DBNL RNA-Seq in HepG2

General Information


RBP	DBNL
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DBNL-BGHcLV29-HepG2
ENCODE_series_ID	ENCSR980ERC
Batch_ID	BGHcLV29
Pool ID	Pool-211117
Local_Set_Name	set50_H
ENCODE_KD_Exp_ID	ENCSR256UIA
ENCODE_CN_Exp_ID	ENCSR462MFN
Rep1	DBNL-BGHcLV29-59
Rep2	DBNL-BGHcLV29-60
CN1	NT-BGHcLV29-1
CN2	NT-BGHcLV29-2
Rep1_qPCR	23.4
Rep2_qPCR	25.4
Rep1_WB	64.8
Rep2_WB	64.0
Antibody Cat#	A303-351A
Antibody Lot#	LOT #1
Antibody DCC ID
Status	Submitted
Project	ENCODE4
ID	862

Experiment Information (Status: Released)

	BGHcLV29-59	BGHcLV29-60
idx	898	899
TRCN#_or_BGC#	BGC#0000735	BGC#0000735
shRNA_or_gRNA_sequence	TTTAATCTCAGACACGGCAT	TTTAATCTCAGACACGGCAT
PAM	TGG	TGG
Name	DBNL_91	DBNL_91
Sample_ID	BGHcLV29-59	BGHcLV29-60
transduction_Date	7/20	7/20
days	D6	D6
RBP_name	DBNL	DBNL
qPCR_result	23.4	25.4
Ave_qPCR	24.4
RT-qPCR_primer-F	acctccagagcaggagacct
RT-qPCR_primer-R	gaatgtggtggtcaatgtgc
protein_conc	3636	5025
WB_result	64.8	64.0
Ave_WB	64.4
WB_DONE_date	10/14/21
MW	48KD
IP	Rabbit / I
antibody_Cat#	A303-351A	LOT #1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/5/21	11/5/21
repeat_library
Note
ID	7077	7078

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV29-59	BGHcLV29-60
Sample_ID	BGHcLV29-59	BGHcLV29-60
Sample Name
Sample Name	DBNL-BGHcLV29-59	DBNL-BGHcLV29-60
RBP	DBNL	DBNL
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	10009	10010

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV29-59	BGHcLV29-60
Sample #	37	38
Sample Name	DBNL-BGHcLV29-59	DBNL-BGHcLV29-60
Sample_Name_Alias
Index Well Position	E05	F05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-11-01	2021-11-01
Lib_ID	Lib-211101	Lib-211101
Tecan_Location
Tecan
Tecan_date
Size_bp	302	294
Peak_Molarity	43.80	39.00
libSampleQC_DNA_Well	DNA_Library_set50/set1/E5.png	DNA_Library_set50/set1/F5.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set50/set1/E11.png	RNA_Library_set50/set2/G12.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGHcLV29-59	BGHcLV29-60
RBP	DBNL	DBNL
Batch_ID	BGHcLV29	BGHcLV29
WB_result	64.800	64.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3124	3125

Sequencing Information

	BGHcLV29-59	BGHcLV29-60
Sample_ID	BGHcLV29-59	BGHcLV29-60
Sample Name	DBNL-BGHcLV29-59	DBNL-BGHcLV29-60
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_H	set50_H
total_reads	74,503,042	65,805,378
total_aligned_reads	69,029,676	61,029,270
unique_aligned_reads	65,050,790	57,555,578
percent_uniqueAligned	0.87313	0.87463
correlation_replicates	0.998446	0.998446
spikein_reads	9,426	9,764
percent_spikeins	0.00013	0.00015
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1905	1906

