DCTN2 RNA-Seq in K562

General Information


RBP	DCTN2
Cell_Line	K562
Method	CRISPR
Exp_Name	DCTN2-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	DCTN2-BGKcLV35-23
Rep2	DCTN2-BGKcLV35-24
CN1	NT-BGKcLV35-1
CN2	NT-BGKcLV35-2
Rep1_qPCR	27.7
Rep2_qPCR	25.3
Rep1_WB	55.2
Rep2_WB	57.3
Antibody Cat#	A303-488A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB127PWU
Status	Submitted
Project	ENCORE2
ID	957

Experiment Information (Status: Submitting)

	BGKcLV35-23	BGKcLV35-23	BGKcLV35-24	BGKcLV35-24
idx	1300	1300	1301	1301
TRCN#_or_BGC#	BGC#0000741	BGC#0000741	BGC#0000741	BGC#0000741
shRNA_or_gRNA_sequence	AACTCCGCTTGATCATCCTC	AACTCCGCTTGATCATCCTC	AACTCCGCTTGATCATCCTC	AACTCCGCTTGATCATCCTC
PAM	AGG	AGG	AGG	AGG
Name	DCTN2_91	DCTN2_91	DCTN2_91	DCTN2_91
Sample_ID	BGKcLV35-23	BGKcLV35-23	BGKcLV35-24	BGKcLV35-24
transduction_Date	4/28/22	4/28/22	4/28/22	4/28/22
days	D6	D6	D6	D6
RBP_name	DCTN2	DCTN2	DCTN2	DCTN2
qPCR_result	27.7	27.7	25.3	25.3
Ave_qPCR	26.5	26.5
RT-qPCR_primer-F	gaccagatgctgcaatcaac	gaccagatgctgcaatcaac
RT-qPCR_primer-R	atccccctttgctgttcttt	atccccctttgctgttcttt
protein_conc	2820	2820	3151	3151
WB_result	55.2	50.2	57.3	52.7
Ave_WB	56.3	51.5
WB_DONE_date	5/18/22	6/16/22
MW	44KD	44KD
IP
antibody_Cat#	A303-488A	A303-489A	LOT #1	LOT #1
Antibody DCC ID	ENCAB127PWU	ENCAB872COD
submitted_to_DCC_date	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	5444	5446	5445	5447

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DCTN2	Product_ID: A303-488A Lot_ID: 1 Source: Bethyl Labs Target Name: DCTN2-human
DCTN2	Product_ID: A303-489A Lot_ID: 1 Source: Bethyl Labs Target Name: DCTN2-human

Experiment Status

	BGKcLV35-23	BGKcLV35-24
Sample_ID	BGKcLV35-23	BGKcLV35-24
Sample Name
Sample Name	DCTN2-BGKcLV35-23	DCTN2-BGKcLV35-24
RBP	DCTN2	DCTN2
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10871	10872

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV35-23	BGKcLV35-24
Sample #	37	38
Sample Name	DCTN2-BGKcLV35-23	DCTN2-BGKcLV35-24
Sample_Name_Alias
Index Well Position	E05	F05
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	278	282
Peak_Molarity	82.50	17.50
libSampleQC_DNA_Well	DNA_Library_set54-56/set3/E9.png	DNA_Library_set54-56/set3/F9.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_set54-56/set2/E5.png	RNA_Library_set54-56/set2/F5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-06-20	2022-06-20
Sample_ID	BGKcLV35-23	BGKcLV35-24
RBP	DCTN2	DCTN2
Batch_ID	BGKcLV35	BGKcLV35
WB_result	55.200	57.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3354	3355

Sequencing Information

	BGKcLV35-23	BGKcLV35-24
Sample_ID	BGKcLV35-23	BGKcLV35-24
Sample Name	DCTN2-BGKcLV35-23	DCTN2-BGKcLV35-24
Pool ID	Pool-220720	Pool-220720
LocalServer_folder	set54	set54
total_reads	76,488,104	47,438,570
total_aligned_reads	68,984,376	41,207,304
unique_aligned_reads	63,076,936	38,021,576
percent_uniqueAligned	0.82466	0.80149
correlation_replicates	0.994943	0.994943
spikein_reads	3,436	3,408
percent_spikeins	0.00004	0.00007
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2233	2234

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
DCTN2-BGKcLV35-23_S39_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2233	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	8494
DCTN2-BGKcLV35-23_S39_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2233	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	8544
DCTN2-BGKcLV35-23_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	2233					GRCh38	V40	DCTN2-BGKcLV35-23/Aligned.sortedByCoord.out.bam		ENCORE2	17740
DCTN2-BGKcLV35-23_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	2233					GRCh38	V40	DCTN2-BGKcLV35-23/Aligned.sortedByCoord.out.bam		ENCORE2	17790
DCTN2-BGKcLV35-23_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	2233					GRCh38	V40	DCTN2-BGKcLV35-23/Aligned.sortedByCoord.out.bam		ENCORE2	17840
DCTN2-BGKcLV35-23_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	2233					GRCh38	V40	DCTN2-BGKcLV35-23/Aligned.sortedByCoord.out.bam		ENCORE2	17890
DCTN2-BGKcLV35-23_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2233					GRCh38	V40	DCTN2-BGKcLV35-23_S39_R1_001.filtered.trimmed.paired.fastq.gz,DCTN2-BGKcLV35-23_S39_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17940
DCTN2-BGKcLV35-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2233					GRCh38	V40	DCTN2-BGKcLV35-23_S39_R1_001.filtered.trimmed.paired.fastq.gz,DCTN2-BGKcLV35-23_S39_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29281
DCTN2-BGKcLV35-24_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2234	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	8495
DCTN2-BGKcLV35-24_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2234	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	8545
DCTN2-BGKcLV35-24_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	2234					GRCh38	V40	DCTN2-BGKcLV35-24/Aligned.sortedByCoord.out.bam		ENCORE2	17741
DCTN2-BGKcLV35-24_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	2234					GRCh38	V40	DCTN2-BGKcLV35-24/Aligned.sortedByCoord.out.bam		ENCORE2	17791
DCTN2-BGKcLV35-24_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	2234					GRCh38	V40	DCTN2-BGKcLV35-24/Aligned.sortedByCoord.out.bam		ENCORE2	17841
DCTN2-BGKcLV35-24_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	2234					GRCh38	V40	DCTN2-BGKcLV35-24/Aligned.sortedByCoord.out.bam		ENCORE2	17891
DCTN2-BGKcLV35-24_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2234					GRCh38	V40	DCTN2-BGKcLV35-24_S40_R1_001.filtered.trimmed.paired.fastq.gz,DCTN2-BGKcLV35-24_S40_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17941
DCTN2-BGKcLV35-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2234					GRCh38	V40	DCTN2-BGKcLV35-24_S40_R1_001.filtered.trimmed.paired.fastq.gz,DCTN2-BGKcLV35-24_S40_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29282