CELF1 RNA-Seq in HepG2

General Information


RBP	CELF1
Cell_Line	HepG2
Method	shRNA
Exp_Name	CELF1-BGHLV23-HepG2
ENCODE_series_ID	ENCSR955ACR
Batch_ID	BGHLV23
Pool ID	Pool-150701
Local_Set_Name	set23
ENCODE_KD_Exp_ID	ENCSR695XOD
ENCODE_CN_Exp_ID	ENCSR042QTH
Rep1	CUGBP1-BGHLV23-9
Rep2	CUGBP1-BGHLV23-10
CN1	non-target-BGHLV23-1
CN2	non-target-BGHLV23-2
Rep1_qPCR	48.0
Rep2_qPCR	64.2
Rep1_WB	92.1
Rep2_WB	89.5
Antibody Cat#	RN034PW
Antibody Lot#	RN034PW
Antibody DCC ID	ENCAB848AYT
Status	Released
Project	ENCODE3
ID	539

Experiment Information (Status: Released)

	BGHLV23-9	BGHLV23-10
idx	501	502
TRCN#_or_BGC#	TRCN0000017283	TRCN0000017283
shRNA_or_gRNA_sequence	CGGCTTAAAGTGCAGCTCAAA	CGGCTTAAAGTGCAGCTCAAA
PAM
Name	CUGBP1	CUGBP1
Sample_ID	BGHLV23-9	BGHLV23-10
transduction_Date	10/29/2014	10/29/2014
days
RBP_name	CELF1	CELF1
qPCR_result	48.0	64.2
Ave_qPCR	56.1
RT-qPCR_primer-F	CCTTTGGGAATGTCGTGTCT
RT-qPCR_primer-R	GGGCCGAAACAGGATTGT
protein_conc	5198	5027
WB_result	92.1	89.5
Ave_WB	90.8
WB_DONE_date	3/30/2015
MW
IP	1	1
antibody_Cat#	RN034PW	RN034PW
Antibody DCC ID	ENCAB848AYT	ENCAB848AYT
submitted_to_DCC_date	5/6/2015
Rep1_TPM	11.2	0
Rep2_TPM	11.4	0
Action
Library_start_date	6/10/2015	6/10/2015
repeat_library
Note
ID	2576	2577

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

	BGHLV23-9	BGHLV23-10
Sample_ID	BGHLV23-9	BGHLV23-10
Sample Name	CUGBP1-BGHLV23-9	CUGBP1-BGHLV23-10
Sample Name	CUGBP1-BGHLV23-9	CUGBP1-BGHLV23-10
RBP	CELF1	CELF1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	815	814

Library-Prep
Sequencing

Library-Prep Information

	BGHLV23-9	BGHLV23-10
Sample #
Sample Name	CELF1-BGHLV23-9	CELF1-BGHLV23-10
Sample_Name_Alias	CUGBP1-BGHLV23-9	CUGBP1-BGHLV23-10
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-10	2015-06-10
Lib_ID	Lib-150610	Lib-150610
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/E11.png	DNA_Library_LV20-22-23/set1/F11.png
RIN	10.0	9.5
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/H11.png	RNA_Library_LV19-21-24/set2/B5.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV23-9	BGHLV23-10
RBP	CELF1	CELF1
Batch_ID	BGHLV23	BGHLV23
WB_result	92.100	89.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2503	2502

Sequencing Information

	BGHLV23-9	BGHLV23-10
Sample_ID	BGHLV23-9	BGHLV23-10
Sample Name	CUGBP1-BGHLV23-9	CUGBP1-BGHLV23-10
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set23	set23
total_reads	56,870,000	54,500,000
total_aligned_reads	51,769,722	49,912,016
unique_aligned_reads	48,695,884	46,983,002
percent_uniqueAligned	0.85627	0.86207
correlation_replicates	0.998760	0.998760
spikein_reads	369,740	314,804
percent_spikeins	0.00650	0.00578
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1125	1124

Data Submission Information

	BGHLV23-9	BGHLV23-9
ENCODE_alias	brenton-graveley:CUGBP1-BGHLV23	brenton-graveley:CELF1-BGHLV23-HepG2
ENCODE_accession	ENCSR695XOD	ENCSR955ACR
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV23-9	BGHLV23-9
Sample Name	CUGBP1-BGHLV23-9	CUGBP1-BGHLV23-9
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2939	6617

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-BGHLV23-9_CGTACG_L004_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1125	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16653
CUGBP1-BGHLV23-9_CGTACG_L004_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1125	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16691
CUGBP1-BGHLV23-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1125					GRCh38	V40	CUGBP1-BGHLV23-9_CGTACG_L004_R1_001.fastq.gz,CUGBP1-BGHLV23-9_CGTACG_L004_R2_001.fastq.gz		ENCORE2	16729
CUGBP1-BGHLV23-9_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1125					GRCh38	V40	CUGBP1-BGHLV23-9/Aligned.sortedByCoord.out.bam		ENCORE2	16767
CUGBP1-BGHLV23-9_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1125					GRCh38	V40	CUGBP1-BGHLV23-9/Aligned.sortedByCoord.out.bam		ENCORE2	16805
CUGBP1-BGHLV23-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1125					GRCh38	V40	CUGBP1-BGHLV23-9/Aligned.sortedByCoord.out.bam		ENCORE2	16843
CUGBP1-BGHLV23-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1125					GRCh38	V40	CUGBP1-BGHLV23-9/Aligned.sortedByCoord.out.bam		ENCORE2	16881
CUGBP1-BGHLV23-9_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1125					GRCh38	V40	CUGBP1-BGHLV23-9_CGTACG_L004_R1_001.fastq.gz,CUGBP1-BGHLV23-9_CGTACG_L004_R2_001.fastq.gz		ENCORE2	16919
CUGBP1-BGHLV23-10_GAGTGG_L004_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1124	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16652
CUGBP1-BGHLV23-10_GAGTGG_L004_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1124	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16690
CUGBP1-BGHLV23-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1124					GRCh38	V40	CUGBP1-BGHLV23-10_GAGTGG_L004_R1_001.fastq.gz,CUGBP1-BGHLV23-10_GAGTGG_L004_R2_001.fastq.gz		ENCORE2	16728
CUGBP1-BGHLV23-10_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1124					GRCh38	V40	CUGBP1-BGHLV23-10/Aligned.sortedByCoord.out.bam		ENCORE2	16766
CUGBP1-BGHLV23-10_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1124					GRCh38	V40	CUGBP1-BGHLV23-10/Aligned.sortedByCoord.out.bam		ENCORE2	16804
CUGBP1-BGHLV23-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1124					GRCh38	V40	CUGBP1-BGHLV23-10/Aligned.sortedByCoord.out.bam		ENCORE2	16842
CUGBP1-BGHLV23-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1124					GRCh38	V40	CUGBP1-BGHLV23-10/Aligned.sortedByCoord.out.bam		ENCORE2	16880
CUGBP1-BGHLV23-10_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1124					GRCh38	V40	CUGBP1-BGHLV23-10_GAGTGG_L004_R1_001.fastq.gz,CUGBP1-BGHLV23-10_GAGTGG_L004_R2_001.fastq.gz		ENCORE2	16918