CSTF2 RNA-Seq in K562

General Information


RBP	CSTF2
Cell_Line	K562
Method	shRNA
Exp_Name	CSTF2-BGKLV19-K562
ENCODE_series_ID	ENCSR429KKD
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR885YOI
ENCODE_CN_Exp_ID	ENCSR245BNJ
Rep1	CSTF2_BGKLV19_9A
Rep2	CSTF2_BGKLV19_10A
CN1	NT_BGKLV19_1A
CN2	NT_BGKLV19_2A
Rep1_qPCR	62.4
Rep2_qPCR	60.6
Rep1_WB	71.2
Rep2_WB	70.7
Antibody Cat#	A301-092A
Antibody Lot#	A301-092A
Antibody DCC ID	ENCAB117EBX
Status	Released
Project	ENCODE3
ID	464

Experiment Information (Status: Released)

	BGKLV19-9	BGKLV19-10
idx	216	217
TRCN#_or_BGC#	TRCN0000157143	TRCN0000157143
shRNA_or_gRNA_sequence	GAGCAAGTATACAGGGTGGAA	GAGCAAGTATACAGGGTGGAA
PAM
Name	CSTF2	CSTF2
Sample_ID	BGKLV19-9	BGKLV19-10
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	CSTF2	CSTF2
qPCR_result	62.4	60.6
Ave_qPCR	61.5
RT-qPCR_primer-F	gaaccaagtcactccacagga
RT-qPCR_primer-R	ctttgctcaggaggcaacat
protein_conc	3324	2999
WB_result	71.2	70.7
Ave_WB	71.0
WB_DONE_date	12/22/2015
MW
IP	1	1
antibody_Cat#	A301-092A	A301-092A
Antibody DCC ID	ENCAB117EBX	ENCAB117EBX
submitted_to_DCC_date	4/2/2015
Rep1_TPM	7.83221139	0
Rep2_TPM	6.47666684	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	235	236

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

	BGKLV19-9	BGKLV19-10
Sample_ID	BGKLV19-9	BGKLV19-10
Sample Name	CSTF2_BGKLV19_9A	CSTF2_BGKLV19_10A
Sample Name	CSTF2_BGKLV19_10A	CSTF2_BGKLV19_9A
RBP	CSTF2	CSTF2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	659	658

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-9	BGKLV19-10
Sample #
Sample Name	CSTF2-BGKLV19-9	CSTF2-BGKLV19-10
Sample_Name_Alias	CSTF2_BGKLV19_9A	CSTF2_BGKLV19_10A
Index Well Position	S23	S22
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-02	2014-10-02
Lib_ID	Lib-141002	Lib-141002
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/F6.png	DNA_Library_LV18-19/set1/E6.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/C1.png	RNA_Library_LV19-21-24/set1/D1.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-9	BGKLV19-10
RBP	CSTF2	CSTF2
Batch_ID	BGKLV19	BGKLV19
WB_result	71.200	70.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2342	2343

Sequencing Information

	BGKLV19-9	BGKLV19-10
Sample_ID	BGKLV19-9	BGKLV19-10
Sample Name	CSTF2_BGKLV19_9A	CSTF2_BGKLV19_10A
Pool ID	Pool-141010	Pool-141010
LocalServer_folder	set19	set19
total_reads	24,010,000	34,750,000
total_aligned_reads	22,199,790	31,550,794
unique_aligned_reads	20,384,516	28,924,030
percent_uniqueAligned	0.84900	0.83235
correlation_replicates	0.996369	0.996369
spikein_reads	59,266	118,122
percent_spikeins	0.00247	0.00340
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	984	985

Data Submission Information

	BGKLV19-9	BGKLV19-9
ENCODE_alias	brenton-graveley:CSTF2_BGKLV19	brenton-graveley:CSTF2-BGKLV19-K562
ENCODE_accession	ENCSR885YOI	ENCSR429KKD
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-9	BGKLV19-9
Sample Name	CSTF2_BGKLV19_9A	CSTF2_BGKLV19_9A
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-05	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2878	6631

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_BGKLV19_9A_CGTACG_L001_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	984	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1A_ATGTCA_L001_R1_001.fastq.gz,NT_BGKLV19_2A_CCGTCC_L001_R1_001.fastq.gz	ENCODE3	15519
CSTF2_BGKLV19_9A_CGTACG_L001_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	984	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1A_ATGTCA_L001_R2_001.fastq.gz,NT_BGKLV19_2A_CCGTCC_L001_R2_001.fastq.gz	ENCODE3	15529
CSTF2_BGKLV19_9A_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	984					GRCh38	V40	CSTF2_BGKLV19_9A_CGTACG_L001_R1_001.fastq.gz,CSTF2_BGKLV19_9A_CGTACG_L001_R2_001.fastq.gz		ENCORE2	15539
CSTF2_BGKLV19_9A_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	984					GRCh38	V40	CSTF2_BGKLV19_9A/Aligned.sortedByCoord.out.bam		ENCORE2	15549
CSTF2_BGKLV19_9A_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	984					GRCh38	V40	CSTF2_BGKLV19_9A/Aligned.sortedByCoord.out.bam		ENCORE2	15559
CSTF2_BGKLV19_9A_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	984					GRCh38	V40	CSTF2_BGKLV19_9A/Aligned.sortedByCoord.out.bam		ENCORE2	15569
CSTF2_BGKLV19_9A_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	984					GRCh38	V40	CSTF2_BGKLV19_9A/Aligned.sortedByCoord.out.bam		ENCORE2	15579
CSTF2_BGKLV19_9A_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	984					GRCh38	V40	CSTF2_BGKLV19_9A_CGTACG_L001_R1_001.fastq.gz,CSTF2_BGKLV19_9A_CGTACG_L001_R2_001.fastq.gz		ENCORE2	16357
CSTF2_BGKLV19_10A_GAGTGG_L001_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	985	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1A_ATGTCA_L001_R1_001.fastq.gz,NT_BGKLV19_2A_CCGTCC_L001_R1_001.fastq.gz	ENCODE3	15518
CSTF2_BGKLV19_10A_GAGTGG_L001_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	985	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1A_ATGTCA_L001_R2_001.fastq.gz,NT_BGKLV19_2A_CCGTCC_L001_R2_001.fastq.gz	ENCODE3	15528
CSTF2_BGKLV19_10A_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	985					GRCh38	V40	CSTF2_BGKLV19_10A_GAGTGG_L001_R1_001.fastq.gz,CSTF2_BGKLV19_10A_GAGTGG_L001_R2_001.fastq.gz		ENCORE2	15538
CSTF2_BGKLV19_10A_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	985					GRCh38	V40	CSTF2_BGKLV19_10A/Aligned.sortedByCoord.out.bam		ENCORE2	15548
CSTF2_BGKLV19_10A_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	985					GRCh38	V40	CSTF2_BGKLV19_10A/Aligned.sortedByCoord.out.bam		ENCORE2	15558
CSTF2_BGKLV19_10A_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	985					GRCh38	V40	CSTF2_BGKLV19_10A/Aligned.sortedByCoord.out.bam		ENCORE2	15568
CSTF2_BGKLV19_10A_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	985					GRCh38	V40	CSTF2_BGKLV19_10A/Aligned.sortedByCoord.out.bam		ENCORE2	15578
CSTF2_BGKLV19_10A_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	985					GRCh38	V40	CSTF2_BGKLV19_10A_GAGTGG_L001_R1_001.fastq.gz,CSTF2_BGKLV19_10A_GAGTGG_L001_R2_001.fastq.gz		ENCORE2	16356