title: TNF rep3

city: Tianjin

first: Xueyang

last: Pang

state: Tianjin

address: 22 Meteorological Observatory Road, Heping District, Tianjin

institute: TMU

description: Library name: SAMPLES9

data_processing:
The raw data were cleaned by removing the reads containing adapter, poly-N and low-quality reads. The reads were then aligned to the hg38 human reference genome by Hisat2 v2.0.5. Feature Counts v1.5.0-p3 was used to count the reads and calculate the FPKM. DESeq2(1.20.0) was used to analyze the differential expression.
Assembly: hg38
Supplementary files format and content: txt file includes RPKM values for all Samples

growth_protocol: HEK293T was cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS and 1% penicillin-streptomycin. All cells were maintained at 37℃ and 5% CO2.

extract_protocol:
Total RNA was extracted with TriZOL (TransGen, Cat No. Q40831).
The integrity of RNA was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Total RNA was used for library preparation. Briefly, mRNA was isolated from the total RNA using poly-T oligo-attached magnetic beads. The resulting mRNA was then randomly fragmented with divalent cations. The first strand of cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-). Subsequently, the second strand of cDNA was synthesized using DNA Polymerase I and RNase H. The remaining overhangs were converted into blunt ends through exonuclease/polymerase activities. The purified double-stranded cDNA was ligated to the sequencing adapters. AMPure XP beads were used to screen for cDNA with a length of around 370 to 420 bp. Then PCR was performed using Phusion High-Fidelity DNA polymerase, universal PCR primers and index (X) primers. Finally, PCR products were purified using AMPure XP beads to ultimately obtain the library.

treatment_protocol: Plasmids expressing σ3 were transfected into HEK293 cells using PEI. At 48 h post-transfection, cells were treated with 10 ng/ml TNF-α for 3 h.

value: Human embryonic kidney 293

value: WT

value: TNFa


title: Host_IL-2(N88D)

status: Public on Feb 24 2026

type: SRA

city: Palo alto

first: Qinli

last: Sun

address: 279 Campus Drive

country: USA

institute: Stanford University

description: Library name: Sample 2

library_source: transcriptomic single cell

data_processing:
Libraries were sequenced with Illumina NovaSeq X platform. Generated FASTQ files were processed with CellRanger v9.0.1 count pipeline using the GRCm39-2024-A transcriptome reference. Reads mapped to introns were included in the gene-expression calculation.
Assembly: Mouse GRCm39
Supplementary files format and content: Preprocessed Seurat object

molecule: total RNA

organism: Mus musculus

source_name: Lymph node

extract_protocol:
One million sorted Thy1.1⁺ naïve OT-II cells were adoptively transferred into Thy1.2⁺ Foxp3-GFP recipient mice via retro-orbital intravenous injection. This was followed by six intraperitoneal injections of 100 μg OVA protein combined with 50 pmol of the indicated proteins, administered every other day. On day 11, donor OT-II cells and host Foxp3-GFP⁺ CD4⁺ T cells were sorted from the mLNs of the respective treatment groups and submitted to MedGenome, Inc. for library preparation and RNA sequencing.
The library was constructed using 10X Genomics Single Cell 3' v4 (polyA) chemistry according to the manufacturer's protocol.

tag: tissue

value: Lymph node

tag: cell type

value: CD4+ T cells

tag: genotype

value: Foxp3-GFP+ endogenous CD4+ T cells

tag: treatment


title: Coc, scRNAseq

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street, BE208

institute: MUSC

description:
Library name: Sample2
10x Genomics

data_processing:
Raw sequencing data were processed with Cell Ranger (v9.0.0) (PMID: 28091601). Cellranger mkfastq command was used to demultiplex the different samples and cellranger count command was used to generate gene – cell expression matrices. Human Genome hg38 was used for the alignment and gencode.v42  was used for gene annotation and coordinates (PMID: 33270111).Downstream analysis was performed in R with Seurat (v5.3.0) (PMID: 34062119) and customized R scripts.
Assembly: hg38
Supplementary files format and content: h5

organism: Homo sapiens

source_name: PBMC

extract_protocol:
To isolate PBMCs from leftover blood after plasma removal, transfer the blood into 50 mL Falcon tubes and rinse the original tubes with RPMI 1640 (no FBS/antibiotics) to maximize recovery. Dilute the blood 1:2 with room temp RPMI, then gently layer 10 mL of Ficoll underneath the diluted blood. Centrifuge at 1500 rpm (~450 g) for 25 minutes at 20°C with no brake. Carefully extract the cloudy lymphocyte ring using a 10 mL pipette and transfer to a new tube. Wash cells by filling with RPMI to 50 mL, spin at 1500 rpm for 10 min, and then again at 2000 rpm for 10 min to recover more cells. Combine pellets in 10 mL RPMI, count using appropriate dilutions, and spin again at 1500 rpm for 10 min. Discard the supernatant, resuspend the pellet gently, and slowly add freezing buffer (90% HI FBS + 10% DMSO) dropwise (~1 mL per 5–10×10⁷ cells) with gentle shaking. Aliquot 400–500 µL into labeled cryovials and store at –80°C using a freezing container.
Single cells were captured and constructed 3’ single-cell gene expression libraries (the latest GEM-X v4 version) using the 10x Genomics Chromium-X system. The libraries were sequenced with ~500 million PE150 reads per sample on Illumina NovaSeq X Plus.

value: PBMC

value: Cocaine


title: LongRNA_vas RG/PH_rep2

city: Worcester

first: Samantha

last: Ho

state: MA

address: 373 Plantation St.

department: Department of Molecular Medicine

institute: University of Massachusetts Chan Medical School

library_source: transcriptomic

data_processing:
piSet_rnaseq pipeline from GitHub was used to analyze long RNA sequences reads. Steps were: Bowtie2 (Version 2.2.5) was used to map raw sequencing reads to rRNA sequence. Remaining reads were mapped to dm6 and transposon consensus using using STAR (Version 2.5.2b) and Hisat2. Transcript abundance for each gene, transposon, and piRNA cluster (rpkm) was counted using BEDTools (Version 2.27.1).
piSet_srnaseq was used to analyze small RNA sequencing reads. Steps were: the 3ʹ end adaptor (TGGAATTCTCGGG) was removed via cutadapt (Version 1.15) and the raw small RNA-seq reads were mapped to rRNA, miRNA hairpin, snoRNA, snRNA, and tRNA sequence allowing for no mismatches using Bowtie (Version 1.1.0). The remaining reads were mapped to the Drosophila genome (dm6) and transposon consensus sequences. Small RNA abundance was normalized to unique mapping reads.
Assembly: dm6
Supplementary files format and content: tab deliniated txt files containing RMPM values

organism: Drosophila melanogaster

source_name: Ovary

extract_protocol:
Total RNA was extracted from 2-4 day old female ovaries using the MirVana kit (Ambion).
For Long RNA-seq, rRNA was depleted using antisense rRNA oligo hybridization followed by RNase H digestion, RNA Fragmentation, Reverse Transcription, dUTP incorporation, end Repair, size selection using Ampure XP beads, A-tailing, Adaptor ligation, UDG treatment and PCR amplification.
For Small RNA-seq, small RNAs 18-29 nucleotide long were isolated using polyacrylamide gel purification followed by 2S rRNA depletion, 3’ adaptor ligation, 5’ adaptor ligation, reverse transcription, and PCR amplification.

value: Ovary

value: vas RG/PH

tag: age

value: 2-4 day old


title: Ctrl, scRNAseq

description:
Library name: Sample1
10x Genomics

value: Control


title: iMN, Isogenic control, line1, G4C2 probe

city: Baltimore

first: Mingming

last: Liu

state: MD

address: 615 N. Wolfe Street

department: BMB, BSPH

institute: Johns Hopkins University

description: Library name: Isogenic_CTRL1_G4C2

library_source: genomic

data_processing:
Raw sequencing reads were processed with TrimGalore v.0.6.7 and quality of the raw sequencing reads was assessed using FastQC v.0.11.9
The trimmed reads were aligned to the human genome (hg19) using Bowtie v.2.3.5.1
Peaks were identified using the MACS2 v.2.1.1 software and filtered using a q-value cutoff of 0.01
BigWig files were generated using deepTools.
Assembly: hg19
Supplementary files format and content: BigWig files for each sample
Library strategy: ChIRP-seq

molecule: genomic DNA

source_name: iMNs

extract_protocol:
Cells were fixed with 1% glutaraldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a sonicator (Diagenode) until the chromatin DNA was 100–500 bp in size.
ChIRP-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit complemented with  NEBNext Multiplex Oligos for Illumina by following the manufacturer's manual. Libraries were validated using the Agilent High Sensitivity DNA Kit.

tag: cell line

value: iMNs

value: Motor Neuron

value: Isogenic control


title: OT-II_PBS

description: Library name: Sample 3

value: Donor OT-II cells

value: PBS


title: TNF rep2

country: China

description: Library name: SAMPLES8

value: Human embryonic kidney 293


title: CTR rep3

description: Library name: SAMPLES3

value: WT

value: Mock


title: LongRNA_vas RG/PH_rep1


title: Host_PBS

description: Library name: Sample 1

value: Lymph node


title: iMN, Control, line3, Scramble probe

description: Library name: iMN_CTRL3_Scramble


title: CTR rep2

description: Library name: SAMPLES2


title: iMN, Control, line3, Input probe

description: Library name: iMN_CTRL3_Input


title: iMN, Isogenic control, line1, Antisense probe

description: Library name: Isogenic_CTRL1_AS


title: LongRNA_mnk, vas RG/PH_rep2

value: mnk, vas RG/PH


title: LongRNA_mnk; thoc7 d/Df_rep2

value: mnk; thoc7 d/Df


title: LongRNA_thoc7 d/Df_rep2

value: thoc7 d/Df


title: TNF rep1

description: Library name: SAMPLES7

value: TNFa


title: iMN, Control, line2, Scramble probe

description: Library name: iMN_CTRL2_Scramble


title: iMN, Control, line3, G4C2 probe

description: Library name: iMN_CTRL3_G4C2


title: LongRNA_mnk; thoc7 d/Df_rep1

value: Ovary


title: DNA from Panc02 mutagenic agent-derived PDAC cell line

type: genomic

city: Brussels

first: Patrick

last: Jacquemin

address: Avenue Hippocrate 75

country: Belgium

institute: de Duve Institute, Université catholique de Louvain

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: Rnbeads package in R environment

label: Cy3 and Cy5

source_name: mutagenic agent-derived PDAC

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from acinar and ductal cells, PDAC cell line, primary tumor tissues, and orthotopic tumors using the QIAamp DNA Mini Kit and QIAamp DNA Micro Kit (Qiagen), according to the manufacturer’s instructions. Proteinase K digestion and RNAse treatment was performed to all samples. The concentration of double-stranded DNA was quantified using a fluorescence-based assay (QuantiFluor ONE dsDNA System, Promega).

value: mutagenic agent-derived PDAC

value: Kras-mut Smad4-mut


title: CTR rep1

description: Library name: SAMPLES1


title: LongRNA_thoc7 d/Df_rep1

value: 2-4 day old


title: DNA from KC-Pten-4 progenitor-derived PDAC cell line

description: test; Progenitor:Kpten

source_name: progenitor-derived PDAC cell line

value: progenitor-derived PDAC cell line

value: Pdx1Cre; KrasG12D/+; Ptenfl/fl


title: iMN, Control, line2, G4C2 probe

description: Library name: iMN_CTRL2_G4C2

value: iMNs

value: Motor Neuron

value: Control


title: PD, Sample_10

city: Incheon

first: Juwon

last: Kang

address: 85, Songdogwahak-ro

department: College of Pharmacy

country: South Korea

institute: Yonsei University

description: Library name: 13977-3

data_processing:
Trimming: Trimmomatic v0.39-1
Alignment: STAR v2.7.8a (GRCh38.105)
Gene expression quantification: RSEM v1.3.3
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes TPM for each samples

source_name: urothelial carcinoma of bladder

extract_protocol:
Total RNA was extracted from FFPE tumor samples using the RNeasy FFPE kit (Qiagen, Hilden, Germany)
SureSelectXT RNA Direct Reagent Kit

