BCCIP RNA-Seq in K562

General Information


RBP	BCCIP
Cell_Line	K562
Method	shRNA
Exp_Name	BCCIP-BGKLV19-K562
ENCODE_series_ID	ENCSR566QET
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR606QIX
ENCODE_CN_Exp_ID	ENCSR245BNJ
Rep1	BCCIP_BGKLV19_5A
Rep2	BCCIP_BGKLV19_6A
CN1	NT_BGKLV19_1A
CN2	NT_BGKLV19_2A
Rep1_qPCR	94.3
Rep2_qPCR	94.3
Rep1_WB	99.6
Rep2_WB	97.2
Antibody Cat#	A302-196A
Antibody Lot#	A302-196A
Antibody DCC ID	ENCAB586MIB
Status	Released
Project	ENCODE3
ID	462

Experiment Information (Status: Released)

	BGKLV19-5	BGKLV19-6
idx	212	213
TRCN#_or_BGC#	TRCN0000072762	TRCN0000072762
shRNA_or_gRNA_sequence	GCCTTCTCCTAAGTGAAAGAT	GCCTTCTCCTAAGTGAAAGAT
PAM
Name	BCCIP	BCCIP
Sample_ID	BGKLV19-5	BGKLV19-6
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	BCCIP	BCCIP
qPCR_result	94.3	94.3
Ave_qPCR	94.3
RT-qPCR_primer-F	ttaatgtccctccacagatcg
RT-qPCR_primer-R	gcacttcccacatggcttat
protein_conc	2355	2765
WB_result	99.6	97.2
Ave_WB	98.4
WB_DONE_date	1/12/2015
MW
IP	1	1
antibody_Cat#	A302-196A	A302-196A
Antibody DCC ID	ENCAB586MIB	ENCAB586MIB
submitted_to_DCC_date	4/2/2015
Rep1_TPM	97.6351913	0
Rep2_TPM	50.1952552	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	231	232

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
BCCIP	Product_ID: A302-196A Lot_ID: 1 Source: Bethyl Labs Target Name: BCCIP-human

Experiment Status

	BGKLV19-5	BGKLV19-6
Sample_ID	BGKLV19-5	BGKLV19-6
Sample Name	BCCIP_BGKLV19_5A	BCCIP_BGKLV19_6A
Sample Name	BCCIP_BGKLV19_5A	BCCIP_BGKLV19_6A
RBP	BCCIP	BCCIP
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	654	655

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-5	BGKLV19-6
Sample #
Sample Name	BCCIP-BGKLV19-5	BCCIP-BGKLV19-6
Sample_Name_Alias	BCCIP_BGKLV19_5A	BCCIP_BGKLV19_6A
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-02	2014-10-02
Lib_ID	Lib-141002	Lib-141002
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/A6.png	DNA_Library_LV18-19/set1/B6.png
RIN	9.9	9.5
libSample_RNA_Well	RNA_Library_LV18-19/set1/G12.png	RNA_Library_LV18-19/set1/H12.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-5	BGKLV19-6
RBP	BCCIP	BCCIP
Batch_ID	BGKLV19	BGKLV19
WB_result	99.600	97.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2338	2339

Sequencing Information

	BGKLV19-5	BGKLV19-6
Sample_ID	BGKLV19-5	BGKLV19-6
Sample Name	BCCIP_BGKLV19_5A	BCCIP_BGKLV19_6A
Pool ID	Pool-141010	Pool-141010
LocalServer_folder	set19	set19
total_reads	57,060,000	49,250,000
total_aligned_reads	53,296,360	46,100,600
unique_aligned_reads	48,989,500	42,302,024
percent_uniqueAligned	0.85856	0.85892
correlation_replicates	0.997568	0.997568
spikein_reads	174,118	125,932
percent_spikeins	0.00305	0.00256
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	980	981

