CALR RNA-Seq in K562

General Information


RBP	CALR
Cell_Line	K562
Method	CRISPR
Exp_Name	CALR-BGKcLV51-K562
ENCODE_series_ID
Batch_ID	BGKcLV51
Pool ID	Pool-260528
Local_Set_Name	set82
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	CALR-BGKcLV51-19
Rep2	CALR-BGKcLV51-20
CN1	NT-BGKcLV51-1
CN2	NT-BGKcLV51-2
Rep1_qPCR	75.4
Rep2_qPCR	75.9
Rep1_WB	52.3
Rep2_WB	55.4
Antibody Cat#	A301-130A
Antibody Lot#	lot# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1717

Experiment Information (Status: Submitting)

	BGKcLV51-19	BGKcLV51-20
idx	0	0
TRCN#_or_BGC#	BGC#0000170	BGC#0000170
shRNA_or_gRNA_sequence	GTAGACGGCAGGCTCGGCGA	GTAGACGGCAGGCTCGGCGA
PAM	CGG	CGG
Name	CALR-91F	CALR-91F
Sample_ID	BGKcLV51-19	BGKcLV51-20
transduction_Date	9/30/2025	9/30/2025
days	D6	D6
RBP_name	CALR	CALR
qPCR_result	75.4	75.9
Ave_qPCR
RT-qPCR_primer-F	ccgttgcaaggatgatgagt
RT-qPCR_primer-R	cacctggctgttgtcaatctt
protein_conc	2698	2840
WB_result	52.3	55.4
Ave_WB
WB_DONE_date	10/14/25
MW	48kd
IP
antibody_Cat#	A301-130A	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	6256	6257

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CALR	Product_ID: A301-130A Lot_ID: 1 Source: Bethyl Labs Target Name: CALR-human

Experiment Status

	BGKcLV51-19	BGKcLV51-20
Sample_ID	BGKcLV51-19	BGKcLV51-20
Sample Name
Sample Name	CALR-BGKcLV51-19	CALR-BGKcLV51-20
RBP	CALR	CALR
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2026-10-30	2026-10-30
Project	ENCORE2	ENCORE2
Note
ID	14570	14571

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV51-19	BGKcLV51-20
Sample #	5	6
Sample Name	CALR-BGKcLV51-19	CALR-BGKcLV51-20
Sample_Name_Alias
Index Well Position	E01	F01
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2026-05-18	2026-05-18
Lib_ID	Lib-260518	Lib-260518
Tecan_Location
Tecan
Tecan_date
Size_bp	286	284
Peak_Molarity	53.50	63.30
libSampleQC_DNA_Well	DNA_Library_set82/set1/E8.png	DNA_Library_set82/set1/F8.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_set82/set1/E1.png	RNA_Library_set82/set1/F1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2026-05-21	2026-05-21
Sample_ID	BGKcLV51-19	BGKcLV51-20
RBP	CALR	CALR
Batch_ID	BGKcLV51	BGKcLV51
WB_result	52.300	55.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4844	4845

Sequencing Information

	BGKcLV51-19	BGKcLV51-20
Sample_ID	BGKcLV51-19	BGKcLV51-20
Sample Name	CALR-BGKcLV51-19	CALR-BGKcLV51-20
Pool ID	Pool-260528	Pool-260528
LocalServer_folder	set82	set82
total_reads	35,304,600	28,894,399
total_aligned_reads	30,446,445	23,759,565
unique_aligned_reads	28,382,086	22,204,218
percent_uniqueAligned	0.80392	0.76846
correlation_replicates	0.997664	0.997664
spikein_reads	79,174	70,526
percent_spikeins	0.00224	0.00244
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	3545	3546

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
CALR-BGKcLV51-19_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3545	NovaSeq6000	100	paired-ended	1				NT-BGKcLV51-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGKcLV51-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33658
CALR-BGKcLV51-19_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3545	NovaSeq6000	100	paired-ended	2				NT-BGKcLV51-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGKcLV51-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33716
CALR-BGKcLV51-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3545					GRCh38	V40	CALR-BGKcLV51-19_R1.filtered.trimmed.paired.fastq.gz,CALR-BGKcLV51-19_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33774
CALR-BGKcLV51-19_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3545					GRCh38	V40	CALR-BGKcLV51-19_Aligned.sortedByCoord.out.bam		ENCORE2	33832
CALR-BGKcLV51-19_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3545					GRCh38	V40	CALR-BGKcLV51-19_Aligned.sortedByCoord.out.bam		ENCORE2	33890
CALR-BGKcLV51-19_Signal.Unique.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3545					GRCh38	V40	CALR-BGKcLV51-19_Aligned.sortedByCoord.out.bam		ENCORE2	33948
CALR-BGKcLV51-19_Signal.Unique.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3545					GRCh38	V40	CALR-BGKcLV51-19_Aligned.sortedByCoord.out.bam		ENCORE2	34006
CALR-BGKcLV51-19_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3545					GRCh38	V40	CALR-BGKcLV51-19_R1.filtered.trimmed.paired.fastq.gz,CALR-BGKcLV51-19_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34064
CALR-BGKcLV51-20_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3546	NovaSeq6000	100	paired-ended	1				NT-BGKcLV51-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGKcLV51-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33659
CALR-BGKcLV51-20_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3546	NovaSeq6000	100	paired-ended	2				NT-BGKcLV51-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGKcLV51-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33717
CALR-BGKcLV51-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3546					GRCh38	V40	CALR-BGKcLV51-20_R1.filtered.trimmed.paired.fastq.gz,CALR-BGKcLV51-20_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33775
CALR-BGKcLV51-20_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3546					GRCh38	V40	CALR-BGKcLV51-20_Aligned.sortedByCoord.out.bam		ENCORE2	33833
CALR-BGKcLV51-20_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3546					GRCh38	V40	CALR-BGKcLV51-20_Aligned.sortedByCoord.out.bam		ENCORE2	33891
CALR-BGKcLV51-20_Signal.Unique.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3546					GRCh38	V40	CALR-BGKcLV51-20_Aligned.sortedByCoord.out.bam		ENCORE2	33949
CALR-BGKcLV51-20_Signal.Unique.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3546					GRCh38	V40	CALR-BGKcLV51-20_Aligned.sortedByCoord.out.bam		ENCORE2	34007
CALR-BGKcLV51-20_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3546					GRCh38	V40	CALR-BGKcLV51-20_R1.filtered.trimmed.paired.fastq.gz,CALR-BGKcLV51-20_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34065