title: sRNA_mock_3_Plus_PNK

city: Urbana

first: Ruiying

last: Cheng

state: IL

address: B520 Chemical & Life Sciences Laboratory

department: School of Molecular & Cellular Biology

institute: The University of Illinois Urbana-Champaign

description: Library name: sRNA_mock_3_Plus_PNK

data_processing:
Small RNA sequencing (sRNA-seq) reads were processed using a standardized pipeline. Raw single-end reads were trimmed with Trim_Galore to remove adapter sequences and low-quality bases, and read quality was assessed using FastQC. Trimmed reads were aligned to the custom THP1_active_PolIIIgenes_100exp index using Bowtie2/2.3.5.1, and resulting SAM files were converted, sorted, and indexed as BAM files using SAMtools/1.9-IGB-gcc-4.9.4. Genome-normalized coverage tracks were generated using deepTools/3.2.1.  Reads counts at RNA central noncoding genes (gene body +- 50bp) were obtained with BEDTools/2.28.0 (coverage function, -counts mode).
Assembly: GRCh38.109
Supplementary files format and content: counts

growth_protocol: THP−1 cells were obtained from ATCC (Batch# 62454382) and propagated in T-75 flasks between 0.2 and 1 × 106 cells/mL in an RPMI-1640 (Catalog# 11875093, Gibco, Billings, MT, USA) growth medium. THP−1 experiments were conducted on cells between passage 10 and 15.

extract_protocol:
small RNA seq: Total steady-state small RNA was purified from equal numbers (~2 million cells per small RNA-seq experiment) of THP-1 monocytes using the mirVana™ PARIS™ RNA and Native Protein Purification Kit (Catalog# AM1556, Invitrogen) according to manufacturer's protocol for sRNA enrichment .
The small RNA were treated with or without Antartic Phosphatase and PNK and libraries were constructed with the NEBNext Small RNA Sample Prep kit (NEB).

treatment_protocol: control or POLR3G ASO are transfected using Lipofectamine™ RNAiMAX Transfection Reagent acroding to manufacturer's protocol, cells are collected

value: 200nM control ASO


title: PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 20 uM heme and 100 ng/ml LPS (rep2)

status: Public on Jul 09 2026

type: SRA

city: Debrecen

first: Laszlo

last: Nagy

address: Egyetem ter 1.

country: Hungary

institute: University of Debrecen

description: mm_BMDM_WT_PolII_20uM_heme_100ng_LPS_rep2

library_source: genomic

data_processing:
alignment to mm10 reference genome with BWA v0.7.10 using default parameters
bam generation with SAMtools v1.7 using default parameters
tag directory generation with HOMER's makeTagDirectory using -checkGC parameter
generation of coverage (bedgraph) files with HOMER's makeUCSCfile using -fsize 1e50 -norm parameters
Assembly: mm10
Supplementary files format and content: bedgraph

molecule: genomic DNA

organism: Mus musculus

source_name: mouse bone marrow derived macrophages

growth_protocol: Isolation and differentiation were completed as described earlier (Daniel et al., 2014). Isolated bone marrow-derived cells were differentiated for 6 days in the presence of L929 supernatant.

extract_protocol:
Mouse bone marrow-derived macrophages were cross-linked using DSG and formaldehyde-based double cross-linking method and processed for ChIP.
Libraries were prepared with the TruSeq ChIP library systems (Illumina) according to the manufacturer protocol.

treatment_protocol: Treatments of mouse bone marrow-derived macrophages occurred at Day7 of differentiation after an overnight incubation in fresh medium.

tag: cell type

value: bone marrow derived macrophages

tag: strain

tag: chip antibody

value: Rabbit polyclonal to RNA polymerase II CTD repeat YSPTSPS (phospho S2) (Abcam - ab5095)

tag: cell treatment

value: 20μΜ Hemin (Sigma 51280) +100ng/ml LPS-SM Ultrapure (Invivogen-LPS from S. minnesota R595)

tag: duration of_treatment_(hours)


title: PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 20 uM heme and 100 ng/ml LPS (rep1)

description: mm_BMDM_WT_PolII_20uM_heme_100ng_LPS_rep1


title: WOM_F15_2N_MH_D112

city: Nanjing

first: Xuan

last: Li

address: No. 666, Binjiang Avenue, Jiangbei New Area

country: China

institute: Nanjing Agricultural University

description:
Library name: D112
WOM_F15_2N_MH_D112

library_source: transcriptomic

data_processing:
Alignment was performed with STAR (v2.7.11a) against the reference genome using a pre-built STAR genome index. STAR was run with “--outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts” to generate sorted alignment files and gene-level count profiles. Gene-level expression quantification was carried out using RSEM (v1.3.1) with STAR-generated transcriptome BAM files as input (--paired-end --no-bam-output --alignments).
Assembly: Nasonia vitripennis reference genome (RefSeq No. GCF_009193385.2, NCBI GenBank)
Supplementary files format and content: Tab-delimited text file includes raw counts and tpm value for each sample

molecule: polyA RNA

organism: Nasonia vitripennis

source_name: Head

extract_protocol:
RNA extraction was performed using Quick-RNATM Tissue/Insect Microprep (Catalogue No. R2030 Zymo Research, Germany) (without DNase treatment). For sequencing, RNA was resuspended in 10 µL DNase/RNase-free water and the RNA concentration and purity was measured using a fluorometer (Qubit 2.0, Life Technologies); poor quality samples judged by A260/A280 and A260/A230 ratios were discarded. The extracted RNA was sent to Novogene (UK) Company Limited for sequencing. Novogene Hongkong prepared the sample library.
Unique index codes were added to each sample using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, USA). mRNA was purified from total RNA using poly-T magnetic beads, and libraries were prepared according to the manufacturer's instructions (Illumina).

tag: tissue

value: Head

tag: Sex

value: male

tag: age

value: 1 day after emergence

tag: genotype

value: WOM


title: WOM_F15_2N_MH_D113

description:
Library name: D113
WOM_F15_2N_MH_D113


title: WOM_F15_2N_MH_D114

description:
Library name: D114
WOM_F15_2N_MH_D114


title: PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 20 ng/ml IL-4 (rep2)

value: 20ng/mL IL-4 (Peprotech 214-14)


title: sRNA_mock_3_Minus_PNK

country: USA

description: Library name: sRNA_mock_3_Minus_PNK

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: treatment


title: PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 20 ng/ml IFNg (rep2)

value: 20ng/mL IFNgamma (Biotechne 485-MI-100)


title: sRNA_mock_2_Plus_PNK

description: Library name: sRNA_mock_2_Plus_PNK


title: PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 20 ng/ml IL-4 (rep1)


title: PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 1 uM ODN1286 (rep2)

value: 1μΜ ODN1826 (Invivogen tlrl-1826-1)


title: PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 20 ng/ml IFNg (rep1)


title: WOM_F15_2N_MA_D116

description:
Library name: D116
WOM_F15_2N_MA_D116

source_name: Abdomen

value: Abdomen


title: sRNA_mock_2_Minus_PNK

description: Library name: sRNA_mock_2_Minus_PNK


title: C100_5

city: Nantong,Jiangsu,China

first: Xiaorong

last: Zhou

state: Jiangsu province

address: 19 Qixiu Road

institute: Nantong University

description:
Library name: Sample 9
Column name in gene_fpkm.txt: C100_5

data_processing:
Differential expression analysis was performed using the DESeq2 R package, and the genes with adjusted p values < 0.05 and log fold change (logFC) > 1 or < -1 were designated as differentially expressed genes (DEGs).
Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of DEGs were performed using the clusterProfiler package (version 4.8.3) in R.
Enriched GO terms and KEGG pathways were filtered with adjusted P-value < 0.05 and q-value < 0.5. Gene Set Enrichment Analysis (GSEA) was performed using the clusterProfiler package
Assembly: mm10
Supplementary files format and content: csv

source_name: tumor

growth_protocol: All animal-related procedures were performed following the ethical guidelines of the Animal Experimentation Institution of Nantong University, and all animal experiments were approved by the Ethics Committee.

extract_protocol:
Tumors were collected three days after the third cycle of CTX treatment, washed with PBS, and submitted for RNA isolation, quality check, and subsequent RNA sequencing by the Novogene (Beijing, China) on the Illumina platform.
Tumors were collected three days after the third cycle of CTX treatment, washed with PBS, and submitted for RNA isolation, quality check, and subsequent RNA sequencing by the Novogene (Beijing, China) on the Illumina platform.

treatment_protocol: In the subcutaneous tumor formation experiment, 4T1 cells resuspended in 100 μL PBS buffer were inoculated into the subcutaneous mammary gland area of each mice (1×10⁶ cells). Nine days later, when the tumor volume reached approximately 100 mm³, the mice were randomly divided into three groups according to the experimental grouping designing. The control group was intraperitoneally injected with 100 μL PBS, and the experimental groups were intraperitoneally injected with 100 or 140 mg/kg CTX in 100 μL PBS, respectively. All groups were injected once every 6 days. On the third day after the third treatment cycle, the mice were euthanized, and the tumor tissues were harvested for bulk RNA sequencing and scRNA-seq.

value: tumor

value: TNBC cell

value: 100mg/kg CTX


title: WOM_F15_2N_MH_D115

description:
Library name: D115
WOM_F15_2N_MH_D115


title: PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 1 uM ODN1286 (rep1)


title: WOM_F15_2N_MA_D117

description:
Library name: D117
WOM_F15_2N_MA_D117


title: PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 1 ug/ml R848 (rep2)

value: 1μg/mL (Invivogen tlrl-r848-5)


title: PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 1 ug/ml R848 (rep1)


title: WOM_F15_2N_MA_D118

description:
Library name: D118
WOM_F15_2N_MA_D118


title: PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 10 ug/ml HMW:PIC (rep2)

value: 10μg/mL (Invivogen tlrl-pic)


title: sRNA_mock_1_Minus_PNK

description: Library name: sRNA_mock_1_Minus_PNK

value: 200nM control ASO


title: PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 10 ug/ml HMW:PIC (rep1)

value: bone marrow derived macrophages


title: WOM_F3_2N_MH_D11

description:
Library name: D11
WOM_F3_2N_MH_D11


title: sRNA_mock_1_Plus_PNK

description: Library name: sRNA_mock_1_Plus_PNK


title: PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 10 ng/ml IFNb (rep2)

value: Rabbit polyclonal to RNA polymerase II CTD repeat YSPTSPS (phospho S2) (Abcam - ab5095)

value: 10ng/mL IFNbeta (Biotechne 8234-MB)


title: sRNA_G8_3_Plus_PNK

description: Library name: sRNA_G8_3_Plus_PNK


title: WOM_F3_2N_MA_D16

description:
Library name: D16
WOM_F3_2N_MA_D16


title: PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 10 ng/ml IFNb (rep1)


title: PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 100 uM heme (rep2)

value: 100μΜ Hemin (Sigma 51280)


title: sRNA_G8_3_Minus_PNK

description: Library name: sRNA_G8_3_Minus_PNK


title: PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 100 uM heme (rep1)


title: WOM_F2_2N_FH_D24

description:
Library name: D24
WOM_F2_2N_FH_D24

value: Head

value: female


title: PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 100 ng/ml LPS (rep2)

value: 100ng/ml LPS-SM Ultrapure (Invivogen-LPS from S. minnesota R595)


title: WOM_F2_2N_FA_D29

description:
Library name: D29
WOM_F2_2N_FA_D29

value: 1 day after emergence

value: WOM


title: sRNA_G8_2_Plus_PNK

description: Library name: sRNA_G8_2_Plus_PNK


title: PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 100 ng/ml LPS (rep1)


title: BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages treated with 20 ng/ml IL-4 (rep2)

value: a-Bach1 (gift from Dr. C.G. Spilianakis -IMBB-FORTH)

value: 20ng/mL IL-4 (Peprotech 214-14)


title: sRNA_G8_2_Minus_PNK

description: Library name: sRNA_G8_2_Minus_PNK


title: BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages treated with 20 ng/ml IL-4 (rep1)


title: WOM_F2_2N_FA_D30

description:
Library name: D30
WOM_F2_2N_FA_D30

value: Abdomen


title: BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages (rep4, control of IL4-treated sample)