Data Submission Information

	BGKLV19-5	BGKLV19-5
ENCODE_alias	brenton-graveley:BCCIP_BGKLV19	brenton-graveley:BCCIP-BGKLV19-K562
ENCODE_accession	ENCSR606QIX	ENCSR566QET
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-5	BGKLV19-5
Sample Name	BCCIP_BGKLV19_5A	BCCIP_BGKLV19_5A
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-05	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2876	6601

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
BCCIP_BGKLV19_5A_GTCCGC_L001_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	980	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1A_ATGTCA_L001_R1_001.fastq.gz,NT_BGKLV19_2A_CCGTCC_L001_R1_001.fastq.gz	ENCODE3	15514
BCCIP_BGKLV19_5A_GTCCGC_L001_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	980	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1A_ATGTCA_L001_R2_001.fastq.gz,NT_BGKLV19_2A_CCGTCC_L001_R2_001.fastq.gz	ENCODE3	15524
BCCIP_BGKLV19_5A_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	980					GRCh38	V40	BCCIP_BGKLV19_5A_GTCCGC_L001_R1_001.fastq.gz,BCCIP_BGKLV19_5A_GTCCGC_L001_R2_001.fastq.gz		ENCORE2	15534
BCCIP_BGKLV19_5A_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	980					GRCh38	V40	BCCIP_BGKLV19_5A/Aligned.sortedByCoord.out.bam		ENCORE2	15544
BCCIP_BGKLV19_5A_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	980					GRCh38	V40	BCCIP_BGKLV19_5A/Aligned.sortedByCoord.out.bam		ENCORE2	15554
BCCIP_BGKLV19_5A_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	980					GRCh38	V40	BCCIP_BGKLV19_5A/Aligned.sortedByCoord.out.bam		ENCORE2	15564
BCCIP_BGKLV19_5A_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	980					GRCh38	V40	BCCIP_BGKLV19_5A/Aligned.sortedByCoord.out.bam		ENCORE2	15574
BCCIP_BGKLV19_5A_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	980					GRCh38	V40	BCCIP_BGKLV19_5A_GTCCGC_L001_R1_001.fastq.gz,BCCIP_BGKLV19_5A_GTCCGC_L001_R2_001.fastq.gz		ENCORE2	16352
BCCIP_BGKLV19_6A_GTGAAA_L001_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	981	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1A_ATGTCA_L001_R1_001.fastq.gz,NT_BGKLV19_2A_CCGTCC_L001_R1_001.fastq.gz	ENCODE3	15515
BCCIP_BGKLV19_6A_GTGAAA_L001_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	981	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1A_ATGTCA_L001_R2_001.fastq.gz,NT_BGKLV19_2A_CCGTCC_L001_R2_001.fastq.gz	ENCODE3	15525
BCCIP_BGKLV19_6A_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	981					GRCh38	V40	BCCIP_BGKLV19_6A_GTGAAA_L001_R1_001.fastq.gz,BCCIP_BGKLV19_6A_GTGAAA_L001_R2_001.fastq.gz		ENCORE2	15535
BCCIP_BGKLV19_6A_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	981					GRCh38	V40	BCCIP_BGKLV19_6A/Aligned.sortedByCoord.out.bam		ENCORE2	15545
BCCIP_BGKLV19_6A_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	981					GRCh38	V40	BCCIP_BGKLV19_6A/Aligned.sortedByCoord.out.bam		ENCORE2	15555
BCCIP_BGKLV19_6A_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	981					GRCh38	V40	BCCIP_BGKLV19_6A/Aligned.sortedByCoord.out.bam		ENCORE2	15565
BCCIP_BGKLV19_6A_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	981					GRCh38	V40	BCCIP_BGKLV19_6A/Aligned.sortedByCoord.out.bam		ENCORE2	15575
BCCIP_BGKLV19_6A_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	981					GRCh38	V40	BCCIP_BGKLV19_6A_GTGAAA_L001_R1_001.fastq.gz,BCCIP_BGKLV19_6A_GTGAAA_L001_R2_001.fastq.gz		ENCORE2	16353