LARS RNA-Seq in K562

General Information


RBP	LARS
Cell_Line	K562
Method	CRISPR
Exp_Name	LARS-BGKcLV23-K562
ENCODE_series_ID	ENCSR498YMD
Batch_ID	BGKcLV23
Pool ID	Pool-201204
Local_Set_Name	set46_K
ENCODE_KD_Exp_ID	ENCSR381NPB
ENCODE_CN_Exp_ID	ENCSR877JEM
Rep1	LARS-BGKcLV23-45
Rep2	LARS-BGKcLV23-46
CN1	NT-BGKcLV23-1
CN2	NT-BGKcLV23-2
Rep1_qPCR	39.0
Rep2_qPCR	18.0
Rep1_WB	75.9
Rep2_WB	79.6
Antibody Cat#	PA5-98918
Antibody Lot#	LOT#UK2881575
Antibody DCC ID	ENCAB154HAY
Status	Released
Project	ENCODE4
ID	31

Experiment Information (Status: Released)

	BGKcLV23-45	BGKcLV23-45	BGKcLV23-45	BGKcLV23-45	BGKcLV23-46	BGKcLV23-46	BGKcLV23-46	BGKcLV23-46
idx	831	831	831	831	832	832	832	832
TRCN#_or_BGC#	BGC#0000577	BGC#0000577	BGC#0000577	BGC#0000577	BGC#0000577	BGC#0000577	BGC#0000577	BGC#0000577
shRNA_or_gRNA_sequence	GTGTTTACGTAGAACAGACA	GTGTTTACGTAGAACAGACA	GTGTTTACGTAGAACAGACA	GTGTTTACGTAGAACAGACA	GTGTTTACGTAGAACAGACA	GTGTTTACGTAGAACAGACA	GTGTTTACGTAGAACAGACA	GTGTTTACGTAGAACAGACA
PAM	GGG	GGG	GGG	GGG	GGG	GGG	GGG	GGG
Name	LARS_83	LARS_83	LARS_83	LARS_83	LARS_83	LARS_83	LARS_83	LARS_83
Sample_ID	BGKcLV23-45	BGKcLV23-45	BGKcLV23-45	BGKcLV23-45	BGKcLV23-46	BGKcLV23-46	BGKcLV23-46	BGKcLV23-46
transduction_Date	9/17/20	9/17/20	9/17/20	9/17/20	9/17/20	9/17/20	9/17/20	9/17/20
days	Day 6	Day 6	Day 6	Day 6	Day 6	Day 6	Day 6	Day 6
RBP_name	LARS	LARS	LARS	LARS	LARS	LARS	LARS	LARS
qPCR_result	39.0	39.0	39.0	39.0	18.0	18.0	18.0	18.0
Ave_qPCR	28.5	28.5	28.5	28.5
RT-qPCR_primer-F	GGGCCTCGTATTCTGGATTT	GGGCCTCGTATTCTGGATTT	GGGCCTCGTATTCTGGATTT	GGGCCTCGTATTCTGGATTT
RT-qPCR_primer-R	CTGCTTCGGAGGCAAACTT	CTGCTTCGGAGGCAAACTT	CTGCTTCGGAGGCAAACTT	CTGCTTCGGAGGCAAACTT
protein_conc	2285	2285	2285	2285	2401	2401	2401	2401
WB_result	75.9	93.5	86.5	87.9	79.6	92.58	84.0941	86.8596
Ave_WB	77.8	93.0	85.3	87.4
WB_DONE_date	10/13/20	6/27/23	7/19/23	4/5/24
MW	134.5KD	134.5KD	134.5KD	134.5KD
IP	Rabbit / I
antibody_Cat#	PA5-98918	83439S	A304-316A	86132S	LOT#UK2881575	LOT# 1	LOT# 1	LOT# 1
Antibody DCC ID	ENCAB154HAY
submitted_to_DCC_date	11/16/20	1/8/24	1/8/24
Rep1_TPM	0	0	0	0	0	0	0	0
Rep2_TPM	0	0	0	0	0	0	0	0
Action	Ready				Ready
Library_start_date	11/24/20				11/24/20
repeat_library
Note
ID	4955	4957	4959	4961	4956	4958	4960	4962

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
LARS	Product_ID: PA5-98918 Lot_ID: UK2881575 Source: Thermo Fisher Target Name: LARS-human
LARS	Product_ID: 83439S Lot_ID: 1 Source: Cell Signaling Technology Target Name: LARS-human
LARS	Product_ID: A304-316A Lot_ID: 1 Source: Bethyl Labs Target Name: LARS-human
LARS	Product_ID: 35509S Lot_ID: 1 Source: Cell Signaling Technology Target Name: LARS-human

Experiment Status

	BGKcLV23-45	BGKcLV23-46
Sample_ID	BGKcLV23-45	BGKcLV23-46
Sample Name
Sample Name	LARS-BGKcLV23-45	LARS-BGKcLV23-46
RBP	LARS	LARS
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7451	7452

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV23-45	BGKcLV23-46
Sample #	53	54
Sample Name	LARS-BGKcLV23-45	LARS-BGKcLV23-46
Sample_Name_Alias
Index Well Position	E07	F07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-11-24	2020-11-24
Lib_ID	Lib-201124	Lib-201124
Tecan_Location
Tecan
Tecan_date
Size_bp	285	288
Peak_Molarity	131.00	124.00
libSampleQC_DNA_Well	DNA_Library_set46/set1/E7.png	DNA_Library_set46/set1/F7.png
RIN	8.7	9.4
libSample_RNA_Well	RNA_Library_set46/set2/E11.png	RNA_Library_set46/set2/F11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGKcLV23-45	BGKcLV23-46
RBP	LARS	LARS
Batch_ID	BGKcLV23	BGKcLV23
WB_result	75.900	79.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1428	1429

