CIZ1 RNA-Seq in K562

General Information


RBP	CIZ1
Cell_Line	K562
Method	CRISPR
Exp_Name	CIZ1-BGKcLV19-K562
ENCODE_series_ID	ENCSR737UDV
Batch_ID	BGKcLV19
Pool ID	Pool-200928
Local_Set_Name	set45_K
ENCODE_KD_Exp_ID	ENCSR765HSN
ENCODE_CN_Exp_ID	ENCSR978MMZ
Rep1	CIZ1-BGKcLV19-9
Rep2	CIZ1-BGKcLV19-10
CN1	NT-BGKcLV19-1
CN2	NT-BGKcLV19-2
Rep1_qPCR	0
Rep2_qPCR	0
Rep1_WB	69.0
Rep2_WB	71.8
Antibody Cat#	PA5-27625
Antibody Lot#	LOT# UF2796672B
Antibody DCC ID	ENCAB411FAE
Status	Released
Project	ENCODE4
ID	51

Experiment Information (Status: Released)

	BGKcLV19-9	BGKcLV19-10
idx	679	680
TRCN#_or_BGC#	BGC#0000465	BGC#0000465
shRNA_or_gRNA_sequence	ACTCACCTTTCGATTGGGGG	ACTCACCTTTCGATTGGGGG
PAM	TGG	TGG
Name	CIZ1_89	CIZ1_89
Sample_ID	BGKcLV19-9	BGKcLV19-10
transduction_Date	11/6/19	11/6/19
days	Day 6	Day 6
RBP_name	CIZ1	CIZ1
qPCR_result	0	0
Ave_qPCR	0.0
RT-qPCR_primer-F	CCAGCACTCCCTCTAAGCAG
RT-qPCR_primer-R	CGACATGTGGTCCTGGAACT
protein_conc	3950	4429
WB_result	69.0	71.8
Ave_WB	70.4
WB_DONE_date	2/4/21	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	185.9	0
Rep2_TPM	202.5	0
Action	Ready	Ready
Library_start_date	09/24/20	09/24/20
repeat_library
Note
ID	4799	4800

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

	BGKcLV19-9	BGKcLV19-10
Sample_ID	BGKcLV19-9	BGKcLV19-10
Sample Name
Sample Name	CIZ1-BGKcLV19-9	CIZ1-BGKcLV19-10
RBP	CIZ1	CIZ1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	5695	5696

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV19-9	BGKcLV19-10
Sample #	9	10
Sample Name	CIZ1-BGKcLV19-9	CIZ1-BGKcLV19-10
Sample_Name_Alias
Index Well Position	C01	D01
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	318	311
Peak_Molarity	105.00	140.00
libSampleQC_DNA_Well	DNA_Library_set45/set1/C1.png	DNA_Library_set45/set2/G9.png
RIN	9.4	8.8
libSample_RNA_Well	RNA_Library_set45/set1/C1.png	RNA_Library_set45/set1/D1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGKcLV19-9	BGKcLV19-10
RBP	CIZ1	CIZ1
Batch_ID	BGKcLV19	BGKcLV19
WB_result	76.100	76.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	783	784

Sequencing Information

	BGKcLV19-9	BGKcLV19-10
Sample_ID	BGKcLV19-9	BGKcLV19-10
Sample Name	CIZ1-BGKcLV19-9	CIZ1-BGKcLV19-10
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_K	set45_K
total_reads	79,042,588	149,918,178
total_aligned_reads	74,910,308	143,749,636
unique_aligned_reads	68,755,312	131,838,108
percent_uniqueAligned	0.86985	0.87940
correlation_replicates	0.994619	0.994619
spikein_reads	68,798	112,354
percent_spikeins	0.00087	0.00075
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	414	415

