CSTF2T RNA-Seq in K562

General Information


RBP	CSTF2T
Cell_Line	K562
Method	shRNA
Exp_Name	CSTF2T-BGKLV13-K562
ENCODE_series_ID	ENCSR093BFT
Batch_ID	BGKLV13
Pool ID	Pool-140901
Local_Set_Name	set13
ENCODE_KD_Exp_ID	ENCSR286OKW
ENCODE_CN_Exp_ID	ENCSR815CVQ
Rep1	CSTF2T_BGKLV13_43
Rep2	CSTF2T_BGKLV13_44
CN1	NT_BGKLV13_1
CN2	NT_BGKLV13_2
Rep1_qPCR	64.0
Rep2_qPCR	66.8
Rep1_WB	79.2
Rep2_WB	74.0
Antibody Cat#	A301-487A
Antibody Lot#	A301-487A
Antibody DCC ID	ENCAB005DBK
Status	Released
Project	ENCODE3
ID	373

Experiment Information (Status: Released)

	BGKLV13-43	BGKLV13-44
idx	178	179
TRCN#_or_BGC#	TRCN0000145349	TRCN0000145349
shRNA_or_gRNA_sequence	GCGTCTGTTCACTTTAAGTTA	GCGTCTGTTCACTTTAAGTTA
PAM
Name	CSTF2T	CSTF2T
Sample_ID	BGKLV13-43	BGKLV13-44
transduction_Date	6/13/2014	6/13/2014
days
RBP_name	CSTF2T	CSTF2T
qPCR_result	64.0	66.8
Ave_qPCR	65.4
RT-qPCR_primer-F	tcccaggcaaatctcagtct
RT-qPCR_primer-R	ggaggattctgctggttcag
protein_conc	2106	2043
WB_result	79.2	74.0
Ave_WB	76.6
WB_DONE_date	7/23/2014
MW	64kDa
IP	1	1
antibody_Cat#	A301-487A	A301-487A
Antibody DCC ID	ENCAB005DBK	ENCAB005DBK
submitted_to_DCC_date	5/4/2015
Rep1_TPM	13.3738272	0
Rep2_TPM	12.6713311	0
Action
Library_start_date	7/27/2014	7/27/2014
repeat_library
Note
ID	197	198

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CSTF2T	Product_ID: A301-487A Lot_ID: 3 Source: Bethyl Labs Target Name: CSTF2T-human

Experiment Status

	BGKLV13-43	BGKLV13-44
Sample_ID	BGKLV13-43	BGKLV13-44
Sample Name	CSTF2T_BGKLV13_43	CSTF2T_BGKLV13_44
Sample Name	CSTF2T_BGKLV13_43	CSTF2T_BGKLV13_44
RBP	CSTF2T	CSTF2T
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-10-29	2014-10-29
Project	ENCODE3	ENCODE3
Note
ID	440	441

Library-Prep
Sequencing

Library-Prep Information

	BGKLV13-43	BGKLV13-44
Sample #
Sample Name	CSTF2T-BGKLV13-43	CSTF2T-BGKLV13-44
Sample_Name_Alias	CSTF2T_BGKLV13_43	CSTF2T_BGKLV13_44
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-07-27	2014-07-27
Lib_ID	Lib-140727	Lib-140727
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/F4.png	DNA_Library_LV13-14/set1/G4.png
RIN	9.4	9.3
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/A1.png	RNA_Library_LV13-14-16/set1/B1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV13-43	BGKLV13-44
RBP	CSTF2T	CSTF2T
Batch_ID	BGKLV13	BGKLV13
WB_result	79.200	74.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2148	2149

Sequencing Information

	BGKLV13-43	BGKLV13-44
Sample_ID	BGKLV13-43	BGKLV13-44
Sample Name	CSTF2T_BGKLV13_43	CSTF2T_BGKLV13_44
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set13	set13
total_reads	48,110,000	53,720,000
total_aligned_reads	44,587,110	49,231,842
unique_aligned_reads	40,991,848	45,161,216
percent_uniqueAligned	0.85204	0.84068
correlation_replicates	0.999104	0.999104
spikein_reads	260,354	114,068
percent_spikeins	0.00541	0.00212
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	790	791

Data Submission Information

	BGKLV13-43	BGKLV13-43
ENCODE_alias	brenton-graveley:CSTF2T_BGKLV13	brenton-graveley:CSTF2T-BGKLV13-K562
ENCODE_accession	ENCSR286OKW	ENCSR093BFT
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV13-43	BGKLV13-43
Sample Name	CSTF2T_BGKLV13_43	CSTF2T_BGKLV13_43
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2769	6633

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
CSTF2T_BGKLV13_43_ACAGTG_L005_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	790	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13368
CSTF2T_BGKLV13_43_ACAGTG_L005_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	790	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13420
CSTF2T_BGKLV13_43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	790					GRCh38	V40	CSTF2T_BGKLV13_43_ACAGTG_L005_R1_001.fastq.gz,CSTF2T_BGKLV13_43_ACAGTG_L005_R2_001.fastq.gz		ENCORE2	13472
CSTF2T_BGKLV13_43_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	790					GRCh38	V40	CSTF2T_BGKLV13_43/Aligned.sortedByCoord.out.bam		ENCORE2	13524
CSTF2T_BGKLV13_43_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	790					GRCh38	V40	CSTF2T_BGKLV13_43/Aligned.sortedByCoord.out.bam		ENCORE2	13576
CSTF2T_BGKLV13_43_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	790					GRCh38	V40	CSTF2T_BGKLV13_43/Aligned.sortedByCoord.out.bam		ENCORE2	13628
CSTF2T_BGKLV13_43_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	790					GRCh38	V40	CSTF2T_BGKLV13_43/Aligned.sortedByCoord.out.bam		ENCORE2	13680
CSTF2T_BGKLV13_43_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	790					GRCh38	V40	CSTF2T_BGKLV13_43_ACAGTG_L005_R1_001.fastq.gz,CSTF2T_BGKLV13_43_ACAGTG_L005_R2_001.fastq.gz		ENCORE2	13732
CSTF2T_BGKLV13_44_GCCAAT_L005_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	791	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13369
CSTF2T_BGKLV13_44_GCCAAT_L005_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	791	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13421
CSTF2T_BGKLV13_44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	791					GRCh38	V40	CSTF2T_BGKLV13_44_GCCAAT_L005_R1_001.fastq.gz,CSTF2T_BGKLV13_44_GCCAAT_L005_R2_001.fastq.gz		ENCORE2	13473
CSTF2T_BGKLV13_44_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	791					GRCh38	V40	CSTF2T_BGKLV13_44/Aligned.sortedByCoord.out.bam		ENCORE2	13525
CSTF2T_BGKLV13_44_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	791					GRCh38	V40	CSTF2T_BGKLV13_44/Aligned.sortedByCoord.out.bam		ENCORE2	13577
CSTF2T_BGKLV13_44_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	791					GRCh38	V40	CSTF2T_BGKLV13_44/Aligned.sortedByCoord.out.bam		ENCORE2	13629
CSTF2T_BGKLV13_44_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	791					GRCh38	V40	CSTF2T_BGKLV13_44/Aligned.sortedByCoord.out.bam		ENCORE2	13681
CSTF2T_BGKLV13_44_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	791					GRCh38	V40	CSTF2T_BGKLV13_44_GCCAAT_L005_R1_001.fastq.gz,CSTF2T_BGKLV13_44_GCCAAT_L005_R2_001.fastq.gz		ENCORE2	13733