Data Submission Information

	BGHcLV29-59	BGHcLV29-59	BGHcLV29-59	BGHcLV29-59	BGHcLV29-59	BGHcLV29-59	BGHcLV29-60	BGHcLV29-60	BGHcLV29-60	BGHcLV29-60
ENCODE_alias	brenton-graveley:DBNL-BGHcLV29	brenton-graveley:DBNL-BGHcLV29-59	brenton-graveley:L-DBNL-BGHcLV29-59	brenton-graveley:DBNL-BGHcLV29-59_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DBNL-BGHcLV29-59_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DBNL-BGHcLV29-HepG2	brenton-graveley:DBNL-BGHcLV29-60	brenton-graveley:L-DBNL-BGHcLV29-60	brenton-graveley:DBNL-BGHcLV29-60_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DBNL-BGHcLV29-60_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR256UIA	ENCBS811ACC	ENCLB766WPP	ENCFF530UTJ	ENCFF983QDR	ENCSR980ERC	ENCBS839YIC	ENCLB922HEC	ENCFF395UPF	ENCFF898QCA
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV29-59	BGHcLV29-59	BGHcLV29-59	BGHcLV29-59	BGHcLV29-59	BGHcLV29-59	BGHcLV29-60	BGHcLV29-60	BGHcLV29-60	BGHcLV29-60
Sample Name	DBNL-BGHcLV29-59	DBNL-BGHcLV29-59	DBNL-BGHcLV29-59	DBNL-BGHcLV29-59	DBNL-BGHcLV29-59	DBNL-BGHcLV29-59	DBNL-BGHcLV29-60	DBNL-BGHcLV29-60	DBNL-BGHcLV29-60	DBNL-BGHcLV29-60
Selected	Yes	No	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
			LV50H_library_protocol					LV50H_library_protocol
protocol_URL			L-DBNL-BGHcLV29-59.pdf					L-DBNL-BGHcLV29-60.pdf
ID	5860	5913	5985	6057	6129	6183	5914	5986	6058	6130

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
DBNL-BGHcLV29-59_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1905	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5793
DBNL-BGHcLV29-59_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1905	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5835
DBNL-BGHcLV29-59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1905					GRCh38	V40	DBNL-BGHcLV29-59_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz,DBNL-BGHcLV29-59_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18960
DBNL-BGHcLV29-59_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1905					GRCh38	V40	DBNL-BGHcLV29-59/Aligned.sortedByCoord.out.bam		ENCORE2	19018
DBNL-BGHcLV29-59_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1905					GRCh38	V40	DBNL-BGHcLV29-59/Aligned.sortedByCoord.out.bam		ENCORE2	19064
DBNL-BGHcLV29-59_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1905					GRCh38	V40	DBNL-BGHcLV29-59/Aligned.sortedByCoord.out.bam		ENCORE2	19110
DBNL-BGHcLV29-59_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1905					GRCh38	V40	DBNL-BGHcLV29-59/Aligned.sortedByCoord.out.bam		ENCORE2	19156
DBNL-BGHcLV29-59_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1905					GRCh38	V40	DBNL-BGHcLV29-59_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz,DBNL-BGHcLV29-59_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19202
DBNL-BGHcLV29-60_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1906	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5794
DBNL-BGHcLV29-60_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1906	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5836
DBNL-BGHcLV29-60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1906					GRCh38	V40	DBNL-BGHcLV29-60_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz,DBNL-BGHcLV29-60_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18961
DBNL-BGHcLV29-60_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1906					GRCh38	V40	DBNL-BGHcLV29-60/Aligned.sortedByCoord.out.bam		ENCORE2	19019
DBNL-BGHcLV29-60_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1906					GRCh38	V40	DBNL-BGHcLV29-60/Aligned.sortedByCoord.out.bam		ENCORE2	19065
DBNL-BGHcLV29-60_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1906					GRCh38	V40	DBNL-BGHcLV29-60/Aligned.sortedByCoord.out.bam		ENCORE2	19111
DBNL-BGHcLV29-60_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1906					GRCh38	V40	DBNL-BGHcLV29-60/Aligned.sortedByCoord.out.bam		ENCORE2	19157
DBNL-BGHcLV29-60_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1906					GRCh38	V40	DBNL-BGHcLV29-60_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz,DBNL-BGHcLV29-60_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19203