SSRP1 RNA-Seq in HepG2

General Information


RBP	SSRP1
Cell_Line	HepG2
Method	shRNA
Exp_Name	SSRP1-BGHLV27-HepG2
ENCODE_series_ID	ENCSR789DBN
Batch_ID	BGHLV27
Pool ID	Pool-151201
Local_Set_Name	set27
ENCODE_KD_Exp_ID	ENCSR422JMS
ENCODE_CN_Exp_ID	ENCSR246RRQ
Rep1	SSRP1_BGHLV27-51
Rep2	SSRP1_BGHLV27-52
CN1	non-target_BGHLV27-1
CN2	non-target_BGHLV27-2
Rep1_qPCR	71.1
Rep2_qPCR	66.2
Rep1_WB	75.1
Rep2_WB	68.2
Antibody Cat#	GTX111816
Antibody Lot#	GTX111816
Antibody DCC ID	ENCAB983GBT
Status	Released
Project	ENCODE3
ID	644

Experiment Information (Status: Released)

	BGHLV27-51	BGHLV27-52
idx	671	672
TRCN#_or_BGC#	TRCN0000019272	>TRCN0000019272
shRNA_or_gRNA_sequence	CGCTTCGATGAGATCTCCTTT	CGCTTCGATGAGATCTCCTTT
PAM
Name	SSRP1	SSRP1
Sample_ID	BGHLV27-51	BGHLV27-52
transduction_Date	6/9/2015	6/9/2015
days
RBP_name	SSRP1	SSRP1
qPCR_result	71.1	66.2
Ave_qPCR	68.7
RT-qPCR_primer-F	acagctcaaaaaggccaaga
RT-qPCR_primer-R	gtatgcagacatgggcctct
protein_conc	4324	4066
WB_result	75.1	68.2
Ave_WB	71.6
WB_DONE_date	7/24/2015
MW	81kDa
IP	1MB	1MB
antibody_Cat#	GTX111816	GTX111816
Antibody DCC ID	ENCAB983GBT	ENCAB983GBT
submitted_to_DCC_date	8/6/2015
Rep1_TPM	38.6	0
Rep2_TPM	33.4	0
Action
Library_start_date	9/28/2015	9/28/2015
repeat_library
Note	x	x
ID	2758	2759

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SSRP1	Product_ID: GTX111816 Lot_ID: 40079 Source: GeneTex Target Name: SSRP1-human

Experiment Status

	BGHLV27-51	BGHLV27-52
Sample_ID	BGHLV27-51	BGHLV27-52
Sample Name	SSRP1_BGHLV27-51	SSRP1_BGHLV27-52
Sample Name	SSRP1_BGHLV27-51	SSRP1_BGHLV27-52
RBP	SSRP1	SSRP1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-01-16	2016-01-16
Project	ENCODE3	ENCODE3
Note
ID	974	975

Library-Prep
Sequencing

Library-Prep Information

	BGHLV27-51	BGHLV27-52
Sample #
Sample Name	SSRP1-BGHLV27-51	SSRP1-BGHLV27-52
Sample_Name_Alias	SSRP1_BGHLV27-51	SSRP1_BGHLV27-52
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-28	2015-09-28
Lib_ID	Lib-150928	Lib-150928
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV27/set1/E2.png	DNA_Library_LV27/set1/F2.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/G5.png	RNA_Library_LV26-27-28-29/set1/H5.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV27-51	BGHLV27-52
RBP	SSRP1	SSRP1
Batch_ID	BGHLV27	BGHLV27
WB_result	75.100	68.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2666	2667

Sequencing Information

	BGHLV27-51	BGHLV27-52
Sample_ID	BGHLV27-51	BGHLV27-52
Sample Name	SSRP1_BGHLV27-51	SSRP1_BGHLV27-52
Pool ID	Pool-151201	Pool-151201
LocalServer_folder	set27	set27
total_reads	70,741,090	97,746,020
total_aligned_reads	65,143,068	90,727,940
unique_aligned_reads	61,103,552	85,022,564
percent_uniqueAligned	0.86376	0.86983
correlation_replicates	0.999123	0.999123
spikein_reads	296,022	406,036
percent_spikeins	0.00418	0.00415
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1308	1309

