DNAJC1 RNA-Seq in K562

General Information


RBP	DNAJC1
Cell_Line	K562
Method	CRISPR
Exp_Name	DNAJC1-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	DNAJC1-BGKcLV38-19
Rep2	DNAJC1-BGKcLV38-20
CN1	NT-BGKcLV38-1
CN2	NT-BGKcLV38-2
Rep1_qPCR	72.3
Rep2_qPCR	63.0
Rep1_WB	63.5
Rep2_WB	65.4
Antibody Cat#	A304-055A
Antibody Lot#	lot# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1026

Experiment Information (Status: Submitting)

	BGKcLV38-19	BGKcLV38-20
idx	1436	1437
TRCN#_or_BGC#	BGC#0000934	BGC#0000934
shRNA_or_gRNA_sequence	TGTGGTTTGGTCAATCTACC	TGTGGTTTGGTCAATCTACC
PAM	tgg	tgg
Name	DNAJC1_91	DNAJC1_91
Sample_ID	BGKcLV38-19	BGKcLV38-20
transduction_Date	10/18/22	10/18/22
days	D6	D6
RBP_name	DNAJC1	DNAJC1
qPCR_result	72.3	63.0
Ave_qPCR	67.7
RT-qPCR_primer-F	tctgcagacatcagaaaagca
RT-qPCR_primer-R	aacttcataaatggccaccaa
protein_conc	2928	3926
WB_result	63.5	65.4
Ave_WB	64.4
WB_DONE_date	10/26/22
MW	64KD
IP
antibody_Cat#	A304-055A	lot# 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5606	5607

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DNAJC1	Product_ID: A304-055A Lot_ID: 1 Source: Bethyl Labs Target Name: DNAJC1-human

Experiment Status

	BGKcLV38-19	BGKcLV38-20
Sample_ID	BGKcLV38-19	BGKcLV38-20
Sample Name
Sample Name	DNAJC1-BGKcLV38-19	DNAJC1-BGKcLV38-20
RBP	DNAJC1	DNAJC1
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11026	11027

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV38-19	BGKcLV38-20
Sample #	61	62
Sample Name	DNAJC1-BGKcLV38-19	DNAJC1-BGKcLV38-20
Sample_Name_Alias
Index Well Position	C09	D09
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	306	305
Peak_Molarity	66.60	66.10
libSampleQC_DNA_Well	DNA_Library_set54-56/set2/C9.png	DNA_Library_set54-56/set2/D9.png
RIN	9.8	10.0
libSample_RNA_Well	RNA_Library_set54-56/set1/E8.png	RNA_Library_set54-56/set1/F8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV38-19	BGKcLV38-20
RBP	DNAJC1	DNAJC1
Batch_ID	BGKcLV38	BGKcLV38
WB_result	63.500	65.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3432	3433

Sequencing Information

	BGKcLV38-19	BGKcLV38-20
Sample_ID	BGKcLV38-19	BGKcLV38-20
Sample Name	DNAJC1-BGKcLV38-19	DNAJC1-BGKcLV38-20
Pool ID	Pool-230127C	Pool-230127C
LocalServer_folder	set56	set56
total_reads	77,109,524	41,425,525
total_aligned_reads	71,007,924	37,539,351
unique_aligned_reads	66,083,946	34,925,537
percent_uniqueAligned	0.85701	0.84309
correlation_replicates	0.996517	0.996517
spikein_reads	11,556	6,650
percent_spikeins	0.00015	0.00016
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2303	2304

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
DNAJC1-BGKcLV38-19_S59_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2303	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	8308
DNAJC1-BGKcLV38-19_S59_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2303	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	8346
DNAJC1-BGKcLV38-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2303					GRCh38	V40	DNAJC1-BGKcLV38-19_S59_L002_R1_001.filtered.trimmed.paired.fastq.gz,DNAJC1-BGKcLV38-19_S59_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16960
DNAJC1-BGKcLV38-19_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	2303					GRCh38	V40	DNAJC1-BGKcLV38-19/Aligned.sortedByCoord.out.bam		ENCORE2	16998
DNAJC1-BGKcLV38-19_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	2303					GRCh38	V40	DNAJC1-BGKcLV38-19/Aligned.sortedByCoord.out.bam		ENCORE2	17036
DNAJC1-BGKcLV38-19_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	2303					GRCh38	V40	DNAJC1-BGKcLV38-19/Aligned.sortedByCoord.out.bam		ENCORE2	17074
DNAJC1-BGKcLV38-19_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	2303					GRCh38	V40	DNAJC1-BGKcLV38-19/Aligned.sortedByCoord.out.bam		ENCORE2	17112
DNAJC1-BGKcLV38-19_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2303					GRCh38	V40	DNAJC1-BGKcLV38-19_S59_L002_R1_001.filtered.trimmed.paired.fastq.gz,DNAJC1-BGKcLV38-19_S59_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17150
DNAJC1-BGKcLV38-20_S60_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2304	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	8309
DNAJC1-BGKcLV38-20_S60_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2304	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	8347
DNAJC1-BGKcLV38-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2304					GRCh38	V40	DNAJC1-BGKcLV38-20_S60_L002_R1_001.filtered.trimmed.paired.fastq.gz,DNAJC1-BGKcLV38-20_S60_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16961
DNAJC1-BGKcLV38-20_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	2304					GRCh38	V40	DNAJC1-BGKcLV38-20/Aligned.sortedByCoord.out.bam		ENCORE2	16999
DNAJC1-BGKcLV38-20_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	2304					GRCh38	V40	DNAJC1-BGKcLV38-20/Aligned.sortedByCoord.out.bam		ENCORE2	17037
DNAJC1-BGKcLV38-20_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	2304					GRCh38	V40	DNAJC1-BGKcLV38-20/Aligned.sortedByCoord.out.bam		ENCORE2	17075
DNAJC1-BGKcLV38-20_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	2304					GRCh38	V40	DNAJC1-BGKcLV38-20/Aligned.sortedByCoord.out.bam		ENCORE2	17113
DNAJC1-BGKcLV38-20_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2304					GRCh38	V40	DNAJC1-BGKcLV38-20_S60_L002_R1_001.filtered.trimmed.paired.fastq.gz,DNAJC1-BGKcLV38-20_S60_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17151