DYNC1LI1 RNA-Seq in K562

General Information


RBP	DYNC1LI1
Cell_Line	K562
Method	CRISPR
Exp_Name	DYNC1LI1-BGKcLV38-K562
ENCODE_series_ID
Batch_ID	BGKcLV38
Pool ID	Pool-230127C
Local_Set_Name	set56
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	DYNC1LI1-BGKcLV38-25
Rep2	DYNC1LI1-BGKcLV38-26
CN1	NT-BGKcLV38-1
CN2	NT-BGKcLV38-2
Rep1_qPCR	67.2
Rep2_qPCR	59.2
Rep1_WB	60.9
Rep2_WB	63.4
Antibody Cat#	A304-209A
Antibody Lot#	lot# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1029

Experiment Information (Status: Submitting)

	BGKcLV38-25	BGKcLV38-25	BGKcLV38-26	BGKcLV38-26
idx	1442	1442	1443	1443
TRCN#_or_BGC#	BGC#0000939	BGC#0000939	BGC#0000939	BGC#0000939
shRNA_or_gRNA_sequence	TAAGTCGAGGATAATCCCGG	TAAGTCGAGGATAATCCCGG	TAAGTCGAGGATAATCCCGG	TAAGTCGAGGATAATCCCGG
PAM	CGG	CGG	CGG	CGG
Name	DYNC1LI1_97	DYNC1LI1_97	DYNC1LI1_97	DYNC1LI1_97
Sample_ID	BGKcLV38-25	BGKcLV38-25	BGKcLV38-26	BGKcLV38-26
transduction_Date	10/18/22	10/18/22	10/18/22	10/18/22
days	D6	D6	D6	D6
RBP_name	DYNC1LI1	DYNC1LI1	DYNC1LI1	DYNC1LI1
qPCR_result	67.2	67.2	59.2	59.2
Ave_qPCR	63.2	63.2
RT-qPCR_primer-F	GCAAAGCAACCACCAACTGCAG	GCAAAGCAACCACCAACTGCAG
RT-qPCR_primer-R	ATGGGTGACACGCTGGCAACAT	ATGGGTGACACGCTGGCAACAT
protein_conc	3146	3146	2945	2945
WB_result	60.9	58.0	63.4	43.7192
Ave_WB	62.1	50.9
WB_DONE_date	10/26/22	7/19/02
MW	57KD	57KD
IP
antibody_Cat#	A304-209A	A304-208A	lot# 1	lot# 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	5616	5618	5617	5619

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DYNC1LI1	Product_ID: A304-209A Lot_ID: 1 Source: Bethyl Labs Target Name: DYNC1LI1-human

Experiment Status

	BGKcLV38-25	BGKcLV38-26
Sample_ID	BGKcLV38-25	BGKcLV38-26
Sample Name
Sample Name	DYNC1LI1-BGKcLV38-25	DYNC1LI1-BGKcLV38-26
RBP	DYNC1LI1	DYNC1LI1
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11032	11033

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV38-25	BGKcLV38-26
Sample #	67	68
Sample Name	DYNC1LI1-BGKcLV38-25	DYNC1LI1-BGKcLV38-26
Sample_Name_Alias
Index Well Position	A10	B10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-01-19	2023-01-19
Lib_ID	Lib-230119	Lib-230119
Tecan_Location
Tecan
Tecan_date
Size_bp	294	290
Peak_Molarity	56.80	64.30
libSampleQC_DNA_Well	DNA_Library_set54-56/set2/A10.png	DNA_Library_set54-56/set2/B10.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set54-56/set1/C9.png	RNA_Library_set54-56/set1/D9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV38-25	BGKcLV38-26
RBP	DYNC1LI1	DYNC1LI1
Batch_ID	BGKcLV38	BGKcLV38
WB_result	60.900	63.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3438	3439