value: No treatment


title: sRNA_G8_1_Plus_PNK

description: Library name: sRNA_G8_1_Plus_PNK


title: WOM_F3_1N_MH_D4

description:
Library name: D4
WOM_F3_1N_MH_D4

value: male


title: BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages treated with 100 ng/ml LPS (rep2)


title: sRNA_G8_1_Minus_PNK

description: Library name: sRNA_G8_1_Minus_PNK


title: WOM_F2_3N_FH_D31

description:
Library name: D31
WOM_F2_3N_FH_D31


title: BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages (rep3, control of IL4-treated sample)


title: BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages (rep6, control of LPS-treated sample)


title: BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages treated with 100 ng/ml LPS (rep1)


title: sRNA_E4_3_Plus_PNK

description: Library name: sRNA_E4_3_Plus_PNK


title: BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages (rep5, control of LPS-treated sample)


title: WOM_F2_3N_FH_D32

description:
Library name: D32
WOM_F2_3N_FH_D32


title: HDAC1 ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages (rep2)

description: mm_BMDM_Bach1KO_HDAC1_ChIPseq_unstim_rep2

value: Anti-HDAC1 antibody (Abcam- ab7028)


title: sRNA_E4_3_Minus_PNK

description: Library name: sRNA_E4_3_Minus_PNK


title: HDAC1 ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages (rep1)

description: mm_BMDM_Bach1KO_HDAC1_ChIPseq_unstim_rep1


title: WOM_F2_3N_FH_D33

description:
Library name: D33
WOM_F2_3N_FH_D33


title: sRNA_E4_2_Plus_PNK

description: Library name: sRNA_E4_2_Plus_PNK


title: HDAC1 ChIP-seq in wild type mouse bone marrow derived macrophages (rep1)


title: HDAC1 ChIP-seq in wild type mouse bone marrow derived macrophages (rep2)


title: WOM_F14_3N_FH_D83B

description:
Library name: D83B
WOM_F14_3N_FH_D83B


title: BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages treated with 100 uM heme (rep2)


title: sRNA_E4_2_Minus_PNK

description: Library name: sRNA_E4_2_Minus_PNK


title: BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages treated with 100 uM heme (rep1)


title: WOM_F14_3N_FA_D89

description:
Library name: D89
WOM_F14_3N_FA_D89


title: BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages (rep8)


title: sRNA_E4_1_Plus_PNK

description: Library name: sRNA_E4_1_Plus_PNK


title: BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages (rep7)


title: WOM_F3_1N_MA_D6

description:
Library name: D6
WOM_F3_1N_MA_D6


title: BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages (rep2)


title: sRNA_E4_1_Minus_PNK

description: Library name: sRNA_E4_1_Minus_PNK


title: WOM_F14_2N_FA_D98

description:
Library name: D98
WOM_F14_2N_FA_D98


title: BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages (rep1)


title: ATAC-seq of day 4 Ly6C low cell populations after CTX injury in Bach1 LysMCre TA muscle samples (rep2)

description: mm_muscle_Bach1_LysMCre_ATAC_CTX_D4_Ly6C_Low_Rep2

source_name: tibialis anterior (TA) muscle

growth_protocol: Tiisue extraction,digestion and FACS-based purification of Ly6C+ and Ly6C- macrophages from CTX-injured TA muscles

extract_protocol:
Mice were anaesthetized with isoflurane (adjusted flow rate or concentration to 1.5%) and 50 µl of cardiotoxin (10x10-6 M in PBS) (Latoxan) was injected in the tibialis anterior (TA) muscle. Muscles were recovered for flow cytometry analysis at day 1,2 and 4 post-injury and were dissociated in RPMI containing 0.2% collagenase B (Roche Diagnostics GmbH) at 37°C for 1 hour and filtered through a 100 µm and a 40 µm filter. CD45+ cells were isolated using magnetic sorting (Miltenyi Biotec). For FACS, macrophages were treated with Fcγ receptor blocking antibodies and with 10% normal rat serum: normal mouse serum 1:1 mix, then stained with a combination of PE-conjugated anti-Ly6C antibody (HK1.4, eBioscience), APC-conjugated F4/80 antibody (BM8, eBioscience) and FITC-conjugated Ly6G antibody (1A8, Biolegend). Ly6Chigh F4/80low macrophages, Ly6Clow F4/80high macrophages and Ly6Ghigh Ly6Cint F4/80- neutrophils were quantified and sorted. For ATAC-seq experiment, ATAC-seq lysis buffer was added, followed by DNA tagmentation according to Buenrostro  et al (PMID: 25559105).
Nextera DNA Library Prep Kit was used for library generation according to manufacturer's protocol.

treatment_protocol: Intramuscular injection of 50 µl of 12 µM cardiotoxin (CTX, L8102-1MG, Latoxan) for 1,2 or 4 days.

value: Bach1 fl/fl;LysM Cre+ (Myeloid specific conditional KO)

value: Ly6C- monocytes from TA muscle

tag: duration of treatment (days)


title: sRNA_con3_Plus_PNK

description: Library name: sRNA_con3_Plus_PNK


title: ATAC-seq of day 4 Ly6C low cell populations after CTX injury in Bach1 LysMCre TA muscle samples (rep1)

description: mm_muscle_Bach1_LysMCre_ATAC_CTX_D4_Ly6C_Low_Rep1

value: Intramuscular injection of 50 µl of 12 µM cardiotoxin (CTX, L8102-1MG, Latoxan)


title: WOM_F14_2N_FA_D99

description:
Library name: D99
WOM_F14_2N_FA_D99


title: sRNA_con3_Minus_PNK

description: Library name: sRNA_con3_Minus_PNK


title: ATAC-seq of day 4 Ly6C high cell populations after CTX injury in Bach1 LysMCre TA muscle samples (rep2)

description: mm_muscle_Bach1_LysMCre_ATAC_CTX_D4_Ly6C_High_Rep2

value: Ly6C+ monocytes from TA muscle


title: WOM_F14_2N_FA_D100

description:
Library name: D100
WOM_F14_2N_FA_D100


title: ATAC-seq of day 4 Ly6C high cell populations after CTX injury in Bach1 LysMCre TA muscle samples (rep1)

description: mm_muscle_Bach1_LysMCre_ATAC_CTX_D4_Ly6C_High_Rep1


title: ATAC-seq of day 2 Ly6C low cell populations after CTX injury in Bach1 LysMCre TA muscle samples (rep2)

description: mm_muscle_Bach1_LysMCre_ATAC_CTX_D2_Ly6C_Low_Rep2


title: ATAC-seq of day 2 Ly6C low cell populations after CTX injury in Bach1 LysMCre TA muscle samples (rep1)

description: mm_muscle_Bach1_LysMCre_ATAC_CTX_D2_Ly6C_Low_Rep1


title: WOM_F15_1N_MH_D101

description:
Library name: D101
WOM_F15_1N_MH_D101


title: ATAC-seq of day 2 Ly6C high cell populations after CTX injury in Bach1 LysMCre TA muscle samples (rep2)

description: mm_muscle_Bach1_LysMCre_ATAC_CTX_D2_Ly6C_High_Rep2


title: sRNA_con2_Plus_PNK

description: Library name: sRNA_con2_Plus_PNK


title: sRNA_con2_Minus_PNK

description: Library name: sRNA_con2_Minus_PNK


title: ATAC-seq of day 2 Ly6C high cell populations after CTX injury in Bach1 LysMCre TA muscle samples (rep1)

description: mm_muscle_Bach1_LysMCre_ATAC_CTX_D2_Ly6C_High_Rep1


title: WOM_F3_1N_MA_D7

description:
Library name: D7
WOM_F3_1N_MA_D7


title: ATAC-seq of day 1 Ly6C high cell populations after CTX injury in Bach1 LysMCre TA muscle samples (rep3)

description: mm_muscle_Bach1_LysMCre_ATAC_CTX_D1_Ly6C_High_Rep3


title: sRNA_con1_Plus_PNK

description: Library name: sRNA_con1_Plus_PNK


title: ATAC-seq of day 1 Ly6C high cell populations after CTX injury in Bach1 LysMCre TA muscle samples (rep2)

description: mm_muscle_Bach1_LysMCre_ATAC_CTX_D1_Ly6C_High_Rep2


title: WOM_F15_1N_MH_D102

description:
Library name: D102
WOM_F15_1N_MH_D102


title: sRNA_con1_Minus_PNK

description: Library name: sRNA_con1_Minus_PNK


title: ATAC-seq of day 4 Ly6C low cell populations after CTX injury in control TA muscle samples (rep2)

description: mm_muscle_Bach1_WT_ATAC_CTX_D4_Ly6C_Low_Rep2

value: Bach1 fl/fl (Control)


title: WOM_F15_1N_MH_D103

description:
Library name: D103
WOM_F15_1N_MH_D103


title: ATAC-seq of day 4 Ly6C low cell populations after CTX injury in control TA muscle samples (rep1)

description: mm_muscle_Bach1_WT_ATAC_CTX_D4_Ly6C_Low_Rep1


title: ATAC-seq of day 1 Ly6C high cell populations after CTX injury in Bach1 LysMCre TA muscle samples (rep1)

description: mm_muscle_Bach1_LysMCre_ATAC_CTX_D1_Ly6C_High_Rep1


title: sRNA_A7_3_Plus_PNK

description: Library name: sRNA_A7_3_Plus_PNK


title: Biol Rep 4 Treg

city: Bonn

first: Dirk

last: Baumjohann

state: NRW

address: Venusberg-Campus 1

department: Medical Clinic III

country: Germany

institute: University Hospital Bonn

description:
Library name: 8983 Treg
Column name in Raw_counts_All_Samples.txt: DE52NGSUKBR147356

data_processing:
Raw sequencing reads in FASTQ format were subjected to quality control using FastQC (v0.12.1).
Adapter sequences and low-quality bases were trimmed using Trimmomatic (v0.39).
Clean reads were aligned to the Mus musculus reference genome (GRCm39, Ensembl release 104) using HISAT2 (v2.2.1) with default parameters.
Read counts per gene were generated using featureCounts (v2.0.1) from the Subread package, based on Ensembl gene annotations.
Assembly: GRCm39 (Ensembl release 104)
Supplementary files format and content: Tab-delimited text file includes raw counts per gene for each sample.

source_name: CD4 T cells

growth_protocol: Treg, Tfr, and Tfh cell subsets were generated in vitro from naive CD4+ T cells obtained from GREAT.Smart-17A.FoxP3hCD2 triple-reporter donor mice.

extract_protocol:
After 3.5 days of cell culture, T cells were harvested, stained, and sorted on a BD FACSAriaFusion cell sorter for FoxP3+CXCR5– (Treg), FoxP3+CXCR5+ (Tfr), and Foxp3–CXCR5+(Tfh) cells among viable CD8–CD19–CD4+ lymphocytes using a 70-micron nozzle. RNA was isolated using TRIzol™ LS Reagent (Invitrogen, #10296028) according to the manufacturer’s instructions. RNA was cleaned up with a RNeasy Mini Kit (catalog #74104) according to the manufacturer’s instructions.
The sequencing library was prepared according to manufacturer´s guidelines with the QuantSeq FWD 3´-mRNA-Seq Kit from Lexogen using 50 ng total RNA as input. Libraries were single-end sequenced with 1x100 bp on a S1 flow cell of an Illumina NovaSeq 6000 instrument to a depth of 10 M raw reads on average at the NGS Core Facility of University Hospital Bonn

value: CD4 T cells

tag: culture condition

value: Treg

value: GREAT (Ifngtm3.1Lky) Smart-17A (Il17atm1.1Lky) Foxp3hCD2 (Foxp3tm1(CD2/CD52)Shori)


title: WOM_F15_1N_MH_D104

description:
Library name: D104
WOM_F15_1N_MH_D104

value: Head


title: ATAC-seq of day 4 Ly6C high cell populations after CTX injury in control TA muscle samples (rep2)

description: mm_muscle_Bach1_WT_ATAC_CTX_D4_Ly6C_High_Rep2


title: ATAC-seq of day 2 Ly6C low cell populations after CTX injury in control TA muscle samples (rep2)

