RTCB RNA-Seq in K562

General Information


RBP	RTCB
Cell_Line	K562
Method	CRISPR
Exp_Name	RTCB-BGKcLV35-K562
ENCODE_series_ID
Batch_ID	BGKcLV35
Pool ID	Pool-220720
Local_Set_Name	set54
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	RTCB-BGKcLV35-63
Rep2	RTCB-BGKcLV35-64
CN1	NT-BGKcLV35-1
CN2	NT-BGKcLV35-2
Rep1_qPCR	77.2
Rep2_qPCR	74.7
Rep1_WB	52.9
Rep2_WB	57.1
Antibody Cat#	A305-078A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB377OYK
Status	Submitted
Project	ENCORE2
ID	962

Experiment Information (Status: Submitting)

	BGKcLV35-63	BGKcLV35-63	BGKcLV35-64	BGKcLV35-64
idx	1340	1340	1341	1341
TRCN#_or_BGC#	BGC#0000834	BGC#0000834	BGC#0000834	BGC#0000834
shRNA_or_gRNA_sequence	TTAAGGAATGCCTGTCGAGG	TTAAGGAATGCCTGTCGAGG	TTAAGGAATGCCTGTCGAGG	TTAAGGAATGCCTGTCGAGG
PAM	TGG	TGG	TGG	TGG
Name	RTCB_89	RTCB_89	RTCB_89	RTCB_89
Sample_ID	BGKcLV35-63	BGKcLV35-63	BGKcLV35-64	BGKcLV35-64
transduction_Date	4/28/22	4/28/22	4/28/22	4/28/22
days	D6	D6	D6	D6
RBP_name	RTCB	RTCB	RTCB	RTCB
qPCR_result	77.2		74.7
Ave_qPCR	76.0
RT-qPCR_primer-F	tgatgctctggagaaattgatg
RT-qPCR_primer-R	attgccaatctgtttcatgg
protein_conc	3442	3442	3981	3981
WB_result	52.9	65.4	57.1	66.7218
Ave_WB	55.0	66.1
WB_DONE_date	5/18/22	6/2/22
MW	55kd	55kd
IP
antibody_Cat#	A305-078A	A305-079A	LOT #1	LOT #1
Antibody DCC ID	ENCAB377OYK	ENCAB418OYG
submitted_to_DCC_date	8/16/22	8/16/22
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	06/17/22		06/17/22
repeat_library
Note
ID	5486	5488	5487	5489

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RTCB	Product_ID: A305-078A Lot_ID: 1 Source: Bethyl Labs Target Name: RTCB-human
RTCB	Product_ID: A305-079A Lot_ID: 1 Source: Bethyl Labs Target Name: RTCB-human

Experiment Status

	BGKcLV35-63	BGKcLV35-63	BGKcLV35-64	BGKcLV35-64
Sample_ID	BGKcLV35-63	BGKcLV35-63	BGKcLV35-64	BGKcLV35-64
Sample Name
Sample Name	RTCB-BGKcLV35-63		RTCB-BGKcLV35-64
RBP	RTCB	RTCB	RTCB	RTCB
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Submitting	NotSatisfied	Submitting	NotSatisfied
Status_date	2023-04-14	2022-06-16	2023-04-14	2022-06-16
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	10881	10923	10882	10924

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV35-63	BGKcLV35-64
Sample #	47	48
Sample Name	RTCB-BGKcLV35-63	RTCB-BGKcLV35-64
Sample_Name_Alias
Index Well Position	G06	H06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-06-17	2022-06-17
Lib_ID	Lib-220617	Lib-220617
Tecan_Location
Tecan
Tecan_date
Size_bp	286	284
Peak_Molarity	42.30	16.30
libSampleQC_DNA_Well	DNA_Library_set54-56/set3/G10.png	DNA_Library_set54-56/set3/H10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set54-56/set2/G6.png	RNA_Library_set54-56/set2/H6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-06-20	2022-06-20
Sample_ID	BGKcLV35-63	BGKcLV35-64
RBP	RTCB	RTCB
Batch_ID	BGKcLV35	BGKcLV35
WB_result	52.900	57.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3364	3365

