SUGP2 RNA-Seq in HepG2

General Information


RBP	SUGP2
Cell_Line	HepG2
Method	shRNA
Exp_Name	SUGP2-BGHLV27-HepG2
ENCODE_series_ID	ENCSR016FXK
Batch_ID	BGHLV27
Pool ID	Pool-151201
Local_Set_Name	set27
ENCODE_KD_Exp_ID	ENCSR837QDN
ENCODE_CN_Exp_ID	ENCSR246RRQ
Rep1	SUGP2_BGHLV27-53
Rep2	SUGP2_BGHLV27-54
CN1	non-target_BGHLV27-1
CN2	non-target_BGHLV27-2
Rep1_qPCR	52.4
Rep2_qPCR	41.9
Rep1_WB	87.7
Rep2_WB	85.2
Antibody Cat#	A301-607A
Antibody Lot#	A301-607A
Antibody DCC ID	ENCAB433XTU
Status	Released
Project	ENCODE3
ID	645

Experiment Information (Status: Released)

	BGHLV27-53	BGHLV27-54
idx	673	674
TRCN#_or_BGC#	TRCN0000152597	TRCN0000152597
shRNA_or_gRNA_sequence	GTCATTGAAGGTTGGCATGAT	GTCATTGAAGGTTGGCATGAT
PAM
Name	SUGP2	SUGP2
Sample_ID	BGHLV27-53	BGHLV27-54
transduction_Date	6/9/2015	6/9/2015
days
RBP_name	SUGP2	SUGP2
qPCR_result	52.4	41.9
Ave_qPCR	47.2
RT-qPCR_primer-F	TGTGTTCCGACAGAGGATGA
RT-qPCR_primer-R	CAATTGCTGCTTCAAGGCTTA
protein_conc	4813	4972
WB_result	87.7	85.2
Ave_WB	86.5
WB_DONE_date	7/24/2015
MW	120kDa
IP	1	1
antibody_Cat#	A301-607A	A301-607A
Antibody DCC ID	ENCAB433XTU	ENCAB433XTU
submitted_to_DCC_date	8/6/2015
Rep1_TPM	8.1	0
Rep2_TPM	11.3	0
Action
Library_start_date	9/28/2015	9/28/2015
repeat_library
Note	x	x
ID	2760	2761

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SUGP2	Product_ID: A301-607A Lot_ID: 1 Source: Bethyl Labs Target Name: SUGP2-human

Experiment Status

	BGHLV27-53	BGHLV27-54
Sample_ID	BGHLV27-53	BGHLV27-54
Sample Name	SUGP2_BGHLV27-53	SUGP2_BGHLV27-54
Sample Name	SUGP2_BGHLV27-53	SUGP2_BGHLV27-54
RBP	SUGP2	SUGP2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-01-16	2016-01-16
Project	ENCODE3	ENCODE3
Note
ID	976	977

Library-Prep
Sequencing

Library-Prep Information

	BGHLV27-53	BGHLV27-54
Sample #
Sample Name	SUGP2-BGHLV27-53	SUGP2-BGHLV27-54
Sample_Name_Alias	SUGP2_BGHLV27-53	SUGP2_BGHLV27-54
Index Well Position	S15	S16
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/G2.png	DNA_Library_LV27/set1/H2.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/H6.png	RNA_Library_LV26-27-28-29/set1/B6.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV27-53	BGHLV27-54
RBP	SUGP2	SUGP2
Batch_ID	BGHLV27	BGHLV27
WB_result	87.700	85.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2668	2669

Sequencing Information

	BGHLV27-53	BGHLV27-54
Sample_ID	BGHLV27-53	BGHLV27-54
Sample Name	SUGP2_BGHLV27-53	SUGP2_BGHLV27-54
Pool ID	Pool-151201	Pool-151201
LocalServer_folder	set27	set27
total_reads	85,015,504	89,713,892
total_aligned_reads	77,953,598	81,778,000
unique_aligned_reads	73,313,136	76,918,636
percent_uniqueAligned	0.86235	0.85738
correlation_replicates	0.998345	0.998345
spikein_reads	380,228	427,962
percent_spikeins	0.00447	0.00477
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1310	1311

