CTCF RNA-Seq in K562

General Information


RBP	CTCF
Cell_Line	K562
Method	CRISPR
Exp_Name	CTCF-BGKcLV17-K562
ENCODE_series_ID	ENCSR040SYA
Batch_ID	BGKcLV17
Pool ID	Pool-200102
Local_Set_Name	set43_K
ENCODE_KD_Exp_ID	ENCSR613LSQ
ENCODE_CN_Exp_ID	ENCSR516TLX
Rep1	CTCF-BGKcLV17-5
Rep2	CTCF-BGKcLV17-6
CN1	NT-BGKcLV17-1
CN2	NT-BGKcLV17-2
Rep1_qPCR	45.8
Rep2_qPCR	39.2
Rep1_WB	61.4
Rep2_WB	69
Antibody Cat#	PA5-17143
Antibody Lot#	lot# UC2731408
Antibody DCC ID	ENCAB363WCM
Status	Released
Project	ENCODE4
ID	141

Experiment Information (Status: Released)

	BGKcLV17-5	BGKcLV17-6
idx	612	613
TRCN#_or_BGC#	BGC#0000445	BGC#0000445
shRNA_or_gRNA_sequence	CTGGCCCAGATGGCGTAGAG	CTGGCCCAGATGGCGTAGAG
PAM	GGG	GGG
Name	CTCF_89	CTCF_89
Sample_ID	BGKcLV17-5	BGKcLV17-6
transduction_Date	7/2/19	7/2/19
days	Day 6	Day 6
RBP_name	CTCF	CTCF
qPCR_result	45.8	39.2
Ave_qPCR	42.5
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	4260	4383
WB_result	61.4	69
Ave_WB	65.3
WB_DONE_date	8/30/19	WES
MW	83KD
IP	Rabbit / I	Polyclonal
antibody_Cat#	PA5-17143	lot# UC2731408
Antibody DCC ID	ENCAB363WCM
submitted_to_DCC_date
Rep1_TPM	26.1	0
Rep2_TPM	27.6	0
Action	Ready	Ready
Library_start_date	12/05/19	12/05/19
repeat_library
Note
ID	4724	4725

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

Experiment Status

	BGKcLV17-5	BGKcLV17-6
Sample_ID	BGKcLV17-5	BGKcLV17-6
Sample Name
Sample Name	CTCF-BGKcLV17-5	CTCF-BGKcLV17-6
RBP	CTCF	CTCF
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5489	5490

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV17-5	BGKcLV17-6
Sample #	79	80
Sample Name	CTCF-BGKcLV17-5	CTCF-BGKcLV17-6
Sample_Name_Alias
Index Well Position	C10	D10
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-E1	1-F1
Tecan	39.68	26.83
Tecan_date	2019-12-10	2019-12-10
Size_bp	274	277
Peak_Molarity	31.40	30.70
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/E6.png	DNA_Library_set43-44/set1/F6.png
RIN	9.4	9.4
libSample_RNA_Well	RNA_Library_set43-44/set4/E1.png	RNA_Library_set43-44/set4/F1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV17-5	BGKcLV17-6
RBP	CTCF	CTCF
Batch_ID	BGKcLV17	BGKcLV17
WB_result	61.400	69.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	655	656

Sequencing Information

	BGKcLV17-5	BGKcLV17-6
Sample_ID	BGKcLV17-5	BGKcLV17-6
Sample Name	CTCF-BGKcLV17-5	CTCF-BGKcLV17-6
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_K	set43_K
total_reads	106,197,702	104,289,108
total_aligned_reads	99,345,504	96,051,126
unique_aligned_reads	90,443,312	87,743,656
percent_uniqueAligned	0.85165	0.84135
correlation_replicates	0.999196	0.999196
spikein_reads	28,970	28,378
percent_spikeins	0.00027	0.00027
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	157	158

