DNAJC1 RNA-Seq in HepG2

General Information


RBP	DNAJC1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DNAJC1-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	DNAJC1-BGHcLV39-27
Rep2	DNAJC1-BGHcLV39-28
CN1	NT-BGHcLV39-1
CN2	NT-BGHcLV39-2
Rep1_qPCR	75.9
Rep2_qPCR	80.1
Rep1_WB	62.3
Rep2_WB	70.6
Antibody Cat#	A304-055A
Antibody Lot#	lot# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1247

Experiment Information (Status: Submitting)

	BGHcLV39-27	BGHcLV39-28
idx	1229	1230
TRCN#_or_BGC#	BGC#0000934	BGC#0000934
shRNA_or_gRNA_sequence	TGTGGTTTGGTCAATCTACC	TGTGGTTTGGTCAATCTACC
PAM	tgg	tgg
Name	DNAJC1_91	DNAJC1_91
Sample_ID	BGHcLV39-27	BGHcLV39-28
transduction_Date	6/10/23	6/10/23
days	D6	D6
RBP_name	DNAJC1	DNAJC1
qPCR_result	75.9	80.1
Ave_qPCR	78.0
RT-qPCR_primer-F	tcaaaactcggtgcttcaga
RT-qPCR_primer-R	gtttgcatggaagcaaatca
protein_conc	1277	1267
WB_result	62.3	70.6
Ave_WB	66.4
WB_DONE_date	7/5/23
MW	64KD
IP
antibody_Cat#	A304-055A	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	7420	7421

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

	BGHcLV39-27	BGHcLV39-28
Sample_ID	BGHcLV39-27	BGHcLV39-28
Sample Name
Sample Name	DNAJC1-BGHcLV39-27	DNAJC1-BGHcLV39-28
RBP	DNAJC1	DNAJC1
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-12-30	2023-12-30
Project	ENCORE2	ENCORE2
Note
ID	11986	11987

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV39-27	BGHcLV39-28
Sample #	13	14
Sample Name	DNAJC1-BGHcLV39-27	DNAJC1-BGHcLV39-28
Sample_Name_Alias
Index Well Position	E02	F02
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	279	281
Peak_Molarity	52.60	64.10
libSampleQC_DNA_Well	DNA_Library_set63/set1/E10.png	DNA_Library_set63/set1/F10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set63/set1/E10.png	RNA_Library_set63/set1/F10.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-08-30	2023-08-30
Sample_ID	BGHcLV39-27	BGHcLV39-28
RBP	DNAJC1	DNAJC1
Batch_ID	BGHcLV39	BGHcLV39
WB_result	62.300	70.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3756	3757

Sequencing Information

	BGHcLV39-27	BGHcLV39-28
Sample_ID	BGHcLV39-27	BGHcLV39-28
Sample Name	DNAJC1-BGHcLV39-27	DNAJC1-BGHcLV39-28
Pool ID	Pool-230830	Pool-230830
LocalServer_folder	set63	set63
total_reads	17,839,130	85,569,905
total_aligned_reads	14,484,825	72,672,634
unique_aligned_reads	13,657,098	68,600,652
percent_uniqueAligned	0.76557	0.80169
correlation_replicates	0.999505	0.999505
spikein_reads	13,338	73,060
percent_spikeins	0.00075	0.00085
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2655	2656

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-BGHcLV39-27_S488_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2655	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	8640
DNAJC1-BGHcLV39-27_S488_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2655	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	8666
DNAJC1-BGHcLV39-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2655					GRCh38	V40	DNAJC1-BGHcLV39-27_S488_L004_R1_001.filtered.trimmed.paired.fastq.gz,DNAJC1-BGHcLV39-27_S488_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9937
DNAJC1-BGHcLV39-27_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	2655					GRCh38	V40	DNAJC1-BGHcLV39-27/Aligned.sortedByCoord.out.bam		ENCORE2	9963
DNAJC1-BGHcLV39-27_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	2655					GRCh38	V40	DNAJC1-BGHcLV39-27/Aligned.sortedByCoord.out.bam		ENCORE2	9989
DNAJC1-BGHcLV39-27_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	2655					GRCh38	V40	DNAJC1-BGHcLV39-27/Aligned.sortedByCoord.out.bam		ENCORE2	10015
DNAJC1-BGHcLV39-27_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	2655					GRCh38	V40	DNAJC1-BGHcLV39-27/Aligned.sortedByCoord.out.bam		ENCORE2	10041
DNAJC1-BGHcLV39-27_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2655					GRCh38	V40	DNAJC1-BGHcLV39-27_S488_L004_R1_001.filtered.trimmed.paired.fastq.gz,DNAJC1-BGHcLV39-27_S488_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10067
DNAJC1-BGHcLV39-28_S9_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2656	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	8641
DNAJC1-BGHcLV39-28_S9_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2656	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	8667
DNAJC1-BGHcLV39-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2656					GRCh38	V40	DNAJC1-BGHcLV39-28_S9_R1_001.filtered.trimmed.paired.fastq.gz,DNAJC1-BGHcLV39-28_S9_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9938
DNAJC1-BGHcLV39-28_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	2656					GRCh38	V40	DNAJC1-BGHcLV39-28/Aligned.sortedByCoord.out.bam		ENCORE2	9964
DNAJC1-BGHcLV39-28_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	2656					GRCh38	V40	DNAJC1-BGHcLV39-28/Aligned.sortedByCoord.out.bam		ENCORE2	9990
DNAJC1-BGHcLV39-28_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	2656					GRCh38	V40	DNAJC1-BGHcLV39-28/Aligned.sortedByCoord.out.bam		ENCORE2	10016
DNAJC1-BGHcLV39-28_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	2656					GRCh38	V40	DNAJC1-BGHcLV39-28/Aligned.sortedByCoord.out.bam		ENCORE2	10042
DNAJC1-BGHcLV39-28_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2656					GRCh38	V40	DNAJC1-BGHcLV39-28_S9_R1_001.filtered.trimmed.paired.fastq.gz,DNAJC1-BGHcLV39-28_S9_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10068