description: mm_muscle_Bach1_WT_ATAC_CTX_D2_Ly6C_Low_Rep2


title: sRNA_A7_3_Minus_PNK

description: Library name: sRNA_A7_3_Minus_PNK


title: WOM_F15_1N_MH_D105

description:
Library name: D105
WOM_F15_1N_MH_D105

value: 1 day after emergence


title: ATAC-seq of day 4 Ly6C high cell populations after CTX injury in control TA muscle samples (rep1)

description: mm_muscle_Bach1_WT_ATAC_CTX_D4_Ly6C_High_Rep1


title: ATAC-seq of day 2 Ly6C low cell populations after CTX injury in control TA muscle samples (rep1)

description: mm_muscle_Bach1_WT_ATAC_CTX_D2_Ly6C_Low_Rep1


title: sRNA_A7_2_Plus_PNK

description: Library name: sRNA_A7_2_Plus_PNK


title: WOM_F15_1N_MA_D106

description:
Library name: D106
WOM_F15_1N_MA_D106

value: WOM


title: ATAC-seq of day 2 Ly6C high cell populations after CTX injury in control TA muscle samples (rep1)

description: mm_muscle_Bach1_WT_ATAC_CTX_D2_Ly6C_High_Rep1


title: sRNA_A7_2_Minus_PNK

description: Library name: sRNA_A7_2_Minus_PNK


title: ATAC-seq of day 1 Ly6C high cell populations after CTX injury in control TA muscle samples (rep3)

description: mm_muscle_Bach1_WT_ATAC_CTX_D1_Ly6C_High_Rep3


title: ATAC-seq of day 2 Ly6C high cell populations after CTX injury in control TA muscle samples (rep2)

description: mm_muscle_Bach1_WT_ATAC_CTX_D2_Ly6C_High_Rep2


title: WOM_F15_1N_MA_D107

description:
Library name: D107
WOM_F15_1N_MA_D107


title: ATAC-seq of day 1 Ly6C high cell populations after CTX injury in control TA muscle samples (rep2)

description: mm_muscle_Bach1_WT_ATAC_CTX_D1_Ly6C_High_Rep2


title: WPL_LSL_1N_MA_B10

description:
Library name: B10
WPL_LSL_1N_MA_B10

value: WPL


title: sRNA_A7_1_Plus_PNK

description: Library name: sRNA_A7_1_Plus_PNK


title: ATAC-seq of day 1 Ly6C high cell populations after CTX injury in control TA muscle samples (rep1)

description: mm_muscle_Bach1_WT_ATAC_CTX_D1_Ly6C_High_Rep1


title: WOM_F15_1N_MA_D108

description:
Library name: D108
WOM_F15_1N_MA_D108


title: ATAC-seq in Bach1-deficient mouse bone marrow derived macrophages treated with 100 uM heme (rep2)

description: mm_BMDM_Bach1cKO_ATACseq_100mM_heme_1h_rep2

source_name: bone marrow derived macrophages

extract_protocol:
Mouse bone marrow-derived macrophages were lysed with the following lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL). After lysis, nuclei were subjected to tagmentation.
Nextera DNA Library Prep Kit was used for library generation according to manufacturer's protocol.

treatment_protocol: No treatment or 100mM Hemin treatment for 1 hour.

value: bone marrow derived macrophages

value: 100μΜ Hemin (Sigma 51280)

tag: duration of treatment (h)


title: sRNA_A4_3_Plus_PNK

description: Library name: sRNA_A4_3_Plus_PNK


title: WOM_F15_1N_MA_D109

description:
Library name: D109
WOM_F15_1N_MA_D109

value: Abdomen


title: ATAC-seq in Bach1-deficient mouse bone marrow derived macrophages veh (rep1)

value: Vehicle


title: sRNA_A7_1_Minus_PNK

description: Library name: sRNA_A7_1_Minus_PNK


title: WOM_F15_1N_MA_D110

description:
Library name: D110
WOM_F15_1N_MA_D110

value: male


title: ATAC-seq in Bach1-deficient mouse bone marrow derived macrophages veh (rep2)

value: Bach1 fl/fl;LysM Cre+ (Myeloid specific conditional KO)


title: ATAC-seq in Bach1-deficient mouse bone marrow derived macrophages treated with 100 uM heme (rep1)

description: mm_BMDM_Bach1cKO_ATACseq_100mM_heme_1h_rep1


title: HEK293T with RNASET2 KD, Palmitate treated, replicate 2

city: Austin

first: Alan

last: Lambowitz

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

description: Library name: KD_PA_2

data_processing:
Illumina TruSeq adapters and PCR primer sequences were trimmed from the reads with Cutadapt v2.8 (https://github.com/marcelm/cutadapt) (sequencing quality score cut-off at 20; p- value <0.01) and reads <15-nt after trimming were discarded. To minimize mismapping, we used a sequential mapping strategy. First, reads were mapped to the human mitochondrial genome (Ensembl GRCh38 Release 93) and the Escherichia coli genome (GeneBank: NC_000913) using HISAT2 v2.1.0 (https://github.com/DaehwanKimLab/hisat2) with customized settings (-k 10 --rfg 1,3 --rdg 1,3 --mp 4,2 --no-mixed --no-discordant -- no-spliced- alignment) to identify reads derived from mitochondrial and E. coli RNAs (denoted Pass 1). Unmapped reads from Pass1 were then mapped to a collection of customized references sequences for human sncRNAs (miRNA, tRNA, Y RNA, Vault RNA, 7SL RNA, 7SK RNA) and rRNAs (2.2-kb 5S rRNA repeats from the 5S rRNA cluster on chromosome 1 (1q42, Gene- Bank: X12811) and 43-kb 45S rRNA containing 5.8S, 18S and 28S rRNAs from clusters on chromosomes 13,14,15, 21, and 22 (GeneBank: U13369), using HISAT2 with the following settings -k 20 --rdg 1,3 --rfg 1,3 --mp 2,1 --no-mixed --no-discordant --no-spliced-alignment -- norc (denoted Pass 2). Unmapped reads from Pass 2 were then mapped to the human genome reference sequence (Ensembl GRCh38 Release 93) using HISAT2 with settings optimized for nonspliced mapping (-k 10 --rdg 1,3 --rfg 1,3 --mp 4,2 --no-mixed --no-discordant --no-spliced- alignment) (denoted Pass 3) followed by splice aware mapping (-k 10 --rdg 1,3 --rfg 1,3 --mp 4,2 --no-mixed --no-discordant --dta) (denoted Pass 4). For reads that mapped to multiple genomic loci with the same mapping score in passes 3 to 4, the alignment with the shortest distance between the two paired ends (i.e., the shortest read span) was selected. In the case of ties (i.e., reads with the same mapping score and read span), reads mapping to a chromosome were selected over reads mapping to scaffold sequences, and in other cases, the read was assigned randomly to one of the tied choices. The filtered multiply mapped reads were then combined with the uniquely mapped reads from Passes 3-4 by using SAMtools v1.10 (https://github.com/samtools/samtools).
To generate counts for different genomic features, the mapped reads were intersected with Ensembl GRCh38 Release 93 gene annotations plus the RNY5 gene and its 10 pseudogenes, which were not annotated in this release. Annotations for repeat elements were from RepBase (https://www.girinst.org/repbase/), and annotations for hairpin miRNA and mature miRNA were from miRBase (https://www.mirbase.org/). Coverage of each feature was calculated by BEDTools v2.29.2 (https://bedtools.readthedocs.io/en/latest/content/bedtools-suite.html). To avoid miscounting reads with embedded sncRNAs that were not filtered out in Pass 2 (e.g., snoRNAs), reads were first intersected with sncRNA annotations, and the remaining reads were then intersected with the annotations for protein-coding gene RNAs, lincRNAs, antisense RNAs, and other lncRNAs to get the read count for each annotated feature.
Read counts were normalized by using DESeq2 (https://github.com/thelovelab/DESeq2) with sample size factors estimated based on counts from nuclear protein-coding genes. Likelihood ratio test (LRT) was then used to identify any genes that show change in expression across datasets with different treatments in different cells.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Embryonic kidney

growth_protocol: HEK 293T cells were cultured in Dulbecco’s Modified Eagle Medium containing 4500 mg/L glucose and 110 mg/L pyruvate supplemented with 10% heat-inactivated FBS and 2 mM glutamine at 37 °C with 5% CO₂.

extract_protocol:
RNA was extracted using TRIzol and the Direct-zol RNA Miniprep kit (Zymo Research R2050).
Total RNA was prepared for TGIRT-seq library preparation using a two-fraction method. Briefly, following treatment with DNase I, rRNA was depleted (Ribocop depletion kit, Lexogen 144.24), and size fractionated into short (<200 nt) and long RNAs fractions according to RCC5 protocol. Long RNAs were fragmented to ~200 nucleotides (NEB Next RNA Fragmentation Module, New England Biolabs E6150S). Small and fragmented large RNAs were pooled prior to treatment with T4 Polynucleotide Kinase (Lucigen P0503K). Each step of RNA processing was evaluated and quantitated using an RNA 6000 Pico Chip mRNA assay on an Agilent 2100 Bioanalyzer. TGIRT-seq library construction was as previously described using the low salt template switching reaction buffer.

treatment_protocol: Actively growing cells (~60-65% confluency) were treated by supplementing growth media with 1 mM palmitic acid freshly complexed with 0.5 mM fatty acid-free BSA as a carrier or with 0.5 mM fatty acid-free BSA as vehicle control, for 8 hours.

value: Embryonic kidney

value: kidney epithelial cells

value: RNASET2 KD

value: Palmitate

tag: batch

tag: treatment time

value: 8 hours treatment


title: ATAC-seq in wild type mouse bone marrow derived macrophages treated with 100 uM heme (rep2)

value: Bach1 fl/fl (Control)


title: sRNA_A4_3_Minus_PNK

description: Library name: sRNA_A4_3_Minus_PNK


title: ATAC-seq in wild type mouse bone marrow derived macrophages treated with 100 uM heme (rep1)


title: WOM_F3_1N_MA_D8

description:
Library name: D8
WOM_F3_1N_MA_D8


title: ATAC-seq in wild type mouse bone marrow derived macrophages veh (rep2)


title: sRNA_A4_2_Plus_PNK

description: Library name: sRNA_A4_2_Plus_PNK


title: ATAC-seq in wild type mouse bone marrow derived macrophages veh (rep1)


title: WOM_F15_2N_MA_D119

description:
Library name: D119
WOM_F15_2N_MA_D119


title: sRNA_A4_2_Minus_PNK

description: Library name: sRNA_A4_2_Minus_PNK


title: ATAC-seq in Bach1-deficient mouse bone marrow derived macrophages unstim (rep1)

value: Bach1-/- (exon 3+4 deletion)

value: No treatment


title: WOM_F15_2N_MA_D120

description:
Library name: D120
WOM_F15_2N_MA_D120

value: 1 day after emergence


title: sRNA_A4_1_Plus_PNK

description: Library name: sRNA_A4_1_Plus_PNK


title: ATAC-seq in wild type mouse bone marrow derived macrophages unstim (rep2)

value: WT


title: ATAC-seq in Bach1-deficient mouse bone marrow derived macrophages unstim (rep2)


title: ATAC-seq in wild type mouse bone marrow derived macrophages unstim (rep1)


title: WOM_F3_1N_MA_D9

description:
Library name: D9
WOM_F3_1N_MA_D9

value: WOM


title: sRNA_A4_1_Minus_PNK

description: Library name: sRNA_A4_1_Minus_PNK


title: Day_5_KO1

city: Kyoto

first: Wooseok

last: Seo

address: Yoshida-Konoe-cho, Sakyo-ku

country: Japan

institute: Kyoto University Graduate School of Medicine

data_processing:
RNA-seq sequence reads were aligned to mouse reference genome release mm10 using HISAT2 (v2.1.0) with default parameters and produced bam files as outputs. Bam Files were used to count reads for genes by using HTSeq (v0.11.1) and produced tab-delimited text files as outputs.  Genome_build: mm10 (GRCm38)  Supplementary_files_format_and_content: *txt: Tab-delimited text files of counted reads for genes (mm10).
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: CD8+ T cells

growth_protocol: Non-applicable

extract_protocol:
Sorted cells were purified by using Trizol (Invitrogen) and Direct-zol RNA kit (Zymo Research) according to the manufacturer’s protocols.
Library construction was conducted by using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s protocol.
Libraries were sequenced to 50 bp read length on a HiSeq2500 (Illumina).

