STIP1 RNA-Seq in K562

General Information


RBP	STIP1
Cell_Line	K562
Method	shRNA
Exp_Name	STIP1-BGKLV24-K562
ENCODE_series_ID	ENCSR575GJA
Batch_ID	BGKLV24
Pool ID	Pool-151101
Local_Set_Name	set24_2
ENCODE_KD_Exp_ID	ENCSR082UWF
ENCODE_CN_Exp_ID	ENCSR419JMU
Rep1	STIP1_BGKLV24_61B
Rep2	STIP1_BGKLV24_62B
CN1	non-target_BGKLV24_1B
CN2	non-target_BGKLV24_2B
Rep1_qPCR	65.9
Rep2_qPCR	75.1
Rep1_WB
Rep2_WB
Antibody Cat#	GTX120608
Antibody Lot#	LOT# 40688
Antibody DCC ID	ENCAB315RZC
Status	Released
Project	ENCODE3
ID	612

Experiment Information (Status: Released)

	BGKLV24-61	BGKLV24-62
idx	398	399
TRCN#_or_BGC#	TRCN0000243098	TRCN0000243098
shRNA_or_gRNA_sequence	ACCCGAAAGATGCCAAATTAT	ACCCGAAAGATGCCAAATTAT
PAM
Name	STIP1	STIP1
Sample_ID	BGKLV24-61	BGKLV24-62
transduction_Date	2/27/2015	2/27/2015
days
RBP_name	STIP1	STIP1
qPCR_result	65.9	75.1
Ave_qPCR	70.5
RT-qPCR_primer-F	ccgaccttcatcaagggtta
RT-qPCR_primer-R	agcgccttctggtacacatc
protein_conc	3795	3934
WB_result
Ave_WB	no clear band
WB_DONE_date	4/7/2015
MW	74kDa
IP	1	1
antibody_Cat#	GTX120608	GTX120608
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	130.364335	0
Rep2_TPM	78.2138385	0
Action
Library_start_date	9/2/2015	9/2/2015
repeat_library
Note
ID	457	458

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV24-61	BGKLV24-62
Sample_ID	BGKLV24-61	BGKLV24-62
Sample Name	STIP1_BGKLV24_61B	STIP1_BGKLV24_62B
Sample Name	STIP1_BGKLV24_61B	STIP1_BGKLV24_62B
RBP	STIP1	STIP1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-12-08	2015-12-08
Project	ENCODE3	ENCODE3
Note
ID	906	907

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-61	BGKLV24-62
Sample #
Sample Name	STIP1-BGKLV24-61B	STIP1-BGKLV24-62B
Sample_Name_Alias	STIP1_BGKLV24_61B	STIP1_BGKLV24_62B
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-02	2015-09-02
Lib_ID	Lib-150902	Lib-150902
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/G7.png	DNA_Library_LV24-25-26/set1/H7.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/A7.png	RNA_Library_LV20-22-24/set1/B7.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-61	BGKLV24-62
RBP	STIP1	STIP1
Batch_ID	BGKLV24	BGKLV24
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2594	2595

Sequencing Information

	BGKLV24-61	BGKLV24-62
Sample_ID	BGKLV24-61	BGKLV24-62
Sample Name	STIP1_BGKLV24_61B	STIP1_BGKLV24_62B
Pool ID	Pool-151101	Pool-151101
LocalServer_folder	set24_2	set24_2
total_reads	77,516,816	65,048,884
total_aligned_reads	74,769,542	62,054,834
unique_aligned_reads	68,009,344	56,511,568
percent_uniqueAligned	0.87735	0.86876
correlation_replicates	0.998605	0.998605
spikein_reads	375,946	207,460
percent_spikeins	0.00485	0.00319
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1236	1237

Data Submission Information

	BGKLV24-61	BGKLV24-61
ENCODE_alias	brenton-graveley:STIP1_BGKLV24_B	brenton-graveley:STIP1-BGKLV24-K562
ENCODE_accession	ENCSR082UWF	ENCSR575GJA
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-61	BGKLV24-61
Sample Name	STIP1_BGKLV24_61B	STIP1_BGKLV24_61B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3002	6987

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_BGKLV24_61B_ACTGAT_L004_001.R1.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1236	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1B_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R1.fastq.gz	ENCODE3	17492
STIP1_BGKLV24_61B_ACTGAT_L004_001.R2.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1236	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1B_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R2.fastq.gz	ENCODE3	17516
STIP1_BGKLV24_61B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1236					GRCh38	V40	STIP1_BGKLV24_61B_ACTGAT_L004_001.R1.fastq.gz,STIP1_BGKLV24_61B_ACTGAT_L004_001.R2.fastq.gz		ENCORE2	17540
STIP1_BGKLV24_61B_Signal.Unique.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1236					GRCh38	V40	STIP1_BGKLV24_61B/Aligned.sortedByCoord.out.bam		ENCORE2	17564
STIP1_BGKLV24_61B_Signal.Unique.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1236					GRCh38	V40	STIP1_BGKLV24_61B/Aligned.sortedByCoord.out.bam		ENCORE2	17588
STIP1_BGKLV24_61B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1236					GRCh38	V40	STIP1_BGKLV24_61B/Aligned.sortedByCoord.out.bam		ENCORE2	17612
STIP1_BGKLV24_61B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1236					GRCh38	V40	STIP1_BGKLV24_61B/Aligned.sortedByCoord.out.bam		ENCORE2	17636
STIP1_BGKLV24_61B_quant.sf	ENCODE_DATA/set24_2/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1236					GRCh38	V40	STIP1_BGKLV24_61B_ACTGAT_L004_001.R1.fastq.gz,STIP1_BGKLV24_61B_ACTGAT_L004_001.R2.fastq.gz		ENCORE2	17660
STIP1_BGKLV24_62B_ATTCCT_L004_001.R1.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1237	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1B_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R1.fastq.gz	ENCODE3	17493
STIP1_BGKLV24_62B_ATTCCT_L004_001.R2.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1237	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1B_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R2.fastq.gz	ENCODE3	17517
STIP1_BGKLV24_62B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1237					GRCh38	V40	STIP1_BGKLV24_62B_ATTCCT_L004_001.R1.fastq.gz,STIP1_BGKLV24_62B_ATTCCT_L004_001.R2.fastq.gz		ENCORE2	17541
STIP1_BGKLV24_62B_Signal.Unique.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1237					GRCh38	V40	STIP1_BGKLV24_62B/Aligned.sortedByCoord.out.bam		ENCORE2	17565
STIP1_BGKLV24_62B_Signal.Unique.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1237					GRCh38	V40	STIP1_BGKLV24_62B/Aligned.sortedByCoord.out.bam		ENCORE2	17589
STIP1_BGKLV24_62B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1237					GRCh38	V40	STIP1_BGKLV24_62B/Aligned.sortedByCoord.out.bam		ENCORE2	17613
STIP1_BGKLV24_62B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1237					GRCh38	V40	STIP1_BGKLV24_62B/Aligned.sortedByCoord.out.bam		ENCORE2	17637
STIP1_BGKLV24_62B_quant.sf	ENCODE_DATA/set24_2/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1237					GRCh38	V40	STIP1_BGKLV24_62B_ATTCCT_L004_001.R1.fastq.gz,STIP1_BGKLV24_62B_ATTCCT_L004_001.R2.fastq.gz		ENCORE2	17661