CIRBP RNA-Seq in HepG2

General Information


RBP	CIRBP
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CIRBP-BGHcLV12-HepG2
ENCODE_series_ID	ENCSR960ZSG
Batch_ID	BGHcLV12
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR010XIH
ENCODE_CN_Exp_ID	ENCSR827PII
Rep1	CIRBP-BGHcLV12-19
Rep2	CIRBP-BGHcLV12-20
CN1	NT-BGHcLV12-1
CN2	NT-BGHcLV12-2
Rep1_qPCR	50.1
Rep2_qPCR	48.6
Rep1_WB	99.7
Rep2_WB	99.7
Antibody Cat#	RN032P
Antibody Lot#
Antibody DCC ID	ENCAB000BFF
Status	Released
Project	ENCODE4
ID	165

Experiment Information (Status: Released)

	BGHcLV12-19	BGHcLV12-20
idx	279	280
TRCN#_or_BGC#	BGC#0000252	BGC#0000252
shRNA_or_gRNA_sequence	AGCGTCGTCAATGTTCTCAA	AGCGTCGTCAATGTTCTCAA
PAM	AGG	AGG
Name	CIRBP_87	CIRBP_87
Sample_ID	BGHcLV12-19	BGHcLV12-20
transduction_Date	8/17/18	8/17/18
days	D6	D6
RBP_name	CIRBP	CIRBP
qPCR_result	50.1	48.6
Ave_qPCR	49.4
RT-qPCR_primer-F	TGTGGTGCGCTGTCTTCC
RT-qPCR_primer-R	AAACTCAGCCCTCCAACAAA
protein_conc	4960	4893
WB_result	99.7	99.7
Ave_WB	99.7
WB_DONE_date	1/28/19
MW	19 kDa
IP
antibody_Cat#	RN032P
Antibody DCC ID	ENCAB000BFF
submitted_to_DCC_date	2/22/19
Rep1_TPM	123	0
Rep2_TPM	96	0
Action	Ready	Ready
Library_start_date	03/13/19	03/13/19
repeat_library
Note
ID	6422	6423

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CIRBP	Product_ID: RN032P Lot_ID: 1 Source: MBLI Target Name: CIRBP-human

Experiment Status

	BGHcLV12-19	BGHcLV12-20
Sample_ID	BGHcLV12-19	BGHcLV12-20
Sample Name	CIRBP-BGHcLV12-19	CIRBP-BGHcLV12-20
Sample Name	CIRBP-BGHcLV12-19	CIRBP-BGHcLV12-20
RBP	CIRBP	CIRBP
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2805	2806

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV12-19	BGHcLV12-20
Sample #	35	36
Sample Name	CIRBP-BGHcLV12-19	CIRBP-BGHcLV12-20
Sample_Name_Alias
Index Well Position	C05	D05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-13	2019-03-13
Lib_ID	Lib-190313	Lib-190313
Tecan_Location	3-C1	3-D1
Tecan	68.12	57.70
Tecan_date	2019-03-13	2019-03-13
Size_bp	300	294
Peak_Molarity	140.00	79.50
libSampleQC_DNA_Well	DNA_Library_set42/set1/C5.png	DNA_Library_set42/set1/D5.png
RIN	9.5	9.8
libSample_RNA_Well	RNA_Library_set42/set1/C5.png	RNA_Library_set42/set1/D5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-13	2019-03-13
Sample_ID	BGHcLV12-19	BGHcLV12-20
RBP	CIRBP	CIRBP
Batch_ID	BGHcLV12	BGHcLV12
WB_result	99.700	99.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	35	36

Sequencing Information

	BGHcLV12-19	BGHcLV12-20
Sample_ID	BGHcLV12-19	BGHcLV12-20
Sample Name	CIRBP-BGHcLV12-19	CIRBP-BGHcLV12-20
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	42,015,718	44,263,526
total_aligned_reads	40,580,390	42,284,630
unique_aligned_reads	38,199,396	39,762,250
percent_uniqueAligned	0.90917	0.89831
correlation_replicates	0.998785	0.998785
spikein_reads	45,178	40,664
percent_spikeins	0.00108	0.00092
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	9	10

