CSTF2T RNA-Seq in HepG2

General Information


RBP	CSTF2T
Cell_Line	HepG2
Method	shRNA
Exp_Name	CSTF2T-BGHLV14-HepG2
ENCODE_series_ID	ENCSR202YZX
Batch_ID	BGHLV14
Pool ID	Pool-140901
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR914WQV
ENCODE_CN_Exp_ID	ENCSR003EKR
Rep1	CSTF2T_BGHLV14-5
Rep2	CSTF2T_BGHLV14-6
CN1	NT_BGHLV14-1_1
CN2	NT_BGHLV14-2_1
Rep1_qPCR	49.7
Rep2_qPCR	54.8
Rep1_WB	85.3
Rep2_WB	91.7
Antibody Cat#	A301-487A
Antibody Lot#	A301-487A
Antibody DCC ID	ENCAB005DBK
Status	Released
Project	ENCODE3
ID	385

Experiment Information (Status: Released)

	BGHLV14-5	BGHLV14-6
idx	99	100
TRCN#_or_BGC#	TRCN0000145349	TRCN0000145349
shRNA_or_gRNA_sequence	GCGTCTGTTCACTTTAAGTTA	GCGTCTGTTCACTTTAAGTTA
PAM
Name	CSTF2T	CSTF2T
Sample_ID	BGHLV14-5	BGHLV14-6
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	CSTF2T	CSTF2T
qPCR_result	49.7	54.8
Ave_qPCR	52.3
RT-qPCR_primer-F	tcccaggcaaatctcagtct
RT-qPCR_primer-R	ggaggattctgctggttcag
protein_conc	4167	4430
WB_result	85.3	91.7
Ave_WB	88.5
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	2.1	0
Rep2_TPM	1.3	0
Action
Library_start_date	7/30/2014	7/30/2014
repeat_library
Note
ID	2156	2157

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

	BGHLV14-5	BGHLV14-6
Sample_ID	BGHLV14-5	BGHLV14-6
Sample Name	CSTF2T_BGHLV14-5	CSTF2T_BGHLV14-6
Sample Name	CSTF2T_BGHLV14-5	CSTF2T_BGHLV14-6
RBP	CSTF2T	CSTF2T
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	492	493

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-5	BGHLV14-6
Sample #
Sample Name	CSTF2T-BGHLV14-5	CSTF2T-BGHLV14-6
Sample_Name_Alias	CSTF2T_BGHLV14-5	CSTF2T_BGHLV14-6
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-07-30	2014-07-30
Lib_ID	Lib-140730	Lib-140730
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/B8.png	DNA_Library_LV13-14/set1/C8.png
RIN	9.4	9.6
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/E4.png	RNA_Library_LV13-14-16/set1/F4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-5	BGHLV14-6
RBP	CSTF2T	CSTF2T
Batch_ID	BGHLV14	BGHLV14
WB_result	85.300	91.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2176	2177

Sequencing Information

	BGHLV14-5	BGHLV14-6
Sample_ID	BGHLV14-5	BGHLV14-6
Sample Name	CSTF2T_BGHLV14-5	CSTF2T_BGHLV14-6
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set14	set14
total_reads	45,360,000	45,600,000
total_aligned_reads	42,673,416	42,812,014
unique_aligned_reads	40,283,222	40,370,956
percent_uniqueAligned	0.88808	0.88533
correlation_replicates	0.995285	0.995285
spikein_reads	268,818	244,038
percent_spikeins	0.00593	0.00535
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	818	819

Data Submission Information

	BGHLV14-5	BGHLV14-5
ENCODE_alias	brenton-graveley:CSTF2T_BGHLV14	brenton-graveley:CSTF2T-BGHLV14-HepG2
ENCODE_accession	ENCSR914WQV	ENCSR202YZX
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-5	BGHLV14-5
Sample Name	CSTF2T_BGHLV14-5	CSTF2T_BGHLV14-5
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2795	6632

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_BGHLV14-5_GATCAG_L008_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	818	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_1_ACAGTG_L008_R1_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R1_001.fastq.gz	ENCODE3	13784
CSTF2T_BGHLV14-5_GATCAG_L008_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	818	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_1_ACAGTG_L008_R2_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R2_001.fastq.gz	ENCODE3	13846
CSTF2T_BGHLV14-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	818					GRCh38	V40	CSTF2T_BGHLV14-5_GATCAG_L008_R1_001.fastq.gz,CSTF2T_BGHLV14-5_GATCAG_L008_R2_001.fastq.gz		ENCORE2	13908
CSTF2T_BGHLV14-5_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	818					GRCh38	V40	CSTF2T_BGHLV14-5/Aligned.sortedByCoord.out.bam		ENCORE2	13970
CSTF2T_BGHLV14-5_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	818					GRCh38	V40	CSTF2T_BGHLV14-5/Aligned.sortedByCoord.out.bam		ENCORE2	14032
CSTF2T_BGHLV14-5_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	818					GRCh38	V40	CSTF2T_BGHLV14-5/Aligned.sortedByCoord.out.bam		ENCORE2	14094
CSTF2T_BGHLV14-5_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	818					GRCh38	V40	CSTF2T_BGHLV14-5/Aligned.sortedByCoord.out.bam		ENCORE2	14156
CSTF2T_BGHLV14-5_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	818					GRCh38	V40	CSTF2T_BGHLV14-5_GATCAG_L008_R1_001.fastq.gz,CSTF2T_BGHLV14-5_GATCAG_L008_R2_001.fastq.gz		ENCORE2	14218
CSTF2T_BGHLV14-6_TAGCTT_L008_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	819	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_1_ACAGTG_L008_R1_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R1_001.fastq.gz	ENCODE3	13785
CSTF2T_BGHLV14-6_TAGCTT_L008_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	819	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_1_ACAGTG_L008_R2_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R2_001.fastq.gz	ENCODE3	13847
CSTF2T_BGHLV14-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	819					GRCh38	V40	CSTF2T_BGHLV14-6_TAGCTT_L008_R1_001.fastq.gz,CSTF2T_BGHLV14-6_TAGCTT_L008_R2_001.fastq.gz		ENCORE2	13909
CSTF2T_BGHLV14-6_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	819					GRCh38	V40	CSTF2T_BGHLV14-6/Aligned.sortedByCoord.out.bam		ENCORE2	13971
CSTF2T_BGHLV14-6_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	819					GRCh38	V40	CSTF2T_BGHLV14-6/Aligned.sortedByCoord.out.bam		ENCORE2	14033
CSTF2T_BGHLV14-6_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	819					GRCh38	V40	CSTF2T_BGHLV14-6/Aligned.sortedByCoord.out.bam		ENCORE2	14095
CSTF2T_BGHLV14-6_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	819					GRCh38	V40	CSTF2T_BGHLV14-6/Aligned.sortedByCoord.out.bam		ENCORE2	14157
CSTF2T_BGHLV14-6_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	819					GRCh38	V40	CSTF2T_BGHLV14-6_TAGCTT_L008_R1_001.fastq.gz,CSTF2T_BGHLV14-6_TAGCTT_L008_R2_001.fastq.gz		ENCORE2	14219