GARS RNA-Seq in HepG2

General Information


RBP	GARS
Cell_Line	HepG2
Method	CRISPR
Exp_Name	GARS-BGHcLV18-HepG2
ENCODE_series_ID	ENCSR896TEE
Batch_ID	BGHcLV18
Pool ID	Pool-200103
Local_Set_Name	set44_H
ENCODE_KD_Exp_ID	ENCSR474EJY
ENCODE_CN_Exp_ID	ENCSR670KAS
Rep1	GARS-BGHcLV18-23
Rep2	GARS-BGHcLV18-24
CN1	NT-BGHcLV18-1
CN2	NT-BGHcLV18-2
Rep1_qPCR	5.2
Rep2_qPCR	0.7
Rep1_WB	93.3
Rep2_WB	91.2
Antibody Cat#	MA5-26714
Antibody Lot#	lot# UA2693064
Antibody DCC ID	ENCAB009SWM
Status	Released
Project	ENCODE4
ID	108

Experiment Information (Status: Released)

	BGHcLV18-23	BGHcLV18-24
idx	516	517
TRCN#_or_BGC#	BGC#0000406	BGC#0000406
shRNA_or_gRNA_sequence	GAGCAGCATGGACGGCGCGG	GAGCAGCATGGACGGCGCGG
PAM	GGG	GGG
Name	GARS_81	GARS_81
Sample_ID	BGHcLV18-23	BGHcLV18-24
transduction_Date	8/13/19	8/13/19
days	D6	D6
RBP_name	GARS	GARS
qPCR_result	5.2	0.7
Ave_qPCR	3.0
RT-qPCR_primer-F	GACCGAGCAAAAATGGAAGA
RT-qPCR_primer-R	CCAACTGGCCCAAAGTCAT
protein_conc	4263	4099
WB_result	93.3	91.2
Ave_WB	92.2
WB_DONE_date	8/28/19	WES
MW	83KD
IP	Mouse / Ig
antibody_Cat#	MA5-26714	lot# UA2693064
Antibody DCC ID	NO ID
submitted_to_DCC_date
Rep1_TPM	125	0
Rep2_TPM	106	0
Action	Ready	Ready
Library_start_date	12/11/19	12/11/19
repeat_library
Note
ID	6669	6670

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
GARS	Product_ID: MA5-26714 Lot_ID: UA2693064 Source: Thermo Fisher Target Name: GARS-human

Experiment Status

	BGHcLV18-23	BGHcLV18-24
Sample_ID	BGHcLV18-23	BGHcLV18-24
Sample Name
Sample Name	GARS-BGHcLV18-23	GARS-BGHcLV18-24
RBP	GARS	GARS
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5633	5634

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV18-23	BGHcLV18-24
Sample #	139	140
Sample Name	GARS-BGHcLV18-23	GARS-BGHcLV18-24
Sample_Name_Alias
Index Well Position	E06	F06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	4-G1	4-H1
Tecan	37.27	33.16
Tecan_date	2019-12-16	2019-12-16
Size_bp	277	278
Peak_Molarity	33.60	34.70
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/E7.png	DNA_Library_set43-44/set2/F7.png
RIN	9.4	9.7
libSample_RNA_Well	RNA_Library_set43-44/set4/A9.png	RNA_Library_set43-44/set4/B9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV18-23	BGHcLV18-24
RBP	GARS	GARS
Batch_ID	BGHcLV18	BGHcLV18
WB_result	93.300	91.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	715	716

Sequencing Information

	BGHcLV18-23	BGHcLV18-24
Sample_ID	BGHcLV18-23	BGHcLV18-24
Sample Name	GARS-BGHcLV18-23	GARS-BGHcLV18-24
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_H	set44_H
total_reads	168,771,876	150,997,978
total_aligned_reads	161,051,970	145,204,346
unique_aligned_reads	150,984,488	136,081,970
percent_uniqueAligned	0.89461	0.90122
correlation_replicates	0.999053	0.999053
spikein_reads	279,176	231,988
percent_spikeins	0.00165	0.00154
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	221	222

