BOP1 RNA-Seq in K562

General Information


RBP	BOP1
Cell_Line	K562
Method	shRNA
Exp_Name	BOP1-BGKLV36-K562
ENCODE_series_ID	ENCSR894YKS
Batch_ID	BGKLV36
Pool ID	Pool-160912
Local_Set_Name	set36
ENCODE_KD_Exp_ID	ENCSR775TMW
ENCODE_CN_Exp_ID	ENCSR424QCW
Rep1	BOP1_BGKLV36-7
Rep2	BOP1_BGKLV36-8
CN1	NT_BGKLV36-1
CN2	NT_BGKLV36-2
Rep1_qPCR	81.7
Rep2_qPCR	85.3
Rep1_WB
Rep2_WB
Antibody Cat#	A302-184A
Antibody Lot#	A302-184A
Antibody DCC ID	wrong AB
Status	Released
Project	ENCODE3
ID	742

Experiment Information (Status: Released)

	BGKLV36-7	BGKLV36-8
idx	730	731
TRCN#_or_BGC#	TRCN0000078069	TRCN0000078069
shRNA_or_gRNA_sequence	CTTGGAGTGGTACGATGACTT	CTTGGAGTGGTACGATGACTT
PAM
Name	BOP1	BOP1
Sample_ID	BGKLV36-7	BGKLV36-8
transduction_Date	5/19/2016	5/19/2016
days
RBP_name	BOP1	BOP1
qPCR_result	81.7	85.3
Ave_qPCR	83.5
RT-qPCR_primer-F	ctgagactgacggatgagca
RT-qPCR_primer-R	ggctcataggggttgaagc
protein_conc	4332	4345
WB_result
Ave_WB		MW is too high?
WB_DONE_date	6/30/16	wes
MW	84kDa
IP	1	1
antibody_Cat#	A302-184A	A302-184A
Antibody DCC ID	wrong AB
submitted_to_DCC_date
Rep1_TPM	56	0
Rep2_TPM	32.8	0
Action
Library_start_date	07/28/16	07/28/16
repeat_library
Note
ID	819	820

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV36-7	BGKLV36-8
Sample_ID	BGKLV36-7	BGKLV36-8
Sample Name	BOP1_BGKLV36-7	BOP1_BGKLV36-8
Sample Name	BOP1_BGKLV36-7	BOP1_BGKLV36-8
RBP	BOP1	BOP1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1275	1276

Library-Prep
Sequencing

Library-Prep Information

	BGKLV36-7	BGKLV36-8
Sample #
Sample Name	BOP1-BGKLV36-7	BOP1-BGKLV36-8
Sample_Name_Alias	BOP1_BGKLV36-7	BOP1_BGKLV36-8
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-07-28	2016-07-28
Lib_ID	Lib-160728	Lib-160728
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV36/set1/C1.png	DNA_Library_LV36/set1/D1.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/E4.png	RNA_Library_LV35_LV36/set1/F4.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV36-7	BGKLV36-8
RBP	BOP1	BOP1
Batch_ID	BGKLV36	BGKLV36
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2960	2961

Sequencing Information

	BGKLV36-7	BGKLV36-8
Sample_ID	BGKLV36-7	BGKLV36-8
Sample Name	BOP1_BGKLV36-7	BOP1_BGKLV36-8
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set36	set36
total_reads	75,649,986	75,916,460
total_aligned_reads	62,116,048	60,456,522
unique_aligned_reads	56,813,800	55,239,212
percent_uniqueAligned	0.75101	0.72763
correlation_replicates	0.998995	0.998995
spikein_reads	119,864	94,280
percent_spikeins	0.00158	0.00124
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1609	1610

Data Submission Information

	BGKLV36-7	BGKLV36-7
ENCODE_alias	brenton-graveley:BOP1_BGKLV36	brenton-graveley:BOP1-BGKLV36-K562
ENCODE_accession	ENCSR775TMW	ENCSR894YKS
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV36-7	BGKLV36-7
Sample Name	BOP1_BGKLV36-7	BOP1_BGKLV36-7
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3177	6605

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
BOP1_BGKLV36-7_GGCTAC_L008_001.R1.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1609	HiSeq2500	100	paired-ended	1				NT_BGKLV36-1_GATCAG_L008_001.R1.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R1.fastq.gz	ENCODE3	21890
BOP1_BGKLV36-7_GGCTAC_L008_001.R2.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1609	HiSeq2500	100	paired-ended	2				NT_BGKLV36-1_GATCAG_L008_001.R2.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R2.fastq.gz	ENCODE3	21908
BOP1_BGKLV36-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1609					GRCh38	V40	BOP1_BGKLV36-7_GGCTAC_L008_001.R1.fastq.gz,BOP1_BGKLV36-7_GGCTAC_L008_001.R2.fastq.gz		ENCORE2	21926
BOP1_BGKLV36-7_Signal.Unique.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1609					GRCh38	V40	BOP1_BGKLV36-7/Aligned.sortedByCoord.out.bam		ENCORE2	21944
BOP1_BGKLV36-7_Signal.Unique.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1609					GRCh38	V40	BOP1_BGKLV36-7/Aligned.sortedByCoord.out.bam		ENCORE2	21962
BOP1_BGKLV36-7_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1609					GRCh38	V40	BOP1_BGKLV36-7/Aligned.sortedByCoord.out.bam		ENCORE2	21980
BOP1_BGKLV36-7_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1609					GRCh38	V40	BOP1_BGKLV36-7/Aligned.sortedByCoord.out.bam		ENCORE2	21998
BOP1_BGKLV36-7_quant.sf	ENCODE_DATA/set36/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1609					GRCh38	V40	BOP1_BGKLV36-7_GGCTAC_L008_001.R1.fastq.gz,BOP1_BGKLV36-7_GGCTAC_L008_001.R2.fastq.gz		ENCORE2	22016
BOP1_BGKLV36-8_CTTGTA_L008_001.R1.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1610	HiSeq2500	100	paired-ended	1				NT_BGKLV36-1_GATCAG_L008_001.R1.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R1.fastq.gz	ENCODE3	21891
BOP1_BGKLV36-8_CTTGTA_L008_001.R2.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1610	HiSeq2500	100	paired-ended	2				NT_BGKLV36-1_GATCAG_L008_001.R2.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R2.fastq.gz	ENCODE3	21909
BOP1_BGKLV36-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1610					GRCh38	V40	BOP1_BGKLV36-8_CTTGTA_L008_001.R1.fastq.gz,BOP1_BGKLV36-8_CTTGTA_L008_001.R2.fastq.gz		ENCORE2	21927
BOP1_BGKLV36-8_Signal.Unique.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1610					GRCh38	V40	BOP1_BGKLV36-8/Aligned.sortedByCoord.out.bam		ENCORE2	21945
BOP1_BGKLV36-8_Signal.Unique.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1610					GRCh38	V40	BOP1_BGKLV36-8/Aligned.sortedByCoord.out.bam		ENCORE2	21963
BOP1_BGKLV36-8_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1610					GRCh38	V40	BOP1_BGKLV36-8/Aligned.sortedByCoord.out.bam		ENCORE2	21981
BOP1_BGKLV36-8_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1610					GRCh38	V40	BOP1_BGKLV36-8/Aligned.sortedByCoord.out.bam		ENCORE2	21999
BOP1_BGKLV36-8_quant.sf	ENCODE_DATA/set36/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1610					GRCh38	V40	BOP1_BGKLV36-8_CTTGTA_L008_001.R1.fastq.gz,BOP1_BGKLV36-8_CTTGTA_L008_001.R2.fastq.gz		ENCORE2	22017