CSTF2 RNA-Seq in HepG2

General Information


RBP	CSTF2
Cell_Line	HepG2
Method	shRNA
Exp_Name	CSTF2-BGHLV17-HepG2
ENCODE_series_ID	ENCSR769MTC
Batch_ID	BGHLV17
Pool ID	Pool-141001
Local_Set_Name	set17
ENCODE_KD_Exp_ID	ENCSR815JDY
ENCODE_CN_Exp_ID	ENCSR856ZRV
Rep1	CSTF2_BGHLV17_9
Rep2	CSTF2_BGHLV17_10
CN1	NT_BGHLV17_63
CN2	NT_BGHLV17_64
Rep1_qPCR	58.1
Rep2_qPCR	61.2
Rep1_WB	91.0
Rep2_WB	86.3
Antibody Cat#	A301-092A
Antibody Lot#	A301-092A
Antibody DCC ID	ENCAB117EBX
Status	Released
Project	ENCODE3
ID	429

Experiment Information (Status: Released)

	BGHLV17-9	BGHLV17-10
idx	245	246
TRCN#_or_BGC#	TRCN0000157143	TRCN0000157143
shRNA_or_gRNA_sequence	GAGCAAGTATACAGGGTGGAA	GAGCAAGTATACAGGGTGGAA
PAM
Name	CSTF2	CSTF2
Sample_ID	BGHLV17-9	BGHLV17-10
transduction_Date	8/19/2014	8/19/2014
days
RBP_name	CSTF2	CSTF2
qPCR_result	58.1	61.2
Ave_qPCR	59.6
RT-qPCR_primer-F	gaaccaagtcactccacagga
RT-qPCR_primer-R	ctttgctcaggaggcaacat
protein_conc	1614	1845
WB_result	91.0	86.3
Ave_WB	88.7
WB_DONE_date	12/4/2015
MW	61kDa
IP	1	1
antibody_Cat#	A301-092A	A301-092A
Antibody DCC ID	ENCAB117EBX	ENCAB117EBX
submitted_to_DCC_date	4/2/2015
Rep1_TPM	2.4	0
Rep2_TPM	1.7	0
Action
Library_start_date	9/26/2014	9/26/2014
repeat_library
Note
ID	2310	2311

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CSTF2	Product_ID: A301-092A Lot_ID: 1 Source: Bethyl Labs Target Name: CSTF2-human

Experiment Status

	BGHLV17-9	BGHLV17-10
Sample_ID	BGHLV17-9	BGHLV17-10
Sample Name	CSTF2_BGHLV17_9	CSTF2_BGHLV17_10
Sample Name	CSTF2_BGHLV17_9	CSTF2_BGHLV17_10
RBP	CSTF2	CSTF2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	585	584

Library-Prep
Sequencing

Library-Prep Information

	BGHLV17-9	BGHLV17-10
Sample #
Sample Name	CSTF2-BGHLV17-9	CSTF2-BGHLV17-10
Sample_Name_Alias	CSTF2_BGHLV17_9	CSTF2_BGHLV17_10
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-26	2014-09-26
Lib_ID	Lib-140926	Lib-140926
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set1/G1.png	DNA_Library_LV16-17/set1/H1.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/G3.png	RNA_Library_LV16-17-18/set1/H3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV17-9	BGHLV17-10
RBP	CSTF2	CSTF2
Batch_ID	BGHLV17	BGHLV17
WB_result	91.000	86.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2269	2268

Sequencing Information

	BGHLV17-9	BGHLV17-10
Sample_ID	BGHLV17-9	BGHLV17-10
Sample Name	CSTF2_BGHLV17_9	CSTF2_BGHLV17_10
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set17	set17
total_reads	28,250,000	25,080,000
total_aligned_reads	25,100,860	22,296,376
unique_aligned_reads	23,624,028	20,985,110
percent_uniqueAligned	0.83625	0.83673
correlation_replicates	0.997524	0.997524
spikein_reads	92,874	59,098
percent_spikeins	0.00329	0.00236
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	911	910

Data Submission Information

	BGHLV17-9	BGHLV17-9
ENCODE_alias	brenton-graveley:CSTF2_BGHLV17	brenton-graveley:CSTF2-BGHLV17-HepG2
ENCODE_accession	ENCSR815JDY	ENCSR769MTC
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV17-9	BGHLV17-9
Sample Name	CSTF2_BGHLV17_9	CSTF2_BGHLV17_9
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2860	6630

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
CSTF2_BGHLV17_9_CAGATC_L001_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	911	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14493
CSTF2_BGHLV17_9_CAGATC_L001_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	911	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14531
CSTF2_BGHLV17_9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	911					GRCh38	V40	CSTF2_BGHLV17_9_CAGATC_L001_R1_001.fastq.gz,CSTF2_BGHLV17_9_CAGATC_L001_R2_001.fastq.gz		ENCORE2	14569
CSTF2_BGHLV17_9_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	911					GRCh38	V40	CSTF2_BGHLV17_9/Aligned.sortedByCoord.out.bam		ENCORE2	14607
CSTF2_BGHLV17_9_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	911					GRCh38	V40	CSTF2_BGHLV17_9/Aligned.sortedByCoord.out.bam		ENCORE2	14645
CSTF2_BGHLV17_9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	911					GRCh38	V40	CSTF2_BGHLV17_9/Aligned.sortedByCoord.out.bam		ENCORE2	14683
CSTF2_BGHLV17_9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	911					GRCh38	V40	CSTF2_BGHLV17_9/Aligned.sortedByCoord.out.bam		ENCORE2	14721
CSTF2_BGHLV17_9_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	911					GRCh38	V40	CSTF2_BGHLV17_9_CAGATC_L001_R1_001.fastq.gz,CSTF2_BGHLV17_9_CAGATC_L001_R2_001.fastq.gz		ENCORE2	14759
CSTF2_BGHLV17_10_ACTTGA_L001_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	910	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14492
CSTF2_BGHLV17_10_ACTTGA_L001_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	910	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14530
CSTF2_BGHLV17_10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	910					GRCh38	V40	CSTF2_BGHLV17_10_ACTTGA_L001_R1_001.fastq.gz,CSTF2_BGHLV17_10_ACTTGA_L001_R2_001.fastq.gz		ENCORE2	14568
CSTF2_BGHLV17_10_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	910					GRCh38	V40	CSTF2_BGHLV17_10/Aligned.sortedByCoord.out.bam		ENCORE2	14606
CSTF2_BGHLV17_10_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	910					GRCh38	V40	CSTF2_BGHLV17_10/Aligned.sortedByCoord.out.bam		ENCORE2	14644
CSTF2_BGHLV17_10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	910					GRCh38	V40	CSTF2_BGHLV17_10/Aligned.sortedByCoord.out.bam		ENCORE2	14682
CSTF2_BGHLV17_10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	910					GRCh38	V40	CSTF2_BGHLV17_10/Aligned.sortedByCoord.out.bam		ENCORE2	14720
CSTF2_BGHLV17_10_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	910					GRCh38	V40	CSTF2_BGHLV17_10_ACTTGA_L001_R1_001.fastq.gz,CSTF2_BGHLV17_10_ACTTGA_L001_R2_001.fastq.gz		ENCORE2	14758