DNAJC2 RNA-Seq in K562

General Information


RBP	DNAJC2
Cell_Line	K562
Method	CRISPR
Exp_Name	DNAJC2-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	DNAJC2-BGKcLV38-21
Rep2	DNAJC2-BGKcLV38-22
CN1	NT-BGKcLV38-1
CN2	NT-BGKcLV38-2
Rep1_qPCR	56.4
Rep2_qPCR	45.8
Rep1_WB	71.0
Rep2_WB	79.7
Antibody Cat#	A303-722A
Antibody Lot#	lot# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1027

Experiment Information (Status: Submitting)

	BGKcLV38-21	BGKcLV38-21	BGKcLV38-22	BGKcLV38-22
idx	1438	0	1439	0
TRCN#_or_BGC#	BGC#0000936	BGC#0000936	BGC#0000936	BGC#0000936
shRNA_or_gRNA_sequence	AGAAGCTGCTCGGTTAGCTA	AGAAGCTGCTCGGTTAGCTA	AGAAGCTGCTCGGTTAGCTA	AGAAGCTGCTCGGTTAGCTA
PAM	AGG	AGG	AGG	AGG
Name	DNAJC2_94	DNAJC2_94	DNAJC2_94	DNAJC2_94
Sample_ID	BGKcLV38-21	BGKcLV38-21	BGKcLV38-22	BGKcLV38-22
transduction_Date	10/18/22	10/18/22	10/18/22	10/18/22
days	D6	D6	D6	D6
RBP_name	DNAJC2	DNAJC2	DNAJC2	DNAJC2
qPCR_result	56.4	56.4	45.8	45.8
Ave_qPCR	51.1	51.1
RT-qPCR_primer-F	gaagctaaacggaaggagca	gaagctaaacggaaggagca
RT-qPCR_primer-R	gcaatgcttgctgtctgact	gcaatgcttgctgtctgact
protein_conc	3621	3621	3477	3477
WB_result	71.0	69.7	79.7	63.9766
Ave_WB	75.4
WB_DONE_date	10/26/22	2/29/24
MW	72KD	72KD
IP
antibody_Cat#	A303-722A	12844S	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	5608	5610	5609	5611

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DNAJC2	Product_ID: A303-722A Lot_ID: 1 Source: Bethyl Labs Target Name: DNAJC2-human
DNAJC2	Product_ID: 12844S Lot_ID: 1 Source: Cell Signaling Technology Target Name: DNAJC2-human

Experiment Status

	BGKcLV38-21	BGKcLV38-22
Sample_ID	BGKcLV38-21	BGKcLV38-22
Sample Name
Sample Name	DNAJC2-BGKcLV38-21	DNAJC2-BGKcLV38-22
RBP	DNAJC2	DNAJC2
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11028	11029

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV38-21	BGKcLV38-22
Sample #	63	64
Sample Name	DNAJC2-BGKcLV38-21	DNAJC2-BGKcLV38-22
Sample_Name_Alias
Index Well Position	E09	F09
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	296
Peak_Molarity	63.80	74.40
libSampleQC_DNA_Well	DNA_Library_set54-56/set2/E9.png	DNA_Library_set54-56/set2/F9.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set54-56/set1/G8.png	RNA_Library_set54-56/set1/H8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV38-21	BGKcLV38-22
RBP	DNAJC2	DNAJC2
Batch_ID	BGKcLV38	BGKcLV38
WB_result	71.000	79.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3434	3435

Sequencing Information

	BGKcLV38-21	BGKcLV38-22
Sample_ID	BGKcLV38-21	BGKcLV38-22
Sample Name	DNAJC2-BGKcLV38-21	DNAJC2-BGKcLV38-22
Pool ID	Pool-230127C	Pool-230127C
LocalServer_folder	set56	set56
total_reads	89,307,721	61,515,753
total_aligned_reads	81,782,035	56,544,327
unique_aligned_reads	76,117,179	52,492,210
percent_uniqueAligned	0.85230	0.85331
correlation_replicates	0.996859	0.996859
spikein_reads	11,540	10,106
percent_spikeins	0.00013	0.00016
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2305	2306

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
DNAJC2-BGKcLV38-21_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2305	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	8310
DNAJC2-BGKcLV38-21_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2305	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	8348
DNAJC2-BGKcLV38-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2305					GRCh38	V40	DNAJC2-BGKcLV38-21_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,DNAJC2-BGKcLV38-21_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16962
DNAJC2-BGKcLV38-21_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	2305					GRCh38	V40	DNAJC2-BGKcLV38-21/Aligned.sortedByCoord.out.bam		ENCORE2	17000
DNAJC2-BGKcLV38-21_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	2305					GRCh38	V40	DNAJC2-BGKcLV38-21/Aligned.sortedByCoord.out.bam		ENCORE2	17038
DNAJC2-BGKcLV38-21_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	2305					GRCh38	V40	DNAJC2-BGKcLV38-21/Aligned.sortedByCoord.out.bam		ENCORE2	17076
DNAJC2-BGKcLV38-21_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	2305					GRCh38	V40	DNAJC2-BGKcLV38-21/Aligned.sortedByCoord.out.bam		ENCORE2	17114
DNAJC2-BGKcLV38-21_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2305					GRCh38	V40	DNAJC2-BGKcLV38-21_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,DNAJC2-BGKcLV38-21_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17152
DNAJC2-BGKcLV38-22_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2306	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	8311
DNAJC2-BGKcLV38-22_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2306	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	8349
DNAJC2-BGKcLV38-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2306					GRCh38	V40	DNAJC2-BGKcLV38-22_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz,DNAJC2-BGKcLV38-22_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16963
DNAJC2-BGKcLV38-22_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	2306					GRCh38	V40	DNAJC2-BGKcLV38-22/Aligned.sortedByCoord.out.bam		ENCORE2	17001
DNAJC2-BGKcLV38-22_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	2306					GRCh38	V40	DNAJC2-BGKcLV38-22/Aligned.sortedByCoord.out.bam		ENCORE2	17039
DNAJC2-BGKcLV38-22_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	2306					GRCh38	V40	DNAJC2-BGKcLV38-22/Aligned.sortedByCoord.out.bam		ENCORE2	17077
DNAJC2-BGKcLV38-22_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	2306					GRCh38	V40	DNAJC2-BGKcLV38-22/Aligned.sortedByCoord.out.bam		ENCORE2	17115
DNAJC2-BGKcLV38-22_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2306					GRCh38	V40	DNAJC2-BGKcLV38-22_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz,DNAJC2-BGKcLV38-22_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17153