RPS5 RNA-Seq in HepG2

General Information


RBP	RPS5
Cell_Line	HepG2
Method	shRNA
Exp_Name	RPS5-BGHLV18-HepG2
ENCODE_series_ID	ENCSR643UXI
Batch_ID	BGHLV18
Pool ID	Pool-141010
Local_Set_Name	set18
ENCODE_KD_Exp_ID	ENCSR838SMC
ENCODE_CN_Exp_ID	ENCSR674KEK
Rep1	RPS5_BGHLV18_57
Rep2	RPS5_BGHLV18_58
CN1	NT_BGHLV18_1
CN2	NT_BGHLV18_2
Rep1_qPCR	59.8
Rep2_qPCR	65.8
Rep1_WB	42.2
Rep2_WB	43.6
Antibody Cat#	A304-010A
Antibody Lot#	A304-010A
Antibody DCC ID	ENCAB780TEB
Status	Released
Project	ENCODE3
ID	461

Experiment Information (Status: Released)

	BGHLV18-57	BGHLV18-58
idx	357	358
TRCN#_or_BGC#	TRCN0000074755	TRCN0000074755
shRNA_or_gRNA_sequence	CGGAACATTAAGACCATTGCT	CGGAACATTAAGACCATTGCT
PAM
Name	RPS5	RPS5
Sample_ID	BGHLV18-57	BGHLV18-58
transduction_Date	8/28/2014	8/28/2014
days
RBP_name	RPS5	RPS5
qPCR_result	59.8	65.8
Ave_qPCR	62.8
RT-qPCR_primer-F	agagacgctcaggctgtgtt
RT-qPCR_primer-R	gtgctccacttcccaaagag
protein_conc	3958	3632
WB_result	42.2	43.6
Ave_WB	42.9
WB_DONE_date	4/15/2015
MW	23kDa
IP	1	1
antibody_Cat#	A304-010A	A304-010A
Antibody DCC ID	ENCAB780TEB	ENCAB780TEB
submitted_to_DCC_date	5/6/2015
Rep1_TPM	565.3	0
Rep2_TPM	618.2	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	2422	2423

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPS5	Product_ID: A304-010A Lot_ID: 1 Source: Bethyl Labs Target Name: RPS5-human

Experiment Status

	BGHLV18-57	BGHLV18-58
Sample_ID	BGHLV18-57	BGHLV18-58
Sample Name	RPS5_BGHLV18_57	RPS5_BGHLV18_58
Sample Name	RPS5_BGHLV18_57	RPS5_BGHLV18_58
RBP	RPS5	RPS5
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	652	653

Library-Prep
Sequencing

Library-Prep Information

	BGHLV18-57	BGHLV18-58
Sample #
Sample Name	RPS5-BGHLV18-57	RPS5-BGHLV18-58
Sample_Name_Alias	RPS5_BGHLV18_57	RPS5_BGHLV18_58
Index Well Position	S13	S14
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/E5.png	DNA_Library_LV18-19/set1/F5.png
RIN	9.5	9.3
libSample_RNA_Well	RNA_Library_LV18-19/set1/C12.png	RNA_Library_LV18-19/set1/D12.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV18-57	BGHLV18-58
RBP	RPS5	RPS5
Batch_ID	BGHLV18	BGHLV18
WB_result	42.200	43.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2336	2337

Sequencing Information

	BGHLV18-57	BGHLV18-58
Sample_ID	BGHLV18-57	BGHLV18-58
Sample Name	RPS5_BGHLV18_57	RPS5_BGHLV18_58
Pool ID	Pool-141010	Pool-141010
LocalServer_folder	set18	set18
total_reads	65,860,000	50,530,000
total_aligned_reads	59,498,318	46,511,658
unique_aligned_reads	56,159,170	43,847,446
percent_uniqueAligned	0.85271	0.86775
correlation_replicates	0.996778	0.996778
spikein_reads	240,606	166,830
percent_spikeins	0.00365	0.00330
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	978	979

Data Submission Information

	BGHLV18-57	BGHLV18-57
ENCODE_alias	brenton-graveley:RPS5_BGHLV18	brenton-graveley:RPS5-BGHLV18-HepG2
ENCODE_accession	ENCSR838SMC	ENCSR643UXI
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV18-57	BGHLV18-57
Sample Name	RPS5_BGHLV18_57	RPS5_BGHLV18_57
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2843	6922

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
RPS5_BGHLV18_57_AGTCAA_L005_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	978	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14826
RPS5_BGHLV18_57_AGTCAA_L005_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	978	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14864
RPS5_BGHLV18_57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	978					GRCh38	V40	RPS5_BGHLV18_57_AGTCAA_L005_R1_001.fastq.gz,RPS5_BGHLV18_57_AGTCAA_L005_R2_001.fastq.gz		ENCORE2	14902
RPS5_BGHLV18_57_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	978					GRCh38	V40	RPS5_BGHLV18_57/Aligned.sortedByCoord.out.bam		ENCORE2	14940
RPS5_BGHLV18_57_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	978					GRCh38	V40	RPS5_BGHLV18_57/Aligned.sortedByCoord.out.bam		ENCORE2	14978
RPS5_BGHLV18_57_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	978					GRCh38	V40	RPS5_BGHLV18_57/Aligned.sortedByCoord.out.bam		ENCORE2	15016
RPS5_BGHLV18_57_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	978					GRCh38	V40	RPS5_BGHLV18_57/Aligned.sortedByCoord.out.bam		ENCORE2	15054
RPS5_BGHLV18_57_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	978					GRCh38	V40	RPS5_BGHLV18_57_AGTCAA_L005_R1_001.fastq.gz,RPS5_BGHLV18_57_AGTCAA_L005_R2_001.fastq.gz		ENCORE2	15092
RPS5_BGHLV18_58_AGTTCC_L005_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	979	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14827
RPS5_BGHLV18_58_AGTTCC_L005_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	979	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14865
RPS5_BGHLV18_58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	979					GRCh38	V40	RPS5_BGHLV18_58_AGTTCC_L005_R1_001.fastq.gz,RPS5_BGHLV18_58_AGTTCC_L005_R2_001.fastq.gz		ENCORE2	14903
RPS5_BGHLV18_58_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	979					GRCh38	V40	RPS5_BGHLV18_58/Aligned.sortedByCoord.out.bam		ENCORE2	14941
RPS5_BGHLV18_58_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	979					GRCh38	V40	RPS5_BGHLV18_58/Aligned.sortedByCoord.out.bam		ENCORE2	14979
RPS5_BGHLV18_58_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	979					GRCh38	V40	RPS5_BGHLV18_58/Aligned.sortedByCoord.out.bam		ENCORE2	15017
RPS5_BGHLV18_58_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	979					GRCh38	V40	RPS5_BGHLV18_58/Aligned.sortedByCoord.out.bam		ENCORE2	15055
RPS5_BGHLV18_58_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	979					GRCh38	V40	RPS5_BGHLV18_58_AGTTCC_L005_R1_001.fastq.gz,RPS5_BGHLV18_58_AGTTCC_L005_R2_001.fastq.gz		ENCORE2	15093