Data Submission Information

	BGHcLV12-19	BGHcLV12-19	BGHcLV12-19	BGHcLV12-19	BGHcLV12-19	BGHcLV12-19	BGHcLV12-20	BGHcLV12-20	BGHcLV12-20	BGHcLV12-20
ENCODE_alias	brenton-graveley:CIRBP-BGHcLV12	brenton-graveley:CIRBP-BGHcLV12-19	brenton-graveley:L-CIRBP-BGHcLV12-19	brenton-graveley:CIRBP-BGHcLV12-19_AGCCTCAT+AGTAGAGA_HK3H2DSXX_S35_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CIRBP-BGHcLV12-19_AGCCTCAT+AGTAGAGA_HK3H2DSXX_S35_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CIRBP-BGHcLV12-HepG2	brenton-graveley:CIRBP-BGHcLV12-20	brenton-graveley:L-CIRBP-BGHcLV12-20	brenton-graveley:CIRBP-BGHcLV12-20_GATTCTGC+GACGAGAG_HK3H2DSXX_S36_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CIRBP-BGHcLV12-20_GATTCTGC+GACGAGAG_HK3H2DSXX_S36_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR010XIH	ENCBS308BII	ENCLB278VFA	ENCFF804KNI	ENCFF758XJP	ENCSR960ZSG	ENCBS035DAB	ENCLB144QOE	ENCFF018ODG	ENCFF258IPH
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV12-19	BGHcLV12-19	BGHcLV12-19	BGHcLV12-19	BGHcLV12-19	BGHcLV12-19	BGHcLV12-20	BGHcLV12-20	BGHcLV12-20	BGHcLV12-20
Sample Name	CIRBP-BGHcLV12-19	CIRBP-BGHcLV12-19	CIRBP-BGHcLV12-19	CIRBP-BGHcLV12-19	CIRBP-BGHcLV12-19	CIRBP-BGHcLV12-19	CIRBP-BGHcLV12-20	CIRBP-BGHcLV12-20	CIRBP-BGHcLV12-20	CIRBP-BGHcLV12-20
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV42_biosample_protocol	LV42_library_protocol				LV42_biosample_protocol	LV42_library_protocol
protocol_URL		CIRBP-BGHcLV12-19.pdf	L-CIRBP-BGHcLV12-19.pdf				CIRBP-BGHcLV12-20.pdf	L-CIRBP-BGHcLV12-20.pdf
ID	747	789	871	959	1041	7138	790	872	960	1042

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-BGHcLV12-19_AGCCTCAT+AGTAGAGA_HK3H2DSXX_S35_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	9	NovaSeq6000	100	paired-ended	1				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	341
CIRBP-BGHcLV12-19_AGCCTCAT+AGTAGAGA_HK3H2DSXX_S35_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	9	NovaSeq6000	100	paired-ended	2				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	423
CIRBP-BGHcLV12-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	9					GRCh38	V40	CIRBP-BGHcLV12-19_AGCCTCAT+AGTAGAGA_HK3H2DSXX_S35_L004_R1_001.filtered.trimmed.paired.fastq.gz,CIRBP-BGHcLV12-19_AGCCTCAT+AGTAGAGA_HK3H2DSXX_S35_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23680
CIRBP-BGHcLV12-19_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	9					GRCh38	V40	CIRBP-BGHcLV12-19/Aligned.sortedByCoord.out.bam		ENCORE2	23762
CIRBP-BGHcLV12-19_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	9					GRCh38	V40	CIRBP-BGHcLV12-19/Aligned.sortedByCoord.out.bam		ENCORE2	23844
CIRBP-BGHcLV12-19_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	9					GRCh38	V40	CIRBP-BGHcLV12-19/Aligned.sortedByCoord.out.bam		ENCORE2	23926
CIRBP-BGHcLV12-19_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	9					GRCh38	V40	CIRBP-BGHcLV12-19/Aligned.sortedByCoord.out.bam		ENCORE2	24008
CIRBP-BGHcLV12-19_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	9					GRCh38	V40	CIRBP-BGHcLV12-19_AGCCTCAT+AGTAGAGA_HK3H2DSXX_S35_L004_R1_001.filtered.trimmed.paired.fastq.gz,CIRBP-BGHcLV12-19_AGCCTCAT+AGTAGAGA_HK3H2DSXX_S35_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24090
CIRBP-BGHcLV12-20_GATTCTGC+GACGAGAG_HK3H2DSXX_S36_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	10	NovaSeq6000	100	paired-ended	1				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	342
CIRBP-BGHcLV12-20_GATTCTGC+GACGAGAG_HK3H2DSXX_S36_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	10	NovaSeq6000	100	paired-ended	2				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	424
CIRBP-BGHcLV12-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	10					GRCh38	V40	CIRBP-BGHcLV12-20_GATTCTGC+GACGAGAG_HK3H2DSXX_S36_L004_R1_001.filtered.trimmed.paired.fastq.gz,CIRBP-BGHcLV12-20_GATTCTGC+GACGAGAG_HK3H2DSXX_S36_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23681
CIRBP-BGHcLV12-20_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	10					GRCh38	V40	CIRBP-BGHcLV12-20/Aligned.sortedByCoord.out.bam		ENCORE2	23763
CIRBP-BGHcLV12-20_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	10					GRCh38	V40	CIRBP-BGHcLV12-20/Aligned.sortedByCoord.out.bam		ENCORE2	23845
CIRBP-BGHcLV12-20_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	10					GRCh38	V40	CIRBP-BGHcLV12-20/Aligned.sortedByCoord.out.bam		ENCORE2	23927
CIRBP-BGHcLV12-20_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	10					GRCh38	V40	CIRBP-BGHcLV12-20/Aligned.sortedByCoord.out.bam		ENCORE2	24009
CIRBP-BGHcLV12-20_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	10					GRCh38	V40	CIRBP-BGHcLV12-20_GATTCTGC+GACGAGAG_HK3H2DSXX_S36_L004_R1_001.filtered.trimmed.paired.fastq.gz,CIRBP-BGHcLV12-20_GATTCTGC+GACGAGAG_HK3H2DSXX_S36_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24091