BCAT2 RNA-Seq in K562

General Information


RBP	BCAT2
Cell_Line	K562
Method	CRISPR
Exp_Name	BCAT2-BGKcLV42-K562
ENCODE_series_ID
Batch_ID	BGKcLV42
Pool ID	Pool-240715
Local_Set_Name	set73
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	BCAT2-BGKcLV42-9
Rep2	BCAT2-BGKcLV42-10
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	39.3
Rep2_qPCR	36.6
Rep1_WB	93.2
Rep2_WB	95.0
Antibody Cat#	79764S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1528

Experiment Information (Status: Submitting)

	BGKcLV42-9	BGKcLV42-10
idx	0	0
TRCN#_or_BGC#	BGC#0001112	BGC#0001112
shRNA_or_gRNA_sequence	ATTTACCGACCACATGCTGA	ATTTACCGACCACATGCTGA
PAM	TGG	TGG
Name	BCAT2_83	BCAT2_83
Sample_ID	BGKcLV42-9	BGKcLV42-10
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	BCAT2	BCAT2
qPCR_result	39.3	36.6
Ave_qPCR	37.9
RT-qPCR_primer-F	ccgctgaatggtgttatcct
RT-qPCR_primer-R	caactgcttcatggtgatcg
protein_conc	2407	2852
WB_result	93.2	95.0
Ave_WB	94.1
WB_DONE_date	5/2/24
MW	39kd
IP
antibody_Cat#	79764S	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5763	5764

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
BCAT2	Product_ID: 79764S Lot_ID: 1 Source: Cell Signaling Technology Target Name: BCAT2-human

Experiment Status

	BGKcLV42-9	BGKcLV42-10
Sample_ID	BGKcLV42-9	BGKcLV42-10
Sample Name
Sample Name	BCAT2-BGKcLV42-9	BCAT2-BGKcLV42-10
RBP	BCAT2	BCAT2
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13050	13051

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-9	BGKcLV42-10
Sample #	7	8
Sample Name	BCAT2-BGKcLV42-9	BCAT2-BGKcLV42-10
Sample_Name_Alias
Index Well Position	G01	H01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-06-21	2024-06-21
Lib_ID	Lib-240621	Lib-240621
Tecan_Location
Tecan
Tecan_date
Size_bp	292	300
Peak_Molarity	47.10	25.00
libSampleQC_DNA_Well	DNA_Library_set73/set1/G1.png	DNA_Library_set73/set1/H1.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set73/set1/G1.png	RNA_Library_set73/set1/H1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-9	BGKcLV42-10
RBP	BCAT2	BCAT2
Batch_ID	BGKcLV42	BGKcLV42
WB_result	93.200	95.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4276	4277

Sequencing Information

	BGKcLV42-9	BGKcLV42-10
Sample_ID	BGKcLV42-9	BGKcLV42-10
Sample Name	BCAT2-BGKcLV42-9	BCAT2-BGKcLV42-10
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	70,066,168	101,605,100
total_aligned_reads	58,903,988	93,557,518
unique_aligned_reads	54,236,306	86,208,853
percent_uniqueAligned	0.77407	0.84847
correlation_replicates	0.995956	0.995956
spikein_reads	7,434	12,456
percent_spikeins	0.00011	0.00012
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3143	3144

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
BCAT2-BGKcLV42-9_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3143	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30345
BCAT2-BGKcLV42-9_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3143	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30435
BCAT2-BGKcLV42-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3143					GRCh38	V40	BCAT2-BGKcLV42-9_L001_R1_001.filtered.trimmed.paired.fastq.gz,BCAT2-BGKcLV42-9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31277
BCAT2-BGKcLV42-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3143					GRCh38	V40	BCAT2-BGKcLV42-9_Aligned.sortedByCoord.out.bam		ENCORE2	31367
BCAT2-BGKcLV42-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3143					GRCh38	V40	BCAT2-BGKcLV42-9_Aligned.sortedByCoord.out.bam		ENCORE2	31457
BCAT2-BGKcLV42-9_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3143					GRCh38	V40	BCAT2-BGKcLV42-9_Aligned.sortedByCoord.out.bam		ENCORE2	31547
BCAT2-BGKcLV42-9_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3143					GRCh38	V40	BCAT2-BGKcLV42-9_Aligned.sortedByCoord.out.bam		ENCORE2	31637
BCAT2-BGKcLV42-9_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3143					GRCh38	V40	BCAT2-BGKcLV42-9_L001_R1_001.filtered.trimmed.paired.fastq.gz,BCAT2-BGKcLV42-9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31727
BCAT2-BGKcLV42-10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3144	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30344
BCAT2-BGKcLV42-10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3144	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30434
BCAT2-BGKcLV42-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3144					GRCh38	V40	BCAT2-BGKcLV42-10_L001_R1_001.filtered.trimmed.paired.fastq.gz,BCAT2-BGKcLV42-10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31276
BCAT2-BGKcLV42-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3144					GRCh38	V40	BCAT2-BGKcLV42-10_Aligned.sortedByCoord.out.bam		ENCORE2	31366
BCAT2-BGKcLV42-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3144					GRCh38	V40	BCAT2-BGKcLV42-10_Aligned.sortedByCoord.out.bam		ENCORE2	31456
BCAT2-BGKcLV42-10_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3144					GRCh38	V40	BCAT2-BGKcLV42-10_Aligned.sortedByCoord.out.bam		ENCORE2	31546
BCAT2-BGKcLV42-10_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3144					GRCh38	V40	BCAT2-BGKcLV42-10_Aligned.sortedByCoord.out.bam		ENCORE2	31636
BCAT2-BGKcLV42-10_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3144					GRCh38	V40	BCAT2-BGKcLV42-10_L001_R1_001.filtered.trimmed.paired.fastq.gz,BCAT2-BGKcLV42-10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31726