DNAJA1 RNA-Seq in HepG2

General Information


RBP	DNAJA1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DNAJA1-BGHcLV39-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV39
Pool ID	Pool-230830
Local_Set_Name	set63
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	DNAJA1-BGHcLV39-25
Rep2	DNAJA1-BGHcLV39-26
CN1	NT-BGHcLV39-1
CN2	NT-BGHcLV39-2
Rep1_qPCR	30.3
Rep2_qPCR	53.8
Rep1_WB	75.9
Rep2_WB	73.4
Antibody Cat#	A304-516A
Antibody Lot#	lot# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1246

Experiment Information (Status: Submitting)

	BGHcLV39-25	BGHcLV39-26
idx	1227	1228
TRCN#_or_BGC#	BGC#0000931	BGC#0000931
shRNA_or_gRNA_sequence	GATGTAAAAGCTGCAACGGA	GATGTAAAAGCTGCAACGGA
PAM	AGG	AGG
Name	DNAJA1_80	DNAJA1_80
Sample_ID	BGHcLV39-25	BGHcLV39-26
transduction_Date	6/10/23	6/10/23
days	D6	D6
RBP_name	DNAJA1	DNAJA1
qPCR_result	30.3	53.8
Ave_qPCR	42.0
RT-qPCR_primer-F	tcgtcatcacctctcatcca
RT-qPCR_primer-R	cgataaattggcatgccttc
protein_conc	1247	1192
WB_result	75.9	73.4
Ave_WB	74.6
WB_DONE_date	7/5/23
MW	45KD
IP
antibody_Cat#	A304-516A	lot# 1
Antibody DCC ID
submitted_to_DCC_date	9/6/23
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	7418	7419

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

	BGHcLV39-25	BGHcLV39-26
Sample_ID	BGHcLV39-25	BGHcLV39-26
Sample Name
Sample Name	DNAJA1-BGHcLV39-25	DNAJA1-BGHcLV39-26
RBP	DNAJA1	DNAJA1
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-12-30	2023-12-30
Project	ENCORE2	ENCORE2
Note
ID	11984	11985

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV39-25	BGHcLV39-26
Sample #	11	12
Sample Name	DNAJA1-BGHcLV39-25	DNAJA1-BGHcLV39-26
Sample_Name_Alias
Index Well Position	C02	D02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-08-28	2023-08-28
Lib_ID	Lib-230828	Lib-230828
Tecan_Location
Tecan
Tecan_date
Size_bp	281	278
Peak_Molarity	64.80	91.10
libSampleQC_DNA_Well	DNA_Library_set63/set1/C10.png	DNA_Library_set63/set1/D10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set63/set1/C10.png	RNA_Library_set63/set1/D10.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-08-30	2023-08-30
Sample_ID	BGHcLV39-25	BGHcLV39-26
RBP	DNAJA1	DNAJA1
Batch_ID	BGHcLV39	BGHcLV39
WB_result	75.900	73.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3754	3755

Sequencing Information

	BGHcLV39-25	BGHcLV39-26
Sample_ID	BGHcLV39-25	BGHcLV39-26
Sample Name	DNAJA1-BGHcLV39-25	DNAJA1-BGHcLV39-26
Pool ID	Pool-230830	Pool-230830
LocalServer_folder	set63	set63
total_reads	54,234,941	13,045,442
total_aligned_reads	45,415,586	10,913,742
unique_aligned_reads	42,810,010	10,294,554
percent_uniqueAligned	0.78934	0.78913
correlation_replicates	0.998700	0.998700
spikein_reads	116,536	10,330
percent_spikeins	0.00215	0.00079
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2653	2654

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-BGHcLV39-25_S8_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2653	NovaSeq6000	100	paired-ended	1				NT-BGHcLV39-1_S476_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8638
DNAJA1-BGHcLV39-25_S8_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2653	NovaSeq6000	100	paired-ended	2				NT-BGHcLV39-1_S476_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8664
DNAJA1-BGHcLV39-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2653					GRCh38	V40	DNAJA1-BGHcLV39-25_S8_R1_001.filtered.trimmed.paired.fastq.gz,DNAJA1-BGHcLV39-25_S8_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9935
DNAJA1-BGHcLV39-25_Signal.Unique.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2653					GRCh38	V40	DNAJA1-BGHcLV39-25/Aligned.sortedByCoord.out.bam		ENCORE2	9961
DNAJA1-BGHcLV39-25_Signal.Unique.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2653					GRCh38	V40	DNAJA1-BGHcLV39-25/Aligned.sortedByCoord.out.bam		ENCORE2	9987
DNAJA1-BGHcLV39-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2653					GRCh38	V40	DNAJA1-BGHcLV39-25/Aligned.sortedByCoord.out.bam		ENCORE2	10013
DNAJA1-BGHcLV39-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2653					GRCh38	V40	DNAJA1-BGHcLV39-25/Aligned.sortedByCoord.out.bam		ENCORE2	10039
DNAJA1-BGHcLV39-25_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2653					GRCh38	V40	DNAJA1-BGHcLV39-25_S8_R1_001.filtered.trimmed.paired.fastq.gz,DNAJA1-BGHcLV39-25_S8_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10065
DNAJA1-BGHcLV39-26_S487_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2654	NovaSeq6000	100	paired-ended	1				NT-BGHcLV39-1_S476_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8639
DNAJA1-BGHcLV39-26_S487_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2654	NovaSeq6000	100	paired-ended	2				NT-BGHcLV39-1_S476_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8665
DNAJA1-BGHcLV39-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2654					GRCh38	V40	DNAJA1-BGHcLV39-26_S487_L004_R1_001.filtered.trimmed.paired.fastq.gz,DNAJA1-BGHcLV39-26_S487_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9936
DNAJA1-BGHcLV39-26_Signal.Unique.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2654					GRCh38	V40	DNAJA1-BGHcLV39-26/Aligned.sortedByCoord.out.bam		ENCORE2	9962
DNAJA1-BGHcLV39-26_Signal.Unique.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2654					GRCh38	V40	DNAJA1-BGHcLV39-26/Aligned.sortedByCoord.out.bam		ENCORE2	9988
DNAJA1-BGHcLV39-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2654					GRCh38	V40	DNAJA1-BGHcLV39-26/Aligned.sortedByCoord.out.bam		ENCORE2	10014
DNAJA1-BGHcLV39-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2654					GRCh38	V40	DNAJA1-BGHcLV39-26/Aligned.sortedByCoord.out.bam		ENCORE2	10040
DNAJA1-BGHcLV39-26_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2654					GRCh38	V40	DNAJA1-BGHcLV39-26_S487_L004_R1_001.filtered.trimmed.paired.fastq.gz,DNAJA1-BGHcLV39-26_S487_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10066