treatment_protocol: Non-applicable

value: peripheral CD8+ T cells

value: spleen


title: WOM_F3_1N_MA_D10

description:
Library name: D10
WOM_F3_1N_MA_D10

value: Abdomen


title: Day_5_KO2


title: Day_5_WT2


title: sRNA_3G_ASO3_Plus_PNK

description: Library name: sRNA_3G_ASO3_Plus_PNK

value: 200nM POLR3G ASO


title: Day_5_WT1


title: sRNA_3G_ASO3_Minus_PNK

description: Library name: sRNA_3G_ASO3_Minus_PNK


title: Day_0_WT2


title: WOM_F3_1N_MH_D1A

description:
Library name: D1A
WOM_F3_1N_MH_D1A

value: Head

value: male


title: Day_0_KO1


title: Day_0_KO2


title: WOM_F3_1N_MH_D1

description:
Library name: D1
WOM_F3_1N_MH_D1


title: sRNA_3G_ASO2_Plus_PNK

description: Library name: sRNA_3G_ASO2_Plus_PNK


title: WOM_F3_2N_MH_D12

description:
Library name: D12
WOM_F3_2N_MH_D12


title: sRNA_3G_ASO2_Minus_PNK

description: Library name: sRNA_3G_ASO2_Minus_PNK


title: KO2_Gfp-_CD25-

data_processing:
RNA-seq sequence reads were aligned to mouse reference genome release mm10 using HISAT2 (v2.1.0) with default parameters and produced bam files as outputs. Bam Files were used to count reads for genes by using HTSeq (v0.11.1) and produced tab-delimited text files as outputs.  Genome_build: mm10 (GRCm38)  Supplementary_files_format_and_content: *txt: Tab-delimited text files of counted reads for genes (mm10).
Genome_build: mm10

source_name: CD4+ T cells

value: peripheral CD4+ T cells


title: KO2_Gfp+_CD25-


title: WOM_F3_2N_MH_D13

description:
Library name: D13
WOM_F3_2N_MH_D13


title: KO2_Gfp+_CD25+


title: sRNA_3G_ASO1_Plus_PNK

description: Library name: sRNA_3G_ASO1_Plus_PNK


title: Day_0_WT1


title: KO1_Gfp-_CD25-


title: WOM_F3_2N_MH_D14

description:
Library name: D14
WOM_F3_2N_MH_D14


title: sRNA_3G_ASO1_Minus_PNK

description: Library name: sRNA_3G_ASO1_Minus_PNK


title: KO1_Gfp+_CD25-


title: KO1_Gfp+_CD25+


title: WOM_F3_2N_MH_D15

description:
Library name: D15
WOM_F3_2N_MH_D15


title: WT2_Gfp-_CD25-


title: WT2_Gfp+_CD25+


title: WOM_F3_2N_MA_D17

description:
Library name: D17
WOM_F3_2N_MA_D17


title: H2B-GFP AICS, 5D CHIR

city: Parkville

first: Kynan

middle: Thomas

last: Lawlor

state: VIC

address: Murdoch Children's Research Institute, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

description: Library name: A676

data_processing:
Files were processed using the nf-core RNA seq pipeline, version 3.12.0
Assembly: GRC38.96
Supplementary files format and content: CSV table of raw counts

source_name: differentiated iPCS cells

extract_protocol:
Thermo purelink RNA mini kit
Illumina stranded mRNA

treatment_protocol: Kidney differentation following Takasato et al 2015

value: differentiated iPCS cells

value: H2B-GFP AICS

value: mesoderm


title: WT1_Gfp-_CD25-


title: MAFB-mtagBFP;GATA3-mCherry, 5D CHIR

description: Library name: A672


title: WT1_Gfp+_CD25+


title: WOM_F3_2N_MA_D18

description:
Library name: D18
WOM_F3_2N_MA_D18


title: CD4+ T cells - KO_rep2

data_processing:
RNA-seq sequence reads were aligned to mouse reference genome release mm10 using HISAT2 (v2.1.0) with default parameters and produced bam files as outputs. Bam Files were used to count reads for genes by using HTSeq (v0.11.1) and produced tab-delimited text files as outputs.
Genome_build: mm10
Supplementary_files_format_and_content: *txt: Tab-delimited text files of counted reads for genes (mm10).

value: Satb1 conditional knockout


title: NG-hiPSC line1B, 5D CHIR

description: Library name: A668

value: NG-hiPSC line1B


title: WOM_F3_2N_MA_D19

description:
Library name: D19
WOM_F3_2N_MA_D19


title: CD4+ T cells - KO_rep1


title: CD4+ T cells - WT_rep2


title: H2B-GFP AICS, 4D CHIR

description: Library name: A664


title: CD4+ T cells - WT_rep1


title: WOM_F3_2N_MA_D20

description:
Library name: D20
WOM_F3_2N_MA_D20


title: MAFB-mtagBFP;GATA3-mCherry, 4D CHIR

description: Library name: A660


title: AbdB RNAi,RNA-seq,Rep3

city: New Orleans

first: Jun-yuan

last: Ji

state: LA

address: 1700 Tulane Avenue

department: Department of Biochemistry and Molecular Biology

institute: Tulane University

description:
Library name: AbdB RNAi 3
dcg_Bi-3

data_processing:
RNA-Star alignment to dm6 reference with default setting
Gathering counts with FeatureCount with default setting
DESeq2 to normalize counts and generate differential gene expression table with p.adj < 0.05 filter
Assembly: dm6
Supplementary files format and content: tab delimited table, count table

organism: Drosophila melanogaster

source_name: 3rd instar larval fat body

extract_protocol:
Total RNA was extracted by standard protocol with Trizol
The library was constructed by standard Illumina buck RNA-seq protocol

value: 3rd instar larval fat body

value: dCG-Gal4>AbdB RNAi


title: AbdB RNAi,RNA-seq,Rep2

description:
Library name: AbdB RNAi 2
dcg_Bi-2


title: WOM_F3_1N_MH_D3

description:
Library name: D3
WOM_F3_1N_MH_D3

value: 1 day after emergence


title: AbdB RNAi,RNA-seq,Rep1

description:
Library name: AbdB RNAi 1
dcg_Bi-1


title: WOM_F2_2N_FH_D21

description:
Library name: D21
WOM_F2_2N_FH_D21

value: female


title: AbdB_GFP-3

description: Library name: AbdB_GFP-3

data_processing:
nf-core/cutandrun for alignment and deduplication
MACS3 for peak calling and pileup
bdgToBigWig for convert pileuped file into bigwig file
Assembly: dm6
Supplementary files format and content: bigwig; pileuped, averaged and normalized target binding signal
Library strategy: CUT&Run

source_name: 3rd instar wing imaginal disc

extract_protocol: We utilized the CUT&RUN assay kit purchased from Cell Signaling Technology (#86652), using IgG from the kit as the negative control, along with the anti-GFP antibody obtained from Abcam (ab290).

value: 3rd instar wing imaginal disc


title: NG-hiPSC line1B, 4D CHIR

description: Library name: A656


title: AbdB_GFP-2

description: Library name: AbdB_GFP-2


title: sDLK_3

city: NEW YORK

first: hao

last: chen

state: NY

address: 413 E 69th ST

department: Brain and mind research institute

institute: Weill Cornell Medicine

description:
Library name: Sample14
mRNA expression in human oligodendrocytes

library_source: transcriptomic single cell

data_processing:
Gene counts were obtained by aligning reads to the mouse genome (mm10) with Cell Ranger software (v.3.1.0) (10× Genomics).
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than two cells, cells with a unique gene count over 8000 or less than 300, and cells with a high fraction of mitochondrial reads (>5%).
Potential doublet cells were predicted and removed using DoubletFinder for each sample.
SoupX was used to identify and remove ambient RNA from the dataset (Young et al., 2020)
Seurat v3.0.182 R package used for analysis
Assembly: GRCm38 (mm10) for mouse tissue and GRCh38 (hg38) for human tissue
Supplementary files format and content: barcodes.tsv.gz: cellular barcodes present in datase
Supplementary files format and content: features.tsv.gz: IDs of quantified genes
Supplementary files format and content: matrix.mtx.gz: a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the cellular barcodes.

molecule: nuclear RNA

source_name: human iPSC derived oligodendrocyte

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics)

value: human iPSC derived oligodendrocyte

value: Male


title: AbdB_GFP-1

description: Library name: AbdB_GFP-1


title: WOM_F2_2N_FH_D22

description:
Library name: D22
WOM_F2_2N_FH_D22

value: WOM


title: AbdB_IgG-3

description: Library name: AbdB_IgG-3


title: sDLK_2

description:
Library name: Sample13
mRNA expression in human oligodendrocytes


title: AbdB_IgG-2

description: Library name: AbdB_IgG-2


title: WOM_F2_2N_FH_D23

description:
Library name: D23
WOM_F2_2N_FH_D23


title: AbdB_IgG-1

description: Library name: AbdB_IgG-1


title: sDLK_1

description:
Library name: Sample12
mRNA expression in human oligodendrocytes


title: WOM_F2_2N_FH_D25

description:
Library name: D25
WOM_F2_2N_FH_D25


title: A673_NChIP-H3K9ac_SW39_rep2

city: Dallas

first: Laura

last: Banaszynski

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center

description: Library name: A673_NChIP-H3K9ac_SW39_rep2

data_processing:
The ChIP-seq reads were aligned to the hg38 human reference genome using the Bowtie2 aligner (Langmead and Salzberg, 2012) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 5-bp windows across the genome using deepTools for presentation as genome browser tracks  (Ramirez et al, 2016).
The seqeunce length was 50 for R1 and 50 for R2 for paired-end data from NextSeq 500. The sequence length was 150 for R1 and 150 for R2 for paired-end data from NovaSeq 6000.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: Ewing sarcoma cell lines were cultured in RPMI (sigma R7256) + 5-10% FBS + 2mM L-glutamine with pen/strep antibiotics.

extract_protocol:
Native ChIP was performed as described (Martire et al. 2019). Briefly, A673 cells were harvested and treated with Mnase, resulting in a population consisting mainly of mono- to trinucleosomes. Chromatin was isolated and used for ChIP according to standard procedures. Cross-linked ChIP was performed as described (Martire et al. 2019). Briefly, A673 cells were cross-linked with 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures.
ChIP-seq libraries were constructed according to the NEBNext protocol.

treatment_protocol: For inhibitor studies, cells were treated for 24 hours with small molecule inhibitors of CDK8 at the described concentrations (100nM for SW393109), or vehicle DMSO at the same final concentration.   For Ewing’s sarcoma cell lines engineered with the auxin inducible degron in the EWSR1-FLI1 fusion, cells were treated with 5-Ph-IAA for 24 hours at a final concentration of 300nM.

