV29-63	BGKLV29-63
ENCODE_alias	brenton-graveley:TRIP6_BGKLV29	brenton-graveley:TRIP6-BGKLV29-K562
ENCODE_accession	ENCSR152IWT	ENCSR468XCA
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV29-63	BGKLV29-63
Sample Name	TRIP6_BGKLV29-63	TRIP6_BGKLV29-63
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3069	7015

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
TRIP6_BGKLV29-63_GGCTAC_L007_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1358	HiSeq2500	100	paired-ended	1				NT_BGKLV29-1_GATCAG_L005_001.R1.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20442
TRIP6_BGKLV29-63_GGCTAC_L007_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1358	HiSeq2500	100	paired-ended	2				NT_BGKLV29-1_GATCAG_L005_001.R2.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	20472
TRIP6_BGKLV29-63_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1358					GRCh38	V40	TRIP6_BGKLV29-63_GGCTAC_L007_001.R1.fastq.gz,TRIP6_BGKLV29-63_GGCTAC_L007_001.R2.fastq.gz		ENCORE2	20502
TRIP6_BGKLV29-63_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1358					GRCh38	V40	TRIP6_BGKLV29-63/Aligned.sortedByCoord.out.bam		ENCORE2	20532
TRIP6_BGKLV29-63_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1358					GRCh38	V40	TRIP6_BGKLV29-63/Aligned.sortedByCoord.out.bam		ENCORE2	20562
TRIP6_BGKLV29-63_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1358					GRCh38	V40	TRIP6_BGKLV29-63/Aligned.sortedByCoord.out.bam		ENCORE2	20592
TRIP6_BGKLV29-63_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1358					GRCh38	V40	TRIP6_BGKLV29-63/Aligned.sortedByCoord.out.bam		ENCORE2	20622
TRIP6_BGKLV29-63_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1358					GRCh38	V40	TRIP6_BGKLV29-63_GGCTAC_L007_001.R1.fastq.gz,TRIP6_BGKLV29-63_GGCTAC_L007_001.R2.fastq.gz		ENCORE2	20652
TRIP6_BGKLV29-64_CTTGTA_L007_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1359	HiSeq2500	100	paired-ended	1				NT_BGKLV29-1_GATCAG_L005_001.R1.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20443
TRIP6_BGKLV29-64_CTTGTA_L007_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1359	HiSeq2500	100	paired-ended	2				NT_BGKLV29-1_GATCAG_L005_001.R2.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	20473
TRIP6_BGKLV29-64_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1359					GRCh38	V40	TRIP6_BGKLV29-64_CTTGTA_L007_001.R1.fastq.gz,TRIP6_BGKLV29-64_CTTGTA_L007_001.R2.fastq.gz		ENCORE2	20503
TRIP6_BGKLV29-64_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1359					GRCh38	V40	TRIP6_BGKLV29-64/Aligned.sortedByCoord.out.bam		ENCORE2	20533
TRIP6_BGKLV29-64_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1359					GRCh38	V40	TRIP6_BGKLV29-64/Aligned.sortedByCoord.out.bam		ENCORE2	20563
TRIP6_BGKLV29-64_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1359					GRCh38	V40	TRIP6_BGKLV29-64/Aligned.sortedByCoord.out.bam		ENCORE2	20593
TRIP6_BGKLV29-64_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1359					GRCh38	V40	TRIP6_BGKLV29-64/Aligned.sortedByCoord.out.bam		ENCORE2	20623
TRIP6_BGKLV29-64_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1359					GRCh38	V40	TRIP6_BGKLV29-64_CTTGTA_L007_001.R1.fastq.gz,TRIP6_BGKLV29-64_CTTGTA_L007_001.R2.fastq.gz		ENCORE2	20653