EED RNA-Seq in K562

General Information


RBP	EED
Cell_Line	K562
Method	CRISPR
Exp_Name	EED-BGKcLV46-K562
ENCODE_series_ID
Batch_ID	BGKcLV46
Pool ID	Pool-250312
Local_Set_Name	set77
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EED-BGKcLV46-25
Rep2	EED-BGKcLV46-26
CN1	NT-BGKcLV46-1
CN2	NT-BGKcLV46-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	53.8
Rep2_WB	68.6
Antibody Cat#	85322S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1639

Experiment Information (Status: Submitting)

	BGKcLV46-25	BGKcLV46-25	BGKcLV46-26	BGKcLV46-26
idx	0	0	0	0
TRCN#_or_BGC#	BGC#0001233	BGC#0001233	BGC#0001233	BGC#0001233
shRNA_or_gRNA_sequence	AGTGTGACATTTGGTACATG	AGTGTGACATTTGGTACATG	AGTGTGACATTTGGTACATG	AGTGTGACATTTGGTACATG
PAM	AGG	AGG	AGG	AGG
Name	EED_66	EED_66	EED_66	EED_66
Sample_ID	BGKcLV46-25	BGKcLV46-25	BGKcLV46-26	BGKcLV46-26
transduction_Date	12/20/24	12/20/24	12/20/24	12/20/24
days	D6	D6	D6	D6
RBP_name	EED	EED	EED	EED
qPCR_result	0.0	0.0	0.0	0.0
Ave_qPCR	0.0	0.0
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	4663	4663	4126	4126
WB_result	53.8		68.6
Ave_WB
WB_DONE_date	1/2/25	1/30/25		no clear band on the
MW	52kd	52kd
IP
antibody_Cat#	85322S	PA5-34430	lot # 1	UK2881462A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	6015	6017	6016	6018

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKcLV46-25	BGKcLV46-26
Sample_ID	BGKcLV46-25	BGKcLV46-26
Sample Name
Sample Name	EED-BGKcLV46-25	EED-BGKcLV46-26
RBP	EED	EED
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	14032	14033

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV46-25	BGKcLV46-26
Sample #	11	12
Sample Name	EED-BGKcLV46-25	EED-BGKcLV46-26
Sample_Name_Alias
Index Well Position	C02	D02
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-02-20	2025-02-20
Lib_ID	Lib-250220	Lib-250220
Tecan_Location
Tecan
Tecan_date
Size_bp	334	309
Peak_Molarity	80.00	91.80
libSampleQC_DNA_Well	DNA_Library_set77/set1/C8.png	DNA_Library_set77/set1/D8.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set77/set1/C2.png	RNA_Library_set77/set1/D2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-02-28	2025-02-28
Sample_ID	BGKcLV46-25	BGKcLV46-26
RBP	EED	EED
Batch_ID	BGKcLV46	BGKcLV46
WB_result	53.800	68.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4670	4671

Sequencing Information

	BGKcLV46-25	BGKcLV46-26
Sample_ID	BGKcLV46-25	BGKcLV46-26
Sample Name	EED-BGKcLV46-25	EED-BGKcLV46-26
Pool ID	Pool-250312	Pool-250312
LocalServer_folder	set77	set77
total_reads	60,441,457	47,989,574
total_aligned_reads	57,316,345	45,044,676
unique_aligned_reads	52,808,938	41,436,336
percent_uniqueAligned	0.87372	0.86344
correlation_replicates	0.997212	0.997212
spikein_reads	188,176	81,358
percent_spikeins	0.00311	0.00170
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3375	3376

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
EED-BGKcLV46-25_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3375	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32156
EED-BGKcLV46-25_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3375	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32206
EED-BGKcLV46-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3375					GRCh38	V40	EED-BGKcLV46-25_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz,EED-BGKcLV46-25_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32256
EED-BGKcLV46-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3375					GRCh38	V40	EED-BGKcLV46-25_Aligned.sortedByCoord.out.bam		ENCORE2	32306
EED-BGKcLV46-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3375					GRCh38	V40	EED-BGKcLV46-25_Aligned.sortedByCoord.out.bam		ENCORE2	32356
EED-BGKcLV46-25_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3375					GRCh38	V40	EED-BGKcLV46-25_Aligned.sortedByCoord.out.bam		ENCORE2	32406
EED-BGKcLV46-25_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3375					GRCh38	V40	EED-BGKcLV46-25_Aligned.sortedByCoord.out.bam		ENCORE2	32456
EED-BGKcLV46-25_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3375					GRCh38	V40	EED-BGKcLV46-25_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz,EED-BGKcLV46-25_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32506
EED-BGKcLV46-26_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3376	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32157
EED-BGKcLV46-26_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3376	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32207
EED-BGKcLV46-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3376					GRCh38	V40	EED-BGKcLV46-26_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz,EED-BGKcLV46-26_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32257
EED-BGKcLV46-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3376					GRCh38	V40	EED-BGKcLV46-26_Aligned.sortedByCoord.out.bam		ENCORE2	32307
EED-BGKcLV46-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3376					GRCh38	V40	EED-BGKcLV46-26_Aligned.sortedByCoord.out.bam		ENCORE2	32357
EED-BGKcLV46-26_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3376					GRCh38	V40	EED-BGKcLV46-26_Aligned.sortedByCoord.out.bam		ENCORE2	32407
EED-BGKcLV46-26_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3376					GRCh38	V40	EED-BGKcLV46-26_Aligned.sortedByCoord.out.bam		ENCORE2	32457
EED-BGKcLV46-26_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3376					GRCh38	V40	EED-BGKcLV46-26_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz,EED-BGKcLV46-26_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32507