value: Ewing sarcoma cell line

value: H3K9ac:Abcam ab10812


title: Ctrl_3

description:
Library name: Sample11
mRNA expression in human oligodendrocytes

value: Ctrl


title: A673_NChIP-H3K9ac_DMSO_rep2

description: Library name: A673_NChIP-H3K9ac_DMSO_rep2

value: DMSO


title: A673_NChIP-H3K9ac_SW39_rep1

description: Library name: A673_NChIP-H3K9ac_SW39_rep1


title: WOM_F2_2N_FA_D26

description:
Library name: D26
WOM_F2_2N_FA_D26

value: Abdomen


title: A673_NChIP-H3K9ac_DMSO_rep1

description: Library name: A673_NChIP-H3K9ac_DMSO_rep1


title: Ctrl_2

description:
Library name: Sample10
mRNA expression in human oligodendrocytes


title: WOM_F2_2N_FA_D27

description:
Library name: D27
WOM_F2_2N_FA_D27


title: A673_EWSFLI-AID_NChIP-Input_DMSO

description: Library name: A673_EWSFLI-AID_NChIP-Input_DMSO

value: EWS-FLI AID


title: Ctrl_1

description:
Library name: Sample9
mRNA expression in human oligodendrocytes


title: A673_EWSFLI-AID_NChIP-H3K27ac_IAA_rep2

description: Library name: A673_EWSFLI-AID_NChIP-H3K27ac_IAA_rep2

value: IAA

value: H3K27ac:Active Motif #39133


title: WOM_F2_2N_FA_D28

description:
Library name: D28
WOM_F2_2N_FA_D28


title: A673_EWSFLI-AID_NChIP-H3K27ac_IAA_rep1

description: Library name: A673_EWSFLI-AID_NChIP-H3K27ac_IAA_rep1


title: bal_028

description:
Library name: sample28
novogene

data_processing:
reads were aligned to the Homo sapiens RCh38 (hg38) reference genome using STAR v2.7.x
follow novogene standard pipeline
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA was harvested by PureLink RNA Mini Kit (Invitrogen, Cat # 12183025), 500ng of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacture's protocol

value: iPSC derived human microglia like cells

value: Ctrl+Etoposide

value: male


title: A673_EWSFLI-AID_NChIP-H3K27ac_DMSO_rep2

description: Library name: A673_EWSFLI-AID_NChIP-H3K27ac_DMSO_rep2


title: WOM_F2_3N_FH_D34

description:
Library name: D34
WOM_F2_3N_FH_D34

value: Head

value: 1 day after emergence


title: bal_027

description:
Library name: sample27
novogene


title: A673_EWSFLI-AID_NChIP-H3K27ac_DMSO_rep1

description: Library name: A673_EWSFLI-AID_NChIP-H3K27ac_DMSO_rep1


title: A673_CnR-CDK8_SW39_rep2

description: Library name: A673_CnR-CDK8_SW39_rep2

data_processing:
The CUT&RUN reads were aligned to the hg38 human reference genome using the Bowtie2 aligner (Langmead and Salzberg, 2012) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 5-bp windows across the genome using deepTools for presentation as genome browser tracks  (Ramirez et al, 2016).
The seqeunce length was 50 for R1 and 50 for R2 for paired-end data from NextSeq 500. The sequence length was 150 for R1 and 150 for R2 for paired-end data from NovaSeq 6000.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Run

extract_protocol:
Samples were prepared according to the Epicypher CUT&RUN protocol.
CUT&RUN libraries were constructed according to the NEBNext protocol.

tag: antibody

value: CDK8 (Proteintech 22067-1-AP)


title: WOM_F2_3N_FH_D35

description:
Library name: D35
WOM_F2_3N_FH_D35

value: female


title: A673_CnR-CDK8_SW39_rep1

description: Library name: A673_CnR-CDK8_SW39_rep1

tag: cell type


title: bal_026

description:
Library name: sample26
novogene


title: A673_CnR-CDK8_DMSO_rep2

description: Library name: A673_CnR-CDK8_DMSO_rep2


title: WOM_F2_3N_FA_D36

description:
Library name: D36
WOM_F2_3N_FA_D36

tag: strain


title: A673_CnR-CDK8_DMSO_rep1

description: Library name: A673_CnR-CDK8_DMSO_rep1


title: bal_025

description:
Library name: sample25
novogene


title: A673_EWSFLI-AID_CnR-CDK8_IAA_rep2

description: Library name: A673_EWSFLI-AID_CnR-CDK8_IAA_rep2


title: A673_EWSFLI-AID_CnR-CDK8_IAA_rep1

description: Library name: A673_EWSFLI-AID_CnR-CDK8_IAA_rep1


title: WOM_F2_3N_FA_D37

description:
Library name: D37
WOM_F2_3N_FA_D37


title: bal_024

description:
Library name: sample24
novogene


title: A673_EWSFLI-AID_CnR-CDK8_DMSO_rep2

description: Library name: A673_EWSFLI-AID_CnR-CDK8_DMSO_rep2


title: WOM_F2_3N_FA_D38

description:
Library name: D38
WOM_F2_3N_FA_D38


title: A673_EWSFLI-AID_CnR-CDK8_DMSO_rep1

description: Library name: A673_EWSFLI-AID_CnR-CDK8_DMSO_rep1


title: bal_023

description:
Library name: sample23
novogene


title: A673_EWSFLI-AID_CnR-FLI_IAA_rep1

description: Library name: A673_EWSFLI-AID_CnR-FLI_IAA_rep1

value: FLI (Santa Cruz sc-53826)


title: WOM_F2_3N_FA_D39

description:
Library name: D39
WOM_F2_3N_FA_D39

value: WOM


title: bal_022

description:
Library name: sample22
novogene


title: A673_EWSFLI-AID_ATAC_IAA_rep3

description: Library name: A673_EWSFLI-AID_ATAC_IAA_rep3

data_processing:
The ATAC-seq reads were aligned to the hg38 human reference genome using the Bowtie2 aligner (Langmead and Salzberg, 2012) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 5-bp windows across the genome using deepTools for presentation as genome browser tracks  (Ramirez et al, 2016).
The seqeunce length was 50 for R1 and 50 for R2 for paired-end data.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Samples were prepared according to the Illumina Nextera protocol
Libraries were constructed according to the Illumina Nextera protocol.

treatment_protocol: Ewing’s sarcoma cell lines engineered with the auxin inducible degron in the EWSR1-FLI1 fusion were treated with 5-Ph-IAA for 24 hours at a final concentration of 300nM.

value: Ewing sarcoma cell line


title: A673_EWSFLI-AID_ATAC_IAA_rep2

description: Library name: A673_EWSFLI-AID_ATAC_IAA_rep2


title: WOM_F2_3N_FA_D40

description:
Library name: D40
WOM_F2_3N_FA_D40


title: A673_EWSFLI-AID_ATAC_IAA_rep1

description: Library name: A673_EWSFLI-AID_ATAC_IAA_rep1


title: bal_021

description:
Library name: sample21
novogene


title: A673_EWSFLI-AID_ATAC_DMSO_rep3

description: Library name: A673_EWSFLI-AID_ATAC_DMSO_rep3


title: A673_EWSFLI-AID_ATAC_DMSO_rep2

description: Library name: A673_EWSFLI-AID_ATAC_DMSO_rep2


title: WOM_F3_1N_MH_D5

description:
Library name: D5
WOM_F3_1N_MH_D5


title: bal_020

description:
Library name: sample20
novogene


title: WOM_F14_3N_FH_D81

description:
Library name: D81
WOM_F14_3N_FH_D81


title: A673_EWSFLI-AID_ATAC_DMSO_rep1

description: Library name: A673_EWSFLI-AID_ATAC_DMSO_rep1


title: bal_019

description:
Library name: sample19
novogene


title: brain_8_BR_Rat, male rat brain sample

city: Madison

first: Hasan

last: Khatib

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin Madison

description:
Library name: 8_BR_Rat
8_BR_Rat

data_processing:
Alignment (STAR)
Read counts (Rsubread)
Differential expression analysis (DEseq2 R package)
Annotation
Assembly: ARS-UI_Ramb_v3.0
Supplementary files format and content: read counts

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
RNA were extracted with either TRIzol reagent  (for sheep samples) or  Zymo Quick-RNA miniprep plus extraction kit (rat samples) followed by DNase I treatment before RNA sequencing.
RNA sequencing was performed for all samples using the NovaSeq X Plus platform with two 25B lanes, using V1.0 sequencing kits, and as 150 bp paired-end reads. Sheep RNA-Seq libraries were prepared with the Kapa Hyper Stranded mRNA library kit. Rat RNA-Seq libraries were prepared with the Watchmaker Stranded mRNA library kit. The libraries were pooled, quantified by qPCR, and sequenced on one 25B lane for 151 cycles from both ends of the fragments.

treatment_protocol: No specific treatment was applied.

value: Brain


title: WOM_F14_3N_FH_D82B

description:
Library name: D82B
WOM_F14_3N_FH_D82B


title: bal_018

description:
Library name: sample18
novogene


title: brain_7_BR_Rat, male rat brain sample

description:
Library name: 7_BR_Rat
7_BR_Rat


title: bal_017

description:
Library name: sample17
novogene


title: brain_5_BR_Rat, male rat brain sample

description:
Library name: 5_BR_Rat
5_BR_Rat


title: WOM_F14_3N_FH_D85

description:
Library name: D85
WOM_F14_3N_FH_D85


title: brain_4_BR_Rat, male rat brain sample

description:
Library name: 4_BR_Rat
4_BR_Rat


title: brain_6_BR_Rat, male rat brain sample

description:
Library name: 6_BR_Rat
6_BR_Rat


title: brain_3_BR_Rat, male rat brain sample

description:
Library name: 3_BR_Rat
3_BR_Rat


title: bal_016

description:
Library name: sample16
novogene


title: WOM_F14_3N_FH_D84

description:
Library name: D84
WOM_F14_3N_FH_D84


title: WOM_F14_3N_FA_D86

description:
Library name: D86
WOM_F14_3N_FA_D86


title: brain_29_BR_Rat, female rat brain sample

description:
Library name: 29_BR_Rat
29_BR_Rat


title: bal_015

description:
Library name: sample15
novogene


title: brain_28_BR_Rat, female rat brain sample

description:
Library name: 28_BR_Rat
28_BR_Rat


title: brain_9_BR_Rat, male rat brain sample

description:
Library name: 9_BR_Rat
9_BR_Rat


title: brain_27_BR_Rat, female rat brain sample

description:
Library name: 27_BR_Rat
27_BR_Rat


title: bal_014

description:
Library name: sample14
novogene


title: WOM_F14_3N_FA_D87

description:
Library name: D87
WOM_F14_3N_FA_D87


title: A673_EWSFLI-AID_NChIP-Input_IAA

description: Library name: A673_EWSFLI-AID_NChIP-Input_IAA


title: WOM_F14_3N_FA_D90A

description:
Library name: D90A
WOM_F14_3N_FA_D90A


title: bal_013

description:
Library name: sample13
novogene


title: brain_26_BR_Rat, female rat brain sample

description:
Library name: 26_BR_Rat
26_BR_Rat


title: brain_25_BR_Rat, female rat brain sample

description:
Library name: 25_BR_Rat
25_BR_Rat


title: brain_24_BR_Rat, female rat brain sample

description:
Library name: 24_BR_Rat
24_BR_Rat


title: WOM_F14_2N_FH_D91

description:
Library name: D91
WOM_F14_2N_FH_D91


title: brain_23_BR_Rat, female rat brain sample

description:
Library name: 23_BR_Rat
23_BR_Rat


title: bal_012

description:
Library name: sample12
novogene


title: WOM_F14_2N_FH_D92

description:
Library name: D92
WOM_F14_2N_FH_D92


title: brain_22_BR_Rat, female rat brain sample

description:
Library name: 22_BR_Rat
22_BR_Rat


title: brain_20_BR_Rat, female rat brain sample

description:
Library name: 20_BR_Rat
20_BR_Rat


title: brain_21_BR_Rat, female rat brain sample

description:
Library name: 21_BR_Rat
21_BR_Rat


title: bal_011

description:
Library name: sample11
novogene


title: WOM_F14_2N_FH_D93

description:
Library name: D93
WOM_F14_2N_FH_D93


title: brain_2_BR_Rat, female rat brain sample

description:
Library name: 2_BR_Rat:
2_BR_Rat:


title: bal_010

description:
Library name: sample10
novogene


title: brain_19_BR_Rat, female rat brain sample

description:
Library name: 19_BR_Rat
19_BR_Rat


title: WOM_F14_2N_FH_D94

description:
Library name: D94
WOM_F14_2N_FH_D94


title: bal_009

description:
Library name: sample9
novogene


title: brain_18_BR_Rat, female rat brain sample

description:
Library name: 18_BR_Rat
18_BR_Rat


title: WOM_F14_2N_FH_D95

description:
Library name: D95
WOM_F14_2N_FH_D95


title: brain_17_BR_Rat, male rat brain sample

description:
Library name: 17_BR_Rat
17_BR_Rat


title: brain_16_BR_Rat, male rat brain sample

description:
Library name: 16_BR_Rat
16_BR_Rat


title: bal_008

description:
Library name: sample8
novogene


title: WOM_F14_2N_FA_D96

description:
Library name: D96
WOM_F14_2N_FA_D96


title: brain_14_BR_Rat, male rat brain sample

description:
Library name: 14_BR_Rat
14_BR_Rat


title: brain_15_BR_Rat, male rat brain sample

description:
Library name: 15_BR_Rat
15_BR_Rat


title: bal_007

description:
Library name: sample7
novogene


title: brain_13_BR_Rat, male rat brain sample

description:
Library name: 13_BR_Rat:
13_BR_Rat:


