CELF1 RNA-Seq in K562

General Information


RBP	CELF1
Cell_Line	K562
Method	shRNA
Exp_Name	CELF1-BGKLV25-K562
ENCODE_series_ID	ENCSR203XSC
Batch_ID	BGKLV25
Pool ID	Pool-151101
Local_Set_Name	set25
ENCODE_KD_Exp_ID	ENCSR605MFS
ENCODE_CN_Exp_ID	ENCSR620PUP
Rep1	CUGBP1_BGKLV25-9
Rep2	CUGBP1_BGKLV25-10
CN1	NT_BGKLV25-1
CN2	NT_BGKLV25-2
Rep1_qPCR	13.0
Rep2_qPCR	3.6
Rep1_WB	51.0
Rep2_WB	51.5
Antibody Cat#	RN034PW
Antibody Lot#	RN034PW
Antibody DCC ID	ENCAB848AYT
Status	Released
Project	ENCODE3
ID	615

Experiment Information (Status: Released)

	BGKLV25-9	BGKLV25-10
idx	410	411
TRCN#_or_BGC#	TRCN0000017283	TRCN0000017283
shRNA_or_gRNA_sequence	CGGCTTAAAGTGCAGCTCAAA	CGGCTTAAAGTGCAGCTCAAA
PAM
Name	CUGBP1	CUGBP1
Sample_ID	BGKLV25-9	BGKLV25-10
transduction_Date	3/17/2015	3/17/2015
days
RBP_name	CELF1	CELF1
qPCR_result	13.0	3.6
Ave_qPCR	8.3
RT-qPCR_primer-F	CCTTTGGGAATGTCGTGTCT
RT-qPCR_primer-R	GGGCCGAAACAGGATTGT
protein_conc	3757	3805
WB_result	51.0	51.5
Ave_WB	51.3
WB_DONE_date	3/30/2015
MW	52kDa
IP	1	1
antibody_Cat#	RN034PW	RN034PW
Antibody DCC ID	ENCAB848AYT	ENCAB848AYT
submitted_to_DCC_date	3/8/2016
Rep1_TPM	23.4487344	0
Rep2_TPM	21.0948271	0
Action
Library_start_date	6/23/2015	6/23/2015
repeat_library
Note
ID	469	470

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CELF1	Product_ID: RN034PW Lot_ID: 1 Source: MBLI Target Name: CELF1-human

Experiment Status

	BGKLV25-9	BGKLV25-10
Sample_ID	BGKLV25-9	BGKLV25-10
Sample Name	CUGBP1_BGKLV25-9	CUGBP1_BGKLV25-10
Sample Name	CUGBP1_BGKLV25-9	CUGBP1_BGKLV25-10
RBP	CELF1	CELF1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-12-08	2015-12-08
Project	ENCODE3	ENCODE3
Note
ID	911	910

Library-Prep
Sequencing

Library-Prep Information

	BGKLV25-9	BGKLV25-10
Sample #
Sample Name	CELF1-BGKLV25-9	CELF1-BGKLV25-10
Sample_Name_Alias	CUGBP1_BGKLV25-9	CUGBP1_BGKLV25-10
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-23	2015-06-23
Lib_ID	Lib-150623	Lib-150623
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set2/D2.png	DNA_Library_LV24-25-26/set1/H1.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/G9.png	RNA_Library_LV22-23-25/set1/H9.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV25-9	BGKLV25-10
RBP	CELF1	CELF1
Batch_ID	BGKLV25	BGKLV25
WB_result	51.000	51.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2601	2600

Sequencing Information

	BGKLV25-9	BGKLV25-10
Sample_ID	BGKLV25-9	BGKLV25-10
Sample Name	CUGBP1_BGKLV25-9	CUGBP1_BGKLV25-10
Pool ID	Pool-151101	Pool-151101
LocalServer_folder	set25	set25
total_reads	123,270,822	139,986,598
total_aligned_reads	125,964,414	144,926,892
unique_aligned_reads	114,376,420	131,820,950
percent_uniqueAligned	0.92785	0.94167
correlation_replicates	0.995820	0.995820
spikein_reads	637,674	668,816
percent_spikeins	0.00517	0.00478
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1243	1242

Data Submission Information

	BGKLV25-9	BGKLV25-9
ENCODE_alias	brenton-graveley:CUGBP1_BGKLV25	brenton-graveley:CELF1-BGKLV25-K562
ENCODE_accession	ENCSR605MFS	ENCSR203XSC
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV25-9	BGKLV25-9
Sample Name	CUGBP1_BGKLV25-9	CUGBP1_BGKLV25-9
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3004	6618

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
CUGBP1_BGKLV25-9_ATGTCA_L005_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1243	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19567
CUGBP1_BGKLV25-9_ATGTCA_L005_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1243	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19603
CUGBP1_BGKLV25-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1243					GRCh38	V40	CUGBP1_BGKLV25-9_ATGTCA_L005_001.R1.fastq.gz,CUGBP1_BGKLV25-9_ATGTCA_L005_001.R2.fastq.gz		ENCORE2	19639
CUGBP1_BGKLV25-9_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1243					GRCh38	V40	CUGBP1_BGKLV25-9/Aligned.sortedByCoord.out.bam		ENCORE2	19675
CUGBP1_BGKLV25-9_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1243					GRCh38	V40	CUGBP1_BGKLV25-9/Aligned.sortedByCoord.out.bam		ENCORE2	19711
CUGBP1_BGKLV25-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1243					GRCh38	V40	CUGBP1_BGKLV25-9/Aligned.sortedByCoord.out.bam		ENCORE2	19747
CUGBP1_BGKLV25-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1243					GRCh38	V40	CUGBP1_BGKLV25-9/Aligned.sortedByCoord.out.bam		ENCORE2	19783
CUGBP1_BGKLV25-9_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1243					GRCh38	V40	CUGBP1_BGKLV25-9_ATGTCA_L005_001.R1.fastq.gz,CUGBP1_BGKLV25-9_ATGTCA_L005_001.R2.fastq.gz		ENCORE2	19973
CUGBP1_BGKLV25-10_CCGTCC_L005_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1242	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19566
CUGBP1_BGKLV25-10_CCGTCC_L005_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1242	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19602
CUGBP1_BGKLV25-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1242					GRCh38	V40	CUGBP1_BGKLV25-10_CCGTCC_L005_001.R1.fastq.gz,CUGBP1_BGKLV25-10_CCGTCC_L005_001.R2.fastq.gz		ENCORE2	19638
CUGBP1_BGKLV25-10_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1242					GRCh38	V40	CUGBP1_BGKLV25-10/Aligned.sortedByCoord.out.bam		ENCORE2	19674
CUGBP1_BGKLV25-10_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1242					GRCh38	V40	CUGBP1_BGKLV25-10/Aligned.sortedByCoord.out.bam		ENCORE2	19710
CUGBP1_BGKLV25-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1242					GRCh38	V40	CUGBP1_BGKLV25-10/Aligned.sortedByCoord.out.bam		ENCORE2	19746
CUGBP1_BGKLV25-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1242					GRCh38	V40	CUGBP1_BGKLV25-10/Aligned.sortedByCoord.out.bam		ENCORE2	19782
CUGBP1_BGKLV25-10_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1242					GRCh38	V40	CUGBP1_BGKLV25-10_CCGTCC_L005_001.R1.fastq.gz,CUGBP1_BGKLV25-10_CCGTCC_L005_001.R2.fastq.gz		ENCORE2	19972