Data Submission Information

	BGKcLV19-9	BGKcLV19-9	BGKcLV19-9	BGKcLV19-9	BGKcLV19-9	BGKcLV19-9	BGKcLV19-10	BGKcLV19-10	BGKcLV19-10	BGKcLV19-10
ENCODE_alias	brenton-graveley:CIZ1-BGKcLV19	brenton-graveley:CIZ1-BGKcLV19-9	brenton-graveley:L-CIZ1-BGKcLV19-9	brenton-graveley:CIZ1-BGKcLV19-9_S3_R1_001.fastq.gz	brenton-graveley:CIZ1-BGKcLV19-9_S3_R2_001.fastq.gz	brenton-graveley:CIZ1-BGKcLV19-K562	brenton-graveley:CIZ1-BGKcLV19-10	brenton-graveley:L-CIZ1-BGKcLV19-10	brenton-graveley:CIZ1-BGKcLV19-10_S4_R1_001.fastq.gz	brenton-graveley:CIZ1-BGKcLV19-10_S4_R2_001.fastq.gz
ENCODE_accession	ENCSR765HSN	ENCBS358YTN	ENCLB056VMX	ENCFF632TTU	ENCFF255QCT	ENCSR737UDV	ENCBS003ASV	ENCLB490YAI	ENCFF516DNX	ENCFF946JAS
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	BGKcLV19-9	BGKcLV19-9	BGKcLV19-9	BGKcLV19-9	BGKcLV19-9	BGKcLV19-9	BGKcLV19-10	BGKcLV19-10	BGKcLV19-10	BGKcLV19-10
Sample Name	CIZ1-BGKcLV19-9	CIZ1-BGKcLV19-9	CIZ1-BGKcLV19-9	CIZ1-BGKcLV19-9	CIZ1-BGKcLV19-9	CIZ1-BGKcLV19-9	CIZ1-BGKcLV19-10	CIZ1-BGKcLV19-10	CIZ1-BGKcLV19-10	CIZ1-BGKcLV19-10
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
		LV45K_biosample_protocol	LV45K_library_protocol				LV45K_biosample_protocol	LV45K_library_protocol
protocol_URL		CIZ1-BGKcLV19-10.pdf	L-CIZ1-BGKcLV19-10.pdf				CIZ1-BGKcLV19-9.pdf	L-CIZ1-BGKcLV19-9.pdf
ID	2091	2137	2207	2277	2347	7141	2138	2208	2278	2348

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-BGKcLV19-9_S3_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	414	NovaSeq6000	100	paired-ended	1				NT-BGKcLV19-1_S1_R1_001.fastq.gz,NT-BGKcLV19-2_S2_R1_001.fastq.gz	ENCODE4	1211
CIZ1-BGKcLV19-9_S3_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	414	NovaSeq6000	100	paired-ended	2				NT-BGKcLV19-1_S1_R2_001.fastq.gz,NT-BGKcLV19-2_S2_R2_001.fastq.gz	ENCODE4	1261
CIZ1-BGKcLV19-9_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	414					GRCh38	V40	CIZ1-BGKcLV19-9_S3_R1_001.filtered.trimmed.paired.fastq.gz,CIZ1-BGKcLV19-9_S3_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25204
CIZ1-BGKcLV19-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	414					GRCh38	V40	CIZ1-BGKcLV19-9_S3_R1_001.filtered.trimmed.paired.fastq.gz,CIZ1-BGKcLV19-9_S3_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27158
CIZ1-BGKcLV19-9_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	414					GRCh38	V40	CIZ1-BGKcLV19-9/Aligned.sortedByCoord.out.bam		ENCORE2	27208
CIZ1-BGKcLV19-9_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	414					GRCh38	V40	CIZ1-BGKcLV19-9/Aligned.sortedByCoord.out.bam		ENCORE2	27258
CIZ1-BGKcLV19-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	414					GRCh38	V40	CIZ1-BGKcLV19-9/Aligned.sortedByCoord.out.bam		ENCORE2	27308
CIZ1-BGKcLV19-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	414					GRCh38	V40	CIZ1-BGKcLV19-9/Aligned.sortedByCoord.out.bam		ENCORE2	27358
CIZ1-BGKcLV19-10_S4_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	415	NovaSeq6000	100	paired-ended	1				NT-BGKcLV19-1_S1_R1_001.fastq.gz,NT-BGKcLV19-2_S2_R1_001.fastq.gz	ENCODE4	1210
CIZ1-BGKcLV19-10_S4_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	415	NovaSeq6000	100	paired-ended	2				NT-BGKcLV19-1_S1_R2_001.fastq.gz,NT-BGKcLV19-2_S2_R2_001.fastq.gz	ENCODE4	1260
CIZ1-BGKcLV19-10_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	415					GRCh38	V40	CIZ1-BGKcLV19-10_S4_R1_001.filtered.trimmed.paired.fastq.gz,CIZ1-BGKcLV19-10_S4_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25203
CIZ1-BGKcLV19-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	415					GRCh38	V40	CIZ1-BGKcLV19-10_S4_R1_001.filtered.trimmed.paired.fastq.gz,CIZ1-BGKcLV19-10_S4_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27157
CIZ1-BGKcLV19-10_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	415					GRCh38	V40	CIZ1-BGKcLV19-10/Aligned.sortedByCoord.out.bam		ENCORE2	27207
CIZ1-BGKcLV19-10_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	415					GRCh38	V40	CIZ1-BGKcLV19-10/Aligned.sortedByCoord.out.bam		ENCORE2	27257
CIZ1-BGKcLV19-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	415					GRCh38	V40	CIZ1-BGKcLV19-10/Aligned.sortedByCoord.out.bam		ENCORE2	27307
CIZ1-BGKcLV19-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	415					GRCh38	V40	CIZ1-BGKcLV19-10/Aligned.sortedByCoord.out.bam		ENCORE2	27357