title: WOM_F14_2N_FA_D97

description:
Library name: D97
WOM_F14_2N_FA_D97


title: brain_12_BR_Rat, male rat brain sample

description:
Library name: 12_BR_Rat:
12_BR_Rat:


title: A673_EWSFLI-AID_CnR-FLI_DMSO_rep1

description: Library name: A673_EWSFLI-AID_CnR-FLI_DMSO_rep1


title: bal_006

description:
Library name: sample6
novogene


title: brain_11_BR_Rat, male rat brain sample

description:
Library name: 11_BR_Rat:
11_BR_Rat:


title: WOM_F15_2N_MH_D111

description:
Library name: D111
WOM_F15_2N_MH_D111


title: brain_10_BR_Rat, male rat brain sample

description:
Library name: 10_BR_Rat:
10_BR_Rat:


title: bal_005

description:
Library name: sample5
novogene


title: brain_1_BR_Rat, female rat brain sample

description:
Library name: 1_BR_Rat
1_BR_Rat


title: WGDL_F2_2N_FH_C21

description:
Library name: C21
WGDL_F2_2N_FH_C21

value: WGDL


title: sperm, 9_Sperm_Rat, rat sperm sample

description:
Library name: 9_Sperm_Rat
9_Sperm_Rat

source_name: Sperm

value: Sperm


title: bal_004

description:
Library name: sample4
novogene

value: Ctrl


title: sperm, 8_Sperm_Rat, rat sperm sample

description:
Library name: 8_Sperm_Rat
8_Sperm_Rat


title: WGDL_F2_2N_FH_C22

description:
Library name: C22
WGDL_F2_2N_FH_C22


title: sperm, 7_Sperm_Rat, rat sperm sample

description:
Library name: 7_Sperm_Rat
7_Sperm_Rat


title: bal_003

description:
Library name: sample3
novogene


title: sperm, 6_Sperm_Rat, rat sperm sample

description:
Library name: 6_Sperm_Rat
6_Sperm_Rat


title: sperm, 5_Sperm_Rat, rat sperm sample

description:
Library name: 5_Sperm_Rat
5_Sperm_Rat


title: WGDL_F2_3N_FH_C33

description:
Library name: C33
WGDL_F2_3N_FH_C33


title: bal_002

description:
Library name: sample2
novogene


title: sperm, 4_Sperm_Rat, rat sperm sample

description:
Library name: 4_Sperm_Rat
4_Sperm_Rat


title: sperm, 17_Sperm_Rat, rat sperm sample

description:
Library name: 17_Sperm_Rat
17_Sperm_Rat


title: sperm, 3_Sperm_Rat, rat sperm sample

description:
Library name: 3_Sperm_Rat
3_Sperm_Rat


title: bal_001

description:
Library name: sample1
novogene


title: WGDL_F2_3N_FH_C34

description:
Library name: C34
WGDL_F2_3N_FH_C34


title: sperm, 16_Sperm_Rat, rat sperm sample

description:
Library name: 16_Sperm_Rat
16_Sperm_Rat


title: WGDL_F2_3N_FH_C35

description:
Library name: C35
WGDL_F2_3N_FH_C35


title: HuH7_si2_4

city: Copenhagen

first: Salvatore

last: Rizza

email: salvatoreri@gmail.com, rizza@cancer.dk

address: Strandboulevarden 49

department: Redox Biology

country: Denmark

institute: Danish Cancer Institute

description:
Library name: Sample 11
Cells were transfected by using RNAiMax, optimem and siRNA2

data_processing:
Data was analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA).
Reads were trimmed using cutadapt.Quality scores were assessed using FastQC.
Reads were aligned to the Homo sapiens genome build GRCh38 using STAR
Individual sample reads were quantified using HTseq and normalized via Relative Log Expression (RLE) using DESeq2 R library
DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction. ≥ 1.5 and  ≤ 1.5 Fold change and pAdj 0.05
Assembly: Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies. The topGO R library, (https://rdrr.io/bioc/topGO/) was used to determine local similarities and dependencies between GO terms in order to perform Elim pruning correction.
Supplementary files format and content: Homo sapiens genome build GRCh38
Supplementary files format and content: tab-delimited text files include log2FoldChange, pvalue and padj for each experimental group

source_name: HuH7 cells

growth_protocol: Cells were plated in DMEM in 6-well cell culture plates and placed in a 5% CO2 37 °C incubator for 48 hours

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
Individual sample reads were quantified using HTseq and normalized via Relative Log Expression (RLE) using DESeq2 R library

treatment_protocol: Cells were transfected for 48h with specific siRNA (20uM), RNAiMAX and optimem

value: HuH7 cells

value: transfected


title: sperm, 15_Sperm_Rat, rat sperm sample

description:
Library name: 15_Sperm_Rat
15_Sperm_Rat


title: WGDL_F2_3N_FA_C36

description:
Library name: C36
WGDL_F2_3N_FA_C36

data_processing:
Alignment was performed with STAR (v2.7.11a) against the reference genome using a pre-built STAR genome index. STAR was run with “--outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts” to generate sorted alignment files and gene-level count profiles. Gene-level expression quantification was carried out using RSEM (v1.3.1) with STAR-generated transcriptome BAM files as input (--paired-end --no-bam-output --alignments).
Assembly: Nasonia vitripennis reference genome (RefSeq No. GCF_009193385.2, NCBI GenBank)
Supplementary files format and content: Tab-delimited text file includes raw counts and tpm value for each sample

extract_protocol:
RNA extraction was performed using Quick-RNATM Tissue/Insect Microprep (Catalogue No. R2030 Zymo Research, Germany) (without DNase treatment). For sequencing, RNA was resuspended in 10 µL DNase/RNase-free water and the RNA concentration and purity was measured using a fluorometer (Qubit 2.0, Life Technologies); poor quality samples judged by A260/A280 and A260/A230 ratios were discarded. The extracted RNA was sent to Novogene (UK) Company Limited for sequencing. Novogene Hongkong prepared the sample library.
Unique index codes were added to each sample using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, USA). mRNA was purified from total RNA using poly-T magnetic beads, and libraries were prepared according to the manufacturer's instructions (Illumina).

value: Abdomen


title: HuH7_si2_3

description:
Library name: Sample 10
Cells were transfected by using RNAiMax, optimem and siRNA2


title: sperm, 14_Sperm_Rat, rat sperm sample

description:
Library name: 14_Sperm_Rat
14_Sperm_Rat


title: sperm, 13_Sperm_Rat, rat sperm sample

description:
Library name: 13_Sperm_Rat
13_Sperm_Rat


title: WGDL_F2_3N_FA_C37

description:
Library name: C37
WGDL_F2_3N_FA_C37


title: sperm, 12_Sperm_Rat, rat sperm sample

description:
Library name: 12_Sperm_Rat
12_Sperm_Rat


title: HuH7_si2_2

description:
Library name: Sample 9
Cells were transfected by using RNAiMax, optimem and siRNA2


title: sperm, 11_Sperm_Rat, rat sperm sample

description:
Library name: 11_Sperm_Rat
11_Sperm_Rat


title: WGDL_F2_3N_FA_C38

description:
Library name: C38
WGDL_F2_3N_FA_C38


title: HuH7_si2_1

description:
Library name: Sample 8
Cells were transfected by using RNAiMax, optimem and siRNA2


title: ovary, 29_Ovary_Rat, female rat ovary sample

description:
Library name: 29_Ovary_Rat
29_Ovary_Rat

source_name: Ovary

value: Ovary


title: sperm, 10_Sperm_Rat, rat sperm sample

description:
Library name: 10_Sperm_Rat
10_Sperm_Rat


title: ovary, 28_Ovary_Rat, female rat ovary sample

description:
Library name: 28_Ovary_Rat
28_Ovary_Rat


title: HuH7_si1_4

description:
Library name: Sample 7
Cells were transfected by using RNAiMax, optimem and siRNA1


title: ovary, 27_Ovary_Rat, female rat ovary sample

description:
Library name: 27_Ovary_Rat
27_Ovary_Rat


title: WGDL_F2_3N_FA_C39

description:
Library name: C39
WGDL_F2_3N_FA_C39


title: ovary, 26_Ovary_Rat, female rat ovary sample

description:
Library name: 26_Ovary_Rat
26_Ovary_Rat


title: HuH7_si1_3

description:
Library name: Sample 6
Cells were transfected by using RNAiMax, optimem and siRNA1


title: ovary, 25_Ovary_Rat, female rat ovary sample

description:
Library name: 25_Ovary_Rat
25_Ovary_Rat


title: WGDL_F2_3N_FA_C40

description:
Library name: C40
WGDL_F2_3N_FA_C40


title: WGDL_F5_1N_MH_C51

description:
Library name: C51
WGDL_F5_1N_MH_C51

source_name: Head


title: ovary, 24_Ovary_Rat, female rat ovary sample

description:
Library name: 24_Ovary_Rat
24_Ovary_Rat


title: HuH7_si1_2

description:
Library name: Sample 5
Cells were transfected by using RNAiMax, optimem and siRNA1


title: ovary, 23_Ovary_Rat, female rat ovary sample

description:
Library name: 23_Ovary_Rat
23_Ovary_Rat


title: WGDL_F5_1N_MH_C52

description:
Library name: C52
WGDL_F5_1N_MH_C52


title: ovary, 22_Ovary_Rat, female rat ovary sample

description:
Library name: 22_Ovary_Rat
22_Ovary_Rat


title: HuH7_siSCR_4

description:
Library name: Sample 4
Cells were transfected by using RNAiMax, optimem and siRNA control

value: wild-type


title: ovary, 21_Ovary_Rat, female rat ovary sample

description:
Library name: 21_Ovary_Rat
21_Ovary_Rat


title: HuH7_siSCR_3

description:
Library name: Sample 3
Cells were transfected by using RNAiMax, optimem and siRNA control


title: WGDL_F2_2N_FH_C23

description:
Library name: C23
WGDL_F2_2N_FH_C23


title: ovary, 20_Ovary_Rat, female rat ovary sample

description:
Library name: 20_Ovary_Rat
20_Ovary_Rat


title: WGDL_F5_1N_MH_C53

description:
Library name: C53
WGDL_F5_1N_MH_C53

value: male


title: ovary, 2_Ovary_Rat, female rat ovary sample

description:
Library name: 2_Ovary_Rat
2_Ovary_Rat


title: HuH7_siSCR_2

description:
Library name: Sample 2
Cells were transfected by using RNAiMax, optimem and siRNA control


title: ovary, 18_Ovary_Rat, female rat ovary sample

description:
Library name: 18_Ovary_Rat
18_Ovary_Rat


title: ovary, 19_Ovary_Rat, female rat ovary sample

description:
Library name: 19_Ovary_Rat
19_Ovary_Rat


title: WGDL_F5_1N_MH_C54

description:
Library name: C54
WGDL_F5_1N_MH_C54

value: Head


title: ovary, 1_Ovary_Rat, female rat ovary sample

description:
Library name: 1_Ovary_Rat
1_Ovary_Rat


title: HuH7_siSCR_1

description:
Library name: Sample 1
Cells were transfected by using RNAiMax, optimem and siRNA control


title: 769-P_si2_4


title: CD4, Constitutive anti-EphA2/IL13RA2 CAR, donor 2U, replicate 2

city: San Francisco

first: Hideho

last: Okada

state: CA

department: Neurological Surgery

institute: University of California, San Francisco

description:
Library name: B11
BSYNC_invitro_RNAseq_StringTie_count_protein_coding_n24.tsv: B11

data_processing:
Quality checking, trimming, and removal of barcodes from FASTQ sequencing reads were performed using fastp (version 0.20.0) with default parameters.
FASTQ reads were aligned to the human reference genome GRCh38.p14 using STAR (v2.7.9a), with transcriptome annotation from GENCODE v49 (gencode.v49.annotation.gtf). Sequences corresponding to BCAN-synNotch and EphA2- IL13Rα2-CAR constructs were incorporated into the reference genome. BAM file sorting and indexing were performed using samtools (v1.22.1).
Gene-level expression counts and transcripts per million (TPM) values were quantified using StringTie (v2.0).
A gene-level expression count data table was prepared by merging all 24 sample count data and excluding irrelevant genes, such as long noncoding genes, based on the GTF annotation.
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: T cells

growth_protocol: Primary human T-cells isolation and culture: Primary CD4+ and CD8+ T-cells were isolated from donor blood after apheresis by negative selection (STEMCELL Technologies). Blood was obtained from StemExpress or Allcells, as approved by the University of California San Francisco (UCSF) institutional review board. T-cells were cryopreserved either in Cellbanker 1 or in RPMI-1640 with 20% human AB serum (Valley Biomedical) and 10% dimethyl sulfoxide. After thawing, T-cells were cultured in human T-cells medium consisting of X-VIVO 15 (Lonza), 5% human AB serum, 55 µM β-mercaptoethanol, and 10 mM neutralized N-acetyl-L-cysteine supplemented with 30 units/ml IL-2.  Lentiviral transduction of human T-cells: Pantropic vesicular stomatitis virus G (VSV-G) pseudotyped lentivirus was produced through transfection of Lenti-X 293T-cells (Takara Bio, catalog no. 632180) with a pHRʹSIN:CSW transgene expression vector and the viral packaging plasmids pCMV and pMD2.G using Fugene HD (Promega) or TransIT-VirusGen (Mirus Bio). Primary T-cells were thawed the same day and, after 24 hours in culture, were stimulated with 25 µl of anti-CD3/CD28 coated beads [Dynabeads Human T-Activator CD3/CD28 (Gibco)] per 1 ×106 T-cells. In some instances, freshly isolated T-cells were used. At 48 hours, viral supernatant was harvested. Primary T-cells were exposed to the lentivirus for 24 hours or spinoculated on retronectin-coated plates. At day 5 after T-cells stimulation, Dynabeads were removed and T-cells were sorted with a BD Biosciences FACSARIA Fusion or Sony SH800S Cell Sorter. T-cells exhibiting basal CAR expression were gated out during sorting. T-cells were expanded until rested and could be used in assays.

