CSDE1 RNA-Seq in K562

General Information


RBP	CSDE1
Cell_Line	K562
Method	CRISPR
Exp_Name	CSDE1-BGKcLV35-K562
ENCODE_series_ID
Batch_ID	BGKcLV35
Pool ID	Pool-220720
Local_Set_Name	set54
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	CSDE1-BGKcLV35-15
Rep2	CSDE1-BGKcLV35-16
CN1	NT-BGKcLV35-1
CN2	NT-BGKcLV35-2
Rep1_qPCR	61.3
Rep2_qPCR	59.7
Rep1_WB	70.7
Rep2_WB	74.1
Antibody Cat#	A303-160A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB259ZCR
Status	Submitted
Project	ENCORE2
ID	954

Experiment Information (Status: Submitting)

	BGKcLV35-15	BGKcLV35-16
idx	1292	1293
TRCN#_or_BGC#	BGC#0000717	BGC#0000717
shRNA_or_gRNA_sequence	ACACCCCTGAAGATGTCGAA	ACACCCCTGAAGATGTCGAA
PAM	GGG	GGG
Name	CSDE1_89	CSDE1_89
Sample_ID	BGKcLV35-15	BGKcLV35-16
transduction_Date	4/28/22	4/28/22
days	D6	D6
RBP_name	CSDE1	CSDE1
qPCR_result	61.3	59.7
Ave_qPCR	60.5
RT-qPCR_primer-F	gccacagtggaatgtgtgaa
RT-qPCR_primer-R	cctcatctcctgcctgtagc
protein_conc	3406	2938
WB_result	70.7	74.1
Ave_WB	72.4
WB_DONE_date	6/2/22
MW	89KD
IP
antibody_Cat#	A303-160A	LOT #1
Antibody DCC ID	ENCAB259ZCR
submitted_to_DCC_date	8/16/22
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/17/22	06/17/22
repeat_library
Note
ID	5436	5437

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CSDE1	Product_ID: A303-160A Lot_ID: 1 Source: Bethyl Labs Target Name: CSDE1-human

Experiment Status

	BGKcLV35-15	BGKcLV35-16
Sample_ID	BGKcLV35-15	BGKcLV35-16
Sample Name
Sample Name	CSDE1-BGKcLV35-15	CSDE1-BGKcLV35-16
RBP	CSDE1	CSDE1
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10865	10866

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV35-15	BGKcLV35-16
Sample #	31	32
Sample Name	CSDE1-BGKcLV35-15	CSDE1-BGKcLV35-16
Sample_Name_Alias
Index Well Position	G04	H04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-06-17	2022-06-17
Lib_ID	Lib-220617	Lib-220617
Tecan_Location
Tecan
Tecan_date
Size_bp	287	283
Peak_Molarity	27.60	15.60
libSampleQC_DNA_Well	DNA_Library_set54-56/set3/G8.png	DNA_Library_set54-56/set3/H8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set54-56/set2/G4.png	RNA_Library_set54-56/set2/H4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-06-20	2022-06-20
Sample_ID	BGKcLV35-15	BGKcLV35-16
RBP	CSDE1	CSDE1
Batch_ID	BGKcLV35	BGKcLV35
WB_result	70.700	74.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3348	3349

Sequencing Information

	BGKcLV35-15	BGKcLV35-16
Sample_ID	BGKcLV35-15	BGKcLV35-16
Sample Name	CSDE1-BGKcLV35-15	CSDE1-BGKcLV35-16
Pool ID	Pool-220720	Pool-220720
LocalServer_folder	set54	set54
total_reads	79,615,684	62,250,740
total_aligned_reads	74,923,872	55,847,336
unique_aligned_reads	68,491,922	51,129,476
percent_uniqueAligned	0.86028	0.82135
correlation_replicates	0.992278	0.992278
spikein_reads	8,626	7,768
percent_spikeins	0.00011	0.00012
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2227	2228

Data Submission Information DCC submission information was not avaliable

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
CSDE1-BGKcLV35-15_S33_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2227	NovaSeq6000	100	paired-ended	1				NT-BGKcLV35-1_S25_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8486
CSDE1-BGKcLV35-15_S33_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2227	NovaSeq6000	100	paired-ended	2				NT-BGKcLV35-1_S25_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8536
CSDE1-BGKcLV35-15_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2227					GRCh38	V40	CSDE1-BGKcLV35-15/Aligned.sortedByCoord.out.bam		ENCORE2	17732
CSDE1-BGKcLV35-15_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2227					GRCh38	V40	CSDE1-BGKcLV35-15/Aligned.sortedByCoord.out.bam		ENCORE2	17782
CSDE1-BGKcLV35-15_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2227					GRCh38	V40	CSDE1-BGKcLV35-15/Aligned.sortedByCoord.out.bam		ENCORE2	17832
CSDE1-BGKcLV35-15_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2227					GRCh38	V40	CSDE1-BGKcLV35-15/Aligned.sortedByCoord.out.bam		ENCORE2	17882
CSDE1-BGKcLV35-15_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2227					GRCh38	V40	CSDE1-BGKcLV35-15_S33_R1_001.filtered.trimmed.paired.fastq.gz,CSDE1-BGKcLV35-15_S33_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17932
CSDE1-BGKcLV35-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2227					GRCh38	V40	CSDE1-BGKcLV35-15_S33_R1_001.filtered.trimmed.paired.fastq.gz,CSDE1-BGKcLV35-15_S33_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29273
CSDE1-BGKcLV35-16_S34_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2228	NovaSeq6000	100	paired-ended	1				NT-BGKcLV35-1_S25_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8487
CSDE1-BGKcLV35-16_S34_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2228	NovaSeq6000	100	paired-ended	2				NT-BGKcLV35-1_S25_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8537
CSDE1-BGKcLV35-16_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2228					GRCh38	V40	CSDE1-BGKcLV35-16/Aligned.sortedByCoord.out.bam		ENCORE2	17733
CSDE1-BGKcLV35-16_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2228					GRCh38	V40	CSDE1-BGKcLV35-16/Aligned.sortedByCoord.out.bam		ENCORE2	17783
CSDE1-BGKcLV35-16_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2228					GRCh38	V40	CSDE1-BGKcLV35-16/Aligned.sortedByCoord.out.bam		ENCORE2	17833
CSDE1-BGKcLV35-16_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2228					GRCh38	V40	CSDE1-BGKcLV35-16/Aligned.sortedByCoord.out.bam		ENCORE2	17883
CSDE1-BGKcLV35-16_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2228					GRCh38	V40	CSDE1-BGKcLV35-16_S34_R1_001.filtered.trimmed.paired.fastq.gz,CSDE1-BGKcLV35-16_S34_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17933
CSDE1-BGKcLV35-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2228					GRCh38	V40	CSDE1-BGKcLV35-16_S34_R1_001.filtered.trimmed.paired.fastq.gz,CSDE1-BGKcLV35-16_S34_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29274