LARS RNA-Seq in HepG2

General Information


RBP	LARS
Cell_Line	HepG2
Method	CRISPR
Exp_Name	LARS-BGHcLV24-HepG2
ENCODE_series_ID	ENCSR723WZK
Batch_ID	BGHcLV24
Pool ID	Pool-210622
Local_Set_Name	set47
ENCODE_KD_Exp_ID	ENCSR213ILK
ENCODE_CN_Exp_ID	ENCSR671FDZ
Rep1	LARS-BGHcLV24-35
Rep2	LARS-BGHcLV24-36
CN1	NT-BGHcLV24-1
CN2	NT-BGHcLV24-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	81.0
Rep2_WB	85.0
Antibody Cat#	PA5-98918
Antibody Lot#	LOT#UK2881575
Antibody DCC ID	ENCAB154HAY
Status	Released
Project	ENCODE4
ID	9

Experiment Information (Status: Released)

	BGHcLV24-35	BGHcLV24-36
idx	693	694
TRCN#_or_BGC#	BGC#0000577	BGC#0000577
shRNA_or_gRNA_sequence	GTGTTTACGTAGAACAGACA	GTGTTTACGTAGAACAGACA
PAM	GGG	GGG
Name	LARS_83	LARS_83
Sample_ID	BGHcLV24-35	BGHcLV24-36
transduction_Date	10/30/20	10/30/20
days	D6	D6
RBP_name	LARS	LARS
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	GGGCCTCGTATTCTGGATTT
RT-qPCR_primer-R	CTGCTTCGGAGGCAAACTT
protein_conc	3952	4409
WB_result	81.0	85.0
Ave_WB	83.0
WB_DONE_date	11/9/20
MW	134.5KD
IP	Rabbit / I
antibody_Cat#	PA5-98918	LOT#UK2881575
Antibody DCC ID	ENCAB154HAY
submitted_to_DCC_date	12/9/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/16/21	06/16/21
repeat_library
Note
ID	6848	6849

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

Experiment Status

	BGHcLV24-35	BGHcLV24-36
Sample_ID	BGHcLV24-35	BGHcLV24-36
Sample Name
Sample Name	LARS-BGHcLV24-35	LARS-BGHcLV24-36
RBP	LARS	LARS
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4
Note
ID	7797	7798

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV24-35	BGHcLV24-36
Sample #	19	20
Sample Name	LARS-BGHcLV24-35	LARS-BGHcLV24-36
Sample_Name_Alias
Index Well Position	C09	D09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-06-04	2021-06-04
Lib_ID	Lib-210604	Lib-210604
Tecan_Location
Tecan
Tecan_date
Size_bp	301	311
Peak_Molarity	87.70	98.10
libSampleQC_DNA_Well	DNA_Library_set47/set1/C6.png	DNA_Library_set47/set1/D6.png
RIN	9.7	9.9
libSample_RNA_Well	RNA_Library_set47/set1/C3.png	RNA_Library_set47/set1/D3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-06-22	2021-06-22
Sample_ID	BGHcLV24-35	BGHcLV24-36
RBP	LARS	LARS
Batch_ID	BGHcLV24	BGHcLV24
WB_result	81.000	85.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1482	1483

Sequencing Information

	BGHcLV24-35	BGHcLV24-36
Sample_ID	BGHcLV24-35	BGHcLV24-36
Sample Name	LARS-BGHcLV24-35	LARS-BGHcLV24-36
Pool ID	Pool-210622	Pool-210622
LocalServer_folder	set47	set47
total_reads	131,200,758	72,538,278
total_aligned_reads	118,918,880	66,417,624
unique_aligned_reads	111,939,498	62,604,062
percent_uniqueAligned	0.85319	0.86305
correlation_replicates	0.997208	0.997208
spikein_reads	52,702	22,860
percent_spikeins	0.00040	0.00032
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	564	565

