LARP4 RNA-Seq in HepG2

General Information


RBP	LARP4
Cell_Line	HepG2
Method	shRNA
Exp_Name	LARP4-BGHLV20-HepG2
ENCODE_series_ID	ENCSR382SKH
Batch_ID	BGHLV20
Pool ID	Pool-160425
Local_Set_Name	set20
ENCODE_KD_Exp_ID	ENCSR744PAQ
ENCODE_CN_Exp_ID	ENCSR135LXL
Rep1	LARP4_BGHLV20-41B
Rep2	LARP4_BGHLV20-42B
CN1	NT_BGHLV20-1B
CN2	NT_BGHLV20-2B
Rep1_qPCR	36.9
Rep2_qPCR	30.7
Rep1_WB	64.0
Rep2_WB	61.0
Antibody Cat#	A303-900A
Antibody Lot#	A303-900A
Antibody DCC ID	ENCAB580XQQ
Status	Released
Project	ENCODE3
ID	594

Experiment Information (Status: Released)

	BGHLV20-41	BGHLV20-42
idx	405	406
TRCN#_or_BGC#	TRCN0000161048	TRCN0000161048
shRNA_or_gRNA_sequence	GCTTTAATTCGCCAGGATCTT	GCTTTAATTCGCCAGGATCTT
PAM
Name	LARP4_48	LARP4_48
Sample_ID	BGHLV20-41	BGHLV20-42
transduction_Date	10/2/2014	10/2/2014
days
RBP_name	LARP4	LARP4
qPCR_result	36.9	30.7
Ave_qPCR	33.8
RT-qPCR_primer-F	aaagtgaaaactgccccaaa
RT-qPCR_primer-R	aagcctgttgtgcatctgtg
protein_conc	3215	2917
WB_result	64.0	61.0
Ave_WB	62.5
WB_DONE_date	7/15/2015
MW	81kDa
IP	1	1
antibody_Cat#	A303-900A	A303-900A
Antibody DCC ID	ENCAB580XQQ	ENCAB580XQQ
submitted_to_DCC_date	8/6/2015
Rep1_TPM	7.3	0
Rep2_TPM	6.9	0
Action
Library_start_date	3/10/2016	3/10/2016
repeat_library
Note	x	x
ID	2470	2471

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
LARP4	Product_ID: A303-900A Lot_ID: 1 Source: Bethyl Labs Target Name: LARP4-human

Experiment Status

	BGHLV20-41	BGHLV20-42
Sample_ID	BGHLV20-41	BGHLV20-42
Sample Name	LARP4_BGHLV20-41B	LARP4_BGHLV20-42B
Sample Name	LARP4_BGHLV20-41B	LARP4_BGHLV20-42B
RBP	LARP4	LARP4
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1213	1214

Library-Prep
Sequencing

Library-Prep Information

	BGHLV20-41	BGHLV20-42
Sample #
Sample Name	LARP4-BGHLV20-41B	LARP4-BGHLV20-42B
Sample_Name_Alias	LARP4_BGHLV20-41B	LARP4_BGHLV20-42B
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-10	2016-03-10
Lib_ID	Lib-160310	Lib-160310
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set2/B2.png	DNA_Library_LV35/set1/E5.png
RIN	9.7	10.0
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/F11.png	RNA_Library_LV35_LV36/set1/G11.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV20-41	BGHLV20-42
RBP	LARP4	LARP4
Batch_ID	BGHLV20	BGHLV20
WB_result	64.000	61.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2890	2891

Sequencing Information

	BGHLV20-41	BGHLV20-42
Sample_ID	BGHLV20-41	BGHLV20-42
Sample Name	LARP4_BGHLV20-41B	LARP4_BGHLV20-42B
Pool ID	Pool-160425	Pool-160425
LocalServer_folder	set20	set20
total_reads	122,910,224	94,289,790
total_aligned_reads	94,756,654	73,426,354
unique_aligned_reads	88,767,090	68,779,654
percent_uniqueAligned	0.72221	0.72945
correlation_replicates	0.999570	0.999570
spikein_reads	205,476	169,778
percent_spikeins	0.00167	0.00180
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1539	1540