value: urothelial carcinoma of bladder

value: primary tumor cells

value: Gemcitabine+Cisplain

tag: group

value: Progressive Disease


title: PD, Sample_9

description: Library name: 25182-12


title: iMN, Control, line2, Input probe

description: Library name: iMN_CTRL2_Input


title: LongRNA_mnk, uap56 sz15/28_rep3

value: mnk, uap56 sz15/28


title: iMN, C9-ALS, line4, Input probe

description: Library name: iMN_C9ALS4_Input


title: LongRNA_mnk, uap56 sz15/28_rep1


title: iMN, C9-ALS, line4, G4C2 probe

description: Library name: iMN_C9ALS4_G4C2


title: iMN, C9-ALS, line4, Scramble probe

description: Library name: iMN_C9ALS4_Scramble


title: PR, Sample_6

description: Library name: 13129-4

value: Partial Response


title: LongRNA_uap56 sz15/28_rep2


title: LongRNA_mnk, uap56 sz15/28_rep2


title: LongRNA_uap56 sz15/28_rep3


title: PR, Sample_7

description: Library name: 23988-1


title: DNA from KC-Pten-3 progenitor-derived PDAC cell line

description: test; Progenitor:Kpten


title: iMN, C9-ALS, line3, Scramble probe

description: Library name: iMN_C9ALS3_Scramble


title: PR, Sample_5

description: Library name: 17198-NG2


title: DNA from KRC_3617 progenitor-derived PDAC cell line

description: test; Progenitor:KR

value: Ptf1aCre; KrasG12D/+; Rnf43fl/fl


title: LongRNA_uap56 sz15/28_rep1


title: PR, Sample_4

description: Library name: 2320-7


title: DNA from 7160c5 progenitor-derived PDAC cell line

description: test; Progenitor:KP

value: Pdx1Cre; KrasG12D/+; Trp53R172H/+


title: iMN, C9-ALS, line3, Input probe

description: Library name: iMN_C9ALS3_Input


title: LongRNA_mnk, rhi 02/KG_rep3

value: Ovary

value: mnk, rhi 02/KG


title: PR, Sample_2

description: Library name: 21470-4


title: iMN, C9-ALS, line3, G4C2 probe

description: Library name: iMN_C9ALS3_G4C2


title: PR, Sample_1

description: Library name: 24397-2


title: LongRNA_mnk, rhi 02/KG_rep1


title: LongRNA_mnk, rhi 02/KG_rep2


title: iMN, C9-ALS, line2, Scramble probe

description: Library name: iMN_C9ALS2_Scramble


title: LongRNA_rhi 02/KG_rep3

value: rhi 02/KG


title: iMN, C9-ALS, line2, G4C2 probe

description: Library name: iMN_C9ALS2_G4C2


title: PR, Sample_3

description: Library name: 13911-3


title: DNA from KC-Pten-2 progenitor-derived PDAC cell line

description: test; Progenitor:Kpten


title: DNA from KPC-T progenitor-derived PDAC cell line

description: test; Progenitor:KP

value: Ptf1aCre; KrasG12D/+; Trp53R172H/+


title: LongRNA_rhi 02/KG_rep2

value: 2-4 day old


title: PD, Sample_8

description: Library name: 14724-2


title: PCS_201_010 cl5 testis-like organoids (day 21)

city: Parkville, Melbourne

first: Svenja

last: Pachernegg

state: VIC

address: 50 Flemington Road

department: Genomic Medicine

country: Australia

institute: Murdoch Children's Research Institute

description: Library name: D21

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation were performed using the Cell Ranger software.
Assembly: Homo_sapiens.GRCH38
Supplementary files format and content: Tab-separated value and matrix files

molecule: polyA RNA

source_name: testis-like organoids

extract_protocol:
Two pooled Day 21 organoids were dissociated with 1 ml of a 1:1 TrypLE/Accutase solution in an 1.5-ml tube at 37°C for 20 min, with occasional mixing (flicking) until large clumps were no longer clearly visible. 1 ml of PBS supplemented with 0.04% BSA was added to the cells before passing through a 40 µl FACS tube cell strainer (Falcon). Following centrifugation at 300 g for 3 min, the supernatant was discarded and cells resuspended in 50 µl PBS with 0.04% BSA. Viability and cell number were assessed.
Libraries for scRNA-seq were prepared using the singlce RNA 3' gene expression kit (10x Genomics) according to the manufacturer's instructions.

value: testis-like organoids

value: testicular cells


title: iMN, C9-ALS, line2, Input probe

description: Library name: iMN_C9ALS2_Input

value: iMNs

value: Motor Neuron


title: LongRNA_rhi 02/KG_rep1


title: DNA from 3616 progenitor-derived PDAC cell line

description: test; Progenitor:KP

value: progenitor-derived PDAC cell line


title: DNA from 6556c4 progenitor-derived PDAC cell line

description: test; Progenitor:KP


title: PCS_201_010 cl5 testis-like organoids (day 18), biol rep 4

description:
Library name: D18.17
Column name in RNA-seq_raw_counts: D18.17

data_processing:
Sequence reads were trimmed for adapter reads/low quality reads and mapped to GRCH38 using Galaxy (https://galaxyproject.org/).
Assembly: Homo_sapiens.GRCH38
Supplementary files format and content: csv file includes raw counts for each sample

extract_protocol:
RNA was extracted using the ReliaPrep RNA Cell Miniprep System (Promega) including DNase treatment (Promega) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using the TruSeq stranded mRNA kit (Illumina) according to the manufacturer's instructions.


title: DNA from 6499c3 progenitor-derived PDAC cell line

description: test; Progenitor:KP


title: iMN, C9-ALS, line1, Sense probe

description: Library name: iMN_C9ALS1_S


title: iMN, C9-ALS, line1, Scramble probe

description: Library name: iMN_C9ALS1_Scramble


title: DNA from KRC_3968 progenitor-derived PDAC cell line

description: test; Progenitor:KR


title: DNA from 6499c4 progenitor-derived PDAC cell line

description: test; Progenitor:KP


title: LongRNA_mnk_rep3

value: mnk


title: iMN, C9-ALS, line1, G4C2 probe

description: Library name: iMN_C9ALS1_G4C2


title: LongRNA_mnk_rep1


title: iMN, C9-ALS, line1, Input probe

description: Library name: iMN_C9ALS1_Input


title: iMN, C9-ALS, line1, HRE-M probe

description: Library name: iMN_C9ALS1_HRE-M


title: PCS_201_010 cl5 testis-like organoids (day 18), biol rep 1

description:
Library name: D18.5
Column name in RNA-seq_raw_counts: D18.5


title: LongRNA_w1_rep3


title: PCS_201_010 cl5 iPSCs, undifferentiated (day -1), biol rep 3

description:
Library name: D_1.3
Column name in RNA-seq_raw_counts: D_1.3

source_name: undifferentiated iPSCs

value: undifferentiated iPSCs

value: human iPSCs


title: iMN, C9-ALS, line1, Antisense probe

description: Library name: iMN_C9ALS1_AS


title: DNA from 3213 progenitor-derived PDAC cell line

description: test; Progenitor:KP


title: PCS_201_010 cl5 testis-like organoids (day 18), biol rep 2

description:
Library name: D18.15
Column name in RNA-seq_raw_counts: D18.15


title: LongRNA_mnk_rep2


title: DNA from KPC792 progenitor-derived PDAC cell line

description: test; Progenitor:KP


title: LongRNA_w1_rep2


title: PCS_201_010 cl5 iPSCs, undifferentiated (day -1), biol rep 2

description:
Library name: D_1.2
Column name in RNA-seq_raw_counts: D_1.2


title: DNA from 6556c3 progenitor-derived PDAC cell line

description: test; Progenitor:KP


title: DNA from aM4222_1 ductal-derived PDAC orthotopic tumor

description: discovery; Ductal1:KP

source_name: ductal-derived PDAC orthotopic tumor in NSG

value: Sox9CreER; KrasG12D/+; Trp53fl/fl


title: LongRNA_w1_rep1


title: PCS_201_010 cl5 iPSCs, undifferentiated (day -1), biol rep 1

description:
Library name: D_1.1
Column name in RNA-seq_raw_counts: D_1.1


title: DNA from 7160c2 progenitor-derived PDAC cell line

description: test; Progenitor:KP


title: B lymhocyte, C9-ALS, line1, G4C2 probe, TPL mock

description: Library name: ChIRP_B_C9ALS1_TPLm

source_name: B lymphocyte

value: B lymphocyte


title: smallRNA_mnk; armi 72.1/1_rep2

value: mnk; armi 72.1/1


title: DNA from aM4222_2 ductal-derived PDAC orthotopic tumor

description: discovery; Ductal1:KP

value: ductal-derived PDAC orthotopic tumor in NSG


title: B lymhocyte, C9-ALS, line1, G4C2 probe, TPL treatment

description: Library name: ChIRP_B_C9ALS1_TPLp

value: 500 nM triptolide (TPL)


title: B lymhocyte, C9-ALS, line1, G4C2 probe, PDS treatment

description: Library name: ChIRP_B_C9ALS1_PDSp

value: 5 µM pyridostatin (PDS)


title: B lymhocyte, C9-ALS, line1, G4C2 probe, PDS mock

description: Library name: ChIRP_B_C9ALS1_PDSm


title: Monocytes, SLE serum, 12hours culture, Biol rep 1

city: Hong Kong

first: Chi Ho

last: Lin

address: 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam

department: Centre for PanorOmic Sciences

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Raw sequencing reads were assigned to respective samples using the Illumina bcl2fastq pipeline and filtered for adapter sequences, low quality sequences, and rRNA sequences.
Human Genome GRCh38 was downloaded from GENCODE and used as reference genome. Filtered quality reads (length ≥ 40bp) were mapped to GRCh38 using STAR Version 2.5.2 (default parameters).
RSEM Version 1.2.31 was used to quantify the expression of genes and transcripts.
Differentially expression analysis was done using DESeq2 for each sample pair. Differentially expressed genes/transcripts were defined as adjusted p-value <0.1.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include normalized reads count for each sample

source_name: Peripheral blood

growth_protocol: 2x10^7 of freshly isolated human monocytes were suspended in complete RPMI medium 1640 supplemented with 10% Fetal Bovine Serum, 1X Non-Essential Amino Acids, 1mM sodium pyruvate, 20mM GlutaMAX™ supplement, 50μM 2-Mercaptoethanol and 100U/mL of penicillin-streptomycin.

extract_protocol:
Total RNA was purified using the Qiagen miRNeasy Mini Kit. 1μg of starting RNA was used for subsequent library contruction
cDNA libraries were prepared from fragmented rRNA-depleted RNA using the NEBNext® Ultra II Directional RNA Library Prep Kit, in accordance to the manufacturer's instruction

treatment_protocol: In the IFN-α culture group, monocytes isolated from three healthy control (HC) donors were cultured for 12 hours with or without IFN-α (250 IU/mL). In the serum culture group, monocytes isolated from one healthy individual were cultured for 12 hours with 10% (v/v) sera obtained from three healthy control (HC) or three SLE subjects.

value: Peripheral blood

value: CD14+ Monocytes

value: 10% SLE patient serum

tag: treatment time


title: Monocytes, SLE serum, 12hours culture, Biol rep 2


title: DNA from J23_697 ductal-derived PDAC primary tumor

description: discovery; Ductal2:KP

source_name: ductal-derived PDAC primary tumor

value: ductal-derived PDAC primary tumor


title: smallRNA_armi 72.1/1_rep2

value: Ovary

value: 2-4 day old


title: Monocytes, SLE serum, 12hours culture, Biol rep 3


title: B lymhocyte, C9-ALS, line1, Input, drug treatment control

description: Library name: ChIRP_B_C9ALS1_Input


title: DNA from J23_554-2_PT ductal-derived PDAC primary tumor

description: discovery; Ductal2:KP


title: smallRNA_armi 72.1/1_rep1


title: DNA from KPC827 progenitor-derived PDAC cell line

description: test; Progenitor:KP

value: Pdx1Cre; KrasG12D/+; Trp53R172H/+


title: smallRNA_mnk; armi 72.1/1_rep1


title: DNA from aF3682 acinar-derived PDAC orthotopic tumor

description: validation; Acinar1:KP

source_name: acinar-derived PDAC orthotopic tumor in NSG

value: ElaCreER; KrasG12D/+; Trp53R172H/+


title: Monocytes, HC serum, 12hours culture, Biol rep 3

value: 10% Healthy donor serum


title: B lymhocyte, Control, line2, Scramble probe

description: Library name: B_CTRL2_Scramble

value: Control


title: B lymhocyte, Control, line2, Input

description: Library name: B_CTRL2_Input


title: smallRNA_mnk; ago3 t2/t3_rep1

value: mnk; ago3 t2/t3


title: Breast cancer tissue

city: Rende

first: Rosamaria

last: Lappano

state: Cs

address: via P. Bucci

country: Italy

institute: University of Calabria

description:
Library name: Sample 1
10x Genomics

data_processing:
Thereafter, single Cell RNA-seq data processing was performed by processing of Chromium single-cell RNA-seq output by Cell Ranger v 3.1.0 to align reads on reference genome (hg38). In particular, Cell Ranger count takes FASTQ files and performs alignment, filtering, barcode counting, and UMI counting. It uses the Chromium cellular barcodes to generate feature-barcode matrices.
Assembly: Homo sapiens hg38
Supplementary files format and content: tab-delimited includes features, barcodes and matrix with raw counts.

source_name: breast tumor

extract_protocol:
The tissue sample was minced into approximately 1–2 mm3 pieces, washed with phosphate-buffered saline (PBS), and placed in Accumax cell detachment solution (Merck Life Science, Milan, Italy) for 45 min at room temperature with gentle but constant mixing. After letting the remaining tissue pieces settle down (for 2 min), the supernatant was filtered to obtain a single-cell suspension. Next, cells were centrifuged (300 rcf for 5 min). After discarding the supernatant, cells were resuspended into chilled 1X DPBS and centrifuged (300 rcf for 5 min). After discarding the supernatant, chilled 100% methanol was added drop by drop to 1×10^6 cells that were stored at -80°C for scRNA-seq library construction and sequencing.
The tube containing methanol-fixed cells, stored at -80°C, was equilibrated to 4°C for 5 min. Fixed cells were centrifugated at 1.000 RCF for 5 min at 4°C. After the supernatant was removed without disrupting the cell pellet, an appropriate volume of Wash-Resuspension Buffer (0.04% BSA - 1mM DTT - 0.2 U/ul RNase Inhibitor in 3X SSC Buffer) was added to obtain the desired cell concentration. Cell concentration was determined using a Countess II Automated Cell Counter (Thermo Fisher Scientific, Waltham, MA). The Trypan Blue staining of the methanol-fixed cells showed that 100% of the cells were dead, indicating that all cells were effectively fixed and permeabilized. For the library preparation and sequencing, Chromium Controller and Chromium NextGEM Single Cell 3’ Reagents Kit v3.1 (10X Genomics, Pleasanton, CA) have been used for partitioning cells into Gel Beads-in-emulsion (GEMs), where all generated cDNA shares a common 10x barcode. Libraries were generated from the cDNA following the manufacturer’s instructions. Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size. TruSeq Read 1 (read 1 primer sequence) is added to the molecules during GEM incubation. P5, P7, a sample index, and TruSeq Read 2 (read 2 primer sequence) are added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers were used in Illumina bridge amplification. After checking with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Agilent Bioanalyzer DNA assay (Agilent Technologies, Santa Clara, CA), libraries were prepared for sequencing and sequenced on paired-end 150 bp mode on NovaSeq6000 (Illumina, San Diego, CA).