Data Submission Information

	BGHcLV18-23	BGHcLV18-23	BGHcLV18-23	BGHcLV18-23	BGHcLV18-23	BGHcLV18-23	BGHcLV18-24	BGHcLV18-24	BGHcLV18-24	BGHcLV18-24
ENCODE_alias	brenton-graveley:GARS-BGHcLV18	brenton-graveley:GARS-BGHcLV18-23	brenton-graveley:L-GARS-BGHcLV18-23	brenton-graveley:GARS-BGHcLV18-23_S55_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GARS-BGHcLV18-23_S55_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GARS-BGHcLV18-HepG2	brenton-graveley:GARS-BGHcLV18-24	brenton-graveley:L-GARS-BGHcLV18-24	brenton-graveley:GARS-BGHcLV18-24_S56_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GARS-BGHcLV18-24_S56_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR474EJY	ENCBS080COY	ENCLB433HDA	ENCFF121APT	ENCFF636IGG	ENCSR896TEE	ENCBS899WLZ	ENCLB473PDT	ENCFF811UZO	ENCFF926TKN
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	BGHcLV18-23	BGHcLV18-23	BGHcLV18-23	BGHcLV18-23	BGHcLV18-23	BGHcLV18-23	BGHcLV18-24	BGHcLV18-24	BGHcLV18-24	BGHcLV18-24
Sample Name	GARS-BGHcLV18-23	GARS-BGHcLV18-23	GARS-BGHcLV18-23	GARS-BGHcLV18-23	GARS-BGHcLV18-23	GARS-BGHcLV18-23	GARS-BGHcLV18-24	GARS-BGHcLV18-24	GARS-BGHcLV18-24	GARS-BGHcLV18-24
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2022-03-02	2020-12-01	2020-12-01	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV44H_biosample_protocol	LV44H_library_protocol				LV44H_biosample_protocol	LV44H_library_protocol
protocol_URL		GARS-BGHcLV18-23.pdf	L-GARS-BGHcLV18-23.pdf				GARS-BGHcLV18-24.pdf	L-GARS-BGHcLV18-24.pdf
ID	55	190	356	606	658	7228	191	357	607	659

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
GARS-BGHcLV18-23_S55_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	221	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	187
GARS-BGHcLV18-23_S55_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	221	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	239
GARS-BGHcLV18-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	221					GRCh38	V40	GARS-BGHcLV18-23_S55_R1_001.filtered.trimmed.paired.fastq.gz,GARS-BGHcLV18-23_S55_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24907
GARS-BGHcLV18-23_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	221					GRCh38	V40	GARS-BGHcLV18-23/Aligned.sortedByCoord.out.bam		ENCORE2	24959
GARS-BGHcLV18-23_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	221					GRCh38	V40	GARS-BGHcLV18-23/Aligned.sortedByCoord.out.bam		ENCORE2	25011
GARS-BGHcLV18-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	221					GRCh38	V40	GARS-BGHcLV18-23/Aligned.sortedByCoord.out.bam		ENCORE2	25063
GARS-BGHcLV18-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	221					GRCh38	V40	GARS-BGHcLV18-23/Aligned.sortedByCoord.out.bam		ENCORE2	25115
GARS-BGHcLV18-23_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	221					GRCh38	V40	GARS-BGHcLV18-23_S55_R1_001.filtered.trimmed.paired.fastq.gz,GARS-BGHcLV18-23_S55_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25167
GARS-BGHcLV18-24_S56_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	222	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	188
GARS-BGHcLV18-24_S56_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	222	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	240
GARS-BGHcLV18-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	222					GRCh38	V40	GARS-BGHcLV18-24_S56_R1_001.filtered.trimmed.paired.fastq.gz,GARS-BGHcLV18-24_S56_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24908
GARS-BGHcLV18-24_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	222					GRCh38	V40	GARS-BGHcLV18-24/Aligned.sortedByCoord.out.bam		ENCORE2	24960
GARS-BGHcLV18-24_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	222					GRCh38	V40	GARS-BGHcLV18-24/Aligned.sortedByCoord.out.bam		ENCORE2	25012
GARS-BGHcLV18-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	222					GRCh38	V40	GARS-BGHcLV18-24/Aligned.sortedByCoord.out.bam		ENCORE2	25064
GARS-BGHcLV18-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	222					GRCh38	V40	GARS-BGHcLV18-24/Aligned.sortedByCoord.out.bam		ENCORE2	25116
GARS-BGHcLV18-24_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	222					GRCh38	V40	GARS-BGHcLV18-24_S56_R1_001.filtered.trimmed.paired.fastq.gz,GARS-BGHcLV18-24_S56_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25168