GATA1 RNA-Seq in K562

General Information


RBP	GATA1
Cell_Line	K562
Method	CRISPR
Exp_Name	GATA1-BGKcLV53-K562
ENCODE_series_ID
Batch_ID	BGKcLV53
Pool ID	Pool-260528
Local_Set_Name	set82
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	GATA1-BGKcLV53-59
Rep2	GATA1-BGKcLV53-60
CN1	NT-BGKcLV53-1
CN2	NT-BGKcLV53-2
Rep1_qPCR	12.0
Rep2_qPCR	28.4
Rep1_WB	88.8
Rep2_WB	91.3
Antibody Cat#	710049
Antibody Lot#	RI243501
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1735

Experiment Information (Status: Submitting)

	BGKcLV53-59	BGKcLV53-60
idx	0	0
TRCN#_or_BGC#	BGC#0001508	BGC#0001508
shRNA_or_gRNA_sequence	TGCGGCACTGGCCTACTACA	TGCGGCACTGGCCTACTACA
PAM	GGG	GGG
Name	GATA1-90	GATA1-90
Sample_ID	BGKcLV53-59	BGKcLV53-60
transduction_Date	2/24/26	2/24/26
days	D6	D6
RBP_name	GATA1	GATA1
qPCR_result	12.0	28.4
Ave_qPCR	20.2
RT-qPCR_primer-F	aggccactacctatgcaacg
RT-qPCR_primer-R	cctgcccgtttactgacaat
protein_conc	921	650
WB_result	88.8	91.3
Ave_WB
WB_DONE_date	3/20/26,3/12/26
MW	43kd
IP
antibody_Cat#	710049	RI243501
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	6421	6422

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
GATA1	Product_ID: 710049 Lot_ID: RI243501 Source: Thermo Fisher Target Name: GATA1-human

Experiment Status

	BGKcLV53-59	BGKcLV53-60
Sample_ID	BGKcLV53-59	BGKcLV53-60
Sample Name
Sample Name	GATA1-BGKcLV53-59	GATA1-BGKcLV53-60
RBP	GATA1	GATA1
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2026-10-30	2026-10-30
Project	ENCORE2	ENCORE2
Note
ID	14794	14795

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV53-59	BGKcLV53-60
Sample #	45	46
Sample Name	GATA1-BGKcLV53-59	GATA1-BGKcLV53-60
Sample_Name_Alias
Index Well Position	C07	D07
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2026-05-26	2026-05-26
Lib_ID	Lib-260526	Lib-260526
Tecan_Location
Tecan
Tecan_date
Size_bp	286	290
Peak_Molarity	63.50	53.90
libSampleQC_DNA_Well	DNA_Library_set82/set2/C10.png	DNA_Library_set82/set2/D10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set82/set2/C7.png	RNA_Library_set82/set2/D7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2026-05-27	2026-05-27
Sample_ID	BGKcLV53-59	BGKcLV53-60
RBP	GATA1	GATA1
Batch_ID	BGKcLV53	BGKcLV53
WB_result	88.800	91.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4884	4885

Sequencing Information

	BGKcLV53-59	BGKcLV53-60
Sample_ID	BGKcLV53-59	BGKcLV53-60
Sample Name	GATA1-BGKcLV53-59	GATA1-BGKcLV53-60
Pool ID	Pool-260528	Pool-260528
LocalServer_folder	set82	set82
total_reads	26,158,590	30,018,713
total_aligned_reads	19,151,859	25,484,245
unique_aligned_reads	17,743,564	23,678,634
percent_uniqueAligned	0.67831	0.78880
correlation_replicates	0.999786	0.999786
spikein_reads	41,444	47,572
percent_spikeins	0.00158	0.00158
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	3585	3586

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
GATA1-BGKcLV53-59_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3585	NovaSeq6000	100	paired-ended	1				NT-BGKcLV53-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGKcLV53-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33668
GATA1-BGKcLV53-59_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3585	NovaSeq6000	100	paired-ended	2				NT-BGKcLV53-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGKcLV53-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33726
GATA1-BGKcLV53-59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3585					GRCh38	V40	GATA1-BGKcLV53-59_R1.filtered.trimmed.paired.fastq.gz,GATA1-BGKcLV53-59_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33784
GATA1-BGKcLV53-59_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3585					GRCh38	V40	GATA1-BGKcLV53-59_Aligned.sortedByCoord.out.bam		ENCORE2	33842
GATA1-BGKcLV53-59_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3585					GRCh38	V40	GATA1-BGKcLV53-59_Aligned.sortedByCoord.out.bam		ENCORE2	33900
GATA1-BGKcLV53-59_Signal.Unique.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3585					GRCh38	V40	GATA1-BGKcLV53-59_Aligned.sortedByCoord.out.bam		ENCORE2	33958
GATA1-BGKcLV53-59_Signal.Unique.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3585					GRCh38	V40	GATA1-BGKcLV53-59_Aligned.sortedByCoord.out.bam		ENCORE2	34016
GATA1-BGKcLV53-59_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3585					GRCh38	V40	GATA1-BGKcLV53-59_R1.filtered.trimmed.paired.fastq.gz,GATA1-BGKcLV53-59_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34074
GATA1-BGKcLV53-60_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3586	NovaSeq6000	100	paired-ended	1				NT-BGKcLV53-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGKcLV53-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33669
GATA1-BGKcLV53-60_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3586	NovaSeq6000	100	paired-ended	2				NT-BGKcLV53-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGKcLV53-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33727
GATA1-BGKcLV53-60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3586					GRCh38	V40	GATA1-BGKcLV53-60_R1.filtered.trimmed.paired.fastq.gz,GATA1-BGKcLV53-60_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33785
GATA1-BGKcLV53-60_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3586					GRCh38	V40	GATA1-BGKcLV53-60_Aligned.sortedByCoord.out.bam		ENCORE2	33843
GATA1-BGKcLV53-60_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3586					GRCh38	V40	GATA1-BGKcLV53-60_Aligned.sortedByCoord.out.bam		ENCORE2	33901
GATA1-BGKcLV53-60_Signal.Unique.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3586					GRCh38	V40	GATA1-BGKcLV53-60_Aligned.sortedByCoord.out.bam		ENCORE2	33959
GATA1-BGKcLV53-60_Signal.Unique.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3586					GRCh38	V40	GATA1-BGKcLV53-60_Aligned.sortedByCoord.out.bam		ENCORE2	34017
GATA1-BGKcLV53-60_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3586					GRCh38	V40	GATA1-BGKcLV53-60_R1.filtered.trimmed.paired.fastq.gz,GATA1-BGKcLV53-60_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34075