value: breast tumor


title: DNA from KPC865 progenitor-derived PDAC cell line

description: test; Progenitor:KP

value: progenitor-derived PDAC cell line


title: DNA from J52_556-2 acinar-derived PDAC primary tumor

description: validation; Acinar2:KP

source_name: acinar-derived PDAC primary tumor

value: acinar-derived PDAC primary tumor

value: Ptf1aCreER; KrasG12D/+; Trp53fl/fl


title: smallRNA_mnk; ago3 t2/t3_rep2


title: B lymhocyte, Control, line1, Scramble probe

description: Library name: B_CTRL1_Scramble

value: B lymphocyte


title: Monocytes, 250IU/mL IFN-alpha, 12hours culture, Biol rep 2

value: 250IU/mL IFN-α


title: B lymhocyte, Control, line2, G4C2 probe

description: Library name: B_CTRL2_G4C2


title: smallRNA_ago3 t2/t3_rep2

value: ago3 t2/t3


title: PCS_201_010 cl5 testis-like organoids (day 18), biol rep 3

description:
Library name: D18.16
Column name in RNA-seq_raw_counts: D18.16

value: testis-like organoids

value: testicular cells


title: smallRNA_ago3 t2/t3_rep1


title: Monocytes, 250IU/mL IFN-alpha, 12hours culture, Biol rep 3

value: Peripheral blood

value: CD14+ Monocytes


title: DNA from J52_267 acinar-derived PDAC primary tumor

description: validation; Acinar2:KP


title: B lymhocyte, C9-ALS, line4, Scramble probe

description: Library name: B_C9ALS4_Scramble


title: smallRNA_mnk, aub HN/QC_rep3

value: Ovary

value: mnk, aub HN/QC

value: 2-4 day old


title: B lymhocyte, Control, line1, HRE-M probe

description: Library name: B_CTRL1_HRE-M


title: smallRNA_mnk, aub HN/QC_rep2


title: Monocytes, 250IU/mL IFN-alpha, 12hours culture, Biol rep 1


title: DNA from J23_553 ductal-derived PDAC cell line

description: discovery; Ductal2:KP

source_name: ductal-derived PDAC cell line

value: ductal-derived PDAC cell line

value: Sox9CreER; KrasG12D/+; Trp53fl/fl


title: Monocytes, Unstimulated, 12hours culture, Biol rep 3

value: Unstimulated


title: DNA from BF5960 ductal-derived PDAC cell line

description: discovery; Ductal2:KP


title: DNA from J23_554-2_CL ductal-derived PDAC cell line

description: discovery; Ductal2:KP


title: B lymhocyte, C9-ALS, line3, Input

description: Library name: B_C9ALS3_Input


title: midAna SHFSCs input in October, male (bio rep 2)

city: Shenyang

first: Huiling

last: Xue

address: 120 Dongling Road,110866 Shenyang,China

institute: Shenyang Agricultural University

description: Library name: Sample 20

data_processing:
SHFSCs were performed using bcl2fast2 for Novaseq output.
Using Skewer v0.2.2, discarding reads left with < 20 bp.
ChlP-seq reads were aligned to the ARS1 (GCA_001704415.1) genome using BWA (0.7.12-r1039). Only uniquely mapping reads with at most two mismatches were retained.
Score representsthe normalized coverage of DNA fragments at a given genomic coordinate. Narrow peak files were generated using MACS v2.1.2 with default settings.
Assembly: ARS1 (GCA_001704415.1)
Supplementary files format and content: bigWig

organism: Capra hircus

source_name: Secondary hair follicle stem cells from goat skin

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicilin/streptomycin. Cells werecultured at 37 ℃ at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysischromatin was sonicated.
The DNA library construction for ChIP sequencing was performed according to the operating instructions for the NEB Next® ChIP-seq Library Prep Kit for Illumina® (NEB, USA).

tag: Sex

value: male

value: Secondary hair follicle stem cells


title: smallRNA_aub HN/QC_rep1

value: aub HN/QC


title: DNA from J52_267-1 acinar-derived PDAC cell line

description: validation; Acinar2:KP

source_name: acinar-derived PDAC cell line

value: acinar-derived PDAC cell line

value: Ptf1aCreER; KrasG12D/+; Trp53fl/fl


title: DNA from J52_530-2 acinar-derived PDAC cell line

description: validation; Acinar2:KP


title: midAna SHFSCs input in October, female (bio rep 1)

description: Library name: Sample 19

value: Secondary hair follicle stem cells from goat skin

value: female


title: smallRNA_mnk, vas PD/PH_rep2

source_name: Ovary

value: mnk, vas PD/PH


title: smallRNA_mnk, vas PD/PH_rep1


title: B lymhocyte, C9-ALS, line3, G4C2 probe

description: Library name: B_C9ALS3_G4C2

value: B lymphocyte


title: smallRNA_mnk, aub HN/QC_rep1


title: DNA from F3513 acinar-derived PDAC cell line

description: discovery; Acinar1:KP

value: ElaCreER; KrasG12D/+; Trp53R172H/+


title: DNA from M4028 ductal-derived PDAC cell line

description: discovery; Ductal1:KP


title: midAna SHFSCs H3K79me2 in October, male (bio rep 2)

description: Library name: Sample 16


title: B lymhocyte, C9-ALS, line2, Scramble probe

description: Library name: B_C9ALS2_Scramble


title: B lymhocyte, C9-ALS, line2, G4C2 probe

description: Library name: B_C9ALS2_G4C2


title: Monocytes, Unstimulated, 12hours culture, Biol rep 2

value: Peripheral blood

value: CD14+ Monocytes


title: midAna SHFSCs H3K4me3 in October, male (bio rep 2)

description: Library name: Sample 18


title: midAna SHFSCs H3K4me3 in October, female (bio rep 1)

description: Library name: Sample 17


title: smallRNA_vas PD/PH_rep1

value: Ovary

value: vas PD/PH


title: smallRNA_vas PD/PH_rep2

value: 2-4 day old


title: smallRNA_aub HN/QC_rep2


title: DNA from Sox9+3 normal ductal cells

description: discovery; Ductal:EGFP

source_name: FACS-purified normal ductal cells

value: FACS-purified normal ductal cells


title: DNA from F3682 acinar-derived PDAC cell line

description: discovery; Acinar1:KP


title: B lymhocyte, C9-ALS, line1, Scramble probe

description: Library name: B_C9ALS1_Scramble


title: DNA from F3199 acinar-derived PDAC cell line

description: discovery; Acinar1:KP


title: smallRNA_mnk, vas RG/PH_rep3

value: mnk, vas RG/PH


title: midAna SHFSCs H3K36me3 in October, male (bio rep 2)

description: Library name: Sample 14

value: male


title: DNA from M4222 ductal-derived PDAC cell line

description: discovery; Ductal1:KP

value: ductal-derived PDAC cell line

value: Sox9CreER; KrasG12D/+; Trp53fl/fl


title: smallRNA_mnk, vas RG/PH_rep2


title: Isogenic control iMNs,S9.6 IP

description: Library name: Isogenic_CTRL1-IP

data_processing:
Raw sequencing reads were processed with TrimGalore v.0.6.7 and quality of the raw sequencing reads was assessed using FastQC v.0.11.9
The processed reads were mapped to the human genome (hg19) using Bowtie2. Duplicated reads and reads aligned to mitochondrial genome were discarded. The retained BAM files were then sorted, indexed, and used to generate bigWig files
BigWig files were generated using deepTools.
Assembly: hg19
Supplementary files format and content: bigwig files for each sample

source_name: iMNs

extract_protocol:
The genomic DNA was purified and digensted with a mix of restriction enzymes [HindIII (ThermoFisher, FD0504), EcoRI (ThermoFisher, FD0274), XbaI (ThermoFisher, FD0684), and BamHI (ThermoFisher, FD0054)] at 37 °C for 2 h. The digested samples were split into two partsparts, and one part was treated with RNase H (NEB, M0297S) for 37 °C for 2 h, followed by purification with Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) (ThermoFisher, 15593031).
The libraries were constrcuted  using the NEBNext® Ultra™ II DNA Library Prep Kit complemented with  NEBNext Multiplex Oligos for Illumina by following the manufacturer's manual.

value: iMNs

value: Motor Neuron

value: Isogenic control


title: B lymhocyte, C9-ALS, line1, HRE-M probe

description: Library name: B_C9ALS1_HRE-M


title: smallRNA_mnk, vas RG/PH_rep1


title: midAna SHFSCs H3K36me3 in October, female (bio rep 1)

description: Library name: Sample 13

value: Secondary hair follicle stem cells from goat skin

value: female

value: Secondary hair follicle stem cells


title: DNA from M4058 ductal-derived PDAC cell line

description: discovery; Ductal1:KP


title: smallRNA_vas RG/PH_rep3

value: vas RG/PH


title: midAna SHFSCs H3K79me2 in October, female (bio rep 1)

description: Library name: Sample 15


title: DNA from Ela+3 normal acinar cells

description: discovery; Acinar:YFP

source_name: FACS-purified normal acinar cells

value: FACS-purified normal acinar cells


title: DNA from J52_529 acinar-derived PDAC cell line

description: validation; Acinar2:KP

value: acinar-derived PDAC cell line

value: Ptf1aCreER; KrasG12D/+; Trp53fl/fl


title: midAna SHFSCs H3K27me3 in October, male (bio rep 2)

description: Library name: Sample 12


title: Isogenic control iMNs, Input.

description: Library name: Isogenic_CTRL1-Input


title: Monocytes, Unstimulated, 12hours culture, Biol rep 1

value: Peripheral blood

value: CD14+ Monocytes

value: Unstimulated


title: midAna SHFSCs H3K27me3 in October, female (bio rep 1)

description: Library name: Sample 11


title: DNA from Sox9+1 normal ductal cells

description: discovery; Ductal:EGFP

value: FACS-purified normal ductal cells


title: DNA from Sox9+2 normal ductal cells

description: discovery; Ductal:EGFP


title: 379_R

city: Oslo

first: Adam

middle: P

last: Sharples

address: 220 Sognsveien

country: Norway

institute: Norwegian School of Sport Sciences

description: Library name: GC-AS-10656-79R_S17

data_processing:
Resulting FastQ files were imported and processed in Partek Flow® software (version 12.4.0; Partek, Inc. Missouri, USA) to filter contaminants (rDNA/tRNA/mtrDNA) using Bowtie 2 (version 2.2.5) and align reads to rn7 Rattus norvegicus genome assembly using Spliced Transcripts Alignment to a Reference (STAR) alignment tool (version 2.7.3a) 75. Total number of pre/post-aligned reads was 49/49 million (59 bp average read length). Phred scores were >33, thus trimming and filtering of reads was not required. Normalized differential gene expression analysis was performed using DESeq2 median of ratios. For differental expression analysis: All experimental conditions in the left limb (atrophy, recovery, repeated atrophy) were normalized to a pooled contralateral non-surgical right limb control. As no differentially expressed genes (DEGs) were detected between sham-operated and contralateral control samples, sham samples were excluded, and contralateral non-surgical limbs were pooled as the control group. Pooling was justified to increase statistical power and reduce variability, given the biological equivalence of these control tissues. Genes with ≥20% fold change (FC) and false discovery rate (FDR) ≤ 0.05 were considered DEGs.
Assembly: rn7 Rattus norvegicus genome assembly
Supplementary files format and content: .txt file contains normalised counts (CPM)

organism: Rattus norvegicus

source_name: Skeletal Muscle

extract_protocol:
Skeletal muscle tissue (tibialis anterior) from aged rats (27 ± 4 mg) was added to 2 ml homogenizing mix tubes (Fisherbrand™, Fisher Scientific) containing 600 μl Buffer RLT (Qiagen) with added 1% β-Mercaptoethanol (β-ME) before transferring to a tissue homogenizing instrument (MagNA Lyser; Roche) for subsequent homogenization (3 × 45 s at 6000 rpm, placing samples on ice for 5 mins between each disruption). Following homogenization, RNA was purified using a RNeasy® Mini kit (Qiagen) and treated with DNase (RNAse-Free DNase Set, Qiagen) as per the manufacturer’s instructions. RNA quantity and purity (406 ± 215 ng/mg tissue, 2.1 ± 0.0 A260/A280 and 2.2 ± 0.2 A260/A230) samples were quantified via spectrophotometry (QIAxpert®, software version 2.4, Qiagen) and concentrations confirmed via fluorometry (Qubit®, Qiagen). RNA integrity prior to sequencing was confirmed via Agilent Bioanalsyer 2100 with RIN scores 8.29 + 0.62 for all samples.
100 ng of total RNA from each sample was used to prepare mRNA libraries using the NEBNext mRNA isolation kit in conjunction with the NEBNext Ultra II Directional RNA Library preparation kit (New England Biolabs, Massachusetts, USA), and samples were randomised before preparation. Fragmentation of isolated mRNA prior to first strand cDNA synthesis was carried out using incubation conditions recommended by the manufacturer for an insert size of 300 bp (94°C for 10 minutes). 13 cycles of PCR were performed for final library amplification. Resulting libraries were quantified using the Qubit 4.0 spectrophotometer (Life Technologies, California, USA) and average fragment size assessed using the Agilent 4200 Tapestation with D1000 screentape (Agilent Technologies, Waldbronn, Germany). A final sequencing pool was created for each project using equimolar quantities of each sample with compatible indexes. 59 bp paired-end reads were generated for each library using the Illumina NextSeq 2000 in conjunction with the NextSeq 2000 P3 100 cycle kit (Illumina Inc., Cambridge, UK).