Data Submission Information

	BGHcLV24-35	BGHcLV24-35	BGHcLV24-35	BGHcLV24-35	BGHcLV24-35	BGHcLV24-35	BGHcLV24-36	BGHcLV24-36	BGHcLV24-36	BGHcLV24-36
ENCODE_alias	brenton-graveley:LARS-BGHcLV24	brenton-graveley:LARS-BGHcLV24-35	brenton-graveley:L-LARS-BGHcLV24-35	brenton-graveley:LARS-BGHcLV24-35_S79_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:LARS-BGHcLV24-35_S79_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:LARS-BGHcLV24-HepG2	brenton-graveley:LARS-BGHcLV24-36	brenton-graveley:L-LARS-BGHcLV24-36	brenton-graveley:LARS-BGHcLV24-36_S80_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:LARS-BGHcLV24-36_S80_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR213ILK	ENCBS428JUW	ENCLB147JVO	ENCFF303BGH	ENCFF750SKQ	ENCSR723WZK	ENCBS195ZYH	ENCLB492RCN	ENCFF216RNI	ENCFF803CAY
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	BGHcLV24-35	BGHcLV24-35	BGHcLV24-35	BGHcLV24-35	BGHcLV24-35	BGHcLV24-35	BGHcLV24-36	BGHcLV24-36	BGHcLV24-36	BGHcLV24-36
Sample Name	LARS-BGHcLV24-35	LARS-BGHcLV24-35	LARS-BGHcLV24-35	LARS-BGHcLV24-35	LARS-BGHcLV24-35	LARS-BGHcLV24-35	LARS-BGHcLV24-36	LARS-BGHcLV24-36	LARS-BGHcLV24-36	LARS-BGHcLV24-36
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2022-03-02	2021-11-04	2021-11-04	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV47_biosample_protocol	LV47_library_protocol				LV47_biosample_protocol	LV47_library_protocol
protocol_URL		LARS-BGHcLV24-35.pdf	L-LARS-BGHcLV24-35.pdf				LARS-BGHcLV24-36.pdf	L-LARS-BGHcLV24-36.pdf
ID	3244	3275	3319	3363	3407	7246	3276	3320	3364	3408

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-BGHcLV24-35_S79_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	564	NovaSeq6000	100	paired-ended	1				NT-BGHcLV24-1_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3722
LARS-BGHcLV24-35_S79_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	564	NovaSeq6000	100	paired-ended	2				NT-BGHcLV24-1_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3768
LARS-BGHcLV24-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	564					GRCh38	V40	LARS-BGHcLV24-35_S79_L002_R1_001.filtered.trimmed.paired.fastq.gz,LARS-BGHcLV24-35_S79_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25411
LARS-BGHcLV24-35_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	564					GRCh38	V40	LARS-BGHcLV24-35_S79_L002_R1_001.filtered.trimmed.paired.fastq.gz,LARS-BGHcLV24-35_S79_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25455
LARS-BGHcLV24-35_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	564					GRCh38	V40	LARS-BGHcLV24-35/Aligned.sortedByCoord.out.bam		ENCORE2	26287
LARS-BGHcLV24-35_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	564					GRCh38	V40	LARS-BGHcLV24-35/Aligned.sortedByCoord.out.bam		ENCORE2	26331
LARS-BGHcLV24-35_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	564					GRCh38	V40	LARS-BGHcLV24-35/Aligned.sortedByCoord.out.bam		ENCORE2	26375
LARS-BGHcLV24-35_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	564					GRCh38	V40	LARS-BGHcLV24-35/Aligned.sortedByCoord.out.bam		ENCORE2	26419
LARS-BGHcLV24-36_S80_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	565	NovaSeq6000	100	paired-ended	1				NT-BGHcLV24-1_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3723
LARS-BGHcLV24-36_S80_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	565	NovaSeq6000	100	paired-ended	2				NT-BGHcLV24-1_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3769
LARS-BGHcLV24-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	565					GRCh38	V40	LARS-BGHcLV24-36_S80_L002_R1_001.filtered.trimmed.paired.fastq.gz,LARS-BGHcLV24-36_S80_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25412
LARS-BGHcLV24-36_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	565					GRCh38	V40	LARS-BGHcLV24-36_S80_L002_R1_001.filtered.trimmed.paired.fastq.gz,LARS-BGHcLV24-36_S80_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25456
LARS-BGHcLV24-36_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	565					GRCh38	V40	LARS-BGHcLV24-36/Aligned.sortedByCoord.out.bam		ENCORE2	26288
LARS-BGHcLV24-36_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	565					GRCh38	V40	LARS-BGHcLV24-36/Aligned.sortedByCoord.out.bam		ENCORE2	26332
LARS-BGHcLV24-36_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	565					GRCh38	V40	LARS-BGHcLV24-36/Aligned.sortedByCoord.out.bam		ENCORE2	26376
LARS-BGHcLV24-36_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	565					GRCh38	V40	LARS-BGHcLV24-36/Aligned.sortedByCoord.out.bam		ENCORE2	26420