TARS RNA-Seq in K562

General Information


RBP	TARS
Cell_Line	K562
Method	CRISPR
Exp_Name	TARS-BGKcLV37-K562
ENCODE_series_ID
Batch_ID	BGKcLV37
Pool ID	Pool-230130
Local_Set_Name	set55
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	TARS-BGKcLV37-51
Rep2	TARS-BGKcLV37-52
CN1	NT-BGKcLV37-1
CN2	NT-BGKcLV37-2
Rep1_qPCR	61.7
Rep2_qPCR	55.3
Rep1_WB	52.6
Rep2_WB	51.9
Antibody Cat#	A304-755A
Antibody Lot#	lot # 1
Antibody DCC ID	NO id
Status	Submitted
Project	ENCORE2
ID	1061

Experiment Information (Status: Submitting)

	BGKcLV37-51	BGKcLV37-52
idx	1403	1404
TRCN#_or_BGC#	BGC#0001066	BGC#0001066
shRNA_or_gRNA_sequence	TCAGAATTCCTCCACGTACT	TCAGAATTCCTCCACGTACT
PAM	GGG	GGG
Name	TARS_90	TARS_90
Sample_ID	BGKcLV37-51	BGKcLV37-52
transduction_Date	9/20/22	9/20/22
days	D6	D6
RBP_name	TARS	TARS
qPCR_result	61.7	55.3
Ave_qPCR	58.5
RT-qPCR_primer-F	tggatccaggctgtacattg
RT-qPCR_primer-R	cccgtggaccttattgtctc
protein_conc	1900	1572
WB_result	52.6	51.9
Ave_WB	52.2
WB_DONE_date	9/27/22	Licor
MW	83kd
IP
antibody_Cat#	A304-755A	lot # 1
Antibody DCC ID	NO id
submitted_to_DCC_date	8/29/23
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5561	5562

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
TARS	Product_ID: A304-755A Lot_ID: 1 Source: Bethyl Labs Target Name: TARS-human

Experiment Status

	BGKcLV37-51	BGKcLV37-52
Sample_ID	BGKcLV37-51	BGKcLV37-52
Sample Name
Sample Name	TARS-BGKcLV37-51	TARS-BGKcLV37-52
RBP	TARS	TARS
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11106	11107

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV37-51	BGKcLV37-52
Sample #	45	46
Sample Name	TARS-BGKcLV37-51	TARS-BGKcLV37-52
Sample_Name_Alias
Index Well Position	E06	F06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-01-13	2023-01-13
Lib_ID	Lib-230113	Lib-230113
Tecan_Location
Tecan
Tecan_date
Size_bp	299	310
Peak_Molarity	61.00	53.50
libSampleQC_DNA_Well	DNA_Library_set54-56/set1/E6.png	DNA_Library_set54-56/set1/F6.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set54-56/set1/E6.png	RNA_Library_set54-56/set1/F6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV37-51	BGKcLV37-52
RBP	TARS	TARS
Batch_ID	BGKcLV37	BGKcLV37
WB_result	52.600	51.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3416	3417

Sequencing Information

	BGKcLV37-51	BGKcLV37-52
Sample_ID	BGKcLV37-51	BGKcLV37-52
Sample Name	TARS-BGKcLV37-51	TARS-BGKcLV37-52
Pool ID	Pool-230130	Pool-230130
LocalServer_folder	set55	set55
total_reads	73,608,222	43,445,356
total_aligned_reads	69,576,271	38,514,197
unique_aligned_reads	64,609,064	35,804,043
percent_uniqueAligned	0.87774	0.82412
correlation_replicates	0.995925	0.995925
spikein_reads	1,902	3,232
percent_spikeins	0.00003	0.00007
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2289	2290

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
TARS-BGKcLV37-51_S45_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2289	NovaSeq6000	100	paired-ended	1				NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8418
TARS-BGKcLV37-51_S45_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2289	NovaSeq6000	100	paired-ended	2				NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8468
TARS-BGKcLV37-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2289					GRCh38	V40	TARS-BGKcLV37-51_S45_L001_R1_001.filtered.trimmed.paired.fastq.gz,TARS-BGKcLV37-51_S45_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25659
TARS-BGKcLV37-51_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2289					GRCh38	V40	TARS-BGKcLV37-51/Aligned.sortedByCoord.out.bam		ENCORE2	25709
TARS-BGKcLV37-51_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2289					GRCh38	V40	TARS-BGKcLV37-51/Aligned.sortedByCoord.out.bam		ENCORE2	25759
TARS-BGKcLV37-51_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2289					GRCh38	V40	TARS-BGKcLV37-51/Aligned.sortedByCoord.out.bam		ENCORE2	25809
TARS-BGKcLV37-51_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2289					GRCh38	V40	TARS-BGKcLV37-51/Aligned.sortedByCoord.out.bam		ENCORE2	25859
TARS-BGKcLV37-51_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2289					GRCh38	V40	TARS-BGKcLV37-51_S45_L001_R1_001.filtered.trimmed.paired.fastq.gz,TARS-BGKcLV37-51_S45_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25909
TARS-BGKcLV37-52_S46_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2290	NovaSeq6000	100	paired-ended	1				NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8419
TARS-BGKcLV37-52_S46_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2290	NovaSeq6000	100	paired-ended	2				NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8469
TARS-BGKcLV37-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2290					GRCh38	V40	TARS-BGKcLV37-52_S46_L001_R1_001.filtered.trimmed.paired.fastq.gz,TARS-BGKcLV37-52_S46_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25660
TARS-BGKcLV37-52_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2290					GRCh38	V40	TARS-BGKcLV37-52/Aligned.sortedByCoord.out.bam		ENCORE2	25710
TARS-BGKcLV37-52_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2290					GRCh38	V40	TARS-BGKcLV37-52/Aligned.sortedByCoord.out.bam		ENCORE2	25760
TARS-BGKcLV37-52_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2290					GRCh38	V40	TARS-BGKcLV37-52/Aligned.sortedByCoord.out.bam		ENCORE2	25810
TARS-BGKcLV37-52_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2290					GRCh38	V40	TARS-BGKcLV37-52/Aligned.sortedByCoord.out.bam		ENCORE2	25860
TARS-BGKcLV37-52_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2290					GRCh38	V40	TARS-BGKcLV37-52_S46_L001_R1_001.filtered.trimmed.paired.fastq.gz,TARS-BGKcLV37-52_S46_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25910