CNDP2 RNA-Seq in K562

General Information


RBP	CNDP2
Cell_Line	K562
Method	CRISPR
Exp_Name	CNDP2-BGKcLV28-K562
ENCODE_series_ID	ENCSR831INO
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR164POA
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	CNDP2-BGKcLV28-27
Rep2	CNDP2-BGKcLV28-28
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	69.0
Rep2_WB	76.1
Antibody Cat#	A305-565A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB798DYU
Status	Released
Project	ENCODE4
ID	830

Experiment Information (Status: Released)

	BGKcLV28-27	BGKcLV28-27	BGKcLV28-28	BGKcLV28-28
idx	963	965	964	966
TRCN#_or_BGC#	BGC#0000704	BGC#0000704	BGC#0000704	BGC#0000704
shRNA_or_gRNA_sequence	GTGCTCCTCTTCCGTGACGG	GTGCTCCTCTTCCGTGACGG	GTGCTCCTCTTCCGTGACGG	GTGCTCCTCTTCCGTGACGG
PAM	CGG	CGG	CGG	CGG
Name	CNDP2_94	CNDP2_94	CNDP2_94	CNDP2_94
Sample_ID	BGKcLV28-27	BGKcLV28-27	BGKcLV28-28	BGKcLV28-28
transduction_Date	7/12/21	7/12/21	7/12/21	7/12/21
days	Day 6	Day 6	Day 6	Day 6
RBP_name	CNDP2	CNDP2	CNDP2	CNDP2
qPCR_result	0.0	0.0	7.9	7.9
Ave_qPCR	4.0	4.0
RT-qPCR_primer-F	tggagtgcagcaacaaagac	tggagtgcagcaacaaagac
RT-qPCR_primer-R	cctcttgtccaccaaagagc	cctcttgtccaccaaagagc
protein_conc	2353	2353	1977	1977
WB_result	69.0	54.9	76.1	72.3944877
Ave_WB	72.5	63.7
WB_DONE_date	6/29/21	2/10/22	JESS
MW	53kd	53kd
IP
antibody_Cat#	A305-565A	A305-566A	LOT #1	LOT #1
Antibody DCC ID	ENCAB798DYU		1/19/22
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	09/23/21		09/23/21
repeat_library
Note
ID	5097	5099	5098	5100

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CNDP2	Product_ID: A305-565A Lot_ID: 1 Source: Bethyl Labs Target Name: CNDP2-human

Experiment Status

	BGKcLV28-27	BGKcLV28-28
Sample_ID	BGKcLV28-27	BGKcLV28-28
Sample Name
Sample Name	CNDP2-BGKcLV28-27	CNDP2-BGKcLV28-28
RBP	CNDP2	CNDP2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9919	9920

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-27	BGKcLV28-28
Sample #	27	28
Sample Name	CNDP2-BGKcLV28-27	CNDP2-BGKcLV28-28
Sample_Name_Alias
Index Well Position	C08	D08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-09-21	2021-09-21
Lib_ID	Lib-210921	Lib-210921
Tecan_Location
Tecan
Tecan_date
Size_bp	309	340
Peak_Molarity	111.00	122.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/C4.png	DNA_Library_set48-49/set3/D4.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set48-49/set2/C4.png	RNA_Library_set48-49/set2/D4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-27	BGKcLV28-28
RBP	CNDP2	CNDP2
Batch_ID	BGKcLV28	BGKcLV28
WB_result	69.000	76.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2088	2089

Sequencing Information

	BGKcLV28-27	BGKcLV28-28
Sample_ID	BGKcLV28-27	BGKcLV28-28
Sample Name	CNDP2-BGKcLV28-27	CNDP2-BGKcLV28-28
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	118,244,508	174,075,316
total_aligned_reads	112,169,548	168,110,730
unique_aligned_reads	102,838,626	154,682,048
percent_uniqueAligned	0.86971	0.88859
correlation_replicates	0.988463	0.988463
spikein_reads	26,686	17,558
percent_spikeins	0.00023	0.00010
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1839	1840