Sequencing Information

	BGKcLV35-63	BGKcLV35-64
Sample_ID	BGKcLV35-63	BGKcLV35-64
Sample Name	RTCB-BGKcLV35-63	RTCB-BGKcLV35-64
Pool ID	Pool-220720	Pool-220720
LocalServer_folder	set54	set54
total_reads	49,415,354	44,324,696
total_aligned_reads	46,564,494	40,715,542
unique_aligned_reads	42,615,622	37,303,658
percent_uniqueAligned	0.86240	0.84160
correlation_replicates	0.987341	0.987341
spikein_reads	5,694	11,696
percent_spikeins	0.00012	0.00026
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2243	2244

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
RTCB-BGKcLV35-63_S49_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2243	NovaSeq6000	100	paired-ended	1				NT-BGKcLV35-1_S25_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8520
RTCB-BGKcLV35-63_S49_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2243	NovaSeq6000	100	paired-ended	2				NT-BGKcLV35-1_S25_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8570
RTCB-BGKcLV35-63_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2243					GRCh38	V40	RTCB-BGKcLV35-63/Aligned.sortedByCoord.out.bam		ENCORE2	17766
RTCB-BGKcLV35-63_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2243					GRCh38	V40	RTCB-BGKcLV35-63/Aligned.sortedByCoord.out.bam		ENCORE2	17816
RTCB-BGKcLV35-63_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2243					GRCh38	V40	RTCB-BGKcLV35-63/Aligned.sortedByCoord.out.bam		ENCORE2	17866
RTCB-BGKcLV35-63_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2243					GRCh38	V40	RTCB-BGKcLV35-63/Aligned.sortedByCoord.out.bam		ENCORE2	17916
RTCB-BGKcLV35-63_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2243					GRCh38	V40	RTCB-BGKcLV35-63_S49_R1_001.filtered.trimmed.paired.fastq.gz,RTCB-BGKcLV35-63_S49_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17966
RTCB-BGKcLV35-63_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2243					GRCh38	V40	RTCB-BGKcLV35-63_S49_R1_001.filtered.trimmed.paired.fastq.gz,RTCB-BGKcLV35-63_S49_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29307
RTCB-BGKcLV35-64_S50_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2244	NovaSeq6000	100	paired-ended	1				NT-BGKcLV35-1_S25_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8521
RTCB-BGKcLV35-64_S50_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2244	NovaSeq6000	100	paired-ended	2				NT-BGKcLV35-1_S25_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8571
RTCB-BGKcLV35-64_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2244					GRCh38	V40	RTCB-BGKcLV35-64/Aligned.sortedByCoord.out.bam		ENCORE2	17767
RTCB-BGKcLV35-64_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2244					GRCh38	V40	RTCB-BGKcLV35-64/Aligned.sortedByCoord.out.bam		ENCORE2	17817
RTCB-BGKcLV35-64_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2244					GRCh38	V40	RTCB-BGKcLV35-64/Aligned.sortedByCoord.out.bam		ENCORE2	17867
RTCB-BGKcLV35-64_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2244					GRCh38	V40	RTCB-BGKcLV35-64/Aligned.sortedByCoord.out.bam		ENCORE2	17917
RTCB-BGKcLV35-64_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2244					GRCh38	V40	RTCB-BGKcLV35-64_S50_R1_001.filtered.trimmed.paired.fastq.gz,RTCB-BGKcLV35-64_S50_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17967
RTCB-BGKcLV35-64_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2244					GRCh38	V40	RTCB-BGKcLV35-64_S50_R1_001.filtered.trimmed.paired.fastq.gz,RTCB-BGKcLV35-64_S50_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29308