CIZ1 RNA-Seq in HepG2

General Information


RBP	CIZ1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CIZ1-BGHcLV20-HepG2
ENCODE_series_ID	ENCSR546WZN
Batch_ID	BGHcLV20
Pool ID	Pool-200928
Local_Set_Name	set45_H
ENCODE_KD_Exp_ID	ENCSR749QMU
ENCODE_CN_Exp_ID	ENCSR306EWE
Rep1	CIZ1-BGHcLV20-3
Rep2	CIZ1-BGHcLV20-4
CN1	NT-BGHcLV20-1
CN2	NT-BGHcLV20-2
Rep1_qPCR	0.0
Rep2_qPCR	15.0
Rep1_WB	74.5
Rep2_WB	81.3
Antibody Cat#	PA5-27625
Antibody Lot#	LOT# UF2796672B
Antibody DCC ID	ENCAB411FAE
Status	Released
Project	ENCODE4
ID	74

Experiment Information (Status: Released)

	BGHcLV20-3	BGHcLV20-4
idx	553	554
TRCN#_or_BGC#	BGC#0000465	BGC#0000465
shRNA_or_gRNA_sequence	ACTCACCTTTCGATTGGGGG	ACTCACCTTTCGATTGGGGG
PAM	TGG	TGG
Name	CIZ1_89	CIZ1_89
Sample_ID	BGHcLV20-3	BGHcLV20-4
transduction_Date	12/10/19	12/10/19
days	D6	D6
RBP_name	CIZ1	CIZ1
qPCR_result	0.0	15.0
Ave_qPCR	7.5
RT-qPCR_primer-F	CCAGCACTCCCTCTAAGCAG
RT-qPCR_primer-R	CGACATGTGGTCCTGGAACT
protein_conc	4418	4370
WB_result	74.5	81.3
Ave_WB	77.9
WB_DONE_date	8/5/20	JESS
MW	100kDa
IP	Rabbit / I
antibody_Cat#	PA5-27625	LOT# UF2796672B
Antibody DCC ID	ENCAB411FAE
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/24/20	09/24/20
repeat_library
Note
ID	6708	6709

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CIZ1	Product_ID: PA5-27625 Lot_ID: UF2796672B Source: Thermo Fisher Target Name: CIZ1-human

Experiment Status

	BGHcLV20-3	BGHcLV20-4
Sample_ID	BGHcLV20-3	BGHcLV20-4
Sample Name
Sample Name	CIZ1-BGHcLV20-3	CIZ1-BGHcLV20-4
RBP	CIZ1	CIZ1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	5809	5810

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV20-3	BGHcLV20-4
Sample #	59	60
Sample Name	CIZ1-BGHcLV20-3	CIZ1-BGHcLV20-4
Sample_Name_Alias
Index Well Position	E07	F07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-09-24	2020-09-24
Lib_ID	Lib-200924	Lib-200924
Tecan_Location
Tecan
Tecan_date
Size_bp	299	310
Peak_Molarity	119.00	79.00
libSampleQC_DNA_Well	DNA_Library_set45/set1/E7.png	DNA_Library_set45/set1/F7.png
RIN	9.8	9.1
libSample_RNA_Well	RNA_Library_set45/set1/E7.png	RNA_Library_set45/set2/B11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGHcLV20-3	BGHcLV20-4
RBP	CIZ1	CIZ1
Batch_ID	BGHcLV20	BGHcLV20
WB_result	74.500	81.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	833	834

Sequencing Information

	BGHcLV20-3	BGHcLV20-4
Sample_ID	BGHcLV20-3	BGHcLV20-4
Sample Name	CIZ1-BGHcLV20-3	CIZ1-BGHcLV20-4
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_H	set45_H
total_reads	84,777,038	139,176,992
total_aligned_reads	80,098,388	125,514,078
unique_aligned_reads	75,650,726	118,576,768
percent_uniqueAligned	0.89235	0.85199
correlation_replicates	0.992043	0.992043
spikein_reads	31,544	54,550
percent_spikeins	0.00037	0.00039
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	464	465

