DYNC1I2 RNA-Seq in K562

General Information


RBP	DYNC1I2
Cell_Line	K562
Method	CRISPR
Exp_Name	DYNC1I2-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	DYNC1I2-BGKcLV38-23
Rep2	DYNC1I2-BGKcLV38-24
CN1	NT-BGKcLV38-1
CN2	NT-BGKcLV38-2
Rep1_qPCR	71.1
Rep2_qPCR	56.3
Rep1_WB	64.4
Rep2_WB	67.1
Antibody Cat#	A304-529A
Antibody Lot#	lot# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1028

Experiment Information (Status: Submitting)

	BGKcLV38-23	BGKcLV38-23	BGKcLV38-24	BGKcLV38-24
idx	1440	1440	1441	1441
TRCN#_or_BGC#	BGC#0000937	BGC#0000937	BGC#0000937	BGC#0000937
shRNA_or_gRNA_sequence	TTTAGGTTTACCTGCCATGG	TTTAGGTTTACCTGCCATGG	TTTAGGTTTACCTGCCATGG	TTTAGGTTTACCTGCCATGG
PAM	CGG	CGG	CGG	CGG
Name	DYNC1I2_81	DYNC1I2_81	DYNC1I2_81	DYNC1I2_81
Sample_ID	BGKcLV38-23	BGKcLV38-23	BGKcLV38-24	BGKcLV38-24
transduction_Date	10/18/22	10/18/22	10/18/22	10/18/22
days	D6	D6	D6	D6
RBP_name	DYNC1I2	DYNC1I2	DYNC1I2	DYNC1I2
qPCR_result	71.1	71.1	56.3	56.3
Ave_qPCR	63.7	63.7
RT-qPCR_primer-F	gggagattggatttgtggaa	gggagattggatttgtggaa
RT-qPCR_primer-R	cttcagaatcacccacagca	cttcagaatcacccacagca
protein_conc	3419	3419	3968	3968
WB_result	64.4	63.8	67.1	74.4978
Ave_WB	65.8	69.1
WB_DONE_date	10/26/22	7/19/23
MW	71KD	71KD
IP
antibody_Cat#	A304-529A	A304-528A	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	5612	5614	5613	5615

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DYNC1I2	Product_ID: A304-529A Lot_ID: 1 Source: Bethyl Labs Target Name: DYNC1I2-human
DYNC1I2	Product_ID: A304-528A Lot_ID: 1 Source: Bethyl Labs Target Name: DYNC1I2-human

Experiment Status

	BGKcLV38-23	BGKcLV38-24
Sample_ID	BGKcLV38-23	BGKcLV38-24
Sample Name
Sample Name	DYNC1I2-BGKcLV38-23	DYNC1I2-BGKcLV38-24
RBP	DYNC1I2	DYNC1I2
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11030	11031

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV38-23	BGKcLV38-24
Sample #	65	66
Sample Name	DYNC1I2-BGKcLV38-23	DYNC1I2-BGKcLV38-24
Sample_Name_Alias
Index Well Position	G09	H09
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	289	296
Peak_Molarity	83.40	64.70
libSampleQC_DNA_Well	DNA_Library_set54-56/set2/G9.png	DNA_Library_set54-56/set2/H9.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set54-56/set1/A9.png	RNA_Library_set54-56/set1/B9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV38-23	BGKcLV38-24
RBP	DYNC1I2	DYNC1I2
Batch_ID	BGKcLV38	BGKcLV38
WB_result	64.400	67.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3436	3437

Sequencing Information

	BGKcLV38-23	BGKcLV38-24
Sample_ID	BGKcLV38-23	BGKcLV38-24
Sample Name	DYNC1I2-BGKcLV38-23	DYNC1I2-BGKcLV38-24
Pool ID	Pool-230127C	Pool-230127C
LocalServer_folder	set56	set56
total_reads	50,751,576	47,787,400
total_aligned_reads	46,304,535	44,224,050
unique_aligned_reads	42,997,676	41,018,780
percent_uniqueAligned	0.84722	0.85836
correlation_replicates	0.997215	0.997215
spikein_reads	10,850	22,734
percent_spikeins	0.00021	0.00048
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2307	2308

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
DYNC1I2-BGKcLV38-23_S63_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2307	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	8312
DYNC1I2-BGKcLV38-23_S63_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2307	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	8350
DYNC1I2-BGKcLV38-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2307					GRCh38	V40	DYNC1I2-BGKcLV38-23_S63_L002_R1_001.filtered.trimmed.paired.fastq.gz,DYNC1I2-BGKcLV38-23_S63_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16964
DYNC1I2-BGKcLV38-23_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	2307					GRCh38	V40	DYNC1I2-BGKcLV38-23/Aligned.sortedByCoord.out.bam		ENCORE2	17002
DYNC1I2-BGKcLV38-23_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	2307					GRCh38	V40	DYNC1I2-BGKcLV38-23/Aligned.sortedByCoord.out.bam		ENCORE2	17040
DYNC1I2-BGKcLV38-23_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	2307					GRCh38	V40	DYNC1I2-BGKcLV38-23/Aligned.sortedByCoord.out.bam		ENCORE2	17078
DYNC1I2-BGKcLV38-23_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	2307					GRCh38	V40	DYNC1I2-BGKcLV38-23/Aligned.sortedByCoord.out.bam		ENCORE2	17116
DYNC1I2-BGKcLV38-23_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2307					GRCh38	V40	DYNC1I2-BGKcLV38-23_S63_L002_R1_001.filtered.trimmed.paired.fastq.gz,DYNC1I2-BGKcLV38-23_S63_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17154
DYNC1I2-BGKcLV38-24_S64_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2308	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	8313
DYNC1I2-BGKcLV38-24_S64_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2308	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	8351
DYNC1I2-BGKcLV38-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2308					GRCh38	V40	DYNC1I2-BGKcLV38-24_S64_L002_R1_001.filtered.trimmed.paired.fastq.gz,DYNC1I2-BGKcLV38-24_S64_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16965
DYNC1I2-BGKcLV38-24_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	2308					GRCh38	V40	DYNC1I2-BGKcLV38-24/Aligned.sortedByCoord.out.bam		ENCORE2	17003
DYNC1I2-BGKcLV38-24_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	2308					GRCh38	V40	DYNC1I2-BGKcLV38-24/Aligned.sortedByCoord.out.bam		ENCORE2	17041
DYNC1I2-BGKcLV38-24_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	2308					GRCh38	V40	DYNC1I2-BGKcLV38-24/Aligned.sortedByCoord.out.bam		ENCORE2	17079
DYNC1I2-BGKcLV38-24_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	2308					GRCh38	V40	DYNC1I2-BGKcLV38-24/Aligned.sortedByCoord.out.bam		ENCORE2	17117
DYNC1I2-BGKcLV38-24_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2308					GRCh38	V40	DYNC1I2-BGKcLV38-24_S64_L002_R1_001.filtered.trimmed.paired.fastq.gz,DYNC1I2-BGKcLV38-24_S64_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17155