BCLAF1 RNA-Seq in K562

General Information


RBP	BCLAF1
Cell_Line	K562
Method	CRISPR
Exp_Name	BCLAF1-BGKcLV40-K562
ENCODE_series_ID
Batch_ID	BGKcLV40
Pool ID	Pool-231226
Local_Set_Name	set67
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	BCLAF1-BGKcLV40-3
Rep2	BCLAF1-BGKcLV40-4
CN1	NT-BGKcLV40-1
CN2	NT-BGKcLV40-2
Rep1_qPCR	76.1
Rep2_qPCR	75.1
Rep1_WB	80.9
Rep2_WB	92.2005
Antibody Cat#	A300-608A
Antibody Lot#	lot # 2
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1356

Experiment Information (Status: Submitting)

	BGKcLV40-3	BGKcLV40-4
idx	1486	1487
TRCN#_or_BGC#	BGC#0000892	BGC#0000892
shRNA_or_gRNA_sequence	TACCTGTTAGAATCATCAAG	TACCTGTTAGAATCATCAAG
PAM	AGG	AGG
Name	BCLAF1_69	BCLAF1_69
Sample_ID	BGKcLV40-3	BGKcLV40-4
transduction_Date	10/31/23	10/31/23
days	D6	D6
RBP_name	BCLAF1	BCLAF1
qPCR_result	76.1	75.1
Ave_qPCR	75.6
RT-qPCR_primer-F	aatggcacctgttcctcttg
RT-qPCR_primer-R	ggatcggaattcttgctcct
protein_conc	3134	3440
WB_result	80.9	92.2005
Ave_WB	86.6
WB_DONE_date	11/8/23,11/17/23
MW	106kd
IP
antibody_Cat#	A300-608A	lot # 2
Antibody DCC ID
submitted_to_DCC_date	1/4/24
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5670	5671

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
BCLAF1	Product_ID: A300-608A Lot_ID: 2 Source: Bethyl Labs Target Name: BCLAF1-human

Experiment Status

	BGKcLV40-3	BGKcLV40-4
Sample_ID	BGKcLV40-3	BGKcLV40-4
Sample Name
Sample Name	BCLAF1-BGKcLV40-3	BCLAF1-BGKcLV40-4
RBP	BCLAF1	BCLAF1
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2024-02-16	2024-02-16
Project	ENCORE2	ENCORE2
Note
ID	12756	12757

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV40-3	BGKcLV40-4
Sample #	3	4
Sample Name	BCLAF1-BGKcLV40-3	BCLAF1-BGKcLV40-4
Sample_Name_Alias
Index Well Position	C01	D01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-12-19	2023-12-19
Lib_ID	Lib-231219	Lib-231219
Tecan_Location
Tecan
Tecan_date
Size_bp	283	288
Peak_Molarity	61.70	74.00
libSampleQC_DNA_Well	DNA_Library_set67/set1/C7.png	DNA_Library_set67/set1/D7.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set67/set1/C1.png	RNA_Library_set67/set1/D1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-12-26	2023-12-26
Sample_ID	BGKcLV40-3	BGKcLV40-4
RBP	BCLAF1	BCLAF1
Batch_ID	BGKcLV40	BGKcLV40
WB_result	80.900	92.201
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4140	4141

Sequencing Information

	BGKcLV40-3	BGKcLV40-4
Sample_ID	BGKcLV40-3	BGKcLV40-4
Sample Name	BCLAF1-BGKcLV40-3	BCLAF1-BGKcLV40-4
Pool ID	Pool-231226	Pool-231226
LocalServer_folder	set67	set67
total_reads	25,540,037	38,897,048
total_aligned_reads	21,411,050	32,898,800
unique_aligned_reads	19,694,391	30,258,658
percent_uniqueAligned	0.77112	0.77792
correlation_replicates	0.996105	0.996105
spikein_reads	3,856	3,042
percent_spikeins	0.00015	0.00008
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	2795	2796

Data Submission Information DCC submission information was not avaliable

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-BGKcLV40-3_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2795	NovaSeq6000	100	paired-ended	1				NT-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28141
BCLAF1-BGKcLV40-3_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2795	NovaSeq6000	100	paired-ended	2				NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28185
BCLAF1-BGKcLV40-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2795					GRCh38	V40	BCLAF1-BGKcLV40-3_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,BCLAF1-BGKcLV40-3_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28229
BCLAF1-BGKcLV40-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2795					GRCh38	V40	BCLAF1-BGKcLV40-3/Aligned.sortedByCoord.out.bam		ENCORE2	28273
BCLAF1-BGKcLV40-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2795					GRCh38	V40	BCLAF1-BGKcLV40-3/Aligned.sortedByCoord.out.bam		ENCORE2	28317
BCLAF1-BGKcLV40-3_Signal.Unique.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2795					GRCh38	V40	BCLAF1-BGKcLV40-3/Aligned.sortedByCoord.out.bam		ENCORE2	28361
BCLAF1-BGKcLV40-3_Signal.Unique.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2795					GRCh38	V40	BCLAF1-BGKcLV40-3/Aligned.sortedByCoord.out.bam		ENCORE2	28405
BCLAF1-BGKcLV40-3_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2795					GRCh38	V40	BCLAF1-BGKcLV40-3_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,BCLAF1-BGKcLV40-3_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28449
BCLAF1-BGKcLV40-4_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2796	NovaSeq6000	100	paired-ended	1				NT-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28142
BCLAF1-BGKcLV40-4_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2796	NovaSeq6000	100	paired-ended	2				NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28186
BCLAF1-BGKcLV40-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2796					GRCh38	V40	BCLAF1-BGKcLV40-4_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz,BCLAF1-BGKcLV40-4_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28230
BCLAF1-BGKcLV40-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2796					GRCh38	V40	BCLAF1-BGKcLV40-4/Aligned.sortedByCoord.out.bam		ENCORE2	28274
BCLAF1-BGKcLV40-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2796					GRCh38	V40	BCLAF1-BGKcLV40-4/Aligned.sortedByCoord.out.bam		ENCORE2	28318
BCLAF1-BGKcLV40-4_Signal.Unique.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2796					GRCh38	V40	BCLAF1-BGKcLV40-4/Aligned.sortedByCoord.out.bam		ENCORE2	28362
BCLAF1-BGKcLV40-4_Signal.Unique.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2796					GRCh38	V40	BCLAF1-BGKcLV40-4/Aligned.sortedByCoord.out.bam		ENCORE2	28406
BCLAF1-BGKcLV40-4_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2796					GRCh38	V40	BCLAF1-BGKcLV40-4_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz,BCLAF1-BGKcLV40-4_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28450