CIRBP RNA-Seq in HepG2

General Information


RBP	CIRBP
Cell_Line	HepG2
Method	shRNA
Exp_Name	CIRBP-BGHLV12-HepG2
ENCODE_series_ID	ENCSR106SDF
Batch_ID	BGHLV12
Pool ID	Pool-140701A
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR230ORC
ENCODE_CN_Exp_ID	ENCSR237YZT
Rep1	CIRBP-BGHLV12-7
Rep2	CIRBP-BGHLV12-8
CN1	NT-BGHLV12-01
CN2	NT-BGHLV12-02
Rep1_qPCR	67.6
Rep2_qPCR	75.3
Rep1_WB
Rep2_WB	no clear bands
Antibody Cat#	RN032P
Antibody Lot#	LOT# 001
Antibody DCC ID	ENCAB000BFF
Status	Archived
Project	ENCODE3
ID	331

Experiment Information (Status: Released)

	BGHLV12-7	BGHLV12-8
idx	7	8
TRCN#_or_BGC#	TRCN0000017265	TRCN0000017265
shRNA_or_gRNA_sequence	GCCATGAATGGGAAGTCTGTA	GCCATGAATGGGAAGTCTGTA
PAM
Name	CIRBP	CIRBP
Sample_ID	BGHLV12-7	BGHLV12-8
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	CIRBP	CIRBP
qPCR_result	67.6	75.3
Ave_qPCR	71.5
RT-qPCR_primer-F	TGTGGTGCGCTGTCTTCC
RT-qPCR_primer-R	AAACTCAGCCCTCCAACAAA
protein_conc	1963	1640
WB_result		no clear bands
Ave_WB	no clear bands
WB_DONE_date	1/20/2015
MW	19kDa
IP	1	1
antibody_Cat#	RN032P	RN032P
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	51.9	0
Rep2_TPM	29.2	0
Action
Library_start_date	6/9/2014	6/9/2014
repeat_library
Note
ID	2054	2055

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV12-7	BGHLV12-8
Sample_ID	BGHLV12-7	BGHLV12-8
Sample Name	CIRBP-BGHLV12-7	CIRBP-BGHLV12-8
Sample Name	CIRBP-BGHLV12-7	CIRBP-BGHLV12-8
RBP	CIRBP	CIRBP
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	376	377

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-7	BGHLV12-8
Sample #
Sample Name	CIRBP-BGHLV12-7	CIRBP-BGHLV12-8
Sample_Name_Alias	CIRBP-BGHLV12-7	CIRBP-BGHLV12-8
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-06-09	2014-06-09
Lib_ID	Lib-140609	Lib-140609
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV12/set1/G1.png	DNA_Library_LV12/set1/H1.png
RIN	9.1	9.2
libSample_RNA_Well	RNA_Library_LV12/set1/G1.png	RNA_Library_LV12/set1/H1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-7	BGHLV12-8
RBP	CIRBP	CIRBP
Batch_ID	BGHLV12	BGHLV12
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1998	1999

Sequencing Information

	BGHLV12-7	BGHLV12-8
Sample_ID	BGHLV12-7	BGHLV12-8
Sample Name	CIRBP-BGHLV12-7	CIRBP-BGHLV12-8
Pool ID	Pool-140701A	Pool-140701A
LocalServer_folder	set12	set12
total_reads	65,120,000	60,010,000
total_aligned_reads	60,523,120	55,799,808
unique_aligned_reads	57,599,382	53,071,428
percent_uniqueAligned	0.88451	0.88438
correlation_replicates	0.994908	0.994908
spikein_reads	572,658	721,182
percent_spikeins	0.00879	0.01202
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	698	699

Data Submission Information

	BGHLV12-7	BGHLV12-7
ENCODE_alias	brenton-graveley:CIRBP-BGHLV12	brenton-graveley:CIRBP-BGHLV12-HepG2
ENCODE_accession	ENCSR230ORC	ENCSR106SDF
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-7	BGHLV12-7
Sample Name	CIRBP-BGHLV12-7	CIRBP-BGHLV12-7
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2737	6619

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
CIRBP-BGHLV12-7_CAGATC_L001_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	698	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12755
CIRBP-BGHLV12-7_CAGATC_L001_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	698	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12824
CIRBP-BGHLV12-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	698					GRCh38	V40	CIRBP-BGHLV12-7_CAGATC_L001_R1_001.fastq.gz,CIRBP-BGHLV12-7_CAGATC_L001_R2_001.fastq.gz		ENCORE2	12894
CIRBP-BGHLV12-7_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	698					GRCh38	V40	CIRBP-BGHLV12-7/Aligned.sortedByCoord.out.bam		ENCORE2	12964
CIRBP-BGHLV12-7_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	698					GRCh38	V40	CIRBP-BGHLV12-7/Aligned.sortedByCoord.out.bam		ENCORE2	13034
CIRBP-BGHLV12-7_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	698					GRCh38	V40	CIRBP-BGHLV12-7/Aligned.sortedByCoord.out.bam		ENCORE2	13104
CIRBP-BGHLV12-7_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	698					GRCh38	V40	CIRBP-BGHLV12-7/Aligned.sortedByCoord.out.bam		ENCORE2	13174
CIRBP-BGHLV12-7_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	698					GRCh38	V40	CIRBP-BGHLV12-7_CAGATC_L001_R1_001.fastq.gz,CIRBP-BGHLV12-7_CAGATC_L001_R2_001.fastq.gz		ENCORE2	13244
CIRBP-BGHLV12-8_ACTTGA_L002_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	699	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12756
CIRBP-BGHLV12-8_ACTTGA_L002_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	699	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12825
CIRBP-BGHLV12-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	699					GRCh38	V40	CIRBP-BGHLV12-8_ACTTGA_L002_R1_001.fastq.gz,CIRBP-BGHLV12-8_ACTTGA_L002_R2_001.fastq.gz		ENCORE2	12895
CIRBP-BGHLV12-8_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	699					GRCh38	V40	CIRBP-BGHLV12-8/Aligned.sortedByCoord.out.bam		ENCORE2	12965
CIRBP-BGHLV12-8_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	699					GRCh38	V40	CIRBP-BGHLV12-8/Aligned.sortedByCoord.out.bam		ENCORE2	13035
CIRBP-BGHLV12-8_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	699					GRCh38	V40	CIRBP-BGHLV12-8/Aligned.sortedByCoord.out.bam		ENCORE2	13105
CIRBP-BGHLV12-8_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	699					GRCh38	V40	CIRBP-BGHLV12-8/Aligned.sortedByCoord.out.bam		ENCORE2	13175
CIRBP-BGHLV12-8_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	699					GRCh38	V40	CIRBP-BGHLV12-8_ACTTGA_L002_R1_001.fastq.gz,CIRBP-BGHLV12-8_ACTTGA_L002_R2_001.fastq.gz		ENCORE2	13245