extract_protocol:
Total RNA was extracted from CD4+ and CD8+ T-cells transduced with either Constitutive CAR or B-SYNC using the RNeasy Mini Kit (Qiagen, 74106) with on-column DNase treatment (RNase-Free DNase Set, Qiagen, 79254) according to the manufacturer’s instructions.
RNA integrity was assessed using an Agilent Bioanalyzer 5400 and confirmed to have a RIN (RNA Integrity Number) value of 7 or greater (range: 7–9.4). RNA quality assessment, library preparation, and sequencing were performed by Novogene (Sacramento, CA). Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, first-strand cDNA synthesis was performed using random hexamer primers, followed by second-strand cDNA synthesis. Libraries were constructed through end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Quality control was conducted using Qubit and real-time PCR for quantification, and Bioanalyzer for size distribution assessment.

value: T cells

tag: transduction

value: Constitutive anti-EphA2/IL13RA2 CAR

tag: donor

value: donor 2U


title: WGDL_F5_1N_MH_C55B

description:
Library name: C55B
WGDL_F5_1N_MH_C55B

value: 1 day after emergence


title: CD4, Constitutive anti-EphA2/IL13RA2 CAR, donor 2U, replicate 1

description:
Library name: B10
BSYNC_invitro_RNAseq_StringTie_count_protein_coding_n24.tsv: B10


title: CD8, Constitutive anti-EphA2/IL13RA2 CAR, donor 2U, replicate 3

description:
Library name: B09
BSYNC_invitro_RNAseq_StringTie_count_protein_coding_n24.tsv: B09


title: 769-P_si2_3


title: CD4, Constitutive anti-EphA2/IL13RA2 CAR, donor 2U, replicate 3

description:
Library name: B12
BSYNC_invitro_RNAseq_StringTie_count_protein_coding_n24.tsv: B12


title: CD8, Constitutive anti-EphA2/IL13RA2 CAR, donor 2U, replicate 1

description:
Library name: B07
BSYNC_invitro_RNAseq_StringTie_count_protein_coding_n24.tsv: B07


title: WGDL_F5_1N_MA_C57

description:
Library name: C57
WGDL_F5_1N_MA_C57

source_name: Abdomen


title: 769-P_si2_2


title: CD8, Constitutive anti-EphA2/IL13RA2 CAR, donor 2U, replicate 2

description:
Library name: B08
BSYNC_invitro_RNAseq_StringTie_count_protein_coding_n24.tsv: B08


title: CD4, BCAN synNotch - anti-EphA2/IL13RA2 CAR, donor 2U, replicate 3

description:
Library name: B06
BSYNC_invitro_RNAseq_StringTie_count_protein_coding_n24.tsv: B06

value: BCAN synNotch - anti-EphA2/IL13RA2 CAR


title: WGDL_F5_1N_MA_C58

description:
Library name: C58
WGDL_F5_1N_MA_C58


title: CD4, BCAN synNotch - anti-EphA2/IL13RA2 CAR, donor 2U, replicate 2

description:
Library name: B05
BSYNC_invitro_RNAseq_StringTie_count_protein_coding_n24.tsv: B05


title: CD4, BCAN synNotch - anti-EphA2/IL13RA2 CAR, donor 2U, replicate 1

description:
Library name: B04
BSYNC_invitro_RNAseq_StringTie_count_protein_coding_n24.tsv: B04


title: 769-P_si2_1

description:
Library name: Sample 8
Cells were transfected by using RNAiMax, optimem and siRNA2


title: WGDL_F5_1N_MA_C59

description:
Library name: C59
WGDL_F5_1N_MA_C59


title: CD8, BCAN synNotch - anti-EphA2/IL13RA2 CAR, donor 2U, replicate 3

description:
Library name: B03
BSYNC_invitro_RNAseq_StringTie_count_protein_coding_n24.tsv: B03


title: 769-P_si1_3

description:
Library name: Sample 7
Cells were transfected by using RNAiMax, optimem and siRNA1


title: CD8, BCAN synNotch - anti-EphA2/IL13RA2 CAR, donor 2U, replicate 2

description:
Library name: B02
BSYNC_invitro_RNAseq_StringTie_count_protein_coding_n24.tsv: B02


title: CD8, BCAN synNotch - anti-EphA2/IL13RA2 CAR, donor 2U, replicate 1

description:
Library name: B01
BSYNC_invitro_RNAseq_StringTie_count_protein_coding_n24.tsv: B01


title: 769-P_si1_2

description:
Library name: Sample 6
Cells were transfected by using RNAiMax, optimem and siRNA1


title: WGDL_F5_1N_MA_C60

description:
Library name: C60
WGDL_F5_1N_MA_C60


title: CD4, Constitutive anti-EphA2/IL13RA2 CAR, donor 2V, replicate 3

description:
Library name: A12
BSYNC_invitro_RNAseq_StringTie_count_protein_coding_n24.tsv: A12

value: donor 2V


title: WGDL_F5_2N_MH_C41

description:
Library name: C41
WGDL_F5_2N_MH_C41


title: CD4, Constitutive anti-EphA2/IL13RA2 CAR, donor 2V, replicate 2

description:
Library name: A11
BSYNC_invitro_RNAseq_StringTie_count_protein_coding_n24.tsv: A11


title: 769-P_si1_1

description:
Library name: Sample 5
Cells were transfected by using RNAiMax, optimem and siRNA1


title: CD4, Constitutive anti-EphA2/IL13RA2 CAR, donor 2V, replicate 1

description:
Library name: A10
BSYNC_invitro_RNAseq_StringTie_count_protein_coding_n24.tsv: A10


title: WGDL_F5_2N_MH_C42

description:
Library name: C42
WGDL_F5_2N_MH_C42


title: CD8, Constitutive anti-EphA2/IL13RA2 CAR, donor 2V, replicate 3

description:
Library name: A09
BSYNC_invitro_RNAseq_StringTie_count_protein_coding_n24.tsv: A09


title: 769-P_siSCR_4

description:
Library name: Sample 4
Cells were transfected by using RNAiMax, optimem and siRNA control


title: CD8, Constitutive anti-EphA2/IL13RA2 CAR, donor 2V, replicate 2

description:
Library name: A08
BSYNC_invitro_RNAseq_StringTie_count_protein_coding_n24.tsv: A08


title: WGDL_F2_2N_FH_C25

description:
Library name: C25
WGDL_F2_2N_FH_C25

value: female


title: CD8, Constitutive anti-EphA2/IL13RA2 CAR, donor 2V, replicate 1

description:
Library name: A07
BSYNC_invitro_RNAseq_StringTie_count_protein_coding_n24.tsv: A07


title: 769-P_siSCR_3

description:
Library name: Sample 3
Cells were transfected by using RNAiMax, optimem and siRNA control


title: CD4, BCAN synNotch - anti-EphA2/IL13RA2 CAR, donor 2V, replicate 3

description:
Library name: A06
BSYNC_invitro_RNAseq_StringTie_count_protein_coding_n24.tsv: A06


title: CD4, BCAN synNotch - anti-EphA2/IL13RA2 CAR, donor 2V, replicate 2

description:
Library name: A05
BSYNC_invitro_RNAseq_StringTie_count_protein_coding_n24.tsv: A05


title: WGDL_F5_2N_MH_C43

description:
Library name: C43
WGDL_F5_2N_MH_C43

value: WGDL


title: 769-P_siSCR_2

description:
Library name: Sample 2
Cells were transfected by using RNAiMax, optimem and siRNA control


title: CD4, BCAN synNotch - anti-EphA2/IL13RA2 CAR, donor 2V, replicate 1

description:
Library name: A04
BSYNC_invitro_RNAseq_StringTie_count_protein_coding_n24.tsv: A04


title: WGDL_F5_2N_MH_C44

description:
Library name: C44
WGDL_F5_2N_MH_C44


title: CD8, BCAN synNotch - anti-EphA2/IL13RA2 CAR, donor 2V, replicate 3

description:
Library name: A03
BSYNC_invitro_RNAseq_StringTie_count_protein_coding_n24.tsv: A03


title: CD8, BCAN synNotch - anti-EphA2/IL13RA2 CAR, donor 2V, replicate 2

description:
Library name: A02
BSYNC_invitro_RNAseq_StringTie_count_protein_coding_n24.tsv: A02


title: WGDL_F5_2N_MH_C45

description:
Library name: C45
WGDL_F5_2N_MH_C45


title: 769-P_siSCR_1

description:
Library name: Sample 1
Cells were transfected by using RNAiMax, optimem and siRNA control


title: CD8, BCAN synNotch - anti-EphA2/IL13RA2 CAR, donor 2V, replicate 1

description:
Library name: A01
BSYNC_invitro_RNAseq_StringTie_count_protein_coding_n24.tsv: A01


title: hippocampal_sclerosis_2

first: Daniel Sebastian

last: Galvis Montes

address: Venusberg Campus 1

institute: Universitätsklinikum Bonn

description:
Library name: DE91NGSUKBR122695
metaData.tsv in column "nCount:RNA" rows "DE91NGSUKBR122695"

data_processing:
Mapping of snRNA-data was performed using Cell Ranger version 6.1.2 (PMID_28091601). The “GRCh38-3.0.0” reference transcriptome for the human genome was downloaded from 10xgenomics here: https://cf.10xgenomics.com/supp/cell-exp/refdata-cellranger-GRCh38-3.0.0.tar.gz. Fastq files of the raw sequencing data for each sample were input into the cellranger “count” subcommand, with parameters –expect set to 7000 and run two times, firstly with “—include-introns” and secondly without “—include-introns”.
The raw feature count matrices were imported into R (v4.0.5) using Seurat (v4.0.2). Matrices were read using ‘read10xCounts’ and converted to SeuratObjects using ‘CreateSeuratObject’.
Contaminated nuclei were identified using DIEM (v2.3.0) with a threshold score of 0.5 (call_targets function) (PMID: 32620816). Cell cycle scoring was performed using ‘CellCycleScoring’ in Seurat with 2019 updated gene lists.
Data normalization and variance stabilization were performed using SCTransform, regressing out cell cycle and mitochondrial effects. Datasets were integrated by sequentially calling ‘SelectIntegrationFeatures’, ‘PrepSCTIntegration’, ‘FindIntegrationAnchors’, and ‘IntegrateData’ (anchor.features = all, normalization.method = SCT).
Quality control filtering excluded nuclei with detected genes <500 or >8000, mitochondrial reads >5%, ribosomal reads >5%, or intron:exon read ratio <1.5. Doublets were identified and removed using DoubletFinder (v2.0.3) (PMID: 30954475) with expected doublet rate set to 4%, parameters pN=0.25, pK=0.09, using 30 PCs.
Assembly: Human GRCh38-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hippocampus