Data Submission Information

	BGKcLV17-5	BGKcLV17-5	BGKcLV17-5	BGKcLV17-5	BGKcLV17-5	BGKcLV17-5	BGKcLV17-6	BGKcLV17-6	BGKcLV17-6	BGKcLV17-6
ENCODE_alias	brenton-graveley:CTCF-BGKcLV17	brenton-graveley:CTCF-BGKcLV17-5	brenton-graveley:L-CTCF-BGKcLV17-5	brenton-graveley:CTCF-BGKcLV17-5_S75_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CTCF-BGKcLV17-5_S75_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CTCF-BGKcLV17-K562	brenton-graveley:CTCF-BGKcLV17-6	brenton-graveley:L-CTCF-BGKcLV17-6	brenton-graveley:CTCF-BGKcLV17-6_S76_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CTCF-BGKcLV17-6_S76_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR613LSQ	ENCBS988SWN	ENCLB846JOE	ENCFF618LQO	ENCFF416VGT	ENCSR040SYA	ENCBS742ULM	ENCLB949WYZ	ENCFF964UJL	ENCFF409UNJ
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	BGKcLV17-5	BGKcLV17-5	BGKcLV17-5	BGKcLV17-5	BGKcLV17-5	BGKcLV17-5	BGKcLV17-6	BGKcLV17-6	BGKcLV17-6	BGKcLV17-6
Sample Name	CTCF-BGKcLV17-5	CTCF-BGKcLV17-5	CTCF-BGKcLV17-5	CTCF-BGKcLV17-5	CTCF-BGKcLV17-5	CTCF-BGKcLV17-5	CTCF-BGKcLV17-6	CTCF-BGKcLV17-6	CTCF-BGKcLV17-6	CTCF-BGKcLV17-6
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	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_biosample_protocol	LV43K_library_protocol				LV43K_biosample_protocol	LV43K_library_protocol
protocol_URL		CTCF-BGKcLV17-5.pdf	L-CTCF-BGKcLV17-5.pdf				CTCF-BGKcLV17-6.pdf	L-CTCF-BGKcLV17-6.pdf
ID	38	158	322	520	572	7162	159	323	521	573

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-BGKcLV17-5_S75_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	157	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	69
CTCF-BGKcLV17-5_S75_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	157	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	121
CTCF-BGKcLV17-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	157					GRCh38	V40	CTCF-BGKcLV17-5_S75_R1_001.filtered.trimmed.paired.fastq.gz,CTCF-BGKcLV17-5_S75_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24360
CTCF-BGKcLV17-5_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	157					GRCh38	V40	CTCF-BGKcLV17-5/Aligned.sortedByCoord.out.bam		ENCORE2	24412
CTCF-BGKcLV17-5_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	157					GRCh38	V40	CTCF-BGKcLV17-5/Aligned.sortedByCoord.out.bam		ENCORE2	24464
CTCF-BGKcLV17-5_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	157					GRCh38	V40	CTCF-BGKcLV17-5/Aligned.sortedByCoord.out.bam		ENCORE2	24516
CTCF-BGKcLV17-5_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	157					GRCh38	V40	CTCF-BGKcLV17-5/Aligned.sortedByCoord.out.bam		ENCORE2	24568
CTCF-BGKcLV17-5_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	157					GRCh38	V40	CTCF-BGKcLV17-5_S75_R1_001.filtered.trimmed.paired.fastq.gz,CTCF-BGKcLV17-5_S75_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24620
CTCF-BGKcLV17-6_S76_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	158	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	70
CTCF-BGKcLV17-6_S76_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	158	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	122
CTCF-BGKcLV17-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	158					GRCh38	V40	CTCF-BGKcLV17-6_S76_R1_001.filtered.trimmed.paired.fastq.gz,CTCF-BGKcLV17-6_S76_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24361
CTCF-BGKcLV17-6_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	158					GRCh38	V40	CTCF-BGKcLV17-6/Aligned.sortedByCoord.out.bam		ENCORE2	24413
CTCF-BGKcLV17-6_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	158					GRCh38	V40	CTCF-BGKcLV17-6/Aligned.sortedByCoord.out.bam		ENCORE2	24465
CTCF-BGKcLV17-6_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	158					GRCh38	V40	CTCF-BGKcLV17-6/Aligned.sortedByCoord.out.bam		ENCORE2	24517
CTCF-BGKcLV17-6_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	158					GRCh38	V40	CTCF-BGKcLV17-6/Aligned.sortedByCoord.out.bam		ENCORE2	24569
CTCF-BGKcLV17-6_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	158					GRCh38	V40	CTCF-BGKcLV17-6_S76_R1_001.filtered.trimmed.paired.fastq.gz,CTCF-BGKcLV17-6_S76_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24621