SRP68 RNA-Seq in HepG2

General Information


RBP	SRP68
Cell_Line	HepG2
Method	shRNA
Exp_Name	SRP68-BGHLV17-HepG2
ENCODE_series_ID	ENCSR579VHH
Batch_ID	BGHLV17
Pool ID	Pool-141001
Local_Set_Name	set17
ENCODE_KD_Exp_ID	ENCSR167JPY
ENCODE_CN_Exp_ID	ENCSR856ZRV
Rep1	SRP68_BGHLV17_29
Rep2	SRP68_BGHLV17_30
CN1	NT_BGHLV17_63
CN2	NT_BGHLV17_64
Rep1_qPCR	78.4
Rep2_qPCR	75.4
Rep1_WB	79.2
Rep2_WB	78.1
Antibody Cat#	A303-955A
Antibody Lot#	A303-955A
Antibody DCC ID	ENCAB434DUK
Status	Released
Project	ENCODE3
ID	438

Experiment Information (Status: Released)

	BGHLV17-29	BGHLV17-30
idx	265	266
TRCN#_or_BGC#	TRCN0000075080	TRCN0000075080
shRNA_or_gRNA_sequence	CCGACTCTATGACATCATCTT	CCGACTCTATGACATCATCTT
PAM
Name	SRP68	SRP68
Sample_ID	BGHLV17-29	BGHLV17-30
transduction_Date	8/19/2014	8/19/2014
days
RBP_name	SRP68	SRP68
qPCR_result	78.4	75.4
Ave_qPCR	76.9
RT-qPCR_primer-F	gagagccagggaaggtgtct
RT-qPCR_primer-R	cctttggccatgttctcatt
protein_conc	2817	3920
WB_result	79.2	78.1
Ave_WB	78.7
WB_DONE_date	3/18/2015
MW	71kDa
IP	1	1
antibody_Cat#	A303-955A	A303-955A
Antibody DCC ID	ENCAB434DUK	ENCAB434DUK
submitted_to_DCC_date	4/2/2015
Rep1_TPM	63.5	0
Rep2_TPM	63.7	0
Action
Library_start_date	9/26/2014	9/26/2014
repeat_library
Note
ID	2330	2331

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SRP68	Product_ID: A303-955A Lot_ID: 1 Source: Bethyl Labs Target Name: SRP68-human

Experiment Status

	BGHLV17-29	BGHLV17-30
Sample_ID	BGHLV17-29	BGHLV17-30
Sample Name	SRP68_BGHLV17_29	SRP68_BGHLV17_30
Sample Name	SRP68_BGHLV17_29	SRP68_BGHLV17_30
RBP	SRP68	SRP68
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	604	605

Library-Prep
Sequencing

Library-Prep Information

	BGHLV17-29	BGHLV17-30
Sample #
Sample Name	SRP68-BGHLV17-29	SRP68-BGHLV17-30
Sample_Name_Alias	SRP68_BGHLV17_29	SRP68_BGHLV17_30
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-26	2014-09-26
Lib_ID	Lib-140926	Lib-140926
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set1/A3.png	DNA_Library_LV16-17/set1/B3.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/A5.png	RNA_Library_LV16-17-18/set1/B5.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV17-29	BGHLV17-30
RBP	SRP68	SRP68
Batch_ID	BGHLV17	BGHLV17
WB_result	79.200	78.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2288	2289

Sequencing Information

	BGHLV17-29	BGHLV17-30
Sample_ID	BGHLV17-29	BGHLV17-30
Sample Name	SRP68_BGHLV17_29	SRP68_BGHLV17_30
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set17	set17
total_reads	60,380,000	69,070,000
total_aligned_reads	54,708,068	62,428,752
unique_aligned_reads	51,614,778	58,867,218
percent_uniqueAligned	0.85483	0.85228
correlation_replicates	0.996628	0.996628
spikein_reads	206,844	151,290
percent_spikeins	0.00343	0.00219
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	930	931

Data Submission Information

	BGHLV17-29	BGHLV17-29
ENCODE_alias	brenton-graveley:SRP68_BGHLV17	brenton-graveley:SRP68-BGHLV17-HepG2
ENCODE_accession	ENCSR167JPY	ENCSR579VHH
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV17-29	BGHLV17-29
Sample Name	SRP68_BGHLV17_29	SRP68_BGHLV17_29
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2869	6963

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
SRP68_BGHLV17_29_GTCCGC_L003_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	930	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14512
SRP68_BGHLV17_29_GTCCGC_L003_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	930	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14550
SRP68_BGHLV17_29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	930					GRCh38	V40	SRP68_BGHLV17_29_GTCCGC_L003_R1_001.fastq.gz,SRP68_BGHLV17_29_GTCCGC_L003_R2_001.fastq.gz		ENCORE2	14588
SRP68_BGHLV17_29_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	930					GRCh38	V40	SRP68_BGHLV17_29/Aligned.sortedByCoord.out.bam		ENCORE2	14626
SRP68_BGHLV17_29_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	930					GRCh38	V40	SRP68_BGHLV17_29/Aligned.sortedByCoord.out.bam		ENCORE2	14664
SRP68_BGHLV17_29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	930					GRCh38	V40	SRP68_BGHLV17_29/Aligned.sortedByCoord.out.bam		ENCORE2	14702
SRP68_BGHLV17_29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	930					GRCh38	V40	SRP68_BGHLV17_29/Aligned.sortedByCoord.out.bam		ENCORE2	14740
SRP68_BGHLV17_29_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	930					GRCh38	V40	SRP68_BGHLV17_29_GTCCGC_L003_R1_001.fastq.gz,SRP68_BGHLV17_29_GTCCGC_L003_R2_001.fastq.gz		ENCORE2	14778
SRP68_BGHLV17_30_GTGAAA_L003_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	931	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14513
SRP68_BGHLV17_30_GTGAAA_L003_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	931	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14551
SRP68_BGHLV17_30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	931					GRCh38	V40	SRP68_BGHLV17_30_GTGAAA_L003_R1_001.fastq.gz,SRP68_BGHLV17_30_GTGAAA_L003_R2_001.fastq.gz		ENCORE2	14589
SRP68_BGHLV17_30_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	931					GRCh38	V40	SRP68_BGHLV17_30/Aligned.sortedByCoord.out.bam		ENCORE2	14627
SRP68_BGHLV17_30_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	931					GRCh38	V40	SRP68_BGHLV17_30/Aligned.sortedByCoord.out.bam		ENCORE2	14665
SRP68_BGHLV17_30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	931					GRCh38	V40	SRP68_BGHLV17_30/Aligned.sortedByCoord.out.bam		ENCORE2	14703
SRP68_BGHLV17_30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	931					GRCh38	V40	SRP68_BGHLV17_30/Aligned.sortedByCoord.out.bam		ENCORE2	14741
SRP68_BGHLV17_30_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	931					GRCh38	V40	SRP68_BGHLV17_30_GTGAAA_L003_R1_001.fastq.gz,SRP68_BGHLV17_30_GTGAAA_L003_R2_001.fastq.gz		ENCORE2	14779