STIP1 RNA-Seq in HepG2

General Information


RBP	STIP1
Cell_Line	HepG2
Method	shRNA
Exp_Name	STIP1-BGHLV22-HepG2
ENCODE_series_ID	ENCSR491IUN
Batch_ID	BGHLV22
Pool ID	Pool-150701
Local_Set_Name	set22
ENCODE_KD_Exp_ID	ENCSR871BXO
ENCODE_CN_Exp_ID	ENCSR279HMU
Rep1	STIP1-BGHLV22-49
Rep2	STIP1-BGHLV22-50
CN1	non-target-BGHLV22-1_17746
CN2	non-target-BGHLV22-2_17747
Rep1_qPCR	71.3
Rep2_qPCR	71.9
Rep1_WB
Rep2_WB	NO CLEAR BAND
Antibody Cat#	GTX120608
Antibody Lot#	LOT# 40688
Antibody DCC ID	ENCAB315RZC
Status	Released
Project	ENCODE3
ID	530

Experiment Information (Status: Released)

	BGHLV22-49	BGHLV22-50
idx	477	478
TRCN#_or_BGC#	TRCN0000243098	TRCN0000243098
shRNA_or_gRNA_sequence	ACCCGAAAGATGCCAAATTAT	ACCCGAAAGATGCCAAATTAT
PAM
Name	STIP1	STIP1
Sample_ID	BGHLV22-49	BGHLV22-50
transduction_Date	10/16/2014	10/16/2014
days
RBP_name	STIP1	STIP1
qPCR_result	71.3	71.9
Ave_qPCR	71.6
RT-qPCR_primer-F	ccgaccttcatcaagggtta
RT-qPCR_primer-R	agcgccttctggtacacatc
protein_conc	6570	5551
WB_result		NO CLEAR BAND
Ave_WB	NO CLEAR BAND
WB_DONE_date	4/7/2015	2/22/2016
MW	74kDa	wes
IP	1	1
antibody_Cat#	GTX120608	GTX120608
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	26.6	0
Rep2_TPM	43.4	0
Action
Library_start_date	6/5/2015	6/5/2015
repeat_library
Note
ID	2552	2553

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV22-49	BGHLV22-50
Sample_ID	BGHLV22-49	BGHLV22-50
Sample Name	STIP1-BGHLV22-49	STIP1-BGHLV22-50
Sample Name	STIP1-BGHLV22-49	STIP1-BGHLV22-50
RBP	STIP1	STIP1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	810	811

Library-Prep
Sequencing

Library-Prep Information

	BGHLV22-49	BGHLV22-50
Sample #
Sample Name	STIP1-BGHLV22-49	STIP1-BGHLV22-50
Sample_Name_Alias	STIP1-BGHLV22-49	STIP1-BGHLV22-50
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-05	2015-06-05
Lib_ID	Lib-150605	Lib-150605
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/A10.png	DNA_Library_LV20-22-23/set1/B10.png
RIN	9.2	9.1
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/A4.png	RNA_Library_LV22-23-25/set1/B4.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV22-49	BGHLV22-50
RBP	STIP1	STIP1
Batch_ID	BGHLV22	BGHLV22
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2496	2497

Sequencing Information

	BGHLV22-49	BGHLV22-50
Sample_ID	BGHLV22-49	BGHLV22-50
Sample Name	STIP1-BGHLV22-49	STIP1-BGHLV22-50
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set22	set22
total_reads	43,850,000	46,090,000
total_aligned_reads	39,957,272	42,232,122
unique_aligned_reads	37,627,128	39,791,212
percent_uniqueAligned	0.85809	0.86334
correlation_replicates	0.997280	0.997280
spikein_reads	304,502	311,466
percent_spikeins	0.00694	0.00676
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1118	1119

Data Submission Information

	BGHLV22-49	BGHLV22-49
ENCODE_alias	brenton-graveley:STIP1-BGHLV22	brenton-graveley:STIP1-BGHLV22-HepG2
ENCODE_accession	ENCSR871BXO	ENCSR491IUN
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV22-49	BGHLV22-49
Sample Name	STIP1-BGHLV22-49	STIP1-BGHLV22-49
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2937	6986

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
STIP1-BGHLV22-49_GATCAG_L003_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1118	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16308
STIP1-BGHLV22-49_GATCAG_L003_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1118	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16348
STIP1-BGHLV22-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1118					GRCh38	V40	STIP1-BGHLV22-49_GATCAG_L003_R1_001.fastq.gz,STIP1-BGHLV22-49_GATCAG_L003_R2_001.fastq.gz		ENCORE2	16446
STIP1-BGHLV22-49_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1118					GRCh38	V40	STIP1-BGHLV22-49/Aligned.sortedByCoord.out.bam		ENCORE2	16486
STIP1-BGHLV22-49_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1118					GRCh38	V40	STIP1-BGHLV22-49/Aligned.sortedByCoord.out.bam		ENCORE2	16526
STIP1-BGHLV22-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1118					GRCh38	V40	STIP1-BGHLV22-49/Aligned.sortedByCoord.out.bam		ENCORE2	16566
STIP1-BGHLV22-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1118					GRCh38	V40	STIP1-BGHLV22-49/Aligned.sortedByCoord.out.bam		ENCORE2	16606
STIP1-BGHLV22-49_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1118					GRCh38	V40	STIP1-BGHLV22-49_GATCAG_L003_R1_001.fastq.gz,STIP1-BGHLV22-49_GATCAG_L003_R2_001.fastq.gz		ENCORE2	16646
STIP1-BGHLV22-50_TAGCTT_L003_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1119	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16309
STIP1-BGHLV22-50_TAGCTT_L003_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1119	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16349
STIP1-BGHLV22-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1119					GRCh38	V40	STIP1-BGHLV22-50_TAGCTT_L003_R1_001.fastq.gz,STIP1-BGHLV22-50_TAGCTT_L003_R2_001.fastq.gz		ENCORE2	16447
STIP1-BGHLV22-50_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1119					GRCh38	V40	STIP1-BGHLV22-50/Aligned.sortedByCoord.out.bam		ENCORE2	16487
STIP1-BGHLV22-50_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1119					GRCh38	V40	STIP1-BGHLV22-50/Aligned.sortedByCoord.out.bam		ENCORE2	16527
STIP1-BGHLV22-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1119					GRCh38	V40	STIP1-BGHLV22-50/Aligned.sortedByCoord.out.bam		ENCORE2	16567
STIP1-BGHLV22-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1119					GRCh38	V40	STIP1-BGHLV22-50/Aligned.sortedByCoord.out.bam		ENCORE2	16607
STIP1-BGHLV22-50_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1119					GRCh38	V40	STIP1-BGHLV22-50_TAGCTT_L003_R1_001.fastq.gz,STIP1-BGHLV22-50_TAGCTT_L003_R2_001.fastq.gz		ENCORE2	16647