Data Submission Information

	BGHcLV20-3	BGHcLV20-3	BGHcLV20-3	BGHcLV20-3	BGHcLV20-3	BGHcLV20-3	BGHcLV20-4	BGHcLV20-4	BGHcLV20-4	BGHcLV20-4
ENCODE_alias	brenton-graveley:CIZ1-BGHcLV20	brenton-graveley:CIZ1-BGHcLV20-3	brenton-graveley:L-CIZ1-BGHcLV20-3	brenton-graveley:CIZ1-BGHcLV20-3_S53_R1_001.fastq.gz	brenton-graveley:CIZ1-BGHcLV20-3_S53_R2_001.fastq.gz	brenton-graveley:CIZ1-BGHcLV20-HepG2	brenton-graveley:CIZ1-BGHcLV20-4	brenton-graveley:L-CIZ1-BGHcLV20-4	brenton-graveley:CIZ1-BGHcLV20-4_S54_R1_001.fastq.gz	brenton-graveley:CIZ1-BGHcLV20-4_S54_R2_001.fastq.gz
ENCODE_accession	ENCSR749QMU	ENCBS005VFH	ENCLB838DBQ	ENCFF781YXM	ENCFF797BTG	ENCSR546WZN	ENCBS100NPF	ENCLB883WXM	ENCFF754GBS	ENCFF707EAV
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	BGHcLV20-3	BGHcLV20-3	BGHcLV20-3	BGHcLV20-3	BGHcLV20-3	BGHcLV20-3	BGHcLV20-4	BGHcLV20-4	BGHcLV20-4	BGHcLV20-4
Sample Name	CIZ1-BGHcLV20-3	CIZ1-BGHcLV20-3	CIZ1-BGHcLV20-3	CIZ1-BGHcLV20-3	CIZ1-BGHcLV20-3	CIZ1-BGHcLV20-3	CIZ1-BGHcLV20-4	CIZ1-BGHcLV20-4	CIZ1-BGHcLV20-4	CIZ1-BGHcLV20-4
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV45H_biosample_protocol	LV45H_library_protocol				LV45H_biosample_protocol	LV45H_library_protocol
protocol_URL		CIZ1-BGHcLV20-3.pdf	L-CIZ1-BGHcLV20-3.pdf				CIZ1-BGHcLV20-4.pdf	L-CIZ1-BGHcLV20-4.pdf
ID	2081	2117	2187	2257	2327	7140	2118	2188	2258	2328

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
CIZ1-BGHcLV20-3_S53_R1_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	464	NovaSeq6000	100	paired-ended	1				NT-BGHcLV20-1_S51_R1_001.fastq.gz,NT-BGHcLV20-2_S52_R1_001.fastq.gz	ENCODE4	1308
CIZ1-BGHcLV20-3_S53_R2_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	464	NovaSeq6000	100	paired-ended	2				NT-BGHcLV20-1_S51_R2_001.fastq.gz,NT-BGHcLV20-2_S52_R2_001.fastq.gz	ENCODE4	1328
CIZ1-BGHcLV20-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	464					GRCh38	V40	CIZ1-BGHcLV20-3_S53_R1_001.filtered.trimmed.paired.fastq.gz,CIZ1-BGHcLV20-3_S53_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24849
CIZ1-BGHcLV20-3_quant.sf	ENCODE_DATA/set45_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	464					GRCh38	V40	CIZ1-BGHcLV20-3_S53_R1_001.filtered.trimmed.paired.fastq.gz,CIZ1-BGHcLV20-3_S53_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24869
CIZ1-BGHcLV20-3_Signal.Unique.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	464					GRCh38	V40	CIZ1-BGHcLV20-3/Aligned.sortedByCoord.out.bam		ENCORE2	25919
CIZ1-BGHcLV20-3_Signal.Unique.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	464					GRCh38	V40	CIZ1-BGHcLV20-3/Aligned.sortedByCoord.out.bam		ENCORE2	25939
CIZ1-BGHcLV20-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	464					GRCh38	V40	CIZ1-BGHcLV20-3/Aligned.sortedByCoord.out.bam		ENCORE2	25959
CIZ1-BGHcLV20-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	464					GRCh38	V40	CIZ1-BGHcLV20-3/Aligned.sortedByCoord.out.bam		ENCORE2	25979
CIZ1-BGHcLV20-4_S54_R1_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	465	NovaSeq6000	100	paired-ended	1				NT-BGHcLV20-1_S51_R1_001.fastq.gz,NT-BGHcLV20-2_S52_R1_001.fastq.gz	ENCODE4	1309
CIZ1-BGHcLV20-4_S54_R2_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	465	NovaSeq6000	100	paired-ended	2				NT-BGHcLV20-1_S51_R2_001.fastq.gz,NT-BGHcLV20-2_S52_R2_001.fastq.gz	ENCODE4	1329
CIZ1-BGHcLV20-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	465					GRCh38	V40	CIZ1-BGHcLV20-4_S54_R1_001.filtered.trimmed.paired.fastq.gz,CIZ1-BGHcLV20-4_S54_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24850
CIZ1-BGHcLV20-4_quant.sf	ENCODE_DATA/set45_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	465					GRCh38	V40	CIZ1-BGHcLV20-4_S54_R1_001.filtered.trimmed.paired.fastq.gz,CIZ1-BGHcLV20-4_S54_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24870
CIZ1-BGHcLV20-4_Signal.Unique.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	465					GRCh38	V40	CIZ1-BGHcLV20-4/Aligned.sortedByCoord.out.bam		ENCORE2	25920
CIZ1-BGHcLV20-4_Signal.Unique.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	465					GRCh38	V40	CIZ1-BGHcLV20-4/Aligned.sortedByCoord.out.bam		ENCORE2	25940
CIZ1-BGHcLV20-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	465					GRCh38	V40	CIZ1-BGHcLV20-4/Aligned.sortedByCoord.out.bam		ENCORE2	25960
CIZ1-BGHcLV20-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	465					GRCh38	V40	CIZ1-BGHcLV20-4/Aligned.sortedByCoord.out.bam		ENCORE2	25980