RPS19 RNA-Seq in HepG2

General Information


RBP	RPS19
Cell_Line	HepG2
Method	shRNA
Exp_Name	RPS19-BGHLV16-HepG2
ENCODE_series_ID	ENCSR424DOB
Batch_ID	BGHLV16
Pool ID	Pool-141001
Local_Set_Name	set16
ENCODE_KD_Exp_ID	ENCSR486AIO
ENCODE_CN_Exp_ID	ENCSR689PHN
Rep1	RPS19_BGHLV16_45
Rep2	RPS19_BGHLV16_46
CN1	NT_BGHLV16_1
CN2	NT_BGHLV16_2
Rep1_qPCR	60.6
Rep2_qPCR	60.6
Rep1_WB	no AB
Rep2_WB	no AB
Antibody Cat#	RN071PW
Antibody Lot#	LOT# 001
Antibody DCC ID	ENCAB123ROG
Status	Released
Project	ENCODE3
ID	423

Experiment Information (Status: Released)

	BGHLV16-45	BGHLV16-46
idx	213	214
TRCN#_or_BGC#	TRCN0000074913	TRCN0000074913
shRNA_or_gRNA_sequence	CTACGATGAGAACTGGTTCTA	CTACGATGAGAACTGGTTCTA
PAM
Name	RPS19_13	RPS19_13
Sample_ID	BGHLV16-45	BGHLV16-46
transduction_Date	7/31/2014	7/31/2014
days
RBP_name	RPS19	RPS19
qPCR_result	60.6	60.6
Ave_qPCR	60.6
RT-qPCR_primer-F	agacgtgaaccagcaggagt
RT-qPCR_primer-R	cttgacggtatccacccatt
protein_conc	2038	1909
WB_result	no AB	no AB
Ave_WB
WB_DONE_date
MW
IP	1	1
antibody_Cat#	RN071PW	RN071PW
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action
Library_start_date	9/23/2014	9/23/2014
repeat_library
Note
ID	2278	2279

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV16-45	BGHLV16-46
Sample_ID	BGHLV16-45	BGHLV16-46
Sample Name	RPS19_BGHLV16_45	RPS19_BGHLV16_46
Sample Name	RPS19_BGHLV16_45	RPS19_BGHLV16_46
RBP	RPS19	RPS19
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	572	573

Library-Prep
Sequencing

Library-Prep Information

	BGHLV16-45	BGHLV16-46
Sample #
Sample Name	RPS19-BGHLV16-45	RPS19-BGHLV16-46
Sample_Name_Alias	RPS19_BGHLV16_45	RPS19_BGHLV16_46
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-23	2014-09-23
Lib_ID	Lib-140923	Lib-140923
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set1/E8.png	DNA_Library_LV16-17/set1/F8.png
RIN	9.1	9.2
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/C2.png	RNA_Library_LV16-17-18/set1/D2.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV16-45	BGHLV16-46
RBP	RPS19	RPS19
Batch_ID	BGHLV16	BGHLV16
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2256	2257

Sequencing Information

	BGHLV16-45	BGHLV16-46
Sample_ID	BGHLV16-45	BGHLV16-46
Sample Name	RPS19_BGHLV16_45	RPS19_BGHLV16_46
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set16	set16
total_reads	47,800,000	39,990,000
total_aligned_reads	42,306,378	35,557,100
unique_aligned_reads	39,858,660	33,506,824
percent_uniqueAligned	0.83386	0.83788
correlation_replicates	0.999546	0.999546
spikein_reads	66,270	63,082
percent_spikeins	0.00139	0.00158
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	898	899

Data Submission Information

	BGHLV16-45	BGHLV16-45
ENCODE_alias	brenton-graveley:RPS19_BGHLV16	brenton-graveley:RPS19-BGHLV16-HepG2
ENCODE_accession	ENCSR486AIO	ENCSR424DOB
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV16-45	BGHLV16-45
Sample Name	RPS19_BGHLV16_45	RPS19_BGHLV16_45
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2854	6916

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
RPS19_BGHLV16_45_CGTACG_L008_R1_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	898	HiSeq2000	100	paired-ended	1				NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE3	14298
RPS19_BGHLV16_45_CGTACG_L008_R2_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	898	HiSeq2000	100	paired-ended	2				NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE3	14324
RPS19_BGHLV16_45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	898					GRCh38	V40	RPS19_BGHLV16_45_CGTACG_L008_R1_001.fastq.gz,RPS19_BGHLV16_45_CGTACG_L008_R2_001.fastq.gz		ENCORE2	14350
RPS19_BGHLV16_45_Signal.Unique.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	898					GRCh38	V40	RPS19_BGHLV16_45/Aligned.sortedByCoord.out.bam		ENCORE2	14376
RPS19_BGHLV16_45_Signal.Unique.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	898					GRCh38	V40	RPS19_BGHLV16_45/Aligned.sortedByCoord.out.bam		ENCORE2	14402
RPS19_BGHLV16_45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	898					GRCh38	V40	RPS19_BGHLV16_45/Aligned.sortedByCoord.out.bam		ENCORE2	14428
RPS19_BGHLV16_45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	898					GRCh38	V40	RPS19_BGHLV16_45/Aligned.sortedByCoord.out.bam		ENCORE2	14454
RPS19_BGHLV16_45_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	898					GRCh38	V40	RPS19_BGHLV16_45_CGTACG_L008_R1_001.fastq.gz,RPS19_BGHLV16_45_CGTACG_L008_R2_001.fastq.gz		ENCORE2	14480
RPS19_BGHLV16_46_GAGTGG_L008_R1_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	899	HiSeq2000	100	paired-ended	1				NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE3	14299
RPS19_BGHLV16_46_GAGTGG_L008_R2_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	899	HiSeq2000	100	paired-ended	2				NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE3	14325
RPS19_BGHLV16_46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	899					GRCh38	V40	RPS19_BGHLV16_46_GAGTGG_L008_R1_001.fastq.gz,RPS19_BGHLV16_46_GAGTGG_L008_R2_001.fastq.gz		ENCORE2	14351
RPS19_BGHLV16_46_Signal.Unique.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	899					GRCh38	V40	RPS19_BGHLV16_46/Aligned.sortedByCoord.out.bam		ENCORE2	14377
RPS19_BGHLV16_46_Signal.Unique.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	899					GRCh38	V40	RPS19_BGHLV16_46/Aligned.sortedByCoord.out.bam		ENCORE2	14403
RPS19_BGHLV16_46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	899					GRCh38	V40	RPS19_BGHLV16_46/Aligned.sortedByCoord.out.bam		ENCORE2	14429
RPS19_BGHLV16_46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	899					GRCh38	V40	RPS19_BGHLV16_46/Aligned.sortedByCoord.out.bam		ENCORE2	14455
RPS19_BGHLV16_46_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	899					GRCh38	V40	RPS19_BGHLV16_46_GAGTGG_L008_R1_001.fastq.gz,RPS19_BGHLV16_46_GAGTGG_L008_R2_001.fastq.gz		ENCORE2	14481