CXXC1 RNA-Seq in K562

General Information


RBP	CXXC1
Cell_Line	K562
Method	CRISPR
Exp_Name	CXXC1-BGKcLV17-K562
ENCODE_series_ID	ENCSR835EFB
Batch_ID	BGKcLV17
Pool ID	Pool-200102
Local_Set_Name	set43_K
ENCODE_KD_Exp_ID	ENCSR416NPL
ENCODE_CN_Exp_ID	ENCSR516TLX
Rep1	CXXC1-BGKcLV17-7
Rep2	CXXC1-BGKcLV17-8
CN1	NT-BGKcLV17-1
CN2	NT-BGKcLV17-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	71.6
Rep2_WB	67.9
Antibody Cat#	PA5-76829
Antibody Lot#	lot# UC2739251A
Antibody DCC ID	ENCAB216VRJ
Status	Released
Project	ENCODE4
ID	142

Experiment Information (Status: Released)

	BGKcLV17-7	BGKcLV17-7	BGKcLV17-8	BGKcLV17-8
idx	614	614	615	615
TRCN#_or_BGC#	BGC#0000431	BGC#0000431	BGC#0000431	BGC#0000431
shRNA_or_gRNA_sequence	AAACGGTCAGCCCGCATGTG	AAACGGTCAGCCCGCATGTG	AAACGGTCAGCCCGCATGTG	AAACGGTCAGCCCGCATGTG
PAM	TGG	TGG	TGG	TGG
Name	CXXC1_97	CXXC1_97	CXXC1_97	CXXC1_97
Sample_ID	BGKcLV17-7	BGKcLV17-7	BGKcLV17-8	BGKcLV17-8
transduction_Date	7/2/19	7/2/19	7/2/19	7/2/19
days	Day 6	Day 6	Day 6	Day 6
RBP_name	CXXC1	CXXC1	CXXC1	CXXC1
qPCR_result	24.7215254	24.7215254	12.15849	12.15849
Ave_qPCR	18.4	18.4
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	4349	4349	4419	4419
WB_result	71.6	49.1	67.9	50.4574
Ave_WB	69.8	49.8
WB_DONE_date	7/23/19	4/5/24
MW	76KD	76KD
IP	Rabbit / I		Polyclonal
antibody_Cat#	PA5-76829	40672S	lot# UC2739251A	lot# 1
Antibody DCC ID	ENCAB216VRJ
submitted_to_DCC_date
Rep1_TPM	37.6	0	0	0
Rep2_TPM	27.5	0	0	0
Action	Ready		Ready
Library_start_date	12/05/19		12/05/19
repeat_library
Note
ID	4726	4728	4727	4729

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CXXC1	Product_ID: 40672S Lot_ID: 1 Source: Cell Signaling Technology Target Name: CXXC1-human

Experiment Status

	BGKcLV17-7	BGKcLV17-8
Sample_ID	BGKcLV17-7	BGKcLV17-8
Sample Name	CXXC1-BGKcLV17-7	CXXC1-BGKcLV17-8
Sample Name	CXXC1-BGKcLV17-7	CXXC1-BGKcLV17-8
RBP	CXXC1	CXXC1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	5491	5492

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV17-7	BGKcLV17-8
Sample #	81	82
Sample Name	CXXC1-BGKcLV17-7	CXXC1-BGKcLV17-8
Sample_Name_Alias
Index Well Position	E10	F10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-31	2020-08-31
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	1-G1	1-H1
Tecan	28.26	32.49
Tecan_date	2019-12-10	2019-12-10
Size_bp	275	279
Peak_Molarity	21.60	28.90
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/G6.png	DNA_Library_set43-44/set1/H6.png
RIN	9.6	9.5
libSample_RNA_Well	RNA_Library_set43-44/set4/G1.png	RNA_Library_set43-44/set4/H1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV17-7	BGKcLV17-8
RBP	CXXC1	CXXC1
Batch_ID	BGKcLV17	BGKcLV17
WB_result	71.600	67.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	657	658

Sequencing Information

	BGKcLV17-7	BGKcLV17-8
Sample_ID	BGKcLV17-7	BGKcLV17-8
Sample Name	CXXC1-BGKcLV17-7	CXXC1-BGKcLV17-8
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_K	set43_K
total_reads	328,933,398	115,739,052
total_aligned_reads	296,556,322	108,757,202
unique_aligned_reads	269,246,412	99,376,116
percent_uniqueAligned	0.81854	0.85862
correlation_replicates	0.998425	0.998425
spikein_reads	41,600	38,490
percent_spikeins	0.00013	0.00033
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	159	160