value: Skeletal Muscle

tag: limb

value: Right

tag: condition

value: control (CTRL)

tag: time

value: Repeated Atrophy


title: Isogenic control iMNs, IgG.

description: Library name: Isogenic_CTRL1-IgG

value: iMNs

value: Motor Neuron


title: smallRNA_vas RG/PH_rep2

value: Ovary

value: 2-4 day old


title: Monocytes, HC serum, 12hours culture, Biol rep 2

value: 10% Healthy donor serum


title: 377_R

description: Library name: GC-AS-10656-77R_S12

value: Recovery


title: earlyAna SHFSCs input in April, female (bio rep 1)

description: Library name: Sample 9

value: Secondary hair follicle stem cells from goat skin

value: female

value: Secondary hair follicle stem cells


title: Isogenic control iMNs, Rnase H, input

description: Library name: Isogenic_CTRL1-H-Input

value: Isogenic control

value: Rnase H


title: earlyAna SHFSCs input in April, male (bio rep 2)

description: Library name: Sample 10

value: male


title: DNA from Ela+2 normal acinar cells

description: discovery; Acinar:YFP

value: FACS-purified normal acinar cells


title: B lymhocyte, C9-ALS, line2, Input

description: Library name: B_C9ALS2_Input

value: B lymphocyte


title: Isogenic control iMNs, Rnase H, S9.6 IP

description: Library name: Isogenic_CTRL1-H-IP


title: smallRNA_vas RG/PH_rep1

value: vas RG/PH


title: Monocytes, HC serum, 12hours culture, Biol rep 1

value: Peripheral blood

value: CD14+ Monocytes


title: B lymhocyte, C9-ALS, line4, Input

description: Library name: B_C9ALS4_Input


title: B lymhocyte, C9-ALS, line3, Scramble probe

description: Library name: B_C9ALS3_Scramble


title: C9-ALS iMNs, S9.6 IP

description: Library name: iMN_C9ALS1-IP

value: iMNs


title: 377_L

description: Library name: GC-AS-10656-77L_S3

value: Skeletal Muscle

value: Left

value: sham


title: C9-ALS iMNs, Input.

description: Library name: iMN_C9ALS1-Input

value: Motor Neuron


title: earlyAna SHFSCs H3K4me3 in April, male (bio rep 2)

description: Library name: Sample 8


title: 372_R

description: Library name: GC-AS-10656-72R_S2

value: Right

value: control (CTRL)

value: Atrophy


title: smallRNA_mnk; thoc7 d/Df_rep1

value: Ovary

value: mnk; thoc7 d/Df

value: 2-4 day old


title: earlyAna SHFSCs H3K4me3 in April, female (bio rep 1)

description: Library name: Sample 7

value: Secondary hair follicle stem cells from goat skin

value: female

value: Secondary hair follicle stem cells


title: DNA from Ela+1 normal acinar cells

description: discovery; Acinar:YFP

value: FACS-purified normal acinar cells


title: earlyAna SHFSCs H3K79me2 in April, male (bio rep 2)

description: Library name: Sample 6

value: male


title: smallRNA_thoc7 d/Df_rep2

value: thoc7 d/Df


title: C9-ALS iMNs, IgG.

description: Library name: iMN_C9ALS1-IgG

value: iMNs


title: 372_L

description: Library name: GC-AS-10656-72L_S11

value: Skeletal Muscle

value: TTX


title: smallRNA_thoc7 d/Df_rep1


title: 371_R

description: Library name: GC-AS-10656-71R_S5

value: Recovery


title: smallRNA_mnk; thoc7 d/Df_rep2


title: earlyAna SHFSCs H3K79me2 in April, female (bio rep 1)

description: Library name: Sample 5


title: 371_L

description: Library name: GC-AS-10656-71L_S23

value: Left

value: TTX+Recovery


title: smallRNA_mnk, uap56 sz15/28_rep3

value: mnk, uap56 sz15/28


title: C9-ALS iMNs, Rnase H-treated input

description: Library name: iMN_C9ALS1-H-Input

value: Motor Neuron

value: Rnase H


title: C9-ALS iMNs, Rnase H, S9.6 IP

description: Library name: iMN_C9ALS1-H-IP


title: Isogenic control iMNs, HMe antibody IP

description: Library name: Isogenic_CTRL1_Me

extract_protocol:
Cells were harvested and genomic DNA was purified with the Genomic DNA Extraction & Purification Kit (NEB, T3010L). Purified genomic DNA was diluted in TE buffer and fragmented to 200-800 bp with a sonicator (Diagenode).
The libraries were constrcuted  using the NEBNext® Ultra™ II DNA Library Prep Kit complemented with  NEBNext Multiplex Oligos for Illumina by following the manufacturer's manual.

value: Isogenic control


title: DNA from J23_499 ductal-derived PDAC primary tumor

description: discovery; Ductal2:KP

value: ductal-derived PDAC primary tumor

value: Sox9CreER; KrasG12D/+; Trp53fl/fl


title: earlyAna SHFSCs H3K36me3 in April, male (bio rep 2)

description: Library name: Sample 4

value: Secondary hair follicle stem cells from goat skin


title: 370_R

description: Library name: GC-AS-10656-70R_S6

value: Right

value: control (CTRL)


title: smallRNA_mnk, uap56 sz15/28_rep2

value: Ovary

value: 2-4 day old


title: 379_L

description: Library name: GC-AS-10656-79L_S21

value: sham

value: Repeated Atrophy


title: 370_L

description: Library name: GC-AS-10656-70L_S20

value: Skeletal Muscle


title: Isogenic control iMNs, Input

description: Library name: Isogenic_CTRL1_Input

value: iMNs


title: earlyAna SHFSCs H3K27me3 in April, male (bio rep 2)

description: Library name: Sample 2

value: male

value: Secondary hair follicle stem cells


title: 367_R

description: Library name: GC-AS-10656-67R_S13

value: Atrophy


title: 369_R

description: Library name: GC-AS-10656-69R_S14

value: Recovery


title: HCT116 dTAG SNIP1_dTAGv-1_RNA_seq_rep2

city: Pamplona

first: Igor

last: Ruiz de los Mozos

state: Nyp

address: C. del Sadar s/n

department: Department of Personalized Medicine

country: Spain

institute: NASERTIC

description:
Library name: SNIP1-dTAGv-1_RNA_seq_rep2
absence of SNIP1 protein

data_processing:
The primary transcript isoforms were determined following established protocols (Caizzi, L. et al. 2021).
RNA-sequencing data was processed using the NF-Core pipeline (Di Tommaso, P. et al. 2017) (Nextflow v23.04.1) from the NF-Core consortium (v3.14, available at https://github.com/nf-core/rnaseq; archived at https://zenodo.org/records/10471647). To identify the predominant isoform for each gene, sequencing reads were mapped with Salmon (Patro, R. & Kingsford, C. 2027) (v1.10.1) against curated UCSC RefSeq annotations (GRCh38, downloaded July 2024).
The isoform exhibiting the highest mean transcript-per-million (TPM) value across all samples was designated as the major isoform, provided it accounted for at least 70% of the gene’s isoform expression. Isoforms associated with overlapping genes and those located on chromosomes X, Y, and M were excluded.
Assembly: GRCh38
Supplementary files format and content: coverage file relative to genes on the forward DNA strand (bigWig)
Supplementary files format and content: coverage file relative to genes on the reverse DNA strand (bigWig)
Supplementary files format and content: Salmon transcript-level quantification of the sample, including feature length, effective length, TPM, and number of reads (quant.sf)

molecule: nuclear RNA

source_name: HCT116 dTAG SNIP1

growth_protocol: To prepare HCT116 dTAG SNIP1 cell line stably expressing inducible degradable SNIP1 protein we utilized CRISPR-Cas9 genome editing with the PITCh system (Sakuma et al., 2016, adopted protocol from Brand and Winter, 2019). Human colorectal HCT116 dTAG SNIP1 cell line was maintained in DMEM/high glucose media supplemented with L-glutamine, sodium pyruvate and 5% FBS at 37°C and 5% CO2.

extract_protocol:
Cells were washed twice with ice-cold PBS, scraped, pelleted at 500g for 3 min and treated for 5 min with 500 µl of cytoplasmic lysis buffer (10 mM Tris-Cl, pH=8, 0.32 M sucrose, 3 mM CaCl2, 2 mM MgCl2, 0.1 mM EDTA, 0.5 % TritonX-100, supplemented with 40 U/ml RNase inhibitor). Cytoplasmic RNA present in the supernatant was removed by centrifugation (500g for 3 min). Nuclear RNA was isolated from the remaining nuclear pellet using Tri-Reagent (Sigma, 93289).
For each sample, 250 ng of DNase treated RNA (Sigma, AMPD1) was used for rRNA depletion using RiboCop rRNA Depletion Kit (Lexogen, #144). Sequencing libraries were prepared using the NEBNext UltraExpress II Directional RNA Library Prep Kit for Illumina (NEB, E3330) according to the manufacturer protocol.

treatment_protocol: The dTAGv-1 was purchased from MedChem Express (HY-145514) and diluted in DMSO. HCT116 dTAG SNIP1 cells were plated onto 10 cm2 plates to reach 50 % confluency at the day of teatment. Next day cells were treated with solvent (DMSO) or 500 nM dTAGv-1 for 2 h.

value: HCT116 dTAG SNIP1

value: human colon

value: dTAG SNIP1

value: dTAGv-1 (500nM)

tag: batch

value: biol. rep 2


title: 369_L

description: Library name: GC-AS-10656-69L_S22

value: Left

value: TTX+Recovery


title: smallRNA_uap56 sz15/28_rep1

value: Ovary


title: Isogenic control iMNs, IgG

description: Library name: Isogenic_CTRL1_IgG

value: Motor Neuron

value: Isogenic control


title: smallRNA_mnk, rhi 02/KG_rep2

value: mnk, rhi 02/KG

value: 2-4 day old


title: earlyAna SHFSCs H3K27me3 in April, female (bio rep 1)

description: Library name: Sample 1

value: Secondary hair follicle stem cells from goat skin

value: female


title: C9-ALS iMNs, Input

description: Library name: iMN_C9ALS1_Input

value: iMNs


title: smallRNA_uap56 sz15/28_rep2


title: smallRNA_mnk, uap56 sz15/28_rep1

value: mnk, uap56 sz15/28


title: HCT116 dTAG SNIP1_dTAGv-1_RNA_seq_rep1

description:
Library name: SNIP1-dTAGv-1_RNA_seq_rep1
absence of SNIP1 protein

value: biol. rep 1


title: 367_L

description: Library name: GC-AS-10656-67L_S9

value: Skeletal Muscle

value: TTX

value: Atrophy


title: Isogenic control iMNs,HMe antibody IP

description: Library name: Isogenic_CTRL1_HMe


title: C9-ALS iMNs, Me antibody IP

description: Library name: iMN_C9ALS1_Me


title: smallRNA_mnk, rhi 02/KG_rep3


title: B lymhocyte, C9-ALS, line4, G4C2 probe

description: Library name: B_C9ALS4_G4C2

value: B lymphocyte


title: HCT116 dTAG SNIP1_DMSO_RNA_seq_rep2

description:
Library name: DMSO_RNA_seq_rep2
presence of SNIP1 protein

value: HCT116 dTAG SNIP1

value: human colon

value: dTAG SNIP1

value: DMSO

value: biol. rep 2


title: earlyAna SHFSCs H3K36me3 in April, female (bio rep 1)

description: Library name: Sample 3

value: Secondary hair follicle stem cells


title: HCT116 dTAG SNIP1_DMSO_RNA_seq_rep1

description:
Library name: DMSO_RNA_seq_rep1
presence of SNIP1 protein


title: C9-ALS iMNs, IgG

description: Library name: iMN_C9ALS1_IgG

value: Motor Neuron


title: 366_R

description: Library name: GC-AS-10656-66R_S4

value: Right

value: control (CTRL)

value: Repeated Atrophy


title: smallRNA_rhi 02/KG_rep3

value: Ovary

value: rhi 02/KG

value: 2-4 day old


title: mRNA-seq, HL60 cells, dCas9-HDAC, replicate 3

city: Bad Nauheim

first: Lei

last: Gu

state: Hessen

address: Parkstraße 1

department: Epigenetics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

description: Library name: dCas9-HDAC-3

data_processing:
Raw reads were trimmed to remove adapter sequences and low-quality bases using Trim Galore v0.6.7 (--stringency 4, --length 35, --quality 25). The quality of the filtered reads was assessed using FastQC v0.11.8 and summarized with MultiQC v1.11. Trimmed reads were aligned to the human hg19 reference genome using HISAT2 v2.2.1 (--dta). Gene-level read counts and expression levels were quantified and normalized using StringTie v2.2.1 with default parameters.
Raw reads were trimmed to remove adapter sequences using Trim Galore v0.6.7 (--stringency 4, --length 35, --quality 20). The trimmed reads were aligned to the Drosophila dm6 reference genome using Bowtie2 v2.4.5 with default parameters. Peaks were identified using MACS2 v2.2.7.1. bigWig files were generated with deepTools bamCoverage v3.5.1, with scores representing normalized fragment coverage at 1 bp resolution.
Assembly: hg19 for RNA-seq; dm6 for ChIP-seq
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: bigWig