Data Submission Information

	BGHLV27-51	BGHLV27-51
ENCODE_alias	brenton-graveley:SSRP1_BGHLV27	brenton-graveley:SSRP1-BGHLV27-HepG2
ENCODE_accession	ENCSR422JMS	ENCSR789DBN
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV27-51	BGHLV27-51
Sample Name	SSRP1_BGHLV27-51	SSRP1_BGHLV27-51
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-01-14	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3034	6982

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
SSRP1_BGHLV27-51_1.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1308	HiSeq2500	100	paired-ended	1	GRCh38	V40		non-target_BGHLV27-1_1.fastq.gz,non-target_BGHLV27-2_1.fastq.gz	ENCODE3	20020
SSRP1_BGHLV27-51_2.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1308	HiSeq2500	100	paired-ended	2				non-target_BGHLV27-1_2.fastq.gz,non-target_BGHLV27-2_2.fastq.gz	ENCODE3	20042
SSRP1_BGHLV27-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1308					GRCh38	V40	SSRP1_BGHLV27-51_1.fastq.gz,SSRP1_BGHLV27-51_2.fastq.gz		ENCORE2	20064
SSRP1_BGHLV27-51_Signal.Unique.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1308					GRCh38	V40	SSRP1_BGHLV27-51/Aligned.sortedByCoord.out.bam		ENCORE2	20086
SSRP1_BGHLV27-51_Signal.Unique.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1308					GRCh38	V40	SSRP1_BGHLV27-51/Aligned.sortedByCoord.out.bam		ENCORE2	20108
SSRP1_BGHLV27-51_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1308					GRCh38	V40	SSRP1_BGHLV27-51/Aligned.sortedByCoord.out.bam		ENCORE2	20130
SSRP1_BGHLV27-51_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1308					GRCh38	V40	SSRP1_BGHLV27-51/Aligned.sortedByCoord.out.bam		ENCORE2	20152
SSRP1_BGHLV27-51_quant.sf	ENCODE_DATA/set27/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1308					GRCh38	V40	SSRP1_BGHLV27-51_1.fastq.gz,SSRP1_BGHLV27-51_2.fastq.gz		ENCORE2	20692
SSRP1_BGHLV27-52_1.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1309	HiSeq2500	100	paired-ended	1	GRCh38	V40		non-target_BGHLV27-1_1.fastq.gz,non-target_BGHLV27-2_1.fastq.gz	ENCODE3	20021
SSRP1_BGHLV27-52_2.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1309	HiSeq2500	100	paired-ended	2				non-target_BGHLV27-1_2.fastq.gz,non-target_BGHLV27-2_2.fastq.gz	ENCODE3	20043
SSRP1_BGHLV27-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1309					GRCh38	V40	SSRP1_BGHLV27-52_1.fastq.gz,SSRP1_BGHLV27-52_2.fastq.gz		ENCORE2	20065
SSRP1_BGHLV27-52_Signal.Unique.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1309					GRCh38	V40	SSRP1_BGHLV27-52/Aligned.sortedByCoord.out.bam		ENCORE2	20087
SSRP1_BGHLV27-52_Signal.Unique.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1309					GRCh38	V40	SSRP1_BGHLV27-52/Aligned.sortedByCoord.out.bam		ENCORE2	20109
SSRP1_BGHLV27-52_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1309					GRCh38	V40	SSRP1_BGHLV27-52/Aligned.sortedByCoord.out.bam		ENCORE2	20131
SSRP1_BGHLV27-52_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1309					GRCh38	V40	SSRP1_BGHLV27-52/Aligned.sortedByCoord.out.bam		ENCORE2	20153
SSRP1_BGHLV27-52_quant.sf	ENCODE_DATA/set27/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1309					GRCh38	V40	SSRP1_BGHLV27-52_1.fastq.gz,SSRP1_BGHLV27-52_2.fastq.gz		ENCORE2	20693