EED RNA-Seq in HepG2

General Information


RBP	EED
Cell_Line	HepG2
Method	CRISPR
Exp_Name	EED-BGHcLV45-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV45
Pool ID	Pool-241205
Local_Set_Name	set76
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EED-BGHcLV45-27
Rep2	EED-BGHcLV45-28
CN1	NT-BGHcLV45-1
CN2	NT-BGHcLV45-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	79.5
Rep2_WB	63.0
Antibody Cat#	85322S
Antibody Lot#	lot# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1622

Experiment Information (Status: Submitting)

	BGHcLV45-27	BGHcLV45-27	BGHcLV45-28	BGHcLV45-28
idx	1217	0	1217	0
TRCN#_or_BGC#	BGC#0000570	BGC#0000570	BGC#0000570	BGC#0000570
shRNA_or_gRNA_sequence	CAATATTTGGAGGCGTAGAA	CAATATTTGGAGGCGTAGAA	CAATATTTGGAGGCGTAGAA	CAATATTTGGAGGCGTAGAA
PAM	GGG	GGG	GGG	GGG
Name	EED_90	EED_90	EED_90	EED_90
Sample_ID	BGHcLV45-27	BGHcLV45-27	BGHcLV45-28	BGHcLV45-28
transduction_Date	10/1/24	10/1/24	10/1/24	10/1/24
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	CTGGTGGCAATATTTGGAGG
RT-qPCR_primer-R	GAATGATCCATACCACAGGACATT
protein_conc	4291	4291	3750	3750
WB_result	79.5	NO CLEAR BAND	63.0
Ave_WB
WB_DONE_date	10/10/24	11/7/24
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	9715	9717	9716	9718

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV45-27	BGHcLV45-27	BGHcLV45-28	BGHcLV45-28
Sample_ID	BGHcLV45-27	BGHcLV45-27	BGHcLV45-28	BGHcLV45-28
Sample Name
Sample Name	EED-BGHcLV45-27		EED-BGHcLV45-28
RBP	EED	EED	EED	EED
Cell_Line	HepG2	HepG2	HepG2	HepG2
Exp UID
Status	Submitting	NotSatisfied	Submitting	NotSatisfied
Status_date	2025-04-21	2024-11-25	2025-04-21	2024-11-25
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	13702	13738	13703	13739

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV45-27	BGHcLV45-28
Sample #	17	18
Sample Name	EED-BGHcLV45-27	EED-BGHcLV45-28
Sample_Name_Alias
Index Well Position	A09	B09
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-12-02	2024-12-02
Lib_ID	Lib-241202	Lib-241202
Tecan_Location
Tecan
Tecan_date
Size_bp	285	286
Peak_Molarity	84.50	72.80
libSampleQC_DNA_Well	DNA_Library_set76/set1/A9.png	DNA_Library_set76/set1/B9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set76/set1/A3.png	RNA_Library_set76/set1/B3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-12-05	2024-12-05
Sample_ID	BGHcLV45-27	BGHcLV45-28
RBP	EED	EED
Batch_ID	BGHcLV45	BGHcLV45
WB_result	79.500	63.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4626	4627

Sequencing Information

	BGHcLV45-27	BGHcLV45-28
Sample_ID	BGHcLV45-27	BGHcLV45-28
Sample Name	EED-BGHcLV45-27	EED-BGHcLV45-28
Pool ID	Pool-241205	Pool-241205
LocalServer_folder	set76	set76
total_reads	37,283,096	32,178,385
total_aligned_reads	33,159,866	28,462,742
unique_aligned_reads	31,160,996	26,762,159
percent_uniqueAligned	0.83579	0.83168
correlation_replicates	0.999378	0.999378
spikein_reads	57,848	28,588
percent_spikeins	0.00155	0.00089
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3337	3338

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-BGHcLV45-27_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3337	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31826
EED-BGHcLV45-27_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3337	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31868
EED-BGHcLV45-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3337					GRCh38	V40	EED-BGHcLV45-27_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz,EED-BGHcLV45-27_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31910
EED-BGHcLV45-27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3337					GRCh38	V40	EED-BGHcLV45-27_Aligned.sortedByCoord.out.bam		ENCORE2	31952
EED-BGHcLV45-27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3337					GRCh38	V40	EED-BGHcLV45-27_Aligned.sortedByCoord.out.bam		ENCORE2	31994
EED-BGHcLV45-27_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3337					GRCh38	V40	EED-BGHcLV45-27_Aligned.sortedByCoord.out.bam		ENCORE2	32036
EED-BGHcLV45-27_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3337					GRCh38	V40	EED-BGHcLV45-27_Aligned.sortedByCoord.out.bam		ENCORE2	32078
EED-BGHcLV45-27_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3337					GRCh38	V40	EED-BGHcLV45-27_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz,EED-BGHcLV45-27_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32120
EED-BGHcLV45-28_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3338	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31827
EED-BGHcLV45-28_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3338	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31869
EED-BGHcLV45-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3338					GRCh38	V40	EED-BGHcLV45-28_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz,EED-BGHcLV45-28_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31911
EED-BGHcLV45-28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3338					GRCh38	V40	EED-BGHcLV45-28_Aligned.sortedByCoord.out.bam		ENCORE2	31953
EED-BGHcLV45-28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3338					GRCh38	V40	EED-BGHcLV45-28_Aligned.sortedByCoord.out.bam		ENCORE2	31995
EED-BGHcLV45-28_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3338					GRCh38	V40	EED-BGHcLV45-28_Aligned.sortedByCoord.out.bam		ENCORE2	32037
EED-BGHcLV45-28_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3338					GRCh38	V40	EED-BGHcLV45-28_Aligned.sortedByCoord.out.bam		ENCORE2	32079
EED-BGHcLV45-28_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3338					GRCh38	V40	EED-BGHcLV45-28_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz,EED-BGHcLV45-28_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32121