Sequencing Information

	BGKcLV23-45	BGKcLV23-46
Sample_ID	BGKcLV23-45	BGKcLV23-46
Sample Name	LARS-BGKcLV23-45	LARS-BGKcLV23-46
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_K	set46_K
total_reads	231,030,260	142,647,758
total_aligned_reads	215,012,452	133,191,846
unique_aligned_reads	195,641,082	120,820,742
percent_uniqueAligned	0.84682	0.84699
correlation_replicates	0.999442	0.999442
spikein_reads	89,032	70,566
percent_spikeins	0.00039	0.00049
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	534	535

Data Submission Information

	BGKcLV23-45	BGKcLV23-45	BGKcLV23-45	BGKcLV23-45	BGKcLV23-45	BGKcLV23-45	BGKcLV23-46	BGKcLV23-46	BGKcLV23-46	BGKcLV23-46
ENCODE_alias	brenton-graveley:LARS-BGKcLV23	brenton-graveley:LARS-BGKcLV23-45	brenton-graveley:L-LARS-BGKcLV23-45	brenton-graveley:LARS-BGKcLV23-45_CAACAATG+CCGTGAAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:LARS-BGKcLV23-45_CAACAATG+CCGTGAAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:LARS-BGKcLV23-K562	brenton-graveley:LARS-BGKcLV23-46	brenton-graveley:L-LARS-BGKcLV23-46	brenton-graveley:LARS-BGKcLV23-46_TGGTGGCA+TTACAGGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:LARS-BGKcLV23-46_TGGTGGCA+TTACAGGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR381NPB	ENCBS365CHW	ENCLB795LDC	ENCFF050IQZ	ENCFF903BWP	ENCSR498YMD	ENCBS504AVE	ENCLB360HKI	ENCFF373HFY	ENCFF435GKI
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	BGKcLV23-45	BGKcLV23-45	BGKcLV23-45	BGKcLV23-45	BGKcLV23-45	BGKcLV23-45	BGKcLV23-46	BGKcLV23-46	BGKcLV23-46	BGKcLV23-46
Sample Name	LARS-BGKcLV23-45	LARS-BGKcLV23-45	LARS-BGKcLV23-45	LARS-BGKcLV23-45	LARS-BGKcLV23-45	LARS-BGKcLV23-45	LARS-BGKcLV23-46	LARS-BGKcLV23-46	LARS-BGKcLV23-46	LARS-BGKcLV23-46
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2022-03-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV46K_biosample_protocol	LV46K_library_protocol				LV46K_biosample_protocol	LV46K_library_protocol
protocol_URL		LARS-BGKcLV23-45.pdf	L-LARS-BGKcLV23-45.pdf				LARS-BGKcLV23-46.pdf	L-LARS-BGKcLV23-46.pdf
ID	2421	2479	2543	2637	2671	7247	2480	2544	2638	2672

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
LARS-BGKcLV23-45_CAACAATG+CCGTGAAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	534	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1398
LARS-BGKcLV23-45_CAACAATG+CCGTGAAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	534	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1462
LARS-BGKcLV23-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	534					GRCh38	V40	LARS-BGKcLV23-45_CAACAATG+CCGTGAAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,LARS-BGKcLV23-45_CAACAATG+CCGTGAAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25301
LARS-BGKcLV23-45_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	534					GRCh38	V40	LARS-BGKcLV23-45_CAACAATG+CCGTGAAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,LARS-BGKcLV23-45_CAACAATG+CCGTGAAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25335
LARS-BGKcLV23-45_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	534					GRCh38	V40	LARS-BGKcLV23-45/Aligned.sortedByCoord.out.bam		ENCORE2	26139
LARS-BGKcLV23-45_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	534					GRCh38	V40	LARS-BGKcLV23-45/Aligned.sortedByCoord.out.bam		ENCORE2	26173
LARS-BGKcLV23-45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	534					GRCh38	V40	LARS-BGKcLV23-45/Aligned.sortedByCoord.out.bam		ENCORE2	26207
LARS-BGKcLV23-45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	534					GRCh38	V40	LARS-BGKcLV23-45/Aligned.sortedByCoord.out.bam		ENCORE2	26241
LARS-BGKcLV23-46_TGGTGGCA+TTACAGGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	535	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1399
LARS-BGKcLV23-46_TGGTGGCA+TTACAGGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	535	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1463
LARS-BGKcLV23-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	535					GRCh38	V40	LARS-BGKcLV23-46_TGGTGGCA+TTACAGGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,LARS-BGKcLV23-46_TGGTGGCA+TTACAGGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25302
LARS-BGKcLV23-46_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	535					GRCh38	V40	LARS-BGKcLV23-46_TGGTGGCA+TTACAGGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,LARS-BGKcLV23-46_TGGTGGCA+TTACAGGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25336
LARS-BGKcLV23-46_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	535					GRCh38	V40	LARS-BGKcLV23-46/Aligned.sortedByCoord.out.bam		ENCORE2	26140
LARS-BGKcLV23-46_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	535					GRCh38	V40	LARS-BGKcLV23-46/Aligned.sortedByCoord.out.bam		ENCORE2	26174
LARS-BGKcLV23-46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	535					GRCh38	V40	LARS-BGKcLV23-46/Aligned.sortedByCoord.out.bam		ENCORE2	26208
LARS-BGKcLV23-46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	535					GRCh38	V40	LARS-BGKcLV23-46/Aligned.sortedByCoord.out.bam		ENCORE2	26242