CTCF RNA-Seq in HepG2

General Information


RBP	CTCF
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CTCF-BGHcLV18-HepG2
ENCODE_series_ID	ENCSR674ZMS
Batch_ID	BGHcLV18
Pool ID	Pool-200103
Local_Set_Name	set44_H
ENCODE_KD_Exp_ID	ENCSR871XPX
ENCODE_CN_Exp_ID	ENCSR670KAS
Rep1	CTCF-BGHcLV18-5
Rep2	CTCF-BGHcLV18-6
CN1	NT-BGHcLV18-1
CN2	NT-BGHcLV18-2
Rep1_qPCR	0.0
Rep2_qPCR	1.6
Rep1_WB	70.2
Rep2_WB	69.5
Antibody Cat#	PA5-17143
Antibody Lot#	lot# UC2731408
Antibody DCC ID	ENCAB363WCM
Status	Released
Project	ENCODE4
ID	100

Experiment Information (Status: Released)

	BGHcLV18-5	BGHcLV18-5	BGHcLV18-6	BGHcLV18-6
idx	498	498	499	499
TRCN#_or_BGC#	BGC#0000444	BGC#0000444	BGC#0000444	BGC#0000444
shRNA_or_gRNA_sequence	AAGCCGCAGGGACGAAGTTG	AAGCCGCAGGGACGAAGTTG	AAGCCGCAGGGACGAAGTTG	AAGCCGCAGGGACGAAGTTG
PAM	GGG	GGG	GGG	GGG
Name	CTCF_91	CTCF_91	CTCF_91	CTCF_91
Sample_ID	BGHcLV18-5	BGHcLV18-5	BGHcLV18-6	BGHcLV18-6
transduction_Date	8/13/19	8/13/19	8/13/19	8/13/19
days	D6	D6	D6	D6
RBP_name	CTCF	CTCF	CTCF	CTCF
qPCR_result	0.0	0.0	1.6	1.6
Ave_qPCR	0.8	0.8
RT-qPCR_primer-F	GGAAGAAAAAGAAAGATGCGCT	GGAAGAAAAAGAAAGATGCGCT
RT-qPCR_primer-R	TCAGGTTCAATTTCTACGGCA	TCAGGTTCAATTTCTACGGCA
protein_conc	3532	3532	3466	3466
WB_result	70.2	91.3	69.5	86.7
Ave_WB	69.9	89.0
WB_DONE_date	8/26/19	4/18/24	WES
MW	83KD	83KD
IP	Rabbit / I		Polyclonal
antibody_Cat#	PA5-17143	3418S	lot# UC2731408	lot# 5
Antibody DCC ID	ENCAB363WCM
submitted_to_DCC_date
Rep1_TPM	39	0	0	0
Rep2_TPM	46	0	0	0
Action	Ready		Ready
Library_start_date	12/11/19		12/11/19
repeat_library
Note
ID	6649	6651	6650	6652

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CTCF	Product_ID: PA5-17143 Lot_ID: UC2731408 Source: Thermo Fisher Target Name: CTCF-human
CTCF	Product_ID: 3418S Lot_ID: 5 Source: Cell Signaling Technology Target Name: CTCF-human

Experiment Status

	BGHcLV18-5	BGHcLV18-6
Sample_ID	BGHcLV18-5	BGHcLV18-6
Sample Name
Sample Name	CTCF-BGHcLV18-5	CTCF-BGHcLV18-6
RBP	CTCF	CTCF
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5617	5618

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV18-5	BGHcLV18-6
Sample #	123	124
Sample Name	CTCF-BGHcLV18-5	CTCF-BGHcLV18-6
Sample_Name_Alias
Index Well Position	E04	F04
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-G1	3-H1
Tecan	38.69	36.97
Tecan_date	2019-12-16	2019-12-16
Size_bp	271	273
Peak_Molarity	25.90	29.20
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/E5.png	DNA_Library_set43-44/set2/F5.png
RIN	9.5	9.7
libSample_RNA_Well	RNA_Library_set43-44/set4/A7.png	RNA_Library_set43-44/set4/B7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV18-5	BGHcLV18-6
RBP	CTCF	CTCF
Batch_ID	BGHcLV18	BGHcLV18
WB_result	70.200	69.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	699	700

Sequencing Information

	BGHcLV18-5	BGHcLV18-6
Sample_ID	BGHcLV18-5	BGHcLV18-6
Sample Name	CTCF-BGHcLV18-5	CTCF-BGHcLV18-6
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_H	set44_H
total_reads	158,878,254	157,434,952
total_aligned_reads	148,938,530	150,247,458
unique_aligned_reads	139,479,382	140,564,670
percent_uniqueAligned	0.87790	0.89284
correlation_replicates	0.999197	0.999197
spikein_reads	191,000	222,272
percent_spikeins	0.00120	0.00141
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	205	206

