BCLAF1 RNA-Seq in K562

General Information


RBP	BCLAF1
Cell_Line	K562
Method	shRNA
Exp_Name	BCLAF1-BGKLV19-K562
ENCODE_series_ID	ENCSR175SZK
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR410ZPU
ENCODE_CN_Exp_ID	ENCSR245BNJ
Rep1	BCLAF1_BGKLV19_7A
Rep2	BCLAF1_BGKLV19_8A
CN1	NT_BGKLV19_1A
CN2	NT_BGKLV19_2A
Rep1_qPCR	61.2
Rep2_qPCR	68.2
Rep1_WB	44.8
Rep2_WB	37.5
Antibody Cat#	A300-608A
Antibody Lot#	A300-608A
Antibody DCC ID	ENCAB012FUX
Status	Released
Project	ENCODE3
ID	463

Experiment Information (Status: Released)

	BGKLV19-7	BGKLV19-8
idx	214	215
TRCN#_or_BGC#	TRCN0000336784	TRCN0000336784
shRNA_or_gRNA_sequence	GCGGTTCACTTCGTATCAGAA	GCGGTTCACTTCGTATCAGAA
PAM
Name	BCLAF1	BCLAF1
Sample_ID	BGKLV19-7	BGKLV19-8
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	BCLAF1	BCLAF1
qPCR_result	61.2	68.2
Ave_qPCR	64.7
RT-qPCR_primer-F	aatggcacctgttcctcttg
RT-qPCR_primer-R	ggatcggaattcttgctcct
protein_conc	3119	3204
WB_result	44.8	37.5
Ave_WB	41.1
WB_DONE_date	3/30/2015
MW	108kDa
IP	1	1
antibody_Cat#	A300-608A	A300-608A
Antibody DCC ID	ENCAB012FUX	ENCAB012FUX
submitted_to_DCC_date	5/4/2015
Rep1_TPM	42.5649821	0
Rep2_TPM	29.1876046	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	235	236

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
BCLAF1	Product_ID: A300-608A Lot_ID: 1 Source: Bethyl Labs Target Name: BCLAF1-human

Experiment Status

	BGKLV19-7	BGKLV19-8
Sample_ID	BGKLV19-7	BGKLV19-8
Sample Name	BCLAF1_BGKLV19_7A	BCLAF1_BGKLV19_8A
Sample Name	BCLAF1_BGKLV19_7A	BCLAF1_BGKLV19_8A
RBP	BCLAF1	BCLAF1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	656	657

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-7	BGKLV19-8
Sample #
Sample Name	BCLAF1-BGKLV19-7	BCLAF1-BGKLV19-8
Sample_Name_Alias	BCLAF1_BGKLV19_7A	BCLAF1_BGKLV19_8A
Index Well Position	S20	S21
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/C6.png	DNA_Library_LV18-19/set1/D6.png
RIN	8.9	9.8
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/A1.png	RNA_Library_LV19-21-24/set1/B1.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-7	BGKLV19-8
RBP	BCLAF1	BCLAF1
Batch_ID	BGKLV19	BGKLV19
WB_result	44.800	37.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2340	2341

Sequencing Information

	BGKLV19-7	BGKLV19-8
Sample_ID	BGKLV19-7	BGKLV19-8
Sample Name	BCLAF1_BGKLV19_7A	BCLAF1_BGKLV19_8A
Pool ID	Pool-141010	Pool-141010
LocalServer_folder	set19	set19
total_reads	46,460,000	53,960,000
total_aligned_reads	43,234,794	49,769,652
unique_aligned_reads	39,629,466	45,678,942
percent_uniqueAligned	0.85298	0.84653
correlation_replicates	0.999357	0.999357
spikein_reads	136,770	148,540
percent_spikeins	0.00294	0.00275
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	982	983