extract_protocol:
Nuclei were extracted in lysis buffer (nuclei extraction buffer (Miltenyi Biotex) with RNase inhibitor (Promega, N2615)) using a gentleMACS dissociator (Miltenyi Biotec). The nuclei suspension was then filtered through a MACS SmartStrainer (70 µm) with the strainer rinsed with lysis buffer. The filtered suspension was centrifuged at 300 x g for 5 min at 4 °C. The pellet was resuspended in 3 ml resuspension buffer (PBS + 0.04 % BSA + 0.2U/ul RNAse inhibitor), and filtered through a MACS SmartStrainer (30 µm). The collected nuclei suspension was immediately processed for debris removal using density gradient centrifugation. For debris removal, the nuclei suspension was centrifuged at 300 x g for 10 min at 4 °C, resuspended in 900 µl PBS, and gently layered with 355 µl debris removal solution (Milteny), followed by 4 ml PBS. Density gradient centrifugation was performed at 3000 x g for 10 min at 4 °C. The two top phases were aspirated, and the tube was filled up with 15 ml PBS, inverted to mix, and centrifuged again at 1000 x g for 10 min at 4°C. The final nuclei pellet was resuspended in 500 µl resuspension buffer and stained with DAPI (1.7µg/ml, Sigma-Aldrich). Nuclei were sorted using BD FACSAria III (100 µm nozzle size, 20psi, 4°C).
Nuclei were prepared using the dual-index Chromium Next GEM Single Cell 3’ Kit v3.1 (10xGenomics) with a target nuclei load of approximately 16,000 per sample. Sequencing was performed on a Novaseq6000 (28/8/91, Illumina) using S2 flow cell with a target of 50,000 reads per nucleus following standard protocols.

value: Hippocampus

tag: pathology


title: WGDL_F5_2N_MA_C46

description:
Library name: C46
WGDL_F5_2N_MA_C46

tag: tissue


title: ML6_25uM_4h_2

description: Library name: THP1_ML6_2

data_processing:
FASTQ files were generated and demultiplexed using Illumina bcl2fastq v2.20 conversion software. Reads were subsequently trimmed with TrimGalore, mapped to the hg38 transcriptome, and quantified using Salmon. Differentially expressed genes were identified using DESeq2.
Assembly: hg38
Supplementary files format and content: Supplementary files format and content: raw counts, and Transcribe per milion in CSV format

growth_protocol: HEK293Tcells were obtained from ATCC (CRL-3216, Batch#70049877) and grown in 10 cm BioLite™   Cell Culture   Treated   Dishes   (Catalog# 12-556-002 Thermo   Scientific)   in Dulbecco’s Modified Eagle Medium, high glucose (Catalog# 11965092, Gibco). HEK293T experiments were conducted on cells between passage 10-25. THP-1 monocytes were obtained from ATCC (TIB-202 Batch# 62454382) and propagated in T-75 flasks between 0.2 and 1 × 10e6 cells/mL in an RPMI-1640 (Catalog# 11875093, Gibco, Billings, MT, USA) growth medium. THP-1 experiments were conducted on cells between passage 10 and 15.

extract_protocol:
E.Z.N.A.® Total RNA Kit I (Catalog# R6834-01, Omega), with 100% ethanol instead of 70% at the binding step to enrich small RNA.
Libraries were prepared with the Kapa Hyper Stranded mRNA library kit (Roche) and sequenced on two 10B lanes for 151 cycles from both ends of the fragments on a NovaSeq X Plus with V1.0 sequencing kits.

treatment_protocol: siRNA and ASO transfected using Lipofectamine® RNAiMax (cat # 13778150) with standard protocol, Overexpression sample are transfected using Lipofectamine 3000 (cat #L3000015)

value: Monocyte


title: ML6_25uM_4h_1

description: Library name: THP1_ML6_1


title: ML6_25uM_4h_3

description: Library name: THP1_ML6_3


title: WGDL_F5_2N_MA_C47

description:
Library name: C47
WGDL_F5_2N_MA_C47

tag: Sex


title: lesion_associated_1

description:
Library name: DE75NGSUKBR122692
metaData.tsv in column "nCount:RNA" rows "DE75NGSUKBR122692"


title: anti-GAD65+_1

description:
Library name: DE64NGSUKBR122696
metaData.tsv in column "nCount:RNA" rows "DE64NGSUKBR122696"

value: anti-GAD65+ TLE


title: DMSO_2

description: Library name: THP1_DMSO_2


title: WGDL_F5_1N_MA_C56

description:
Library name: C56
WGDL_F5_1N_MA_C56

tag: age


title: DMSO_3

description: Library name: THP1_DMSO_3


title: WGDL_F5_2N_MA_C48

description:
Library name: C48
WGDL_F5_2N_MA_C48

tag: genotype


title: DMSO_1

description: Library name: THP1_DMSO_1

tag: cell line


title: lesion_associated_2

description:
Library name: DE48NGSUKBR122693
metaData.tsv in column "nCount:RNA" rows "DE48NGSUKBR122693"


title: CHX_10ug_per_ml_4.5h_ML625uM_4h_3

description: Library name: THP1_CHX_ML6_3

tag: treatment


title: WGDL_F5_2N_MA_C49

description:
Library name: C49
WGDL_F5_2N_MA_C49


title: CHX_10ug_per_ml_4.5h_ML625uM_4h_2

description: Library name: THP1_CHX_ML6_2


title: CHX_10ug_per_ml_4.5h_ML625uM_4h_1

description: Library name: THP1_CHX_ML6_1


title: WGDL_F5_2N_MA_C50

description:
Library name: C50
WGDL_F5_2N_MA_C50


title: anti-GAD65+_2

description:
Library name: DE37NGSUKBR122697
metaData.tsv in column "nCount:RNA" rows "DE37NGSUKBR122697"


title: CHX_10ug_per_ml_4.5h_3

description: Library name: THP1_CHX_3


title: anti-Drebrin+_1

description:
Library name: DE32NGSUKBR122690
metaData.tsv in column "nCount:RNA" rows "DE32NGSUKBR122690"

value: anti-Drebrin+ TLE


title: CHX_10ug_per_ml_4.5h_2

description: Library name: THP1_CHX_2


title: WGDL_F14_3N_FH_C61

description:
Library name: C61
WGDL_F14_3N_FH_C61


title: CHX_10ug_per_ml_4.5h_1

description: Library name: THP1_CHX_1


title: hippocampal_sclerosis_1

description:
Library name: DE21NGSUKBR122694
metaData.tsv in column "nCount:RNA" rows "DE21NGSUKBR122694"


title: WGDL_F14_3N_FH_C62

description:
Library name: C62
WGDL_F14_3N_FH_C62


title: MAF1_OE_48h_3

description: Library name: MAF1_OE_3

value: Kidney


title: MAF1_OE_48h_2

description: Library name: MAF1_OE_2


title: MAF1_OE_48h_1

description: Library name: MAF1_OE_1


title: anti-Drebrin+_2

description:
Library name: DE05NGSUKBR122691
metaData.tsv in column "nCount:RNA" rows "DE05NGSUKBR122691"


title: WGDL_F2_2N_FA_C27

description:
Library name: C27
WGDL_F2_2N_FA_C27

value: Abdomen


title: A673_XChIP-INPUT_SW39

description: Library name: A673_XChIP-INPUT_SW39

value: Ewing sarcoma cell line


title: control_eGFP_OE_48h_3

description: Library name: eGFP_OE_3


title: control_eGFP_OE_48h_2

description: Library name: eGFP_OE_2


title: control_eGFP_OE_48h_1

description: Library name: eGFP_OE_1


title: WGDL_F14_3N_FH_C63

description:
Library name: C63
WGDL_F14_3N_FH_C63


title: A673_XChIP-INPUT_DMSO

description: Library name: A673_XChIP-INPUT_DMSO

value: DMSO


title: Scramble_ASO_200nM_48h_3

description: Library name: ASOPOLR3G_control_3


title: POLR3G_ASO_200nM_ 48h_3

description: Library name: ASOPOLR3G_ASO3G_3

value: POLR3G_ASO_200nM_ 48h_3


title: WGDL_F14_3N_FH_C64

description:
Library name: C64
WGDL_F14_3N_FH_C64

value: Head


title: A673_XChIP-MED1_SW39_rep2

description: Library name: A673_XChIP-MED1_SW39_rep2

tag: chip antibody

value: MED1:Bethyl A300-793A lot 11


title: POLR3G_ASO_200nM_ 48h_2

description: Library name: ASOPOLR3G_ASO3G_2

value: POLR3G_ASO_200nM_ 48h_2


title: WGDL_F14_3N_FA_C66

description:
Library name: C66
WGDL_F14_3N_FA_C66

value: 1 day after emergence


title: POLR3G_ASO_200nM_ 48h_1

description: Library name: ASOPOLR3G_ASO3G_1

value: POLR3G_ASO_200nM_ 48h_1


title: A673_XChIP-MED1_SW39_rep1

description: Library name: A673_XChIP-MED1_SW39_rep1


title: siPOLR3GL_siE8_25nM 48 h_3

description: Library name: siPOLR3GL_siE8_3

value: siPOLR3GL_siE8_25nM 48 h_3


title: WGDL_F14_3N_FA_C67

description:
Library name: C67
WGDL_F14_3N_FA_C67

value: female


title: siPOLR3GL_siE8_25nM 48 h_2

description: Library name: siPOLR3GL_siE8_2

value: siPOLR3GL_siE8_25nM 48 h_2


title: A673_XChIP-MED1_DMSO_rep2

description: Library name: A673_XChIP-MED1_DMSO_rep2


title: siPOLR3GL_siE8_25nM 48 h_1

description: Library name: siPOLR3GL_siE8_1

value: siPOLR3GL_siE8_25nM 48 h_1


title: WGDL_F14_3N_FA_C68

description:
Library name: C68
WGDL_F14_3N_FA_C68

value: WGDL


title: siPOLR3GL_siE6_25nM 48 h_3

description: Library name: siPOLR3GL_siE6_3

value: siPOLR3GL_siE6_25nM 48 h_3


title: A673_XChIP-MED1_DMSO_rep1

description: Library name: A673_XChIP-MED1_DMSO_rep1


title: siPOLR3GL_siE6_25nM 48 h_2

description: Library name: siPOLR3GL_siE6_2

value: siPOLR3GL_siE6_25nM 48 h_2


title: WGDL_F14_3N_FA_C69

description:
Library name: C69
WGDL_F14_3N_FA_C69


title: siPOLR3GL_siE6_25nM 48 h_1

description: Library name: siPOLR3GL_siE6_1

value: Kidney

value: siPOLR3GL_siE6_25nM 48 h_1


title: A673_NChIP-Input_SW39

description: Library name: A673_NChIP-Input_SW39

value: Ewing sarcoma cell line


title: siPOLR3GL_siE4_25nM 48 h_3

description: Library name: siPOLR3GL_siE4_3

value: siPOLR3GL_siE4_25nM 48 h_3


title: WGDL_F14_2N_FH_C71

description:
Library name: C71
WGDL_F14_2N_FH_C71


title: siPOLR3GL_siE4_25nM 48 h_2

description: Library name: siPOLR3GL_siE4_2

value: siPOLR3GL_siE4_25nM 48 h_2


title: A673_NChIP-Input_DMSO

description: Library name: A673_NChIP-Input_DMSO

value: DMSO


title: WGDL_F14_2N_FH_C72

description:
Library name: C72
WGDL_F14_2N_FH_C72

value: Head


title: control siRNA 25nM 48 h_3

description: Library name: siPOLR3GL_control_3

value: control siRNA 25nM 48 h_3


title: siPOLR3GL_siE4_25nM 48 h_1

description: Library name: siPOLR3GL_siE4_1

value: siPOLR3GL_siE4_25nM 48 h_1


title: A673_NChIP-H3K27ac_SW39_rep2

description: Library name: A673_NChIP-H3K27ac_SW39_rep2

value: H3K27ac (Active Motif #39133)


title: control siRNA 25nM 48 h_2

description: Library name: siPOLR3GL_control_2

value: control siRNA 25nM 48 h_2