DCTN2 RNA-Seq in HepG2

General Information


RBP	DCTN2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DCTN2-BGHcLV29-HepG2
ENCODE_series_ID	ENCSR768GEJ
Batch_ID	BGHcLV29
Pool ID	Pool-211117
Local_Set_Name	set50_H
ENCODE_KD_Exp_ID	ENCSR146ITQ
ENCODE_CN_Exp_ID	ENCSR462MFN
Rep1	DCTN2-BGHcLV29-65
Rep2	DCTN2-BGHcLV29-66
CN1	NT-BGHcLV29-1
CN2	NT-BGHcLV29-2
Rep1_qPCR	0
Rep2_qPCR	0
Rep1_WB	66.6
Rep2_WB	64.6
Antibody Cat#	A303-488A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB127PWU
Status	Submitted
Project	ENCODE4
ID	864

Experiment Information (Status: Released)

	BGHcLV29-65	BGHcLV29-66
idx	906	907
TRCN#_or_BGC#	BGC#0000741	BGC#0000741
shRNA_or_gRNA_sequence	AACTCCGCTTGATCATCCTC	AACTCCGCTTGATCATCCTC
PAM	AGG	AGG
Name	DCTN2_91	DCTN2_91
Sample_ID	BGHcLV29-65	BGHcLV29-66
transduction_Date	7/20	7/20
days	D6	D6
RBP_name	DCTN2	DCTN2
qPCR_result	0	0
Ave_qPCR	0
RT-qPCR_primer-F	gaccagatgctgcaatcaac
RT-qPCR_primer-R	atccccctttgctgttcttt
protein_conc	5011	4735
WB_result	66.6	64.6
Ave_WB	65.6
WB_DONE_date	8/4/21	JESS
MW	44KD
IP	Rabbit / I
antibody_Cat#	A303-488A	LOT #1
Antibody DCC ID	ENCAB127PWU
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/5/21	11/5/21
repeat_library
Note
ID	7085	7086

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

Experiment Status

	BGHcLV29-65	BGHcLV29-66
Sample_ID	BGHcLV29-65	BGHcLV29-66
Sample Name
Sample Name	DCTN2-BGHcLV29-65	DCTN2-BGHcLV29-66
RBP	DCTN2	DCTN2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	10013	10014

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV29-65	BGHcLV29-66
Sample #	41	42
Sample Name	DCTN2-BGHcLV29-65	DCTN2-BGHcLV29-66
Sample_Name_Alias
Index Well Position	A06	B06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-11-01	2021-11-01
Lib_ID	Lib-211101	Lib-211101
Tecan_Location
Tecan
Tecan_date
Size_bp	299	300
Peak_Molarity	55.00	40.20
libSampleQC_DNA_Well	DNA_Library_set50/set1/A6.png	DNA_Library_set50/set1/B6.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set50/set1/A12.png	RNA_Library_set50/set1/B12.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGHcLV29-65	BGHcLV29-66
RBP	DCTN2	DCTN2
Batch_ID	BGHcLV29	BGHcLV29
WB_result	66.600	64.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3128	3129

Sequencing Information

	BGHcLV29-65	BGHcLV29-66
Sample_ID	BGHcLV29-65	BGHcLV29-66
Sample Name	DCTN2-BGHcLV29-65	DCTN2-BGHcLV29-66
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_H	set50_H
total_reads	60,968,014	84,675,602
total_aligned_reads	56,606,034	77,124,546
unique_aligned_reads	53,426,156	72,689,990
percent_uniqueAligned	0.87630	0.85845
correlation_replicates	0.997612	0.997612
spikein_reads	11,984	13,338
percent_spikeins	0.00020	0.00016
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1909	1910