Data Submission Information

	BGKLV19-7	BGKLV19-7
ENCODE_alias	brenton-graveley:BCLAF1_BGKLV19	brenton-graveley:BCLAF1-BGKLV19-K562
ENCODE_accession	ENCSR410ZPU	ENCSR175SZK
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-7	BGKLV19-7
Sample Name	BCLAF1_BGKLV19_7A	BCLAF1_BGKLV19_7A
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-05	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2877	6603

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
BCLAF1_BGKLV19_7A_GTGGCC_L001_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	982	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1A_ATGTCA_L001_R1_001.fastq.gz,NT_BGKLV19_2A_CCGTCC_L001_R1_001.fastq.gz	ENCODE3	15516
BCLAF1_BGKLV19_7A_GTGGCC_L001_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	982	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1A_ATGTCA_L001_R2_001.fastq.gz,NT_BGKLV19_2A_CCGTCC_L001_R2_001.fastq.gz	ENCODE3	15526
BCLAF1_BGKLV19_7A_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	982					GRCh38	V40	BCLAF1_BGKLV19_7A_GTGGCC_L001_R1_001.fastq.gz,BCLAF1_BGKLV19_7A_GTGGCC_L001_R2_001.fastq.gz		ENCORE2	15536
BCLAF1_BGKLV19_7A_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	982					GRCh38	V40	BCLAF1_BGKLV19_7A/Aligned.sortedByCoord.out.bam		ENCORE2	15546
BCLAF1_BGKLV19_7A_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	982					GRCh38	V40	BCLAF1_BGKLV19_7A/Aligned.sortedByCoord.out.bam		ENCORE2	15556
BCLAF1_BGKLV19_7A_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	982					GRCh38	V40	BCLAF1_BGKLV19_7A/Aligned.sortedByCoord.out.bam		ENCORE2	15566
BCLAF1_BGKLV19_7A_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	982					GRCh38	V40	BCLAF1_BGKLV19_7A/Aligned.sortedByCoord.out.bam		ENCORE2	15576
BCLAF1_BGKLV19_7A_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	982					GRCh38	V40	BCLAF1_BGKLV19_7A_GTGGCC_L001_R1_001.fastq.gz,BCLAF1_BGKLV19_7A_GTGGCC_L001_R2_001.fastq.gz		ENCORE2	16354
BCLAF1_BGKLV19_8A_GTTTCG_L001_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	983	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1A_ATGTCA_L001_R1_001.fastq.gz,NT_BGKLV19_2A_CCGTCC_L001_R1_001.fastq.gz	ENCODE3	15517
BCLAF1_BGKLV19_8A_GTTTCG_L001_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	983	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1A_ATGTCA_L001_R2_001.fastq.gz,NT_BGKLV19_2A_CCGTCC_L001_R2_001.fastq.gz	ENCODE3	15527
BCLAF1_BGKLV19_8A_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	983					GRCh38	V40	BCLAF1_BGKLV19_8A_GTTTCG_L001_R1_001.fastq.gz,BCLAF1_BGKLV19_8A_GTTTCG_L001_R2_001.fastq.gz		ENCORE2	15537
BCLAF1_BGKLV19_8A_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	983					GRCh38	V40	BCLAF1_BGKLV19_8A/Aligned.sortedByCoord.out.bam		ENCORE2	15547
BCLAF1_BGKLV19_8A_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	983					GRCh38	V40	BCLAF1_BGKLV19_8A/Aligned.sortedByCoord.out.bam		ENCORE2	15557
BCLAF1_BGKLV19_8A_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	983					GRCh38	V40	BCLAF1_BGKLV19_8A/Aligned.sortedByCoord.out.bam		ENCORE2	15567
BCLAF1_BGKLV19_8A_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	983					GRCh38	V40	BCLAF1_BGKLV19_8A/Aligned.sortedByCoord.out.bam		ENCORE2	15577
BCLAF1_BGKLV19_8A_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	983					GRCh38	V40	BCLAF1_BGKLV19_8A_GTTTCG_L001_R1_001.fastq.gz,BCLAF1_BGKLV19_8A_GTTTCG_L001_R2_001.fastq.gz		ENCORE2	16355