Data Submission Information

	BGHLV20-41
ENCODE_alias	brenton-graveley:LARP4-BGHLV20-HepG2
ENCODE_accession	ENCSR382SKH
object_type	gene_silencing_series
assay_type	knockdown followed by RNA-seq
Sample_ID	BGHLV20-41
Sample Name	LARP4_BGHLV20-41B
Selected	Yes
Status	Released
Status_Date	2022-03-01
Project	ENCODE3

protocol_URL
ID	6795

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
LARP4_BGHLV20-41B_CGTACG_L005_001.R1.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1539	HiSeq2000	100	paired-ended	1				NT_BGHLV20-1B_GTCCGC_L004_001.R1.fastq.gz,NT_BGHLV20-2B_GTGAAA_L004_001.R1.fastq.gz	ENCODE3	15608
LARP4_BGHLV20-41B_CGTACG_L005_001.R2.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1539	HiSeq2000	100	paired-ended	2				NT_BGHLV20-1B_GTCCGC_L004_001.R2.fastq.gz,NT_BGHLV20-2B_GTGAAA_L004_001.R2.fastq.gz	ENCODE3	15650
LARP4_BGHLV20-41B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1539					GRCh38	V40	LARP4_BGHLV20-41B_CGTACG_L005_001.R1.fastq.gz,LARP4_BGHLV20-41B_CGTACG_L005_001.R2.fastq.gz		ENCORE2	15692
LARP4_BGHLV20-41B_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1539					GRCh38	V40	LARP4_BGHLV20-41B/Aligned.sortedByCoord.out.bam		ENCORE2	15734
LARP4_BGHLV20-41B_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1539					GRCh38	V40	LARP4_BGHLV20-41B/Aligned.sortedByCoord.out.bam		ENCORE2	15776
LARP4_BGHLV20-41B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1539					GRCh38	V40	LARP4_BGHLV20-41B/Aligned.sortedByCoord.out.bam		ENCORE2	15818
LARP4_BGHLV20-41B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1539					GRCh38	V40	LARP4_BGHLV20-41B/Aligned.sortedByCoord.out.bam		ENCORE2	15860
LARP4_BGHLV20-41B_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1539					GRCh38	V40	LARP4_BGHLV20-41B_CGTACG_L005_001.R1.fastq.gz,LARP4_BGHLV20-41B_CGTACG_L005_001.R2.fastq.gz		ENCORE2	15902
LARP4_BGHLV20-42B_GAGTGG_L005_001.R1.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1540	HiSeq2000	100	paired-ended	1				NT_BGHLV20-1B_GTCCGC_L004_001.R1.fastq.gz,NT_BGHLV20-2B_GTGAAA_L004_001.R1.fastq.gz	ENCODE3	15609
LARP4_BGHLV20-42B_GAGTGG_L005_001.R2.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1540	HiSeq2000	100	paired-ended	2				NT_BGHLV20-1B_GTCCGC_L004_001.R2.fastq.gz,NT_BGHLV20-2B_GTGAAA_L004_001.R2.fastq.gz	ENCODE3	15651
LARP4_BGHLV20-42B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1540					GRCh38	V40	LARP4_BGHLV20-42B_GAGTGG_L005_001.R1.fastq.gz,LARP4_BGHLV20-42B_GAGTGG_L005_001.R2.fastq.gz		ENCORE2	15693
LARP4_BGHLV20-42B_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1540					GRCh38	V40	LARP4_BGHLV20-42B/Aligned.sortedByCoord.out.bam		ENCORE2	15735
LARP4_BGHLV20-42B_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1540					GRCh38	V40	LARP4_BGHLV20-42B/Aligned.sortedByCoord.out.bam		ENCORE2	15777
LARP4_BGHLV20-42B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1540					GRCh38	V40	LARP4_BGHLV20-42B/Aligned.sortedByCoord.out.bam		ENCORE2	15819
LARP4_BGHLV20-42B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1540					GRCh38	V40	LARP4_BGHLV20-42B/Aligned.sortedByCoord.out.bam		ENCORE2	15861
LARP4_BGHLV20-42B_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1540					GRCh38	V40	LARP4_BGHLV20-42B_GAGTGG_L005_001.R1.fastq.gz,LARP4_BGHLV20-42B_GAGTGG_L005_001.R2.fastq.gz		ENCORE2	15903