Data Submission Information

	BGHcLV29-65	BGHcLV29-65	BGHcLV29-65	BGHcLV29-65	BGHcLV29-65	BGHcLV29-65	BGHcLV29-66	BGHcLV29-66	BGHcLV29-66	BGHcLV29-66
ENCODE_alias	brenton-graveley:DCTN2-BGHcLV29	brenton-graveley:DCTN2-BGHcLV29-65	brenton-graveley:L-DCTN2-BGHcLV29-65	brenton-graveley:DCTN2-BGHcLV29-65_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DCTN2-BGHcLV29-65_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DCTN2-BGHcLV29-HepG2	brenton-graveley:DCTN2-BGHcLV29-66	brenton-graveley:L-DCTN2-BGHcLV29-66	brenton-graveley:DCTN2-BGHcLV29-66_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DCTN2-BGHcLV29-66_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR146ITQ	ENCBS709SAZ	ENCLB940RPR	ENCFF405KEE	ENCFF949FOV	ENCSR768GEJ	ENCBS535IUJ	ENCLB079DGB	ENCFF564ONC	ENCFF096VRG
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV29-65	BGHcLV29-65	BGHcLV29-65	BGHcLV29-65	BGHcLV29-65	BGHcLV29-65	BGHcLV29-66	BGHcLV29-66	BGHcLV29-66	BGHcLV29-66
Sample Name	DCTN2-BGHcLV29-65	DCTN2-BGHcLV29-65	DCTN2-BGHcLV29-65	DCTN2-BGHcLV29-65	DCTN2-BGHcLV29-65	DCTN2-BGHcLV29-65	DCTN2-BGHcLV29-66	DCTN2-BGHcLV29-66	DCTN2-BGHcLV29-66	DCTN2-BGHcLV29-66
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV50H_biosample_protocol	LV50H_library_protocol				LV50H_biosample_protocol	LV50H_library_protocol
protocol_URL		DCTN2-BGHcLV29-65.pdf	L-DCTN2-BGHcLV29-65.pdf				DCTN2-BGHcLV29-66.pdf	L-DCTN2-BGHcLV29-66.pdf
ID	5862	5917	5989	6061	6133	6185	5918	5990	6062	6134

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-BGHcLV29-65_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1909	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5797
DCTN2-BGHcLV29-65_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1909	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5839
DCTN2-BGHcLV29-65_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1909					GRCh38	V40	DCTN2-BGHcLV29-65_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz,DCTN2-BGHcLV29-65_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18964
DCTN2-BGHcLV29-65_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1909					GRCh38	V40	DCTN2-BGHcLV29-65/Aligned.sortedByCoord.out.bam		ENCORE2	19022
DCTN2-BGHcLV29-65_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1909					GRCh38	V40	DCTN2-BGHcLV29-65/Aligned.sortedByCoord.out.bam		ENCORE2	19068
DCTN2-BGHcLV29-65_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1909					GRCh38	V40	DCTN2-BGHcLV29-65/Aligned.sortedByCoord.out.bam		ENCORE2	19114
DCTN2-BGHcLV29-65_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1909					GRCh38	V40	DCTN2-BGHcLV29-65/Aligned.sortedByCoord.out.bam		ENCORE2	19160
DCTN2-BGHcLV29-65_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1909					GRCh38	V40	DCTN2-BGHcLV29-65_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz,DCTN2-BGHcLV29-65_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19206
DCTN2-BGHcLV29-66_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1910	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5798
DCTN2-BGHcLV29-66_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1910	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5840
DCTN2-BGHcLV29-66_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1910					GRCh38	V40	DCTN2-BGHcLV29-66_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz,DCTN2-BGHcLV29-66_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18965
DCTN2-BGHcLV29-66_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1910					GRCh38	V40	DCTN2-BGHcLV29-66/Aligned.sortedByCoord.out.bam		ENCORE2	19023
DCTN2-BGHcLV29-66_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1910					GRCh38	V40	DCTN2-BGHcLV29-66/Aligned.sortedByCoord.out.bam		ENCORE2	19069
DCTN2-BGHcLV29-66_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1910					GRCh38	V40	DCTN2-BGHcLV29-66/Aligned.sortedByCoord.out.bam		ENCORE2	19115
DCTN2-BGHcLV29-66_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1910					GRCh38	V40	DCTN2-BGHcLV29-66/Aligned.sortedByCoord.out.bam		ENCORE2	19161
DCTN2-BGHcLV29-66_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1910					GRCh38	V40	DCTN2-BGHcLV29-66_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz,DCTN2-BGHcLV29-66_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19207