RPS10 RNA-Seq in HepG2

General Information


RBP	RPS10
Cell_Line	HepG2
Method	shRNA
Exp_Name	RPS10-BGHLV14-HepG2
ENCODE_series_ID	ENCSR245WSO
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR410UHJ
ENCODE_CN_Exp_ID	ENCSR491FOC
Rep1	RPS10_BGHLV14-41
Rep2	RPS10_BGHLV14-42
CN1	NT_BGHLV14-1
CN2	NT_BGHLV14-2
Rep1_qPCR	74.5
Rep2_qPCR	67.4
Rep1_WB	50.1
Rep2_WB	49.7
Antibody Cat#	RN070PW
Antibody Lot#	lot #1
Antibody DCC ID	ENCAB391UDZ
Status	Released
Project	ENCODE3
ID	401

Experiment Information (Status: Released)

	BGHLV14-41	BGHLV14-42
idx	137	138
TRCN#_or_BGC#	TRCN0000074810	TRCN0000074810
shRNA_or_gRNA_sequence	CTGGAGACATTTCTACTGGTA	CTGGAGACATTTCTACTGGTA
PAM
Name	RPS10	RPS10
Sample_ID	BGHLV14-41	BGHLV14-42
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	RPS10	RPS10
qPCR_result	74.5	67.4
Ave_qPCR	71.0
RT-qPCR_primer-F	GGGAAGCTGACAGAGATACC
RT-qPCR_primer-R	ACTGGAATTCGGTTGCTGAC
protein_conc	2908	2840
WB_result	50.1	49.7
Ave_WB	49.9
WB_DONE_date	6/14/19
MW	19KD
IP	1	1
antibody_Cat#	RN070PW	lot #1
Antibody DCC ID	ENCAB391UDZ
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action
Library_start_date	8/12/2014	8/12/2014
repeat_library
Note
ID	2198	2199

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPS10	Product_ID: RN070PW Lot_ID: 1 Source: MBLI Target Name: RPS10-human

Experiment Status

	BGHLV14-41	BGHLV14-42
Sample_ID	BGHLV14-41	BGHLV14-42
Sample Name	RPS10_BGHLV14-41	RPS10_BGHLV14-42
Sample Name	RPS10_BGHLV14-41	RPS10_BGHLV14-42
RBP	RPS10	RPS10
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	528	529

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-41	BGHLV14-42
Sample #
Sample Name	RPS10-BGHLV14-41	RPS10-BGHLV14-42
Sample_Name_Alias	RPS10_BGHLV14-41	RPS10_BGHLV14-42
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-08-12	2014-08-12
Lib_ID	Lib-140812	Lib-140812
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/D12.png	DNA_Library_LV13-14/set1/E12.png
RIN	9.4	9.4
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/E8.png	RNA_Library_LV13-14-16/set1/F8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-41	BGHLV14-42
RBP	RPS10	RPS10
Batch_ID	BGHLV14	BGHLV14
WB_result	50.100	49.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2210	2211

Sequencing Information

	BGHLV14-41	BGHLV14-42
Sample_ID	BGHLV14-41	BGHLV14-42
Sample Name	RPS10_BGHLV14-41	RPS10_BGHLV14-42
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	52,460,000	49,920,000
total_aligned_reads	47,343,924	43,710,042
unique_aligned_reads	44,865,300	41,396,530
percent_uniqueAligned	0.85523	0.82926
correlation_replicates	0.997891	0.997891
spikein_reads	288,100	261,254
percent_spikeins	0.00549	0.00523
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	852	853

Data Submission Information

	BGHLV14-41	BGHLV14-41
ENCODE_alias	brenton-graveley:RPS10_BGHLV14	brenton-graveley:RPS10-BGHLV14-HepG2
ENCODE_accession	ENCSR410UHJ	ENCSR245WSO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-41	BGHLV14-41
Sample Name	RPS10_BGHLV14-41	RPS10_BGHLV14-41
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2813	6914

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
RPS10_BGHLV14-41_GTGGCC_L005_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	852	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13820
RPS10_BGHLV14-41_GTGGCC_L005_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	852	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13882
RPS10_BGHLV14-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	852					GRCh38	V40	RPS10_BGHLV14-41_GTGGCC_L005_R1_001.fastq.gz,RPS10_BGHLV14-41_GTGGCC_L005_R2_001.fastq.gz		ENCORE2	13944
RPS10_BGHLV14-41_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	852					GRCh38	V40	RPS10_BGHLV14-41/Aligned.sortedByCoord.out.bam		ENCORE2	14006
RPS10_BGHLV14-41_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	852					GRCh38	V40	RPS10_BGHLV14-41/Aligned.sortedByCoord.out.bam		ENCORE2	14068
RPS10_BGHLV14-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	852					GRCh38	V40	RPS10_BGHLV14-41/Aligned.sortedByCoord.out.bam		ENCORE2	14130
RPS10_BGHLV14-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	852					GRCh38	V40	RPS10_BGHLV14-41/Aligned.sortedByCoord.out.bam		ENCORE2	14192
RPS10_BGHLV14-41_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	852					GRCh38	V40	RPS10_BGHLV14-41_GTGGCC_L005_R1_001.fastq.gz,RPS10_BGHLV14-41_GTGGCC_L005_R2_001.fastq.gz		ENCORE2	14254
RPS10_BGHLV14-42_GTTTCG_L005_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	853	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13821
RPS10_BGHLV14-42_GTTTCG_L005_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	853	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13883
RPS10_BGHLV14-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	853					GRCh38	V40	RPS10_BGHLV14-42_GTTTCG_L005_R1_001.fastq.gz,RPS10_BGHLV14-42_GTTTCG_L005_R2_001.fastq.gz		ENCORE2	13945
RPS10_BGHLV14-42_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	853					GRCh38	V40	RPS10_BGHLV14-42/Aligned.sortedByCoord.out.bam		ENCORE2	14007
RPS10_BGHLV14-42_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	853					GRCh38	V40	RPS10_BGHLV14-42/Aligned.sortedByCoord.out.bam		ENCORE2	14069
RPS10_BGHLV14-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	853					GRCh38	V40	RPS10_BGHLV14-42/Aligned.sortedByCoord.out.bam		ENCORE2	14131
RPS10_BGHLV14-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	853					GRCh38	V40	RPS10_BGHLV14-42/Aligned.sortedByCoord.out.bam		ENCORE2	14193
RPS10_BGHLV14-42_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	853					GRCh38	V40	RPS10_BGHLV14-42_GTTTCG_L005_R1_001.fastq.gz,RPS10_BGHLV14-42_GTTTCG_L005_R2_001.fastq.gz		ENCORE2	14255