Data Submission Information

	BGHcLV18-5	BGHcLV18-5	BGHcLV18-5	BGHcLV18-5	BGHcLV18-5	BGHcLV18-5	BGHcLV18-6	BGHcLV18-6	BGHcLV18-6	BGHcLV18-6
ENCODE_alias	brenton-graveley:CTCF-BGHcLV18	brenton-graveley:CTCF-BGHcLV18-5	brenton-graveley:L-CTCF-BGHcLV18-5	brenton-graveley:CTCF-BGHcLV18-5_S39_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CTCF-BGHcLV18-5_S39_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CTCF-BGHcLV18-HepG2	brenton-graveley:CTCF-BGHcLV18-6	brenton-graveley:L-CTCF-BGHcLV18-6	brenton-graveley:CTCF-BGHcLV18-6_S40_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CTCF-BGHcLV18-6_S40_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR871XPX	ENCBS061ERM	ENCLB739AXP	ENCFF085HUX	ENCFF731VFI	ENCSR674ZMS	ENCBS180SBL	ENCLB011VZC	ENCFF725TDX	ENCFF511LGS
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	BGHcLV18-5	BGHcLV18-5	BGHcLV18-5	BGHcLV18-5	BGHcLV18-5	BGHcLV18-5	BGHcLV18-6	BGHcLV18-6	BGHcLV18-6	BGHcLV18-6
Sample Name	CTCF-BGHcLV18-5	CTCF-BGHcLV18-5	CTCF-BGHcLV18-5	CTCF-BGHcLV18-5	CTCF-BGHcLV18-5	CTCF-BGHcLV18-5	CTCF-BGHcLV18-6	CTCF-BGHcLV18-6	CTCF-BGHcLV18-6	CTCF-BGHcLV18-6
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		CTCF-BGHcLV18-5.pdf	L-CTCF-BGHcLV18-5.pdf				CTCF-BGHcLV18-6.pdf	L-CTCF-BGHcLV18-6.pdf
ID	47	174	340	590	642	7161	175	341	591	643

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
CTCF-BGHcLV18-5_S39_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	205	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	171
CTCF-BGHcLV18-5_S39_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	205	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	223
CTCF-BGHcLV18-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	205					GRCh38	V40	CTCF-BGHcLV18-5_S39_R1_001.filtered.trimmed.paired.fastq.gz,CTCF-BGHcLV18-5_S39_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24891
CTCF-BGHcLV18-5_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	205					GRCh38	V40	CTCF-BGHcLV18-5/Aligned.sortedByCoord.out.bam		ENCORE2	24943
CTCF-BGHcLV18-5_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	205					GRCh38	V40	CTCF-BGHcLV18-5/Aligned.sortedByCoord.out.bam		ENCORE2	24995
CTCF-BGHcLV18-5_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	205					GRCh38	V40	CTCF-BGHcLV18-5/Aligned.sortedByCoord.out.bam		ENCORE2	25047
CTCF-BGHcLV18-5_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	205					GRCh38	V40	CTCF-BGHcLV18-5/Aligned.sortedByCoord.out.bam		ENCORE2	25099
CTCF-BGHcLV18-5_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	205					GRCh38	V40	CTCF-BGHcLV18-5_S39_R1_001.filtered.trimmed.paired.fastq.gz,CTCF-BGHcLV18-5_S39_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25151
CTCF-BGHcLV18-6_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	206	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	172
CTCF-BGHcLV18-6_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	206	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	224
CTCF-BGHcLV18-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	206					GRCh38	V40	CTCF-BGHcLV18-6_S40_R1_001.filtered.trimmed.paired.fastq.gz,CTCF-BGHcLV18-6_S40_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24892
CTCF-BGHcLV18-6_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	206					GRCh38	V40	CTCF-BGHcLV18-6/Aligned.sortedByCoord.out.bam		ENCORE2	24944
CTCF-BGHcLV18-6_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	206					GRCh38	V40	CTCF-BGHcLV18-6/Aligned.sortedByCoord.out.bam		ENCORE2	24996
CTCF-BGHcLV18-6_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	206					GRCh38	V40	CTCF-BGHcLV18-6/Aligned.sortedByCoord.out.bam		ENCORE2	25048
CTCF-BGHcLV18-6_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	206					GRCh38	V40	CTCF-BGHcLV18-6/Aligned.sortedByCoord.out.bam		ENCORE2	25100
CTCF-BGHcLV18-6_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	206					GRCh38	V40	CTCF-BGHcLV18-6_S40_R1_001.filtered.trimmed.paired.fastq.gz,CTCF-BGHcLV18-6_S40_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25152