Data Submission Information

	BGKcLV17-7	BGKcLV17-7	BGKcLV17-7	BGKcLV17-7	BGKcLV17-7	BGKcLV17-7	BGKcLV17-8	BGKcLV17-8	BGKcLV17-8	BGKcLV17-8
ENCODE_alias	brenton-graveley:CXXC1-BGKcLV17	brenton-graveley:CXXC1-BGKcLV17-7	brenton-graveley:L-CXXC1-BGKcLV17-7	brenton-graveley:CXXC1-BGKcLV17-7_S77_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CXXC1-BGKcLV17-7_S77_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CXXC1-BGKcLV17-K562	brenton-graveley:CXXC1-BGKcLV17-8	brenton-graveley:L-CXXC1-BGKcLV17-8	brenton-graveley:CXXC1-BGKcLV17-8_S78_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CXXC1-BGKcLV17-8_S78_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR416NPL	ENCBS312HQY	ENCLB736ZUT	ENCFF283JCY	ENCFF421ZIH	ENCSR835EFB	ENCBS048SGI	ENCLB232QWZ	ENCFF572PEZ	ENCFF471WCH
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	BGKcLV17-7	BGKcLV17-7	BGKcLV17-7	BGKcLV17-7	BGKcLV17-7	BGKcLV17-7	BGKcLV17-8	BGKcLV17-8	BGKcLV17-8	BGKcLV17-8
Sample Name	CXXC1-BGKcLV17-7	CXXC1-BGKcLV17-7	CXXC1-BGKcLV17-7	CXXC1-BGKcLV17-7	CXXC1-BGKcLV17-7	CXXC1-BGKcLV17-7	CXXC1-BGKcLV17-8	CXXC1-BGKcLV17-8	CXXC1-BGKcLV17-8	CXXC1-BGKcLV17-8
Selected	Yes	No	Yes	Yes	Yes	Yes	No	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
			LV43K_library_protocol					LV43K_library_protocol
protocol_URL			L-CXXC1-BGKcLV17-7.pdf					L-CXXC1-BGKcLV17-8.pdf
ID	39	160	324	522	574	7167	161	325	523	575

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
CXXC1-BGKcLV17-7_S77_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	159	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	71
CXXC1-BGKcLV17-7_S77_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	159	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	123
CXXC1-BGKcLV17-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	159					GRCh38	V40	CXXC1-BGKcLV17-7_S77_R1_001.filtered.trimmed.paired.fastq.gz,CXXC1-BGKcLV17-7_S77_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24362
CXXC1-BGKcLV17-7_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	159					GRCh38	V40	CXXC1-BGKcLV17-7/Aligned.sortedByCoord.out.bam		ENCORE2	24414
CXXC1-BGKcLV17-7_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	159					GRCh38	V40	CXXC1-BGKcLV17-7/Aligned.sortedByCoord.out.bam		ENCORE2	24466
CXXC1-BGKcLV17-7_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	159					GRCh38	V40	CXXC1-BGKcLV17-7/Aligned.sortedByCoord.out.bam		ENCORE2	24518
CXXC1-BGKcLV17-7_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	159					GRCh38	V40	CXXC1-BGKcLV17-7/Aligned.sortedByCoord.out.bam		ENCORE2	24570
CXXC1-BGKcLV17-7_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	159					GRCh38	V40	CXXC1-BGKcLV17-7_S77_R1_001.filtered.trimmed.paired.fastq.gz,CXXC1-BGKcLV17-7_S77_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24622
CXXC1-BGKcLV17-8_S78_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	160	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	72
CXXC1-BGKcLV17-8_S78_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	160	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	124
CXXC1-BGKcLV17-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	160					GRCh38	V40	CXXC1-BGKcLV17-8_S78_R1_001.filtered.trimmed.paired.fastq.gz,CXXC1-BGKcLV17-8_S78_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24363
CXXC1-BGKcLV17-8_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	160					GRCh38	V40	CXXC1-BGKcLV17-8/Aligned.sortedByCoord.out.bam		ENCORE2	24415
CXXC1-BGKcLV17-8_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	160					GRCh38	V40	CXXC1-BGKcLV17-8/Aligned.sortedByCoord.out.bam		ENCORE2	24467
CXXC1-BGKcLV17-8_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	160					GRCh38	V40	CXXC1-BGKcLV17-8/Aligned.sortedByCoord.out.bam		ENCORE2	24519
CXXC1-BGKcLV17-8_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	160					GRCh38	V40	CXXC1-BGKcLV17-8/Aligned.sortedByCoord.out.bam		ENCORE2	24571
CXXC1-BGKcLV17-8_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	160					GRCh38	V40	CXXC1-BGKcLV17-8_S78_R1_001.filtered.trimmed.paired.fastq.gz,CXXC1-BGKcLV17-8_S78_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24623