Data Submission Information

	BGHLV27-53	BGHLV27-53
ENCODE_alias	brenton-graveley:SUGP2_BGHLV27	brenton-graveley:SUGP2-BGHLV27-HepG2
ENCODE_accession	ENCSR837QDN	ENCSR016FXK
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV27-53	BGHLV27-53
Sample Name	SUGP2_BGHLV27-53	SUGP2_BGHLV27-53
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-01-14	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3035	6992

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
SUGP2_BGHLV27-53_1.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1310	HiSeq2500	100	paired-ended	1	GRCh38	V40		non-target_BGHLV27-1_1.fastq.gz,non-target_BGHLV27-2_1.fastq.gz	ENCODE3	20022
SUGP2_BGHLV27-53_2.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1310	HiSeq2500	100	paired-ended	2				non-target_BGHLV27-1_2.fastq.gz,non-target_BGHLV27-2_2.fastq.gz	ENCODE3	20044
SUGP2_BGHLV27-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1310					GRCh38	V40	SUGP2_BGHLV27-53_1.fastq.gz,SUGP2_BGHLV27-53_2.fastq.gz		ENCORE2	20066
SUGP2_BGHLV27-53_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	1310					GRCh38	V40	SUGP2_BGHLV27-53/Aligned.sortedByCoord.out.bam		ENCORE2	20088
SUGP2_BGHLV27-53_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	1310					GRCh38	V40	SUGP2_BGHLV27-53/Aligned.sortedByCoord.out.bam		ENCORE2	20110
SUGP2_BGHLV27-53_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	1310					GRCh38	V40	SUGP2_BGHLV27-53/Aligned.sortedByCoord.out.bam		ENCORE2	20132
SUGP2_BGHLV27-53_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	1310					GRCh38	V40	SUGP2_BGHLV27-53/Aligned.sortedByCoord.out.bam		ENCORE2	20154
SUGP2_BGHLV27-53_quant.sf	ENCODE_DATA/set27/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1310					GRCh38	V40	SUGP2_BGHLV27-53_1.fastq.gz,SUGP2_BGHLV27-53_2.fastq.gz		ENCORE2	20694
SUGP2_BGHLV27-54_1.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1311	HiSeq2500	100	paired-ended	1	GRCh38	V40		non-target_BGHLV27-1_1.fastq.gz,non-target_BGHLV27-2_1.fastq.gz	ENCODE3	20023
SUGP2_BGHLV27-54_2.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1311	HiSeq2500	100	paired-ended	2				non-target_BGHLV27-1_2.fastq.gz,non-target_BGHLV27-2_2.fastq.gz	ENCODE3	20045
SUGP2_BGHLV27-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1311					GRCh38	V40	SUGP2_BGHLV27-54_1.fastq.gz,SUGP2_BGHLV27-54_2.fastq.gz		ENCORE2	20067
SUGP2_BGHLV27-54_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	1311					GRCh38	V40	SUGP2_BGHLV27-54/Aligned.sortedByCoord.out.bam		ENCORE2	20089
SUGP2_BGHLV27-54_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	1311					GRCh38	V40	SUGP2_BGHLV27-54/Aligned.sortedByCoord.out.bam		ENCORE2	20111
SUGP2_BGHLV27-54_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	1311					GRCh38	V40	SUGP2_BGHLV27-54/Aligned.sortedByCoord.out.bam		ENCORE2	20133
SUGP2_BGHLV27-54_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	1311					GRCh38	V40	SUGP2_BGHLV27-54/Aligned.sortedByCoord.out.bam		ENCORE2	20155
SUGP2_BGHLV27-54_quant.sf	ENCODE_DATA/set27/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1311					GRCh38	V40	SUGP2_BGHLV27-54_1.fastq.gz,SUGP2_BGHLV27-54_2.fastq.gz		ENCORE2	20695