CTNND1 RNA-Seq in K562

General Information


RBP	CTNND1
Cell_Line	K562
Method	CRISPR
Exp_Name	CTNND1-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	CTNND1-BGKcLV35-19
Rep2	CTNND1-BGKcLV35-20
CN1	NT-BGKcLV35-1
CN2	NT-BGKcLV35-2
Rep1_qPCR	xx
Rep2_qPCR	xx
Rep1_WB	65.4
Rep2_WB	55.1
Antibody Cat#	A300-976A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB598HFH
Status	Submitted
Project	ENCORE2
ID	956

Experiment Information (Status: Submitting)

	BGKcLV35-19	BGKcLV35-20
idx	1296	1297
TRCN#_or_BGC#	BGC#0000726	BGC#0000726
shRNA_or_gRNA_sequence	ACTGACGTGCGGAAGCTCAA	ACTGACGTGCGGAAGCTCAA
PAM	GGG	GGG
Name	CTNND1_91	CTNND1_91
Sample_ID	BGKcLV35-19	BGKcLV35-20
transduction_Date	4/28/22	4/28/22
days	D6	D6
RBP_name	CTNND1	CTNND1
qPCR_result	57.4	62.4
Ave_qPCR	59.9
RT-qPCR_primer-F	caacgaggttatcgctgaga
RT-qPCR_primer-R	gctgctgctcgaacttcttt
protein_conc	3155	3058
WB_result	65.4	55.1
Ave_WB	60.3
WB_DONE_date	5/18/22
MW	108KD
IP
antibody_Cat#	A300-976A	LOT #1
Antibody DCC ID	ENCAB598HFH
submitted_to_DCC_date	7/26/22
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/17/22	06/17/22
repeat_library
Note
ID	5440	5441

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CTNND1	Product_ID: A300-976A Lot_ID: 1 Source: Bethyl Labs Target Name: CTNND1-human

Experiment Status

	BGKcLV35-19	BGKcLV35-20
Sample_ID	BGKcLV35-19	BGKcLV35-20
Sample Name
Sample Name	CTNND1-BGKcLV35-19	CTNND1-BGKcLV35-20
RBP	CTNND1	CTNND1
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10869	10870

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV35-19	BGKcLV35-20
Sample #	35	36
Sample Name	CTNND1-BGKcLV35-19	CTNND1-BGKcLV35-20
Sample_Name_Alias
Index Well Position	C05	D05
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	280
Peak_Molarity	15.60	59.10
libSampleQC_DNA_Well	DNA_Library_set54-56/set3/C9.png	DNA_Library_set54-56/set3/D9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set54-56/set2/C5.png	RNA_Library_set54-56/set2/D5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-06-20	2022-06-20
Sample_ID	BGKcLV35-19	BGKcLV35-20
RBP	CTNND1	CTNND1
Batch_ID	BGKcLV35	BGKcLV35
WB_result	65.400	55.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3352	3353

Sequencing Information

	BGKcLV35-19	BGKcLV35-20
Sample_ID	BGKcLV35-19	BGKcLV35-20
Sample Name	CTNND1-BGKcLV35-19	CTNND1-BGKcLV35-20
Pool ID	Pool-220720	Pool-220720
LocalServer_folder	set54	set54
total_reads	38,280,558	29,151,598
total_aligned_reads	33,645,460	25,741,366
unique_aligned_reads	30,961,130	23,542,448
percent_uniqueAligned	0.80880	0.80759
correlation_replicates	0.997778	0.997778
spikein_reads	1,850	1,444
percent_spikeins	0.00005	0.00005
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2231	2232

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
CTNND1-BGKcLV35-19_S37_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2231	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	8492
CTNND1-BGKcLV35-19_S37_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2231	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	8542
CTNND1-BGKcLV35-19_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	2231					GRCh38	V40	CTNND1-BGKcLV35-19/Aligned.sortedByCoord.out.bam		ENCORE2	17738
CTNND1-BGKcLV35-19_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	2231					GRCh38	V40	CTNND1-BGKcLV35-19/Aligned.sortedByCoord.out.bam		ENCORE2	17788
CTNND1-BGKcLV35-19_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	2231					GRCh38	V40	CTNND1-BGKcLV35-19/Aligned.sortedByCoord.out.bam		ENCORE2	17838
CTNND1-BGKcLV35-19_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	2231					GRCh38	V40	CTNND1-BGKcLV35-19/Aligned.sortedByCoord.out.bam		ENCORE2	17888
CTNND1-BGKcLV35-19_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2231					GRCh38	V40	CTNND1-BGKcLV35-19_S37_R1_001.filtered.trimmed.paired.fastq.gz,CTNND1-BGKcLV35-19_S37_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17938
CTNND1-BGKcLV35-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2231					GRCh38	V40	CTNND1-BGKcLV35-19_S37_R1_001.filtered.trimmed.paired.fastq.gz,CTNND1-BGKcLV35-19_S37_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29279
CTNND1-BGKcLV35-20_S38_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2232	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	8493
CTNND1-BGKcLV35-20_S38_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2232	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	8543
CTNND1-BGKcLV35-20_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	2232					GRCh38	V40	CTNND1-BGKcLV35-20/Aligned.sortedByCoord.out.bam		ENCORE2	17739
CTNND1-BGKcLV35-20_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	2232					GRCh38	V40	CTNND1-BGKcLV35-20/Aligned.sortedByCoord.out.bam		ENCORE2	17789
CTNND1-BGKcLV35-20_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	2232					GRCh38	V40	CTNND1-BGKcLV35-20/Aligned.sortedByCoord.out.bam		ENCORE2	17839
CTNND1-BGKcLV35-20_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	2232					GRCh38	V40	CTNND1-BGKcLV35-20/Aligned.sortedByCoord.out.bam		ENCORE2	17889
CTNND1-BGKcLV35-20_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2232					GRCh38	V40	CTNND1-BGKcLV35-20_S38_R1_001.filtered.trimmed.paired.fastq.gz,CTNND1-BGKcLV35-20_S38_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17939
CTNND1-BGKcLV35-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2232					GRCh38	V40	CTNND1-BGKcLV35-20_S38_R1_001.filtered.trimmed.paired.fastq.gz,CTNND1-BGKcLV35-20_S38_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29280