GARS RNA-Seq in K562

General Information


RBP	GARS
Cell_Line	K562
Method	CRISPR
Exp_Name	GARS-BGKcLV17-K562
ENCODE_series_ID	ENCSR574XXD
Batch_ID	BGKcLV17
Pool ID	Pool-200103
Local_Set_Name	set44_K
ENCODE_KD_Exp_ID	ENCSR503VIZ
ENCODE_CN_Exp_ID	ENCSR516TLX
Rep1	GARS-BGKcLV17-23
Rep2	GARS-BGKcLV17-24
CN1	NT-BGKcLV17-1
CN2	NT-BGKcLV17-2
Rep1_qPCR	0.0
Rep2_qPCR	23.0
Rep1_WB	74.1
Rep2_WB	74.1
Antibody Cat#	MA5-26714
Antibody Lot#	lot# UA2693064
Antibody DCC ID	ENCAB009SWM
Status	Released
Project	ENCODE4
ID	86

Experiment Information (Status: Released)

	BGKcLV17-23	BGKcLV17-24
idx	630	631
TRCN#_or_BGC#	BGC#0000406	BGC#0000406
shRNA_or_gRNA_sequence	GAGCAGCATGGACGGCGCGG	GAGCAGCATGGACGGCGCGG
PAM	GGG	GGG
Name	GARS_81	GARS_81
Sample_ID	BGKcLV17-23	BGKcLV17-24
transduction_Date	7/2/19	7/2/19
days	Day 6	Day 6
RBP_name	GARS	GARS
qPCR_result	0.0	23.0
Ave_qPCR	11.5
RT-qPCR_primer-F	GACCGAGCAAAAATGGAAGA
RT-qPCR_primer-R	CCAACTGGCCCAAAGTCAT
protein_conc	3920	3750
WB_result	74.1	74.1
Ave_WB	74.1
WB_DONE_date	7/10/19	WES
MW	83KD
IP	Mouse / Ig
antibody_Cat#	MA5-26714	lot# UA2693064
Antibody DCC ID	ENCAB009SWM
submitted_to_DCC_date	8/20/19
Rep1_TPM	472	0
Rep2_TPM	518.5	0
Action	Ready	Ready
Library_start_date	12/05/19	12/05/19
repeat_library
Note
ID	4746	4747

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

	BGKcLV17-23	BGKcLV17-24
Sample_ID	BGKcLV17-23	BGKcLV17-24
Sample Name
Sample Name	GARS-BGKcLV17-23	GARS-BGKcLV17-24
RBP	GARS	GARS
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5505	5506

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV17-23	BGKcLV17-24
Sample #	95	96
Sample Name	GARS-BGKcLV17-23	GARS-BGKcLV17-24
Sample_Name_Alias
Index Well Position	E12	F12
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	1-C2	1-D2
Tecan	31.35	32.34
Tecan_date	2019-12-16	2019-12-16
Size_bp	276	277
Peak_Molarity	33.50	35.40
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/E8.png	DNA_Library_set43-44/set1/F8.png
RIN	9.6	9.4
libSample_RNA_Well	RNA_Library_set43-44/set4/E3.png	RNA_Library_set43-44/set4/F3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV17-23	BGKcLV17-24
RBP	GARS	GARS
Batch_ID	BGKcLV17	BGKcLV17
WB_result	74.100	74.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	671	672

Sequencing Information

	BGKcLV17-23	BGKcLV17-24
Sample_ID	BGKcLV17-23	BGKcLV17-24
Sample Name	GARS-BGKcLV17-23	GARS-BGKcLV17-24
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_K	set44_K
total_reads	270,160,426	264,190,070
total_aligned_reads	245,490,306	250,027,032
unique_aligned_reads	222,591,220	226,377,704
percent_uniqueAligned	0.82392	0.85687
correlation_replicates	0.999678	0.999678
spikein_reads	51,202	73,360
percent_spikeins	0.00019	0.00028
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	177	178

