CXXC1 RNA-Seq in HepG2

General Information


RBP	CXXC1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CXXC1-BGHcLV18-HepG2
ENCODE_series_ID	ENCSR812QUI
Batch_ID	BGHcLV18
Pool ID	Pool-200103
Local_Set_Name	set44_H
ENCODE_KD_Exp_ID	ENCSR666FOS
ENCODE_CN_Exp_ID	ENCSR670KAS
Rep1	CXXC1-BGHcLV18-7
Rep2	CXXC1-BGHcLV18-8
CN1	NT-BGHcLV18-1
CN2	NT-BGHcLV18-2
Rep1_qPCR	83.4
Rep2_qPCR	83.2
Rep1_WB	86.8
Rep2_WB	91.2
Antibody Cat#	PA5-76829
Antibody Lot#	lot# UC2739251A
Antibody DCC ID	ENCAB216VRJ
Status	Released
Project	ENCODE4
ID	101

Experiment Information (Status: Released)

	BGHcLV18-7	BGHcLV18-8
idx	500	501
TRCN#_or_BGC#	BGC#0000431	BGC#0000431
shRNA_or_gRNA_sequence	AAACGGTCAGCCCGCATGTG	AAACGGTCAGCCCGCATGTG
PAM	TGG	TGG
Name	CXXC1_97	CXXC1_97
Sample_ID	BGHcLV18-7	BGHcLV18-8
transduction_Date	8/13/19	8/13/19
days	D6	D6
RBP_name	CXXC1	CXXC1
qPCR_result	83.4	83.2
Ave_qPCR	83.3
RT-qPCR_primer-F	AACAAGATCCGGCAGAAGTG
RT-qPCR_primer-R	cactggtgagagcgaggaa
protein_conc	4468	4816
WB_result	86.8	91.2
Ave_WB	89.0
WB_DONE_date	8/28/19	WES
MW	76KD
IP	Rabbit / I	Polyclonal
antibody_Cat#	PA5-76829	lot# UC2739251A
Antibody DCC ID	ENCAB216VRJ
submitted_to_DCC_date
Rep1_TPM	64	0
Rep2_TPM	33	0
Action	Ready	Ready
Library_start_date	12/11/19	12/11/19
repeat_library
Note
ID	6653	6654

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CXXC1	Product_ID: PA5-76829 Lot_ID: UC2739251A Source: Thermo Fisher Target Name: CXXC1-human

Experiment Status

	BGHcLV18-7	BGHcLV18-8
Sample_ID	BGHcLV18-7	BGHcLV18-8
Sample Name	CXXC1-BGHcLV18-7	CXXC1-BGHcLV18-8
Sample Name	CXXC1-BGHcLV18-7	CXXC1-BGHcLV18-8
RBP	CXXC1	CXXC1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5619	5620

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV18-7	BGHcLV18-8
Sample #	125	126
Sample Name	CXXC1-BGHcLV18-7	CXXC1-BGHcLV18-8
Sample_Name_Alias
Index Well Position	G04	H04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	3-A2	3-B2
Tecan	40.20	36.51
Tecan_date	2019-12-16	2019-12-16
Size_bp	270	269
Peak_Molarity	29.00	28.20
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/G5.png	DNA_Library_set43-44/set2/H5.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_set43-44/set4/C7.png	RNA_Library_set43-44/set4/D7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV18-7	BGHcLV18-8
RBP	CXXC1	CXXC1
Batch_ID	BGHcLV18	BGHcLV18
WB_result	86.800	91.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	701	702

Sequencing Information

	BGHcLV18-7	BGHcLV18-8
Sample_ID	BGHcLV18-7	BGHcLV18-8
Sample Name	CXXC1-BGHcLV18-7	CXXC1-BGHcLV18-8
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_H	set44_H
total_reads	149,704,138	163,469,940
total_aligned_reads	138,377,732	155,841,678
unique_aligned_reads	129,431,240	145,724,286
percent_uniqueAligned	0.86458	0.89144
correlation_replicates	0.998451	0.998451
spikein_reads	214,964	223,248
percent_spikeins	0.00144	0.00137
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	207	208

