MARS RNA-Seq in K562

General Information


RBP	MARS
Cell_Line	K562
Method	CRISPR
Exp_Name	MARS-BGKcLV46-K562
ENCODE_series_ID
Batch_ID	BGKcLV46
Pool ID	Pool-250312
Local_Set_Name	set77
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	MARS-BGKcLV46-45
Rep2	MARS-BGKcLV46-46
CN1	NT-BGKcLV46-1
CN2	NT-BGKcLV46-2
Rep1_qPCR	60.3
Rep2_qPCR	57.4
Rep1_WB	87.7
Rep2_WB	87.5
Antibody Cat#	A303-960A
Antibody Lot#	lot# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1643

Experiment Information (Status: Submitting)

	BGKcLV46-45	BGKcLV46-46
idx	0	0
TRCN#_or_BGC#	BGC#0001030	BGC#0001030
shRNA_or_gRNA_sequence	ATGAGACTGTTCGTGAGTGA	ATGAGACTGTTCGTGAGTGA
PAM	TGG	TGG
Name	MARS_82	MARS_82
Sample_ID	BGKcLV46-45	BGKcLV46-46
transduction_Date	12/20/24	12/20/24
days	D6	D6
RBP_name	MARS	MARS
qPCR_result	60.3	57.4
Ave_qPCR	58.8
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3944	4905
WB_result	87.7	87.5
Ave_WB
WB_DONE_date	1/6/25
MW	101kd
IP
antibody_Cat#	A303-960A	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	6039	6040

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKcLV46-45	BGKcLV46-46
Sample_ID	BGKcLV46-45	BGKcLV46-46
Sample Name
Sample Name	MARS-BGKcLV46-45	MARS-BGKcLV46-46
RBP	MARS	MARS
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	14040	14041

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV46-45	BGKcLV46-46
Sample #	19	20
Sample Name	MARS-BGKcLV46-45	MARS-BGKcLV46-46
Sample_Name_Alias
Index Well Position	C03	D03
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-02-20	2025-02-20
Lib_ID	Lib-250220	Lib-250220
Tecan_Location
Tecan
Tecan_date
Size_bp	297	304
Peak_Molarity	91.10	81.50
libSampleQC_DNA_Well	DNA_Library_set77/set1/C9.png	DNA_Library_set77/set1/D9.png
RIN	9.8	10.0
libSample_RNA_Well	RNA_Library_set77/set1/C3.png	RNA_Library_set77/set1/D3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-02-28	2025-02-28
Sample_ID	BGKcLV46-45	BGKcLV46-46
RBP	MARS	MARS
Batch_ID	BGKcLV46	BGKcLV46
WB_result	87.700	87.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4678	4679

Sequencing Information

	BGKcLV46-45	BGKcLV46-46
Sample_ID	BGKcLV46-45	BGKcLV46-46
Sample Name	MARS-BGKcLV46-45	MARS-BGKcLV46-46
Pool ID	Pool-250312	Pool-250312
LocalServer_folder	set77	set77
total_reads	56,054,594	48,110,441
total_aligned_reads	50,103,295	44,040,441
unique_aligned_reads	46,104,061	40,615,015
percent_uniqueAligned	0.82248	0.84420
correlation_replicates	0.997007	0.997007
spikein_reads	130,794	53,892
percent_spikeins	0.00233	0.00112
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3383	3384

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
MARS-BGKcLV46-45_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3383	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32164
MARS-BGKcLV46-45_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3383	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32214
MARS-BGKcLV46-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3383					GRCh38	V40	MARS-BGKcLV46-45_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz,MARS-BGKcLV46-45_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32264
MARS-BGKcLV46-45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3383					GRCh38	V40	MARS-BGKcLV46-45_Aligned.sortedByCoord.out.bam		ENCORE2	32314
MARS-BGKcLV46-45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3383					GRCh38	V40	MARS-BGKcLV46-45_Aligned.sortedByCoord.out.bam		ENCORE2	32364
MARS-BGKcLV46-45_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3383					GRCh38	V40	MARS-BGKcLV46-45_Aligned.sortedByCoord.out.bam		ENCORE2	32414
MARS-BGKcLV46-45_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3383					GRCh38	V40	MARS-BGKcLV46-45_Aligned.sortedByCoord.out.bam		ENCORE2	32464
MARS-BGKcLV46-45_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3383					GRCh38	V40	MARS-BGKcLV46-45_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz,MARS-BGKcLV46-45_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32514
MARS-BGKcLV46-46_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3384	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32165
MARS-BGKcLV46-46_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3384	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32215
MARS-BGKcLV46-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3384					GRCh38	V40	MARS-BGKcLV46-46_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz,MARS-BGKcLV46-46_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32265
MARS-BGKcLV46-46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3384					GRCh38	V40	MARS-BGKcLV46-46_Aligned.sortedByCoord.out.bam		ENCORE2	32315
MARS-BGKcLV46-46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3384					GRCh38	V40	MARS-BGKcLV46-46_Aligned.sortedByCoord.out.bam		ENCORE2	32365
MARS-BGKcLV46-46_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3384					GRCh38	V40	MARS-BGKcLV46-46_Aligned.sortedByCoord.out.bam		ENCORE2	32415
MARS-BGKcLV46-46_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3384					GRCh38	V40	MARS-BGKcLV46-46_Aligned.sortedByCoord.out.bam		ENCORE2	32465
MARS-BGKcLV46-46_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3384					GRCh38	V40	MARS-BGKcLV46-46_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz,MARS-BGKcLV46-46_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32515