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen). RNA quality (RIN > 9) was assessed using the TapeStation 4200 system (Agilent Technologies). Approximately 1 μg of RNA was used for sequencing library preparation.
Adult fruit flies were homogenized using a Dounce tissue grinder. Cells were fixed with 1% formaldehyde for 10 minutes, followed by quenching and cell lysis. Chromatin was then digested with micrococcal nuclease (MNase) at 37 °C for 15 minutes.
Preparation of RNA library and transcriptome sequencing was conducted by Biomarker Technologies (BMK) GmbH (Münster, Germany).
Preparation of ChIP library and sequencing was conducted by Biomarker Technologies (BMK) GmbH (Münster, Germany).


title: smallRNA_mnk, rhi 02/KG_rep1

value: mnk, rhi 02/KG


title: C9-ALS iMNs, HMe antibody IP

description: Library name: iMN_C9ALS1_HMe

value: iMNs


title: Isogenic CTRL, iMNs, scrambled probe

description: Library name: RAP_Isogenic_CTRL1_iMN_Scramble

extract_protocol:
Cells were fixed, lysed, and sonicated, followed by TURBO Dnase to get fragmented DNA.
The libraries were constrcuted  using the NEBNext® Ultra™ II DNA Library Prep Kit complemented with  NEBNext Multiplex Oligos for Illumina by following the manufacturer's manual.

value: Isogenic control


title: mRNA-seq, HL60 cells, control, replicate 3

description: Library name: Control-3


title: 365_R

description: Library name: GC-AS-10656-65R_S1

value: Skeletal Muscle


title: mRNA-seq, HL60 cells, dCas9-HDAC, replicate 2

description: Library name: dCas9-HDAC-2


title: smallRNA_rhi 02/KG_rep2


title: 365_L

description: Library name: GC-AS-10656-65L_S18

value: Left

value: Repeated TTX (RTTX)


title: Isogenic CTRL, iMNs,G4C2 probe

description: Library name: RAP_Isogenic_CTRL1_iMN_G4C2


title: 364_R

description: Library name: GC-AS-10656-64R_S24


title: smallRNA_rhi 02/KG_rep1


title: 364_L

description: Library name: GC-AS-10656-64L_S16


title: mRNA-seq, HL60 cells, control, replicate 1

description: Library name: Control-1


title: smallRNA_mnk_rep3

value: mnk


title: Isogenic CTRL, iMNs, input

description: Library name: RAP_Isogenic_CTRL1_iMN_Input


title: smallRNA_mnk_rep2


title: smallRNA_mnk_rep1


title: 366_L

description: Library name: GC-AS-10656-66L_S10


title: C9-ALS, iMNs, scrambled probe

description: Library name: RAP_C9ALS1_iMN_Scramble


title: 362_R

description: Library name: GC-AS-10656-62R_S15

value: Atrophy


title: E. coli, Sfx deletion R6K, Psfx-sfx-FLAG, rep 2 (Input)

city: Columbus

first: Irina

last: Artsimovitch

state: Ohio

address: 318 W 12th Ave

department: Microbiology

institute: The Ohio State University

description:
Library name: Sfx_Eco_WT_5CB
Sfx_Eco_WT_2_FE.bw

data_processing:
Adapter and low-quality reads were trimmed using TrimGalore v0.6.7 in paired-end mode; additionally, one base was trimmed from the 5' end of all reads. Parameters: --paired --trim-n ("--2colour 30" was added to the parameters if PolyG was present in the reads). For RNA ChIP-seq reads, parameters "--trim-n -q 28 --clip_R1 1 --clip_R2 1 --paired" were used.
Reads were aligned using bowtie2 v2.4.4 with very sensitive, end-to-end alignment, and dovetailed alignments allowed. Parameters: --very-sensitive --no-mixed --no-discordant --dovetail -X 1000
Peak calling was done by MACS3 v3.0.3 with a significance 10-7. Motif searching was done using peaks discovered by MACS3 on the chromosome by HOMER v5.1. The fold enrichment (FE = ChIP/Input) was calculated by MACS3 and converted to bigWig files by bedGraphToBigWig v2.10.
Assembly: Escherichia coli K-12 substr. BW25113 (ASM75055v1), plasmid Sfx deletion R6K (pIA1548; sequence is attached in the accompanying manuscript)
Supplementary files format and content: bigWig, fold enrichment (ChIP/Input) at given genomic coordinates, linked to the corresponding ChIP sample records

organism: Escherichia coli K-12

source_name: strain

growth_protocol: Bacterial cells transformed with selected plasmids were grown in LB medium at 37 ℃ and 250 rpm overnight (~16 hours). The medium was supplemented with 100 μg/ml carbenicillin and 30 μg/ml chloramphenicol when needed.

extract_protocol:
ChIP-seq samples of FLAG-tagged Sfx and H-NS. The crosslinked cell pellets were resuspended in 1x IP buffer (200 mM Tris, pH 8.0, 600 mM NaCl, 4% Triton X-100, 2x ProBlock Gold 2D Protease Inhibitor Cocktail). The resuspended cells were subjected to sonication to yield DNA fragments ranging from 100 to 500 bp. The cells were kept in an ice-water bath throughout sonication. After sonication, 0.1 volume of cell lysate, which is used as the input sample, was kept at 4 ℃ until reverse-crosslinking. The remaining cell lysate was mixed with MonoRab anti-DYKDDDDK magnetic beads (GenScript). After an overnight incubation at 4 ℃, the magnetic beads were subjected to sequential washes, with 1 ml used per wash: 1) 1x Wash buffer A (100 mM Tris-HCl, pH 8.0, 250 mM LiCl, 2% Triton X-100, 1 mM EDTA); 2) 1x Wash buffer B (100 mM Tris-HCl, pH 8.0, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM EDTA); 3) 1x Wash buffer C (10 mM Tris-HCl, pH 8.0, 500 mM NaCl, 1% Triton X-100, 1 mM EDTA); 4) 1x TE (10 mM Tris-HCl, pH 8.0, 1 mM EDTA). The antigens were eluted in 1 ml of elution buffer (50 mM Tris, pH 8.0; 10 mM EDTA; 1% SDS, 5 U/ml proteinase K (NEB, cat# P8107S)) by a one-hour incubation at 65 ℃, with vigorous vortexing every 10 minutes. The input samples were diluted 10 times with elution buffer and subjected to the same treatment as the ChIP samples from now on. The samples were incubated at 65 ℃ overnight to reverse the crosslinking. To digest the RNA, 100 μg/ml of RNase A (ThermoFisher) was added for 2 h incubation at 37 ℃, followed by 2 h incubation at 50 ℃ with 5 U/ml of proteinase K (NEB). Finally, DNA was recovered using QIAquick PCR Purification Kit (QIAGEN).
ChIP-seq samples of RNAP. The protocol is largely the same as FLAG-tagged ChIP-seq samples except for the incubation with antibodies. The samples were first incubated with Protein A/G MagBeads (GenScript) for 3 hours at 4℃, and then the protein A/G MagBeads were removed. Anti-E. coli RNA polymerase β antibody was added to the samples for an overnight incubation. The next day, Protein A/G MagBeads were added again. After 3 hours of incubation, the magnetic beads were washed as above.
RNA ChIP-seq samples. The protocol is largely the same as FLAG-tagged ChIP-seq sample preparation with the following changes. After reverse crosslinking, the samples were treated with Turbo DNase (ThermoFisher) and then the RNA was purified by Monarch Total RNA Miniprep Kit (NEB).
DNA and RNA libraries were prepared using Illumina DNA Prep, (M) Tagmentation kit and Illumina Stranded mRNA Prep kit, respectively, following the manufacturer's protocols.

treatment_protocol: The overnight cultures were mixed with formaldehyde/sodium phosphate (pH 7.4) buffer to yield a final concentration of 10 mM NaPO4 and 1% (v/v) formaldehyde. The cells were crosslinked for 5 min at 37 ℃, 250 rpm. The crosslinking was stopped by adding 0.33 M glycine, followed by a 30-min incubation in an ice-water bath. The crosslinked cells were collected by centrifugation, washed three times with PBS, and stored at -80 ℃.

value: strain

value: E. coli carrying plasmid Sfx deletion R6K and plasmid p451 (Psfx-sfx-FLAG)


title: C9-ALS, iMNs,G4C2 probe

description: Library name: RAP_C9ALS1_iMN_G4C2

value: Motor Neuron


title: mRNA-seq, HL60 cells, control, replicate 2

description: Library name: Control-2


title: Isogenic control iMNs, MAZ antibody IP

description: Library name: Isogenic_CTRL1_MAZ

extract_protocol:
Cells were fixed with 1% glutaraldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a sonicator (Diagenode) until the chromatin DNA was 100–500 bp in size.
The libraries were constrcuted  using the NEBNext® Ultra™ II DNA Library Prep Kit complemented with  NEBNext Multiplex Oligos for Illumina by following the manufacturer's manual.


title: E. coli, Sfx deletion R6K, Psfx-sfx-FLAG, rep 1 (Input)

description:
Library name: Sfx_Eco_WT_5CA
Sfx_Eco_WT_1_FE.bw


title: 362_L

description: Library name: GC-AS-10656-62L_S19

value: TTX


title: C9-ALS, iMNs, input

description: Library name: RAP_C9ALS1_iMN_Input


title: 354_R

description: Library name: GC-AS-10656-54R_S7

value: Right

value: control (CTRL)


title: smallRNA_w1_rep2

extract_protocol:
Total RNA was extracted from 2-4 day old female ovaries using the MirVana kit (Ambion).
For Long RNA-seq, rRNA was depleted using antisense rRNA oligo hybridization followed by RNase H digestion, RNA Fragmentation, Reverse Transcription, dUTP incorporation, end Repair, size selection using Ampure XP beads, A-tailing, Adaptor ligation, UDG treatment and PCR amplification.
For Small RNA-seq, small RNAs 18-29 nucleotide long were isolated using polyacrylamide gel purification followed by 2S rRNA depletion, 3’ adaptor ligation, 5’ adaptor ligation, reverse transcription, and PCR amplification.

value: Ovary


title: E. coli, Sfx deletion R6K, Psfx-sfx-FLAG, rep 1 (ChIP)

description:
Library name: Sfx_Eco_WT_5EA
Sfx_Eco_WT_1_FE.bw


title: 354_L

description: Library name: GC-AS-10656-54L_S8

value: sham


title: Isogenic control iMNs, Input, bioreplicate 2

description: Library name: Isogenic_CTRL1_Input


title: Isogenic control iMNs, IgG, bioreplicate 2

description: Library name: Isogenic_CTRL1_IgG


title: E. coli Hha deletion, Sfx deletion R6K, Psfx-sfx-FLAG, rep 1 (Input)

description:
Library name: Sfx_Eco_dHha_7CA
Sfx_Eco_dHha_1_FE.bw

value: E. coli Hha deletion carrying plasmid Sfx deletion R6K and plasmid p451 (Psfx-sfx-FLAG)


title: E. coli, Sfx deletion R6K, Psfx-sfx-FLAG, rep 2 (ChIP)

description:
Library name: Sfx_Eco_WT_5EB
Sfx_Eco_WT_2_FE.bw


title: smallRNA_w1_rep3

value: 2-4 day old


title: smallRNA_w1_rep1


title: 369_L_rpt

description: Library name: GC-AS-10657-369-L_S2

data_processing:
Reduced representation bisulfite sequencing (RRBS) libraries were processed using a standard workflow. Raw base-call files were demultiplexed using Illumina bcl2fastq /2.19.1, and unique molecular identifiers (UMIs) were extracted using umi_tools 81. Reads were adapter and quality-trimmed (minimum phred score 30) with trim_galore (https://doi.org/10.5281/zenodo.5127898). in RRBS mode, reads less than 15 bp after trimming were discarded. Trimmed reads were aligned to the rat genome Rn6 using bismark/0.22.1 82 with bowtie2, with the PBAT option enabled. PCR duplicates were removed with deduplicate_bismark in a UMI-aware manner. CpG methylation calls were obtained using bismark_methylation_extractor. Differential methylation analysis performed can be found in the weblink / citation to the published manuscript.
Assembly: rat genome Rn6
Supplementary files format and content: pe.bismark.cov.gz (Bismark coverage files)

extract_protocol:
Skeletal muscle tissue derived from aged rats (12 ± 2 mg) was added to 2 mL homogenizing mix tubes (Fisherbrand™, Fisher Scientific) containing 180 μl Buffer ATL (Qiagen, Hilden, Germany) before transferring to a tissue homogenizing instrument (MagNA Lyser; Roche, Basel, Switzerland) for subsequent homogenization (3 × 45 s at 6000 rpm, placing samples on ice for 5 mins between each disruption). Following homogenization, 20 μl proteinase K (Qiagen) was added and samples were incubated at 56°C until complete lysis (≈ 30-60 mins) before continuing with DNA purification using a DNeasy® Blood & Tissue kit (Qiagen) as per the manufacturer’s instructions. DNA quantity and quality (1427 ± 426 ng/mg tissue, 2 ± 0 A260/A280 &  2 ± 0.1 A260/A230) samples were quantified using spectrophotometry (NanoDrop™ 2000; Thermo Fisher Scientific) and concentrations confirmed via fluorometry (Qubit®, Qiagen). DNA integrity was confirmed prior to sequencing via Agilent Bioanalsyer 2100 with DIN scores 7.22 ± 0.23.
RREM (reduced-representation enzymatic methyl-seq) libraries were prepared using 100 ng of genomic DNA in conjunction with the NEBNext Enzymatic Methyl-Seq kit (New England Biolabs, Massachusetts, USA). Briefly, DNA samples were digested using MspI restriction enzyme followed by end-repair and adapter ligation. A two step enzymatic conversion is then performed by Oxidation of 5mC and 5hmC using TET2 and glucosylation of 5hmC using T4-BGT. Deamination of unmodified cytosines was subsequently performed using APOBEC. Converted samples were then uniquely barcoded and amplified by PCR prior to sequencing. Sequencing was performed on an Illumina NextSeq 2000 with P4 XLEAP 100-cycle sequencing kit, generating 50bp paired-end reads.