Data Submission Information

	BGKcLV17-23	BGKcLV17-23	BGKcLV17-23	BGKcLV17-23	BGKcLV17-23	BGKcLV17-23	BGKcLV17-24	BGKcLV17-24	BGKcLV17-24	BGKcLV17-24
ENCODE_alias	brenton-graveley:GARS-BGKcLV17	brenton-graveley:GARS-BGKcLV17-23	brenton-graveley:L-GARS-BGKcLV17-23	brenton-graveley:GARS-BGKcLV17-23_S7_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GARS-BGKcLV17-23_S7_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GARS-BGKcLV17-K562	brenton-graveley:GARS-BGKcLV17-24	brenton-graveley:L-GARS-BGKcLV17-24	brenton-graveley:GARS-BGKcLV17-24_S8_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GARS-BGKcLV17-24_S8_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR503VIZ	ENCBS609YII	ENCLB809TRL	ENCFF008KMF	ENCFF156XPL	ENCSR574XXD	ENCBS521NGU	ENCLB129ZUM	ENCFF784DCC	ENCFF089QLK
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	BGKcLV17-23	BGKcLV17-23	BGKcLV17-23	BGKcLV17-23	BGKcLV17-23	BGKcLV17-23	BGKcLV17-24	BGKcLV17-24	BGKcLV17-24	BGKcLV17-24
Sample Name	GARS-BGKcLV17-23	GARS-BGKcLV17-23	GARS-BGKcLV17-23	GARS-BGKcLV17-23	GARS-BGKcLV17-23	GARS-BGKcLV17-23	GARS-BGKcLV17-24	GARS-BGKcLV17-24	GARS-BGKcLV17-24	GARS-BGKcLV17-24
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
		LV44K_biosample_protocol	LV44K_library_protocol				LV44K_biosample_protocol	LV44K_library_protocol
protocol_URL		GARS-BGKcLV17-23.pdf	L-GARS-BGKcLV17-23.pdf				GARS-BGKcLV17-24.pdf	L-GARS-BGKcLV17-24.pdf
ID	72	224	390	692	722	7229	225	391	693	723

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-BGKcLV17-23_S7_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	177	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	279
GARS-BGKcLV17-23_S7_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	177	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	309
GARS-BGKcLV17-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	177					GRCh38	V40	GARS-BGKcLV17-23_S7_R1_001.filtered.trimmed.paired.fastq.gz,GARS-BGKcLV17-23_S7_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24675
GARS-BGKcLV17-23_Signal.Unique.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	177					GRCh38	V40	GARS-BGKcLV17-23/Aligned.sortedByCoord.out.bam		ENCORE2	24705
GARS-BGKcLV17-23_Signal.Unique.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	177					GRCh38	V40	GARS-BGKcLV17-23/Aligned.sortedByCoord.out.bam		ENCORE2	24735
GARS-BGKcLV17-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	177					GRCh38	V40	GARS-BGKcLV17-23/Aligned.sortedByCoord.out.bam		ENCORE2	24765
GARS-BGKcLV17-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	177					GRCh38	V40	GARS-BGKcLV17-23/Aligned.sortedByCoord.out.bam		ENCORE2	24795
GARS-BGKcLV17-23_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	177					GRCh38	V40	GARS-BGKcLV17-23_S7_R1_001.filtered.trimmed.paired.fastq.gz,GARS-BGKcLV17-23_S7_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24825
GARS-BGKcLV17-24_S8_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	178	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	280
GARS-BGKcLV17-24_S8_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	178	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	310
GARS-BGKcLV17-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	178					GRCh38	V40	GARS-BGKcLV17-24_S8_R1_001.filtered.trimmed.paired.fastq.gz,GARS-BGKcLV17-24_S8_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24676
GARS-BGKcLV17-24_Signal.Unique.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	178					GRCh38	V40	GARS-BGKcLV17-24/Aligned.sortedByCoord.out.bam		ENCORE2	24706
GARS-BGKcLV17-24_Signal.Unique.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	178					GRCh38	V40	GARS-BGKcLV17-24/Aligned.sortedByCoord.out.bam		ENCORE2	24736
GARS-BGKcLV17-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	178					GRCh38	V40	GARS-BGKcLV17-24/Aligned.sortedByCoord.out.bam		ENCORE2	24766
GARS-BGKcLV17-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	178					GRCh38	V40	GARS-BGKcLV17-24/Aligned.sortedByCoord.out.bam		ENCORE2	24796
GARS-BGKcLV17-24_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	178					GRCh38	V40	GARS-BGKcLV17-24_S8_R1_001.filtered.trimmed.paired.fastq.gz,GARS-BGKcLV17-24_S8_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24826