DNAJA1 RNA-Seq in K562

General Information


RBP	DNAJA1
Cell_Line	K562
Method	CRISPR
Exp_Name	DNAJA1-BGKcLV40-K562
ENCODE_series_ID
Batch_ID	BGKcLV40
Pool ID	Pool-231226
Local_Set_Name	set67
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	DNAJA1-BGKcLV40-9
Rep2	DNAJA1-BGKcLV40-10
CN1	NT-BGKcLV40-1
CN2	NT-BGKcLV40-2
Rep1_qPCR	71.1
Rep2_qPCR	70.5
Rep1_WB	58.7
Rep2_WB	53.8
Antibody Cat#	A304-516A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1357

Experiment Information (Status: Submitting)

	BGKcLV40-9	BGKcLV40-10
idx	1492	1493
TRCN#_or_BGC#	BGC#0000931	BGC#0000931
shRNA_or_gRNA_sequence	GATGTAAAAGCTGCAACGGA	GATGTAAAAGCTGCAACGGA
PAM	AGG	AGG
Name	DNAJA1_80	DNAJA1_80
Sample_ID	BGKcLV40-9	BGKcLV40-10
transduction_Date	10/31/23	10/31/23
days	D6	D6
RBP_name	DNAJA1	DNAJA1
qPCR_result	71.1	70.5
Ave_qPCR	70.8
RT-qPCR_primer-F	tcgtcatcacctctcatcca
RT-qPCR_primer-R	cgataaattggcatgccttc
protein_conc	3085	3299
WB_result	58.7	53.8
Ave_WB	56.2
WB_DONE_date	11/17/23
MW	45kd
IP
antibody_Cat#	A304-516A	lot # 1
Antibody DCC ID
submitted_to_DCC_date	1/4/24
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5678	5679

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DNAJA1	Product_ID: A304-516A Lot_ID: 1 Source: Bethyl Labs Target Name: DNAJA1-human

Experiment Status

	BGKcLV40-9	BGKcLV40-10
Sample_ID	BGKcLV40-9	BGKcLV40-10
Sample Name
Sample Name	DNAJA1-BGKcLV40-9	DNAJA1-BGKcLV40-10
RBP	DNAJA1	DNAJA1
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2024-02-16	2024-02-16
Project	ENCORE2	ENCORE2
Note
ID	12758	12759

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV40-9	BGKcLV40-10
Sample #	5	6
Sample Name	DNAJA1-BGKcLV40-9	DNAJA1-BGKcLV40-10
Sample_Name_Alias
Index Well Position	E01	F01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-12-19	2023-12-19
Lib_ID	Lib-231219	Lib-231219
Tecan_Location
Tecan
Tecan_date
Size_bp	295	287
Peak_Molarity	61.70	60.50
libSampleQC_DNA_Well	DNA_Library_set67/set1/E7.png	DNA_Library_set67/set1/F7.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set67/set1/E1.png	RNA_Library_set67/set1/F1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-12-26	2023-12-26
Sample_ID	BGKcLV40-9	BGKcLV40-10
RBP	DNAJA1	DNAJA1
Batch_ID	BGKcLV40	BGKcLV40
WB_result	58.700	53.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4142	4143

Sequencing Information

	BGKcLV40-9	BGKcLV40-10
Sample_ID	BGKcLV40-9	BGKcLV40-10
Sample Name	DNAJA1-BGKcLV40-9	DNAJA1-BGKcLV40-10
Pool ID	Pool-231226	Pool-231226
LocalServer_folder	set67	set67
total_reads	36,861,482	38,055,920
total_aligned_reads	31,425,549	32,034,087
unique_aligned_reads	28,952,834	29,467,904
percent_uniqueAligned	0.78545	0.77433
correlation_replicates	0.998809	0.998809
spikein_reads	4,324	9,344
percent_spikeins	0.00012	0.00025
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	2797	2798

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
DNAJA1-BGKcLV40-9_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2797	NovaSeq6000	100	paired-ended	1				NT-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28144
DNAJA1-BGKcLV40-9_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2797	NovaSeq6000	100	paired-ended	2				NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28188
DNAJA1-BGKcLV40-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2797					GRCh38	V40	DNAJA1-BGKcLV40-9_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz,DNAJA1-BGKcLV40-9_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28232
DNAJA1-BGKcLV40-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2797					GRCh38	V40	DNAJA1-BGKcLV40-9/Aligned.sortedByCoord.out.bam		ENCORE2	28276
DNAJA1-BGKcLV40-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2797					GRCh38	V40	DNAJA1-BGKcLV40-9/Aligned.sortedByCoord.out.bam		ENCORE2	28320
DNAJA1-BGKcLV40-9_Signal.Unique.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2797					GRCh38	V40	DNAJA1-BGKcLV40-9/Aligned.sortedByCoord.out.bam		ENCORE2	28364
DNAJA1-BGKcLV40-9_Signal.Unique.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2797					GRCh38	V40	DNAJA1-BGKcLV40-9/Aligned.sortedByCoord.out.bam		ENCORE2	28408
DNAJA1-BGKcLV40-9_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2797					GRCh38	V40	DNAJA1-BGKcLV40-9_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz,DNAJA1-BGKcLV40-9_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28452
DNAJA1-BGKcLV40-10_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2798	NovaSeq6000	100	paired-ended	1				NT-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28143
DNAJA1-BGKcLV40-10_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2798	NovaSeq6000	100	paired-ended	2				NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28187
DNAJA1-BGKcLV40-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2798					GRCh38	V40	DNAJA1-BGKcLV40-10_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz,DNAJA1-BGKcLV40-10_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28231
DNAJA1-BGKcLV40-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2798					GRCh38	V40	DNAJA1-BGKcLV40-10/Aligned.sortedByCoord.out.bam		ENCORE2	28275
DNAJA1-BGKcLV40-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2798					GRCh38	V40	DNAJA1-BGKcLV40-10/Aligned.sortedByCoord.out.bam		ENCORE2	28319
DNAJA1-BGKcLV40-10_Signal.Unique.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2798					GRCh38	V40	DNAJA1-BGKcLV40-10/Aligned.sortedByCoord.out.bam		ENCORE2	28363
DNAJA1-BGKcLV40-10_Signal.Unique.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2798					GRCh38	V40	DNAJA1-BGKcLV40-10/Aligned.sortedByCoord.out.bam		ENCORE2	28407
DNAJA1-BGKcLV40-10_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2798					GRCh38	V40	DNAJA1-BGKcLV40-10_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz,DNAJA1-BGKcLV40-10_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28451