Data Submission Information

	BGKcLV28-27	BGKcLV28-27	BGKcLV28-27	BGKcLV28-27	BGKcLV28-27	BGKcLV28-27	BGKcLV28-28	BGKcLV28-28	BGKcLV28-28	BGKcLV28-28
ENCODE_alias	brenton-graveley:CNDP2-BGKcLV28	brenton-graveley:CNDP2-BGKcLV28-27	brenton-graveley:L-CNDP2-BGKcLV28-27	brenton-graveley:CNDP2-BGKcLV28-27_S109_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CNDP2-BGKcLV28-27_S109_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CNDP2-BGKcLV28-K562	brenton-graveley:CNDP2-BGKcLV28-28	brenton-graveley:L-CNDP2-BGKcLV28-28	brenton-graveley:CNDP2-BGKcLV28-28_S110_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CNDP2-BGKcLV28-28_S110_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR164POA	ENCBS051GWD	ENCLB303SJT	ENCFF637IST	ENCFF940AWH	ENCSR831INO	ENCBS383JOT	ENCLB160TEX	ENCFF023GNJ	ENCFF249QKX
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	BGKcLV28-27	BGKcLV28-27	BGKcLV28-27	BGKcLV28-27	BGKcLV28-27	BGKcLV28-27	BGKcLV28-28	BGKcLV28-28	BGKcLV28-28	BGKcLV28-28
Sample Name	CNDP2-BGKcLV28-27	CNDP2-BGKcLV28-27	CNDP2-BGKcLV28-27	CNDP2-BGKcLV28-27	CNDP2-BGKcLV28-27	CNDP2-BGKcLV28-27	CNDP2-BGKcLV28-28	CNDP2-BGKcLV28-28	CNDP2-BGKcLV28-28	CNDP2-BGKcLV28-28
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-01-29	2022-01-29	2022-01-29	2022-01-29	2022-01-29	2022-03-02	2022-01-29	2022-01-29	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV49_biosample_protocol	LV49_library_protocol				LV49_biosample_protocol	LV49_library_protocol
protocol_URL		CNDP2-BGKcLV28-27.pdf	L-CNDP2-BGKcLV28-27.pdf				CNDP2-BGKcLV28-28.pdf	L-CNDP2-BGKcLV28-28.pdf
ID	3484	3602	3736	3870	4004	7146	3603	3737	3871	4005

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
CNDP2-BGKcLV28-27_S109_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1839	NovaSeq6000	100	paired-ended	1				NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3956
CNDP2-BGKcLV28-27_S109_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1839	NovaSeq6000	100	paired-ended	2				NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	4014
CNDP2-BGKcLV28-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1839					GRCh38	V40	CNDP2-BGKcLV28-27_S109_L004_R1_001.filtered.trimmed.paired.fastq.gz,CNDP2-BGKcLV28-27_S109_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19238
CNDP2-BGKcLV28-27_Signal.Unique.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1839					GRCh38	V40	CNDP2-BGKcLV28-27/Aligned.sortedByCoord.out.bam		ENCORE2	19296
CNDP2-BGKcLV28-27_Signal.Unique.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1839					GRCh38	V40	CNDP2-BGKcLV28-27/Aligned.sortedByCoord.out.bam		ENCORE2	19354
CNDP2-BGKcLV28-27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1839					GRCh38	V40	CNDP2-BGKcLV28-27/Aligned.sortedByCoord.out.bam		ENCORE2	19412
CNDP2-BGKcLV28-27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1839					GRCh38	V40	CNDP2-BGKcLV28-27/Aligned.sortedByCoord.out.bam		ENCORE2	19470
CNDP2-BGKcLV28-27_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1839					GRCh38	V40	CNDP2-BGKcLV28-27_S109_L004_R1_001.filtered.trimmed.paired.fastq.gz,CNDP2-BGKcLV28-27_S109_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19528
CNDP2-BGKcLV28-28_S110_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1840	NovaSeq6000	100	paired-ended	1				NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3957
CNDP2-BGKcLV28-28_S110_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1840	NovaSeq6000	100	paired-ended	2				NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	4015
CNDP2-BGKcLV28-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1840					GRCh38	V40	CNDP2-BGKcLV28-28_S110_L004_R1_001.filtered.trimmed.paired.fastq.gz,CNDP2-BGKcLV28-28_S110_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19239
CNDP2-BGKcLV28-28_Signal.Unique.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1840					GRCh38	V40	CNDP2-BGKcLV28-28/Aligned.sortedByCoord.out.bam		ENCORE2	19297
CNDP2-BGKcLV28-28_Signal.Unique.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1840					GRCh38	V40	CNDP2-BGKcLV28-28/Aligned.sortedByCoord.out.bam		ENCORE2	19355
CNDP2-BGKcLV28-28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1840					GRCh38	V40	CNDP2-BGKcLV28-28/Aligned.sortedByCoord.out.bam		ENCORE2	19413
CNDP2-BGKcLV28-28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1840					GRCh38	V40	CNDP2-BGKcLV28-28/Aligned.sortedByCoord.out.bam		ENCORE2	19471
CNDP2-BGKcLV28-28_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1840					GRCh38	V40	CNDP2-BGKcLV28-28_S110_L004_R1_001.filtered.trimmed.paired.fastq.gz,CNDP2-BGKcLV28-28_S110_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19529