DARS RNA-Seq in HepG2

General Information


RBP	DARS
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DARS-BGHcLV29-HepG2
ENCODE_series_ID	ENCSR073ZUO
Batch_ID	BGHcLV29
Pool ID	Pool-211117
Local_Set_Name	set50_H
ENCODE_KD_Exp_ID	ENCSR574ZTO
ENCODE_CN_Exp_ID	ENCSR462MFN
Rep1	DARS-BGHcLV29-57
Rep2	DARS-BGHcLV29-58
CN1	NT-BGHcLV29-1
CN2	NT-BGHcLV29-2
Rep1_qPCR	0
Rep2_qPCR	0
Rep1_WB	51.2
Rep2_WB	54.2
Antibody Cat#	A304-799A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB187BNV
Status	Submitted
Project	ENCODE4
ID	861

Experiment Information (Status: Released)

	BGHcLV29-57	BGHcLV29-58
idx	896	897
TRCN#_or_BGC#	BGC#0000733	BGC#0000733
shRNA_or_gRNA_sequence	GTCCAGGCTCTTGTGGCGGT	GTCCAGGCTCTTGTGGCGGT
PAM	GGG	GGG
Name	DARS1_86	DARS1_86
Sample_ID	BGHcLV29-57	BGHcLV29-58
transduction_Date	7/20	7/20
days	D6	D6
RBP_name	DARS	DARS
qPCR_result	0	0
Ave_qPCR	0
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3307	3918
WB_result	51.2	54.2
Ave_WB	52.7
WB_DONE_date	8/2/21	JESS
MW	57KD
IP	Rabbit / I
antibody_Cat#	A304-799A	LOT #1
Antibody DCC ID	ENCAB187BNV
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	7075	7076

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DARS	Product_ID: A304-799A Lot_ID: 1 Source: Bethyl Labs Target Name: DARS-human

Experiment Status

	BGHcLV29-57	BGHcLV29-58
Sample_ID	BGHcLV29-57	BGHcLV29-58
Sample Name
Sample Name	DARS-BGHcLV29-57	DARS-BGHcLV29-58
RBP	DARS	DARS
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	10007	10008

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV29-57	BGHcLV29-58
Sample #	35	36
Sample Name	DARS-BGHcLV29-57	DARS-BGHcLV29-58
Sample_Name_Alias
Index Well Position	C05	D05
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	300	299
Peak_Molarity	34.10	25.70
libSampleQC_DNA_Well	DNA_Library_set50/set1/C5.png	DNA_Library_set50/set1/D5.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set50/set1/C11.png	RNA_Library_set50/set1/D11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGHcLV29-57	BGHcLV29-58
RBP	DARS	DARS
Batch_ID	BGHcLV29	BGHcLV29
WB_result	51.200	54.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3122	3123

Sequencing Information

	BGHcLV29-57	BGHcLV29-58
Sample_ID	BGHcLV29-57	BGHcLV29-58
Sample Name	DARS-BGHcLV29-57	DARS-BGHcLV29-58
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_H	set50_H
total_reads	82,876,644	95,103,088
total_aligned_reads	75,255,466	87,151,968
unique_aligned_reads	70,950,716	82,017,158
percent_uniqueAligned	0.85610	0.86240
correlation_replicates	0.992228	0.992228
spikein_reads	15,634	8,738
percent_spikeins	0.00019	0.00009
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1903	1904

Data Submission Information

	BGHcLV29-57	BGHcLV29-57	BGHcLV29-57	BGHcLV29-57	BGHcLV29-57	BGHcLV29-57	BGHcLV29-58	BGHcLV29-58	BGHcLV29-58	BGHcLV29-58
ENCODE_alias	brenton-graveley:DARS-BGHcLV29	brenton-graveley:DARS-BGHcLV29-57	brenton-graveley:L-DARS-BGHcLV29-57	brenton-graveley:DARS-BGHcLV29-57_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DARS-BGHcLV29-57_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DARS-BGHcLV29-HepG2	brenton-graveley:DARS-BGHcLV29-58	brenton-graveley:L-DARS-BGHcLV29-58	brenton-graveley:DARS-BGHcLV29-58_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DARS-BGHcLV29-58_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR574ZTO	ENCBS993GYU	ENCLB766JBZ	ENCFF108BLS	ENCFF367TUN	ENCSR073ZUO	ENCBS735KRY	ENCLB880BBL	ENCFF517ILP	ENCFF389XFB
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	BGHcLV29-57	BGHcLV29-57	BGHcLV29-57	BGHcLV29-57	BGHcLV29-57	BGHcLV29-57	BGHcLV29-58	BGHcLV29-58	BGHcLV29-58	BGHcLV29-58
Sample Name	DARS-BGHcLV29-57	DARS-BGHcLV29-57	DARS-BGHcLV29-57	DARS-BGHcLV29-57	DARS-BGHcLV29-57	DARS-BGHcLV29-57	DARS-BGHcLV29-58	DARS-BGHcLV29-58	DARS-BGHcLV29-58	DARS-BGHcLV29-58
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	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_biosample_protocol	LV50H_library_protocol				LV50H_biosample_protocol	LV50H_library_protocol
protocol_URL		DARS-BGHcLV29-57.pdf	L-DARS-BGHcLV29-57.pdf				DARS-BGHcLV29-58.pdf	L-DARS-BGHcLV29-58.pdf
ID	5859	5911	5983	6055	6127	6182	5912	5984	6056	6128

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
DARS-BGHcLV29-57_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1903	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	5791
DARS-BGHcLV29-57_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1903	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	5833
DARS-BGHcLV29-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1903					GRCh38	V40	DARS-BGHcLV29-57_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,DARS-BGHcLV29-57_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18958
DARS-BGHcLV29-57_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	1903					GRCh38	V40	DARS-BGHcLV29-57/Aligned.sortedByCoord.out.bam		ENCORE2	19016
DARS-BGHcLV29-57_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	1903					GRCh38	V40	DARS-BGHcLV29-57/Aligned.sortedByCoord.out.bam		ENCORE2	19062
DARS-BGHcLV29-57_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	1903					GRCh38	V40	DARS-BGHcLV29-57/Aligned.sortedByCoord.out.bam		ENCORE2	19108
DARS-BGHcLV29-57_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	1903					GRCh38	V40	DARS-BGHcLV29-57/Aligned.sortedByCoord.out.bam		ENCORE2	19154
DARS-BGHcLV29-57_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1903					GRCh38	V40	DARS-BGHcLV29-57_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,DARS-BGHcLV29-57_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19200
DARS-BGHcLV29-58_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1904	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	5792
DARS-BGHcLV29-58_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1904	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	5834
DARS-BGHcLV29-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1904					GRCh38	V40	DARS-BGHcLV29-58_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz,DARS-BGHcLV29-58_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18959
DARS-BGHcLV29-58_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	1904					GRCh38	V40	DARS-BGHcLV29-58/Aligned.sortedByCoord.out.bam		ENCORE2	19017
DARS-BGHcLV29-58_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	1904					GRCh38	V40	DARS-BGHcLV29-58/Aligned.sortedByCoord.out.bam		ENCORE2	19063
DARS-BGHcLV29-58_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	1904					GRCh38	V40	DARS-BGHcLV29-58/Aligned.sortedByCoord.out.bam		ENCORE2	19109
DARS-BGHcLV29-58_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	1904					GRCh38	V40	DARS-BGHcLV29-58/Aligned.sortedByCoord.out.bam		ENCORE2	19155
DARS-BGHcLV29-58_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1904					GRCh38	V40	DARS-BGHcLV29-58_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz,DARS-BGHcLV29-58_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19201