value: TTX+Recovery

value: Recovery


title: E. coli Hha deletion, Sfx deletion R6K, Psfx-sfx-FLAG, rep 2 (ChIP)

description:
Library name: Sfx_Eco_dHha_7EB
Sfx_Eco_dHha_2_FE.bw


title: 370_R_rpt

description: Library name: GC-AS-10657-370-R_S1

value: Skeletal Muscle


title: w1_HS1hr37C_24hRec_rep3_LongRNA

treatment_protocol: Heat shock was carried on 2-4 day old flies with yeast for 1 hour in a water bath kept at 37oC. Flies were allowed to recover at room temp for designated times before proceeding with extraction and library construction.  No Shock control flies were kept at room temp as controls.

value: Heat Shock for 1 hour at 37oC

tag: recovory time_after_heat_stress

value: 24 hour recovoery after heat stress


title: smallRNA_aub HN/QC_rep3

value: aub HN/QC


title: C9-ALS iMNs,MAZ antibody IP

description: Library name: iMN_C9ALS1_MAZ

value: iMNs


title: w1_HS1hr37C_24hRec_rep2_LongRNA


title: w1_HS1hr37C_24hRec_rep1_LongRNA


title: C9-ALS iMNs, IgG, bioreplicate 2

description: Library name: iMN_C9ALS1_IgG


title: 364_L_rpt

description: Library name: GC-AS-10657-364-L_S3

value: Left

value: Repeated TTX (RTTX)

value: Repeated Atrophy


title: w1_HS1hr37C_12hRec_rep3_LongRNA

value: 12 hour recovoery after heat stress


title: 364_R_rpt

description: Library name: GC-AS-10657-364-R_S4

value: Right


title: E. coli Hha deletion, Sfx deletion R6K, Psfx-sfx-FLAG, rep 2 (Input)

description:
Library name: Sfx_Eco_dHha_7CB
Sfx_Eco_dHha_2_FE.bw

value: strain


title: C9-ALS iMNs, Input, bioreplicate 2

description: Library name: iMN_C9ALS1_Input

value: Motor Neuron


title: Isogenic CTRL, iMNs, bioreplicate 2

description: Library name: Isogenic_CTRL1_r2

data_processing:
Raw sequencing reads were processed with TrimGalore v.0.6.7 and quality of the raw sequencing reads was assessed using FastQC v.0.11.9
The clipped reads were aligned to the hg19 genome through Bowtie2, with these mapping parameters: -very-sensitive -X 2000. The uniquely mapped reads from each background were merged and called peaks using MACS2, with parameters: --nomodel -q 0.05 --shift -100 --extsize 200 --broad.
The combined BAM files and peak set were further processed with TOBIAS ATACorrect to generate the bigwig files.
Assembly: hg19
Supplementary files format and content: bigwig files for each sample

extract_protocol:
Approximately 50,000 nuclei were collected, washed, and incubated in Tagmentation buffer with 5 µl of Tn5 transpose mix (TruePrep DNA Library Prep Kit V2 for Illumina, TD501, Vazyme) at 37°C for 30 min. The fragmented DNA was purified using VAHTS DNA Clean Beads (#N411, Vazyme).
The DNA fragments were amplified with TruePrep DNA Library Prep Kit V2 for Illumina (TD501, Vazyme). The universal adapter primer and a barcoded primer (TruePrep Index Kit V2 for Illumina, TD202, Vazyme) were incorporated into the PCR products.

value: Isogenic CTRL


title: w1_HS1hr37C_12hRec_rep2_LongRNA

value: Ovary


title: 379_R

description: Library name: GC-AS-10657-379-R_S42

value: control (CTRL)


title: E. coli Hha deletion, Sfx deletion R6K, Psfx-sfx-FLAG, rep 1 (ChIP)

description:
Library name: Sfx_Eco_dHha_7EA
Sfx_Eco_dHha_1_FE.bw

value: E. coli Hha deletion carrying plasmid Sfx deletion R6K and plasmid p451 (Psfx-sfx-FLAG)


title: E. coli, Sfx deletion R6K, RNAP ChIP-seq, rep 2 (Input)

description:
Library name: RNAP_RI3
RNAP_2_FE.bw

treatment_protocol: Cells were treated with 150 μg/ml rifampicin for 10 min at OD600 ~0.4. The treated cells were crosslinked and washed as H-NS ChIP-seq samples.

value: E. coli carrying plasmid Sfx deletion R6K


title: Isogenic CTRL, iMNs, bioreplicate 1

description: Library name: Isogenic_CTRL1_r1


title: E. coli, Sfx deletion R6K, RNAP ChIP-seq, rep 1 (Input)

description:
Library name: RNAP_RI2
RNAP_1_FE.bw


title: C9-ALS, iMNs, line 1, bioreplicate 2

description: Library name: iMN_C9ALS1_r2


title: E. coli, Sfx deletion R6K, RNAP ChIP-seq, rep 2 (ChIP)

description:
Library name: RNAP_RC3
RNAP_2_FE.bw


title: w1_HS1hr37C_12hRec_rep1_LongRNA

value: 2-4 day old


title: 377_R

description: Library name: GC-AS-10657-377-R_S37

value: Skeletal Muscle

value: Recovery


title: w1_HS1hr37C_8hRec_rep2_LongRNA

value: Heat Shock for 1 hour at 37oC

value: 8 hour recovoery after heat stress


title: 379_L

description: Library name: GC-AS-10657-379-L_S43

value: Left

value: sham


title: C9-ALS, iMNs, line 1, bioreplicate 1

description: Library name: iMN_C9ALS1_r1

value: iMNs


title: w1_HS1hr37C_8hRec_rep1_LongRNA


title: CTRL, iMNs, line 4, bioreplicate2

description: Library name: CTRL4_r2

value: CTRL


title: w1_HS1hr37C_6hRec_rep2_LongRNA

value: 6 hour recovoery after heat stress


title: 372_R

description: Library name: GC-AS-10657-372-R_S24

value: Right

value: Atrophy


title: CTRL, iMNs, line 4, bioreplicate1

description: Library name: CTRL4_r1

value: Motor Neuron


title: 377_L

description: Library name: GC-AS-10657-377-L_S11


title: E. coli, Sfx deletion R6K, Psfx-sfx-FLAG, RNA ChIP-seq (Input)

description:
Library name: RNA_ChIP_SC2
RNA_ChIP_1_FE.bw
RNA_ChIP_2_FE.bw

value: strain

value: E. coli carrying plasmid Sfx deletion R6K and plasmid p451 (Psfx-sfx-FLAG)


title: E. coli, Sfx deletion R6K, RNAP ChIP-seq, rep 1 (ChIP)

description:
Library name: RNAP_RC2
RNAP_1_FE.bw


title: CTRL, iMNs, line 2

description: Library name: CTRL2


title: 372_L

description: Library name: GC-AS-10657-372-L_S26

value: TTX


title: E. coli, Sfx deletion R6K, Psfx-sfx-FLAG, RNA ChIP-seq, rep 2 (ChIP)

description:
Library name: RNA_ChIP_SR2
RNA_ChIP_2_FE.bw


title: 371_R

description: Library name: GC-AS-10657-371-R_S36

value: control (CTRL)


title: w1_HS1hr37C_4hRec_rep2_LongRNA

value: Ovary

value: 2-4 day old

value: 4 hour recovoery after heat stress


title: E. coli, Sfx deletion R6K, Psfx-sfx-FLAG, RNA ChIP-seq, rep 1 (ChIP)

description:
Library name: RNA_ChIP_R35
RNA_ChIP_1_FE.bw


title: C9-ALS, iMNs, line 6

description: Library name: C9ALS6


title: 371_L

description: Library name: GC-AS-10657-371-L_S32

value: Skeletal Muscle

value: TTX+Recovery

value: Recovery


title: E. coli hns-3xFLAG, R6K, rep 2 (Input)

description:
Library name: HNS_HI2
HNS_2_FE.bw

value: E. coli hns-3xFLAG carrying plasmid R6K


title: w1_HS1hr37C_4hRec_rep1_LongRNA

value: Heat Shock for 1 hour at 37oC


title: w1_HS1hr37C_6hRec_rep1_LongRNA


title: C9-ALS, iMNs, line 5

description: Library name: C9ALS5

value: iMNs


title: w1_HS1hr37C_2hRec_rep2_LongRNA

value: 2 hour recovoery after heat stress


title: E. coli hns-3xFLAG, R6K, rep 1 (Input)

description:
Library name: HNS_HI1
HNS_1_FE.bw


title: 370_L

description: Library name: GC-AS-10657-370-L_S47

value: Left


title: C9-ALS, iMNs, line 2

description: Library name: C9ALS2


title: E. coli hns-3xFLAG, R6K, rep 2 (ChIP)

description:
Library name: HNS_HC2
HNS_2_FE.bw


title: w1_HS1hr37C_2hRec_rep1_LongRNA


title: w1_HS1hr37C_1hRec_rep4_LongRNA

value: 1 hour recovoery after heat stress


title: S9.6 REO rep2

description: Library name: SAMPLES8

data_processing:
The CUT&Tag reads were checked for quality and trimmed using Fastp. Reads were aligned to the Ensembl hg38 human reference genome using Bowtie2 (version 2.4.4) with the options “--very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700 -p 12”. Duplicate reads were removed using Picard tools for downstream analyses. Samtools was used to convert the read format and sort the reads. To visualize the genomic occupancy from the transcription start site (TSS) to the transcription end site (TES), bam files were converted into BigWig files using the bamCoverage function from deepTools, with the parameter set to 'normalizeUsing RPGC'. Subsequently, computeMatrix and plotHeatmap from deeptools were used with the options “--beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros -o”. SEACR was employed for peak scanning across the entire genome with the option of “0.05 non stringent”. Deseq2 was used for differential analysis. bedtools was used to find the overlaps. ChIPseeker was used to annotate the positions of peaks within genomic features.
Assembly: hg38
Supplementary files format and content: BigWig
Library strategy: Cut&Tag

extract_protocol:
The CUT&Tag assay was conducted using Hyperactive Universal the CUT&Tag Assay Kit for Illumina (Vazyme, Cat No. TD903) according to the manufacturer’s instructions.
80,000 cells were harvested and washed twice in wash buffer. Concanavalin A beads were then added to the cell suspension and incubated at room temperature for 10 mins. Bead-bound cells were separated from the supernatant and were resuspended in antibody buffer. Antibodies against S9.6 (Absoluteantibody, Cat No. AB01137, with 1 μg) were added to the cells, and incubated at 4°C overnight. The following day, the secondary antibody diluted in dig-wash buffer was added to the beads and incubated at room temperature for 1 h. After incubation, beads were washed three times with dig-wash buffer. pA/G-Tnp transposomes diluted in dig-300 buffer were incubated with beads at room temperature for 1 h. After three washes with dig-300 buffer, samples were then tagmented with TTBL from the kit. After 1 h of tagmentation, proteinase K and spike-in were added. Fragmented DNA was purified using DNA Extract Beads. The eluted DNA was amplified using Illumina i7/i5 indexed primers. After that, VAHTS DNA Clean Beads (Vazyme #N411) were employed for the purification of the libraries, which were then subjected to quality control and Illumina sequencing.

treatment_protocol: 293T cells were treated with TNF-α(10 ng/ml) and IFN-β(10 ng/ml) for 3 hours, or infected with T1L-WT(MOI 10) for 6 hours.