Data Submission Information

	BGHcLV18-7	BGHcLV18-7	BGHcLV18-7	BGHcLV18-7	BGHcLV18-7	BGHcLV18-7	BGHcLV18-8	BGHcLV18-8	BGHcLV18-8	BGHcLV18-8
ENCODE_alias	brenton-graveley:CXXC1-BGHcLV18	brenton-graveley:CXXC1-BGHcLV18-7	brenton-graveley:L-CXXC1-BGHcLV18-7	brenton-graveley:CXXC1-BGHcLV18-7_S41_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CXXC1-BGHcLV18-7_S41_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CXXC1-BGHcLV18-HepG2	brenton-graveley:CXXC1-BGHcLV18-8	brenton-graveley:L-CXXC1-BGHcLV18-8	brenton-graveley:CXXC1-BGHcLV18-8_S42_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CXXC1-BGHcLV18-8_S42_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR666FOS	ENCBS285GCD	ENCLB653BOA	ENCFF251IUX	ENCFF755ZKE	ENCSR812QUI	ENCBS083QAV	ENCLB465QNE	ENCFF267VOH	ENCFF496JDK
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	BGHcLV18-7	BGHcLV18-7	BGHcLV18-7	BGHcLV18-7	BGHcLV18-7	BGHcLV18-7	BGHcLV18-8	BGHcLV18-8	BGHcLV18-8	BGHcLV18-8
Sample Name	CXXC1-BGHcLV18-7	CXXC1-BGHcLV18-7	CXXC1-BGHcLV18-7	CXXC1-BGHcLV18-7	CXXC1-BGHcLV18-7	CXXC1-BGHcLV18-7	CXXC1-BGHcLV18-8	CXXC1-BGHcLV18-8	CXXC1-BGHcLV18-8	CXXC1-BGHcLV18-8
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2022-03-02	2020-12-01	2020-12-01	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV44H_biosample_protocol	LV44H_library_protocol				LV44H_biosample_protocol	LV44H_library_protocol
protocol_URL		CXXC1-BGHcLV18-7.pdf	L-CXXC1-BGHcLV18-7.pdf				CXXC1-BGHcLV18-8.pdf	L-CXXC1-BGHcLV18-8.pdf
ID	48	176	342	592	644	7166	177	343	593	645

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-BGHcLV18-7_S41_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	207	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	173
CXXC1-BGHcLV18-7_S41_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	207	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	225
CXXC1-BGHcLV18-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	207					GRCh38	V40	CXXC1-BGHcLV18-7_S41_R1_001.filtered.trimmed.paired.fastq.gz,CXXC1-BGHcLV18-7_S41_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24893
CXXC1-BGHcLV18-7_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	207					GRCh38	V40	CXXC1-BGHcLV18-7/Aligned.sortedByCoord.out.bam		ENCORE2	24945
CXXC1-BGHcLV18-7_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	207					GRCh38	V40	CXXC1-BGHcLV18-7/Aligned.sortedByCoord.out.bam		ENCORE2	24997
CXXC1-BGHcLV18-7_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	207					GRCh38	V40	CXXC1-BGHcLV18-7/Aligned.sortedByCoord.out.bam		ENCORE2	25049
CXXC1-BGHcLV18-7_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	207					GRCh38	V40	CXXC1-BGHcLV18-7/Aligned.sortedByCoord.out.bam		ENCORE2	25101
CXXC1-BGHcLV18-7_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	207					GRCh38	V40	CXXC1-BGHcLV18-7_S41_R1_001.filtered.trimmed.paired.fastq.gz,CXXC1-BGHcLV18-7_S41_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25153
CXXC1-BGHcLV18-8_S42_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	208	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	174
CXXC1-BGHcLV18-8_S42_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	208	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	226
CXXC1-BGHcLV18-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	208					GRCh38	V40	CXXC1-BGHcLV18-8_S42_R1_001.filtered.trimmed.paired.fastq.gz,CXXC1-BGHcLV18-8_S42_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24894
CXXC1-BGHcLV18-8_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	208					GRCh38	V40	CXXC1-BGHcLV18-8/Aligned.sortedByCoord.out.bam		ENCORE2	24946
CXXC1-BGHcLV18-8_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	208					GRCh38	V40	CXXC1-BGHcLV18-8/Aligned.sortedByCoord.out.bam		ENCORE2	24998
CXXC1-BGHcLV18-8_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	208					GRCh38	V40	CXXC1-BGHcLV18-8/Aligned.sortedByCoord.out.bam		ENCORE2	25050
CXXC1-BGHcLV18-8_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	208					GRCh38	V40	CXXC1-BGHcLV18-8/Aligned.sortedByCoord.out.bam		ENCORE2	25102
CXXC1-BGHcLV18-8_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	208					GRCh38	V40	CXXC1-BGHcLV18-8_S42_R1_001.filtered.trimmed.paired.fastq.gz,CXXC1-BGHcLV18-8_S42_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25154