LARP7 RNA-Seq in HepG2

General Information


RBP	LARP7
Cell_Line	HepG2
Method	shRNA
Exp_Name	LARP7-BGHLV18-HepG2
ENCODE_series_ID	ENCSR365KBY
Batch_ID	BGHLV18
Pool ID	Pool-141010
Local_Set_Name	set18
ENCODE_KD_Exp_ID	ENCSR624FBY
ENCODE_CN_Exp_ID	ENCSR674KEK
Rep1	LARP7_BGHLV18_19
Rep2	LARP7_BGHLV18_20
CN1	NT_BGHLV18_1
CN2	NT_BGHLV18_2
Rep1_qPCR	70.7
Rep2_qPCR	84.5
Rep1_WB	88.6
Rep2_WB	95.9
Antibody Cat#	A303-723A
Antibody Lot#	A303-723A
Antibody DCC ID	ENCAB568DRS
Status	Released
Project	ENCODE3
ID	448

Experiment Information (Status: Released)

	BGHLV18-19	BGHLV18-20
idx	319	320
TRCN#_or_BGC#	TRCN0000122544	TRCN0000122544
shRNA_or_gRNA_sequence	CTTGAGCTGTTCTTGGGAGAT	CTTGAGCTGTTCTTGGGAGAT
PAM
Name	LARP7	LARP7
Sample_ID	BGHLV18-19	BGHLV18-20
transduction_Date	8/28/2014	8/28/2014
days
RBP_name	LARP7	LARP7
qPCR_result	70.7	84.5
Ave_qPCR	77.6
RT-qPCR_primer-F	gctggaaactcgagatccttt
RT-qPCR_primer-R	ttttcccgaggctgattaag
protein_conc	4173	4309
WB_result	88.6	95.9
Ave_WB	92.3
WB_DONE_date	3/19/2015
MW	67kDa
IP	1	1
antibody_Cat#	A303-723A	A303-723A
Antibody DCC ID	ENCAB568DRS	ENCAB568DRS
submitted_to_DCC_date	4/2/2015
Rep1_TPM	27.8	0
Rep2_TPM	27.6	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	2384	2385

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
LARP7	Product_ID: A303-723A Lot_ID: 1 Source: Bethyl Labs Target Name: LARP7-human

Experiment Status

	BGHLV18-19	BGHLV18-20
Sample_ID	BGHLV18-19	BGHLV18-20
Sample Name	LARP7_BGHLV18_19	LARP7_BGHLV18_20
Sample Name	LARP7_BGHLV18_19	LARP7_BGHLV18_20
RBP	LARP7	LARP7
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	624	625

Library-Prep
Sequencing

Library-Prep Information

	BGHLV18-19	BGHLV18-20
Sample #
Sample Name	LARP7-BGHLV18-19	LARP7-BGHLV18-20
Sample_Name_Alias	LARP7_BGHLV18_19	LARP7_BGHLV18_20
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-02	2014-10-02
Lib_ID	Lib-141002	Lib-141002
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/C2.png	DNA_Library_LV18-19/set1/D2.png
RIN	9.2	9.4
libSample_RNA_Well	RNA_Library_LV18-19/set1/A9.png	RNA_Library_LV18-19/set1/B9.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV18-19	BGHLV18-20
RBP	LARP7	LARP7
Batch_ID	BGHLV18	BGHLV18
WB_result	88.600	95.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2308	2309

Sequencing Information

	BGHLV18-19	BGHLV18-20
Sample_ID	BGHLV18-19	BGHLV18-20
Sample Name	LARP7_BGHLV18_19	LARP7_BGHLV18_20
Pool ID	Pool-141010	Pool-141010
LocalServer_folder	set18	set18
total_reads	44,590,000	49,700,000
total_aligned_reads	40,280,578	45,202,298
unique_aligned_reads	38,060,418	42,735,836
percent_uniqueAligned	0.85356	0.85988
correlation_replicates	0.999599	0.999599
spikein_reads	107,846	164,006
percent_spikeins	0.00242	0.00330
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	950	951

Data Submission Information

	BGHLV18-19	BGHLV18-19
ENCODE_alias	brenton-graveley:LARP7_BGHLV18	brenton-graveley:LARP7-BGHLV18-HepG2
ENCODE_accession	ENCSR624FBY	ENCSR365KBY
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV18-19	BGHLV18-19
Sample Name	LARP7_BGHLV18_19	LARP7_BGHLV18_19
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2829	6797

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
LARP7_BGHLV18_19_GGCTAC_L002_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	950	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14798
LARP7_BGHLV18_19_GGCTAC_L002_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	950	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14836
LARP7_BGHLV18_19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	950					GRCh38	V40	LARP7_BGHLV18_19_GGCTAC_L002_R1_001.fastq.gz,LARP7_BGHLV18_19_GGCTAC_L002_R2_001.fastq.gz		ENCORE2	14874
LARP7_BGHLV18_19_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	950					GRCh38	V40	LARP7_BGHLV18_19/Aligned.sortedByCoord.out.bam		ENCORE2	14912
LARP7_BGHLV18_19_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	950					GRCh38	V40	LARP7_BGHLV18_19/Aligned.sortedByCoord.out.bam		ENCORE2	14950
LARP7_BGHLV18_19_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	950					GRCh38	V40	LARP7_BGHLV18_19/Aligned.sortedByCoord.out.bam		ENCORE2	14988
LARP7_BGHLV18_19_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	950					GRCh38	V40	LARP7_BGHLV18_19/Aligned.sortedByCoord.out.bam		ENCORE2	15026
LARP7_BGHLV18_19_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	950					GRCh38	V40	LARP7_BGHLV18_19_GGCTAC_L002_R1_001.fastq.gz,LARP7_BGHLV18_19_GGCTAC_L002_R2_001.fastq.gz		ENCORE2	15064
LARP7_BGHLV18_20_CTTGTA_L002_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	951	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14799
LARP7_BGHLV18_20_CTTGTA_L002_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	951	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14837
LARP7_BGHLV18_20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	951					GRCh38	V40	LARP7_BGHLV18_20_CTTGTA_L002_R1_001.fastq.gz,LARP7_BGHLV18_20_CTTGTA_L002_R2_001.fastq.gz		ENCORE2	14875
LARP7_BGHLV18_20_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	951					GRCh38	V40	LARP7_BGHLV18_20/Aligned.sortedByCoord.out.bam		ENCORE2	14913
LARP7_BGHLV18_20_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	951					GRCh38	V40	LARP7_BGHLV18_20/Aligned.sortedByCoord.out.bam		ENCORE2	14951
LARP7_BGHLV18_20_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	951					GRCh38	V40	LARP7_BGHLV18_20/Aligned.sortedByCoord.out.bam		ENCORE2	14989
LARP7_BGHLV18_20_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	951					GRCh38	V40	LARP7_BGHLV18_20/Aligned.sortedByCoord.out.bam		ENCORE2	15027
LARP7_BGHLV18_20_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	951					GRCh38	V40	LARP7_BGHLV18_20_CTTGTA_L002_R1_001.fastq.gz,LARP7_BGHLV18_20_CTTGTA_L002_R2_001.fastq.gz		ENCORE2	15065