value: Human embryonic kidney 293

value: WT

value: REO


title: 369_R

description: Library name: GC-AS-10657-369-R_S33

value: Right


title: yfjW inserted into R6K, E. coli wild type, Psfx-sfx-FLAG (ChIP)

description:
Library name: DNA_swap_Sfx_S43
DNA_swap_Sfx_FE.bw

value: strain

value: E. coli carrying plasmid Sfx deletion R6K with yfjW inserted (pIA1710) and plasmid p451 (Psfx-sfx-FLAG)


title: 369_L

description: Library name: GC-AS-10657-369-L_S14


title: E. coli hns-3xFLAG, R6K, rep 1 (ChIP)

description:
Library name: HNS_HC1
HNS_1_FE.bw


title: S9.6 REO rep1

description: Library name: SAMPLES7


title: mRNA-seq, HL60 cells, dCas9-HDAC, replicate 1

description: Library name: dCas9-HDAC-1


title: 370_R

description: Library name: GC-AS-10657-370-R_S4

value: control (CTRL)


title: S9.6 IFN  rep2

description: Library name: SAMPLES6

value: IFN


title: w1_HS1hr37C_1hRec_rep2_LongRNA

data_processing:
piSet_rnaseq pipeline from GitHub was used to analyze long RNA sequences reads. Steps were: Bowtie2 (Version 2.2.5) was used to map raw sequencing reads to rRNA sequence. Remaining reads were mapped to dm6 and transposon consensus using using STAR (Version 2.5.2b) and Hisat2. Transcript abundance for each gene, transposon, and piRNA cluster (rpkm) was counted using BEDTools (Version 2.27.1).
piSet_srnaseq was used to analyze small RNA sequencing reads. Steps were: the 3ʹ end adaptor (TGGAATTCTCGGG) was removed via cutadapt (Version 1.15) and the raw small RNA-seq reads were mapped to rRNA, miRNA hairpin, snoRNA, snRNA, and tRNA sequence allowing for no mismatches using Bowtie (Version 1.1.0). The remaining reads were mapped to the Drosophila genome (dm6) and transposon consensus sequences. Small RNA abundance was normalized to unique mapping reads.
Assembly: dm6
Supplementary files format and content: tab deliniated txt files containing RMPM values

value: Ovary

value: 2-4 day old


title: R6K, rep2

description: Library name: SF4

data_processing:
Adapter and low-quality reads were trimmed using TrimGalore v0.6.7 in paired-end mode; additionally, one base was trimmed from the 5' end of all reads. Parameters: --paired --trim-n -clip_R1 1 --clip_R2 1
Reads were aligned using bowtie2 v2.4.4 with very sensitive, end-to-end alignment, and dovetailed alignments allowed. Parameters: --very-sensitive --no-mixed --no-discordant --dovetail -X 1000
The alignment files were subjected to quantification using featureCounts v2.0.3 with the --countReadPairs option
Assembly: Escherichia coli K-12 substr. BW25113 (ASM75055v1), plasmid Sfx deletion R6K (pIA1548; sequence is provided in the accompanying manuscript)
Supplementary files format and content: The tab-delimited text file includes raw counts for each sample.

growth_protocol: Cells carrying different R6K derivatives were grown in LB medium supplemented with 100 μg/ml carbenicillin at 37 ℃ and 250 rpm. Cells were collected by centrifugation when the OD600 reached 0.6.

extract_protocol:
Total RNA was first extracted with RNAzol RT (Sigma), and the top water phase was fed into Monarch Total RNA Miniprep Kit (NEB). The extracted RNA was further treated with DNase I. The rRNA was removed by using NEBNext rRNA Depletion Kit (Bacteria) (NEB) following the manufacturer's protocol.
RNA library is prepared using Illumina Stranded mRNA Prep following the manufacturer's protocol.

value: carrying plasmid R6K


title: S9.6 IFN  rep1

description: Library name: SAMPLES5


title: S9.6 TNF rep2

description: Library name: SAMPLES4

value: TNF


title: w1_HS1hr37C_1hRec_rep3_LongRNA

value: Heat Shock for 1 hour at 37oC


title: 367_L

description: Library name: GC-AS-10657-367-L_S3

value: Skeletal Muscle

value: TTX

value: Atrophy


title: w1_HS1hr37C_1hRec_rep1_LongRNA

value: 1 hour recovoery after heat stress


title: 367_R

description: Library name: GC-AS-10657-367-R_S46


title: 366_R

description: Library name: GC-AS-10657-366-R_S15

value: Repeated Atrophy


title: R6K, rep1

description: Library name: SF3


title: yfjW inserted into R6K, E. coli hns-3xFLAG, Psfx-sfx (ChIP)

description:
Library name: DNA_swap_HNS_H45
DNA_swap_HNS_FE.bw

value: E. coli hns-3xFLAG carrying plasmid Sfx deletion R6K with yfjW inserted (pIA1710) and plasmid p452 (Psfx-sfx)


title: w1_HS1hr37C_0hRec_rep1_LongRNA

value: 0 hour recovoery after heat stress


title: S9.6 TNF rep1

description: Library name: SAMPLES3

value: Human embryonic kidney 293

value: WT


title: S9.6 CTR rep2

description: Library name: SAMPLES2

value: Mock


title: w1_HS1hr37C_0hRec_rep2_LongRNA


title: 366_L

description: Library name: GC-AS-10657-366-L_S44

value: Left

value: Repeated TTX (RTTX)


title: Sfx deletion R6K, rep1

description: Library name: SF1

value: strain

value: carrying plasmid Sfx deletion R6K


title: Sfx deletion R6K, rep2

description: Library name: SF2


title: w1_noHS_control_rep1_LongRNA

value: Ovary

value: 2-4 day old

value: No heat shock


title: C. elegans N2 L4 LISA treatment 12 h replicate 3

city: San Francisco

first: Junqiang

state: CA - California

address: 555 Mission Bay Blvd South

institute: University of California, San Francisco

description:
Library name: Sta_3
Standing replicate 3

data_processing:
Sequencing libraries were prepared and sequenced (paired-end, 150 bp) on the DNBseq platform (Innomics).
Assembly: WBcel235
Supplementary files format and content: csv files include FPKM values for all Samples.
Supplementary files format and content: fpkm.csv

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: C. elegans N2 animals were maintained at 20 °C.

extract_protocol:
Total RNA was extracted using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (RC112-01, Vazyme) according to the manufacturer’s instructions. RNA quantity and purity were assessed using a NanoDrop spectrophotometer, and RNA integrity was evaluated by agarose gel electrophoresis.
For each sample, 1 µg of total RNA was used for sequencing library construction. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For liquid-induced suspended animation (LISA) treatment, synchronized L4 larvae were either subjected to LISA 12 hours or maintained under control conditions prior to collection.

value: Whole worm

value: Wild-type worms

value: Synchronized L4 larvae were exposed to high-density liquid conditions for 12 hours


title: 42ABDfxw1-F1s_rep3_smallRNA


title: 364_R

description: Library name: GC-AS-10657-364-R_S39

value: Skeletal Muscle

value: Right

value: control (CTRL)


title: 42ABDfxw1-F1s_rep2_smallRNA


title: S9.6 CTR rep1

description: Library name: SAMPLES1


title: C. elegans N2 L4 control replicate 3

description:
Library name: Con_3
Control replicate 3

value: Synchronized L4 larvae under normal conditions


title: C. elegans N2 L4 LISA treatment 12 h replicate 2

description:
Library name: Sta_2
Standing replicate 2


title: 362_R

description: Library name: GC-AS-10657-362-R_S1

value: Atrophy


title: 362_L

description: Library name: GC-AS-10657-362-L_S38

value: TTX


title: HEL cells, TAL1 siPool 2, bio rep 1

city: Charlottesville

first: Francine

middle: E.

last: Garrett-Bakelman

state: VA

address: 1340 Jefferson park Ave.

department: Medicine and BMG

institute: University of Virginia

description:
Library name: H3
HEL cells electroporated with siTAL1 targeting siRNAs

data_processing:
Qualtiy was assessed using FastQC and aligned to the hg19 human genome using STAR. Differential expression analysis was conducted using MultiRankSeq.
Assembly: hg19
Supplementary files format and content: HEL siTAL1 FeatureCounts with reads aligned to each annotated gene in the hg19 genome. K562 LMO2-degron FRKM aligned to hg19. K562 shLDB1 TPM aligned to hg19.

source_name: HEL

extract_protocol:
RNA was extracted using phenol-chloroform/Trizol
HEL libraries were prepared using Fast RNA-seq Lib Prep Kit V2(Abclonal RK20306) by Novogene and K562 libraries were prepared for Illumina preparation by Azenta.

value: HEL

value: siTAL1 pool 2


title: 365_R

description: Library name: GC-AS-10657-365-R_S16

value: Repeated Atrophy


title: w1x42ABDf-F1s_rep2_smallRNA


title: HEL cells, TAL1 siPool 1, bio rep 3

description:
Library name: H8
HEL cells electroporated with siTAL1 targeting siRNAs

value: siTAL1 pool 1


title: 364_L

description: Library name: GC-AS-10657-364-L_S23

value: Left

value: Repeated TTX (RTTX)


title: w1x42ABDf-F1s_rep3_smallRNA

value: Ovary

value: 2-4 day old


title: 365_L

description: Library name: GC-AS-10657-365-L_S21


title: HEL cells, TAL1 siPool 2, bio rep 3

description:
Library name: H9
HEL cells electroporated with siTAL1 targeting siRNAs


title: C. elegans N2 L4 control replicate 2

description:
Library name: Con_2
Control replicate 2

value: Whole worm

value: WT


title: HEL cells, TAL1 siPool 1, bio rep 1

description:
Library name: H2
HEL cells electroporated with siTAL1 targeting siRNAs


title: w1x42ABDf-F1s_rep1_smallRNA

value: No heat shock


title: C. elegans N2 L4 control replicate 1

description:
Library name: Con_1
Control replicate 1

value: Wild-type worms


title: 42ABDfxw1-F1s_rep1_smallRNA


title: 354_R

description: Library name: GC-AS-10657-354-R_S45

value: Skeletal Muscle

value: Right


title: 42ABDfxOreR-F1s_rep3_smallRNA


title: 354_L

description: Library name: GC-AS-10657-354-L_S48

value: sham


title: Input ChIP-seq, fly adult, day 63

description: Library name: day63-input

source_name: whole body

value: whole body


title: HEL cells, TAL1 siPool 1, bio rep 2

description:
Library name: H5
HEL cells electroporated with siTAL1 targeting siRNAs


title: HEL cells, Non-Targeting Control pool, bio rep 3

description:
Library name: H7
HEL cells electroporated with non-targeting siRNAs

value: Non-targeting siRNA


title: RAM_BAL_KO_d21_rep4

city: Aurora

first: Qihua

last: Ye

state: CO

address: Research Complex II  12700 East 19th Avenue

department: Pulmonary

institute: University of Colorado Anschutz Medical Campus

description: Library name: RAM_BAL_KO_d21_rep4

data_processing:
Raw fastq files were trimmed using cutadapt (4.2)
Aligned to reference genome GRCm38/mm10 using STAR (2.7.10b).
Picardtool (2.27.5) was used to collect strandedness information for each sample.
Raw gene-level counts were filtered to remove genes with low expression, retaining only those with >10 raw counts in at least 10 of the 27 total samples. This strategy removes genes with limited and inconsistent expression across the dataset while preserving those robustly detected across multiple samples.
Normalized counts were acquired using DESeq2 (1.38.2) in R (4.2.2).
The log fold change shrunk gene set enrichment analysis (GSEA) was performed using fgsea (1.24.0) in R (4.2.2).
Assembly: GRCm38/mm10
Supplementary files format and content: .csv file for raw counts, normalized counts

source_name: lung lavage

extract_protocol:
RNA was isolated from freshly sorted cells using micro RNA kit (Qiagen, Germantown, MD), following manufacturer's protocols.
RNA purity, quantity, and integrity were determined by NanoDrop (ThermoFisher Scientific, Waltham, MA) and TapeStation 4200 (Agilent, Santa Clara, CA) analyses prior to RNA-seq library preparation. MGIEasy RNA Library Prep Set (3.1, cat. 1000006384) was used to generate libraries with an input of 100 ng of total RNA.

