QKI RNA-Seq in HepG2

General Information


RBP	QKI
Cell_Line	HepG2
Method	shRNA
Exp_Name	QKI-BGHLV12-HepG2
ENCODE_series_ID	ENCSR010BGO
Batch_ID	BGHLV12
Pool ID	Pool-140701A
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR330YOU
ENCODE_CN_Exp_ID	ENCSR603TCV
Rep1	QKI-BGHLV12-61
Rep2	QKI-BGHLV12-62
CN1	NT-BGHLV12-93
CN2	NT-BGHLV12-94
Rep1_qPCR	68.8
Rep2_qPCR	77.0
Rep1_WB	59.7
Rep2_WB	52.7
Antibody Cat#	A300-183A
Antibody Lot#	A300-183A
Antibody DCC ID	ENCAB494QSS
Status	Released
Project	ENCODE3
ID	349

Experiment Information (Status: Released)

	BGHLV12-61	BGHLV12-62
idx	61	62
TRCN#_or_BGC#	TRCN0000015184	TRCN0000015184
shRNA_or_gRNA_sequence	CCCTACCATAATGCCTTTGAT	CCCTACCATAATGCCTTTGAT
PAM
Name	QKI	QKI
Sample_ID	BGHLV12-61	BGHLV12-62
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	QKI	QKI
qPCR_result	68.8	77.0
Ave_qPCR	72.9
RT-qPCR_primer-F	ACGATATGCGTGTCCATCCT
RT-qPCR_primer-R	GGGTGAAGAGTTCAGAGGTCA
protein_conc	3413	1708
WB_result	59.7	52.7
Ave_WB	56.2
WB_DONE_date	7/27/2015
MW	39kDa
IP	1	1
antibody_Cat#	A300-183A	A300-183A
Antibody DCC ID	ENCAB494QSS	ENCAB494QSS
submitted_to_DCC_date	8/6/2015
Rep1_TPM	16.7	0
Rep2_TPM	18	0
Action
Library_start_date	6/12/2014	6/12/2014
repeat_library
Note
ID	2114	2115

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
QKI	Product_ID: A300-183A Lot_ID: 2 Source: Bethyl Labs Target Name: QKI-human

Experiment Status

	BGHLV12-61	BGHLV12-62
Sample_ID	BGHLV12-61	BGHLV12-62
Sample Name	QKI-BGHLV12-61	QKI-BGHLV12-62
Sample Name	QKI-BGHLV12-61	QKI-BGHLV12-62
RBP	QKI	QKI
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	418	419

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-61	BGHLV12-62
Sample #
Sample Name	QKI-BGHLV12-61	QKI-BGHLV12-62
Sample_Name_Alias	QKI-BGHLV12-61	QKI-BGHLV12-62
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-06-12	2014-06-12
Lib_ID	Lib-140612	Lib-140612
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV12/set3/G2.png	DNA_Library_LV12/set3/H2.png
RIN	9.2	9.5
libSample_RNA_Well	RNA_Library_LV12/set1/G6.png	RNA_Library_LV12/set1/H6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-61	BGHLV12-62
RBP	QKI	QKI
Batch_ID	BGHLV12	BGHLV12
WB_result	59.700	52.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2042	2043

Sequencing Information

	BGHLV12-61	BGHLV12-62
Sample_ID	BGHLV12-61	BGHLV12-62
Sample Name	QKI-BGHLV12-61	QKI-BGHLV12-62
Pool ID	Pool-140701A	Pool-140701A
LocalServer_folder	set12	set12
total_reads	75,760,000	74,400,000
total_aligned_reads	69,577,738	68,364,692
unique_aligned_reads	65,924,642	64,728,172
percent_uniqueAligned	0.87018	0.87000
correlation_replicates	0.991411	0.991411
spikein_reads	391,164	498,506
percent_spikeins	0.00516	0.00670
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	740	741

Data Submission Information

	BGHLV12-61	BGHLV12-61
ENCODE_alias	brenton-graveley:QKI-BGHLV12	brenton-graveley:QKI-BGHLV12-HepG2
ENCODE_accession	ENCSR330YOU	ENCSR010BGO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-61	BGHLV12-61
Sample Name	QKI-BGHLV12-61	QKI-BGHLV12-61
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2758	6885

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
QKI-BGHLV12-61_ACTGAT_L007_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	740	HiSeq2000	100	paired-ended	1				NT-BGHLV12-93_GTGGCC_L007_R1_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R1_001.fastq.gz	ENCODE3	12801
QKI-BGHLV12-61_ACTGAT_L007_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	740	HiSeq2000	100	paired-ended	2				NT-BGHLV12-93_GTGGCC_L007_R2_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R2_001.fastq.gz	ENCODE3	12870
QKI-BGHLV12-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	740					GRCh38	V40	QKI-BGHLV12-61_ACTGAT_L007_R1_001.fastq.gz,QKI-BGHLV12-61_ACTGAT_L007_R2_001.fastq.gz		ENCORE2	12940
QKI-BGHLV12-61_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	740					GRCh38	V40	QKI-BGHLV12-61/Aligned.sortedByCoord.out.bam		ENCORE2	13010
QKI-BGHLV12-61_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	740					GRCh38	V40	QKI-BGHLV12-61/Aligned.sortedByCoord.out.bam		ENCORE2	13080
QKI-BGHLV12-61_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	740					GRCh38	V40	QKI-BGHLV12-61/Aligned.sortedByCoord.out.bam		ENCORE2	13150
QKI-BGHLV12-61_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	740					GRCh38	V40	QKI-BGHLV12-61/Aligned.sortedByCoord.out.bam		ENCORE2	13220
QKI-BGHLV12-61_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	740					GRCh38	V40	QKI-BGHLV12-61_ACTGAT_L007_R1_001.fastq.gz,QKI-BGHLV12-61_ACTGAT_L007_R2_001.fastq.gz		ENCORE2	13290
QKI-BGHLV12-62_ATTCCT_L007_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	741	HiSeq2000	100	paired-ended	1				NT-BGHLV12-93_GTGGCC_L007_R1_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R1_001.fastq.gz	ENCODE3	12802
QKI-BGHLV12-62_ATTCCT_L007_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	741	HiSeq2000	100	paired-ended	2				NT-BGHLV12-93_GTGGCC_L007_R2_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R2_001.fastq.gz	ENCODE3	12871
QKI-BGHLV12-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	741					GRCh38	V40	QKI-BGHLV12-62_ATTCCT_L007_R1_001.fastq.gz,QKI-BGHLV12-62_ATTCCT_L007_R2_001.fastq.gz		ENCORE2	12941
QKI-BGHLV12-62_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	741					GRCh38	V40	QKI-BGHLV12-62/Aligned.sortedByCoord.out.bam		ENCORE2	13011
QKI-BGHLV12-62_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	741					GRCh38	V40	QKI-BGHLV12-62/Aligned.sortedByCoord.out.bam		ENCORE2	13081
QKI-BGHLV12-62_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	741					GRCh38	V40	QKI-BGHLV12-62/Aligned.sortedByCoord.out.bam		ENCORE2	13151
QKI-BGHLV12-62_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	741					GRCh38	V40	QKI-BGHLV12-62/Aligned.sortedByCoord.out.bam		ENCORE2	13221
QKI-BGHLV12-62_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	741					GRCh38	V40	QKI-BGHLV12-62_ATTCCT_L007_R1_001.fastq.gz,QKI-BGHLV12-62_ATTCCT_L007_R2_001.fastq.gz		ENCORE2	13291