Sequencing Information

	BGKcLV38-25	BGKcLV38-26
Sample_ID	BGKcLV38-25	BGKcLV38-26
Sample Name	DYNC1LI1-BGKcLV38-25	DYNC1LI1-BGKcLV38-26
Pool ID	Pool-230127C	Pool-230127C
LocalServer_folder	set56	set56
total_reads	40,903,814	72,031,539
total_aligned_reads	37,370,842	66,825,346
unique_aligned_reads	34,755,104	62,049,449
percent_uniqueAligned	0.84968	0.86142
correlation_replicates	0.998574	0.998574
spikein_reads	20,608	25,182
percent_spikeins	0.00050	0.00035
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2309	2310

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
DYNC1LI1-BGKcLV38-25_S65_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2309	NovaSeq6000	100	paired-ended	1				NT-BGKcLV38-1_S51_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8314
DYNC1LI1-BGKcLV38-25_S65_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2309	NovaSeq6000	100	paired-ended	2				NT-BGKcLV38-1_S51_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8352
DYNC1LI1-BGKcLV38-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2309					GRCh38	V40	DYNC1LI1-BGKcLV38-25_S65_L002_R1_001.filtered.trimmed.paired.fastq.gz,DYNC1LI1-BGKcLV38-25_S65_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16966
DYNC1LI1-BGKcLV38-25_Signal.Unique.strand+.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2309					GRCh38	V40	DYNC1LI1-BGKcLV38-25/Aligned.sortedByCoord.out.bam		ENCORE2	17004
DYNC1LI1-BGKcLV38-25_Signal.Unique.strand-.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2309					GRCh38	V40	DYNC1LI1-BGKcLV38-25/Aligned.sortedByCoord.out.bam		ENCORE2	17042
DYNC1LI1-BGKcLV38-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2309					GRCh38	V40	DYNC1LI1-BGKcLV38-25/Aligned.sortedByCoord.out.bam		ENCORE2	17080
DYNC1LI1-BGKcLV38-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2309					GRCh38	V40	DYNC1LI1-BGKcLV38-25/Aligned.sortedByCoord.out.bam		ENCORE2	17118
DYNC1LI1-BGKcLV38-25_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2309					GRCh38	V40	DYNC1LI1-BGKcLV38-25_S65_L002_R1_001.filtered.trimmed.paired.fastq.gz,DYNC1LI1-BGKcLV38-25_S65_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17156
DYNC1LI1-BGKcLV38-26_S66_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2310	NovaSeq6000	100	paired-ended	1				NT-BGKcLV38-1_S51_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8315
DYNC1LI1-BGKcLV38-26_S66_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2310	NovaSeq6000	100	paired-ended	2				NT-BGKcLV38-1_S51_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8353
DYNC1LI1-BGKcLV38-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2310					GRCh38	V40	DYNC1LI1-BGKcLV38-26_S66_L002_R1_001.filtered.trimmed.paired.fastq.gz,DYNC1LI1-BGKcLV38-26_S66_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16967
DYNC1LI1-BGKcLV38-26_Signal.Unique.strand+.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2310					GRCh38	V40	DYNC1LI1-BGKcLV38-26/Aligned.sortedByCoord.out.bam		ENCORE2	17005
DYNC1LI1-BGKcLV38-26_Signal.Unique.strand-.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2310					GRCh38	V40	DYNC1LI1-BGKcLV38-26/Aligned.sortedByCoord.out.bam		ENCORE2	17043
DYNC1LI1-BGKcLV38-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2310					GRCh38	V40	DYNC1LI1-BGKcLV38-26/Aligned.sortedByCoord.out.bam		ENCORE2	17081
DYNC1LI1-BGKcLV38-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2310					GRCh38	V40	DYNC1LI1-BGKcLV38-26/Aligned.sortedByCoord.out.bam		ENCORE2	17119
DYNC1LI1-BGKcLV38-26_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2310					GRCh38	V40	DYNC1LI1-BGKcLV38-26_S66_L002_R1_001.filtered.trimmed.paired.fastq.gz,DYNC1LI1-BGKcLV38-26_S66_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17157