value: lung lavage

value: RAMs

value: KO

value: PPE

tag: timepoint (day)


title: Input ChIP-seq, fly adult, day 60

description: Library name: day60-input


title: HEL cells, Non-Targeting Control pool, bio rep 2

description:
Library name: H4
HEL cells electroporated with non-targeting siRNAs

value: HEL


title: C. elegans N2 L4 LISA treatment 12 h replicate 1

description:
Library name: Sta_1
Standing replicate 1

value: Synchronized L4 larvae were exposed to high-density liquid conditions for 12 hours


title: Input ChIP-seq, fly adult, day 55

description: Library name: day55-input


title: RAM_BAL_KO_d21_rep3

description: Library name: RAM_BAL_KO_d21_rep3


title: HEL cells, TAL1 siPool 2, bio rep 2

description:
Library name: H6
HEL cells electroporated with siTAL1 targeting siRNAs

value: siTAL1 pool 2


title: RAM_BAL_WT_d21_rep3

description: Library name: RAM_BAL_WT_d21_rep3


title: HEL cells, Non-Targeting Control pool, bio rep 1

description:
Library name: H1
HEL cells electroporated with non-targeting siRNAs


title: Input ChIP-seq, fly adult, day 33

description: Library name: day33-input


title: SNCA triplication 3, scRNAseq

city: Erlangen

first: Bruno

last: Ghirotto

address: Kussmaulalle 4

description:
Library name: 3x_4 mutant
10x Genomics

data_processing:
The fastq files were processed using CellRanger (v7.1.0) from 10X Genomics, with reads aligned to the GRCh38 genome assembly to generate gene counts per cell. Subsequent processing, analysis, and visualization were performed in R (v4.3.3) using Seurat (v5.1.0). To ensure quality control, outlier cells with < 200 genes, > 7500 reads or a mitochondrial percentage > 5% were filtered out. Potential doublets were removed using scDblfinder.  Following quality control, batch effect across samples was mitigated using Seurat’s integration workflow. Data normalization was carried out using the SCTransform algorithm. Features to use when integrating multiple datasets were identified using SelectIntegrationFeatures. Integration anchors computed using the FindIntegrationAnchors function were subsequently used by the IntegrateData function to generate a batch-corrected, integrated expression matrix.
Assembly: GRCh38
Supplementary files format and content: .tar files containing matrix, barcode and feature data

source_name: SNCA triplication 3

extract_protocol:
On day 70 of differentiation, we obtained single cells from iPSC-ENLs using a papain-DNAse digestion protocol. Cells were then cryopreserved in a medium containing 90% fetal bovine serum and 10% DMSO and sent out for library preparation and sequencing at GENEWIZ (Leipzig, Germany) with 6000 cells targeted per sample and 50,000 reads targeted per cell.  RNA samples were quantified using Qubit 4.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with RNA Kit on Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA).
rRNA depletion was performed using NEBNext rRNA Depletion Kit (Human/Mouse/Rat). RNA sequencing library preparation used NEBNext Ultra RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, enriched RNAs were fragmented according to manufacturer’s instruction. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA).

value: SNCA triplication 3

value: enteric neural lineage

value: SNCA triplication


title: OreRx42ABDf-F1s_rep3_smallRNA

value: Ovary

value: 2-4 day old

value: No heat shock


title: OreRx42ABDf-F1s_rep2_smallRNA


title: 42ABDfxOreR-F1s_rep2_smallRNA


title: 42ABDfxOreR-F1s_rep1_smallRNA


title: Isogenic control 3, scRNAseq

description:
Library name: 3x_4 isogenic
10x Genomics

source_name: Isogenic 3

value: Isogenic 3

value: isogenic control


title: RAM_BAL_WT_d21_rep2

description: Library name: RAM_BAL_WT_d21_rep2

value: WT


title: RAM_BAL_KO_d21_rep2

description: Library name: RAM_BAL_KO_d21_rep2


title: Input ChIP-seq, fly adult, day 45

description: Library name: day45-input

value: whole body


title: RAM_BAL_WT_d21_rep1

description: Library name: RAM_BAL_WT_d21_rep1

value: lung lavage


title: Input ChIP-seq, fly adult, day 20

description: Library name: day20-input


title: OreRx42ABDf-F1s_rep1_smallRNA


title: 42ABDf_rep3_smallRNA


title: SNCA triplication 2, scRNAseq

description:
Library name: 3x_2 mutant
10x Genomics

source_name: SNCA triplication 2

value: SNCA triplication 2


title: Isogenic control 2, scRNAseq

description:
Library name: 3x_2 isogenic
10x Genomics

source_name: Isogenic 2

value: Isogenic 2


title: RAM_BAL_KO_d7_rep5

description: Library name: RAM_BAL_KO_d7_rep5

value: RAMs

value: KO

value: PPE


title: Input ChIP-seq, fly adult, day 5

description: Library name: day5-input


title: SNCA triplication 1, scRNAseq

description:
Library name: 3x_1 mutant
10x Genomics

source_name: SNCA triplication 1

value: SNCA triplication 1


title: Input ChIP-seq, fly adult, day 3

description: Library name: day3-input


title: 42ABDf_rep2_smallRNA


title: RAM_BAL_KO_d7_rep4

description: Library name: RAM_BAL_KO_d7_rep4


title: OreR_rep3_smallRNA

value: OreR


title: RAM_BAL_KO_d7_rep3

description: Library name: RAM_BAL_KO_d7_rep3


title: 42ABDf_rep1_smallRNA


title: Input ChIP-seq, fly adult, day 13

description: Library name: day13-input


title: Isogenic control 1, scRNAseq

description:
Library name: 3x_1 isogenic
10x Genomics

source_name: Isogenic 1

value: Isogenic 1

value: enteric neural lineage


title: H3K4me3WT rep2

city: Tianjin

first: Xueyang

last: Pang

address: 22 Meteorological Observatory Road, Heping District, Tianjin

institute: TMU

description: Library name: SAMPLES18

data_processing:
The CUT&Tag reads were checked for quality and trimmed using Fastp. Reads were aligned to the Ensembl hg38 human reference genome using Bowtie2 (version 2.4.4) with the options “--very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700 -p 12”. Duplicate reads were removed using Picard tools for downstream analyses. Samtools was used to convert the read format and sort the reads. To visualize the genomic occupancy from the transcription start site (TSS) to the transcription end site (TES), bam files were converted into BigWig files using the bamCoverage function from deepTools, with the parameter set to 'normalizeUsing RPKM'. Subsequently, computeMatrix and plotHeatmap from deeptools were used with the options “--beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros -o”. Then MACS2 was employed for peak scanning across the entire genome with the option of “q 0.05”. ChIPseeker was used to annotate the positions of peaks within genomic features.
Assembly: hg38
Supplementary files format and content: BigWig

extract_protocol:
The CUT&Tag assay was conducted using Hyperactive Universal the CUT&Tag Assay Kit for Illumina (Vazyme, Cat No. TD903) according to the manufacturer’s instructions.
80,000 cells were harvested and washed twice in wash buffer. Concanavalin A beads were then added to the cell suspension and incubated at room temperature for 10 mins. Bead-bound cells were separated from the supernatant and were resuspended in antibody buffer. Antibodies against RNA Pol II (Cell Signaling Technology, Cat No.14958, at 1:50 dilution), H3K4Me3 (Abcam, Cat No. ab12209, 1 μg), S9.6 (Absoluteantibody, Cat No. AB01137, with 1 μg), or IgG control (Cell Signaling Technology, Cat No.2729s, with 1 μg) were added to the cells, and incubated at 4°C overnight. For S9.6 CUT & Tag, 10 μg/μl of RNase A was supplemented as negative control. The following day, the secondary antibody diluted in dig-wash buffer was added to the beads and incubated at room temperature for 1 h. After incubation, beads were washed three times with dig-wash buffer. pA/G-Tnp transposomes diluted in dig-300 buffer were incubated with beads at room temperature for 1 h. After three washes with dig-300 buffer, samples were then tagmented with TTBL from the kit. After 1 h of tagmentation, proteinase K and spike-in were added. Fragmented DNA was purified using DNA Extract Beads. The eluted DNA was amplified using Illumina i7/i5 indexed primers. After that, VAHTS DNA Clean Beads (Vazyme #N411) were employed for the purification of the libraries, which were then subjected to quality control and Illumina sequencing.

treatment_protocol: HEK293 cells were transfected with pcDNA3.1 or pcDNA3.1-sigma3 (either WT or K287T mutant). At 48 h post-transfection, cells were treated with TNFa at 10 ng/ μl for 3 h

value: Human embryonic kidney 293

value: SIGMA3 OVEREXPRESSION

value: TNF


title: igG

description: Library name: SAMPLES19

value: Mock


title: RAM_BAL_KO_d7_rep2

description: Library name: RAM_BAL_KO_d7_rep2


title: Input ChIP-seq, fly adult, day 1

description: Library name: day1-input


title: H3K27ac ChIP-seq, fly adult, day63, replicate 3

description: Library name: day63-rep3-ip


title: OreR_rep1_smallRNA

city: Worcester

first: Samantha

address: 373 Plantation St.

source_name: Ovary

value: Ovary

value: 2-4 day old

value: No heat shock


title: OreR_rep2_smallRNA


title: RAM_BAL_WT_d7_rep3

description: Library name: RAM_BAL_WT_d7_rep3

value: lung lavage

value: WT


title: w1_HS1hr37C_1hRec_rep1_smallRNA

value: Heat Shock for 1 hour at 37oC

value: 1 hour recovoery after heat stress


title: H3K27ac ChIP-seq, fly adult, day60, replicate 3

description: Library name: day60-rep3-ip

value: whole body


title: H3K27ac ChIP-seq, fly adult, day63, replicate 2

description: Library name: day63-rep2-ip


title: RAM_BAL_KO_d7_rep1

description: Library name: RAM_BAL_KO_d7_rep1

value: RAMs

value: KO

value: PPE


title: H3K4me3empty rep2

description: Library name: SAMPLES17


title: H3K4me3WT rep1

description: Library name: SAMPLES15


title: RAM_BAL_WT_d7_rep1

description: Library name: RAM_BAL_WT_d7_rep1


title: w1_HS1hr37C_1hRec_rep2_smallRNA


title: H3K27ac ChIP-seq, fly adult, day63, replicate 1

description: Library name: day63-rep1-ip


title: w1_noHS_control_rep2_smallRNA


title: H3K27ac ChIP-seq, fly adult, day60, replicate 2

description: Library name: day60-rep2-ip


title: RAM_BAL_WT_d7_rep2

description: Library name: RAM_BAL_WT_d7_rep2


title: H3K4me3empty rep1

description: Library name: SAMPLES14


title: H3K4me3mock rep1

description: Library name: SAMPLES13


title: H3K4me3mock rep2

description: Library name: SAMPLES16


title: w1_noHS_control_rep1_smallRNA


title: H3K27ac ChIP-seq, fly adult, day60, replicate 1

description: Library name: day60-rep1-ip


title: RAM_BAL_KO_d3_rep5

description: Library name: RAM_BAL_KO_d3_rep5


title: RAM_BAL_KO_d3_rep4

description: Library name: RAM_BAL_KO_d3_rep4


title: H3K27ac ChIP-seq, fly adult, day55, replicate 3

description: Library name: day55-rep3-ip


title: smallRNA_mnk, uap56 sz15/28_rep4

value: mnk, uap56 sz15/28


title: RAM_BAL_KO_d3_rep1

description: Library name: RAM_BAL_KO_d3_rep1


title: w1_HS1hr37C_24hRec_antiRhi_rep2

data_processing:
Cut and Run analysis was performed using piSet_chipseq pipeline on GitHub. Briefly, Bowtie2 (Version 2.2.5) was used to map sequencing reads to the Drosophila genome (dm6) and transposon consensus sequence, signal mapping to transposons were normalized to total number of genome mapping Cut and Run reads.
Assembly: dm6
Supplementary files format and content: bigWig files
Library strategy: CUT and RUN

extract_protocol:
Ovaries were dissected from 2-4 day flies and bound to ConA beads, incubated with primary antibody, DNA digested with pAMA and DNA was recovered.
Recovered DNA undergone library construction with the following steps: end repair, A-tailing, adaptor ligation, and PCR amplification.

value: 24 hour recovoery after heat stress

tag: cut-and-run antibody

value: Rhino


title: S9.6empty rep2

description: Library name: SAMPLES11

value: Human embryonic kidney 293


title: RAM_BAL_WT_d3_rep4

description: Library name: RAM_BAL_WT_d3_rep4


title: w1_HS1hr37C_24hRec_antiRhi_rep1


title: H3K27ac ChIP-seq, fly adult, day55, replicate 1

description: Library name: day55-rep1-ip


title: H3K27ac ChIP-seq, fly adult, day55, replicate 2

description: Library name: day55-rep2-ip


title: w1_HS1hr37C_24hRec_antiIgG_rep2

value: guinea pig IgG


title: S9.6WT rep1

description: Library name: SAMPLES9

value: SIGMA3 OVEREXPRESSION

value: TNF


title: RAM_BAL_WT_d3_rep3

description: Library name: RAM_BAL_WT_d3_rep3


title: w1_HS1hr37C_24hRec_antiIgG_rep1

value: Ovary

value: 2-4 day old


title: S9.6mock rep2

description: Library name: SAMPLES10

value: Mock


title: RAM_BAL_WT_d3_rep2

description: Library name: RAM_BAL_WT_d3_rep2

value: lung lavage

value: WT


title: RAM_BAL_WT_d3_rep1

description: Library name: RAM_BAL_WT_d3_rep1


title: H3K27ac ChIP-seq, fly adult, day45, replicate 2

description: Library name: day45-rep2-ip


title: H3K27ac ChIP-seq, fly adult, day45, replicate 1

description: Library name: day45-rep1-ip


title: w1_HS1hr37C_12hRec_antiRhi_rep1

value: Heat Shock for 1 hour at 37oC

value: 12 hour recovoery after heat stress


title: RAM_BAL_KO_naive_rep3

description: Library name: RAM_BAL_KO_naive_rep3

value: RAMs

value: naïve


title: RAM_BAL_KO_naive_rep2

description: Library name: RAM_BAL_KO_naive_rep2

value: KO


title: RNAPolIIK287T rep2

description: Library name: SAMPLES6

value: SIGMA3K287T OVEREXPRESSION


title: w1_HS1hr37C_12hRec_antiIgG_rep1


title: S9.6WT rep2

description: Library name: SAMPLES12


title: S9.6empty rep1

description: Library name: SAMPLES8


title: w1_HS1hr37C_1hRec_antiRhi_rep1

value: 1 hour recovoery after heat stress


title: S9.6mock rep1

description: Library name: SAMPLES7


title: RNAPolIIWT rep2

description: Library name: SAMPLES5


title: w1_HS1hr37C_1hRec_antiRhi_rep2

value: Rhino