title: RAW264.7 cells, Sync-label Enrich, Blank, rep3

description:
5_RAW_Sync_label_LPS_VS_Blank_DESeq2_DEG.csv
RAW264.7_Sync-label_LPS_and_Blank_Reads_Count.txt
RAW_Sync_Blank_3

source_name: wildtype RAW264.7 cells with Sync-label treatment

value: Sync-label+,LPS-


title: sputum, asthma, rep 16

status: Public on Jun 24 2025

type: SRA

city: New Haven

first: Xiting

last: Yan

state: Connecticut

address: 300 Cedar Street, Ste S441D

department: Internal Medicine

country: USA

institute: Yale School of Medicine

description:
genexSC-16
10x Genomics Chromium 3' V2

library_source: transcriptomic single cell

data_processing:
The demultiplexed, barcoded processing, gene counting and aggregation were made using the Cell Ranger pipeline V3.1.
Assembly: GRCh38
Supplementary files format and content: seurat object V5

molecule: total RNA

organism: Homo sapiens

source_name: sputum

extract_protocol:
Fresh sputum samples with viability >70% was prepared by suspending the cell pellet (~1 x 10^6) in 1ml PBS and processed using the Chromium V2 chips and protocol from 10X Genomics for RNA Seq. Some of the samples were preserved using DMSO and thawed before processing using the protocol.
Library was constructed according to the manufacter's instructions (single cell 3' V2 protocol, 10x Genomics).

tag: tissue

value: sputum

tag: cell line

value: primary cells

tag: cell type

value: immune cells and bronchial epithelial cells

tag: condition

value: asthma


title: RPE_iCut_tracr_10h_LaminB2_R1-gatc.counts.txt.gz

city: Amsterdam

first: Xabier

last: Vergara

state: North Holland

address: Plesmalaan 121

department: Molecular Genetics

country: Netherlands

institute: Netherlands Cancer Institute

description:
Library name: 6604_1_pA-DamID_tracr_10h_R1_AAACATCG_S21_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"

library_source: genomic

data_processing:
We processed the DNA sequencing data using the previously published computational pipeline (https://github.com/vansteensellab/pADamID_ABCB1_Novaseq)
Assembly: hg38
Supplementary files format and content: There are two processed data formats: (1) -gatc.counts.txt.gz, read counts per gatc sequence in the genome used for domainograms and (2) -20kb.bw, bigwig file at 20kb resolution
Library strategy: DamID-Seq

molecule: genomic DNA

growth_protocol: Culturing methods per cell line are described in the manuscript

extract_protocol:
genomic DNA was extracted using the Bioline kit (details in methods section)
We followed pA-DamID library preparation protocol used for NOVAseq (details in methods section)

treatment_protocol: Trearment per sample are described in the manuscript

value: hTERT-immortalized retinal pigment epithelial

tag: genotype

value: wildtype

tag: antibody

tag: transfection

tag: timepoint

tag: treatment

tag: batch


title: 406_1

city: Boston

first: Jiekun

last: Yang

address: 32 Vassar Street

institute: MIT

description:
Sample 19
10x Genomics

data_processing:
We received the sequences, mapped the reads against the GRCh38 human reference genome, and quantified the read counts using Cell Ranger pipeline version 3.1.0 (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Metastatic melanoma

extract_protocol:
We enzymatically digested and dissociated fresh tumor samples according to tissue dissociation kit protocols using the gentleMACS™ Dissociator (Miltenyi). Dissociated tissues were filtered, centrifuged, and the isolated cells were resuspended in 0.1% BSA in PBS.
Briefly, 5000-6000 cells were profiled per sample using the Chromium Single Cell 3’ RNA reagent kit v3 according to the 10X Genomics protocol. The generated cDNA libraries were indexed, pooled, and sequenced in batches.

value: Metastatic melanoma


title: T47D, PRA, 3D, vehicle treated, rep3

city: Minneapolis

first: Noelle

middle: E

last: Gillis

state: Minnesota

address: 2231 6th ST SE, CCRB

institute: University of Minnesota

description: Library name: PRA_3D_veh_rep3

library_source: transcriptomic

data_processing:
Illumina adapters were removed using Trim-Galore.
For alignment and transcript assembly, the sequencing reads were mapped to hg38 using STAR.
Sorted reads were counted using HTSeq.
Normalization and differential expression analysis was performed using DESeq2
Assembly: hg38
Supplementary files format and content: tab delimited text files containing count data for each sample

source_name: ER+ breast cancer

growth_protocol: T47D cells were cultured in MEM 10 (Corning,) containing 5% FBS (Corning), 1% penicillin streptomycin (Gibco), nonessential amino acids (Gibco), and 6 ng/mL of insulin (Gibco). To make PR isoform-specific models, T47D (Y; naturally occurring PR-null variant) cells were transduced with lentiviral pLenti CMV Neo containing PR-A WT, PR-A S294A, PR-B WT, or PR-B S294A cDNA. Cells were selected and maintained with 0.5 mg/ml G418 (Corning).

extract_protocol:
1 ug of total RNA was extracted and purified using RNeasy Plus Kit (Qiagen) according to manufacturer’s protocol.
Libraries were built from individual samples with the TruSeq Stranded mRNA kit (Illumina). RNA-Seq libraries were pooled and sequenced on the Illumina NovaSeq X Plus with 50 bp paired-end reads

treatment_protocol: For experiments with R5020 (PerkinElmer) treatment, cells were hormone-starved in phenol red-free MEM (Gibco) containing 5% dextran-coated charcoal-stripped FBS (HyClone), 1% penicillin streptomycin (Gibco), nonessential amino acids (Gibco), and 6 ng/mL of insulin (Gibco) for 24 hours prior to addition of 10 nM R5020.

value: ER+ breast cancer

tag: pr isoform_expression

value: A

tag: growth condition

value: vehicle


title: 1171_1

description:
Sample 18
10x Genomics


title: RAW264.7 cells, Sync-label Enrich, Blank, rep2

city: Beijing

first: Qidong

last: Deng

address: No.5 Yiheyuan Road Haidian District, Beijing 100871 P.R. China

department: School of Life Sciences

country: China

institute: Peking university

description:
5_RAW_Sync_label_LPS_VS_Blank_DESeq2_DEG.csv
RAW264.7_Sync-label_LPS_and_Blank_Reads_Count.txt
RAW_Sync_Blank_2

data_processing:
Raw reads were trimmed with Trim Galore!(v0.6.7) to remove low-quality bases and adapters and subsequently aligned to the Homo sapiens genome (Ensembl GRCh38.107) or Mus musculus (GRCm38.98) by HISAT2 (v2.2.1) with with ‘-rna-strandness RF’ parameters. After the low-quality reads were filtered out by SAMtools (v1.9), fragments mapped on the exons were processed using featureCounts (v2.0.2) to obtain the gene expression matrix. The R/Bioconductor package DESeq2 (v1.36.0) was used for data normalization and differential expression analysis.
Assembly: hg38, mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Mus musculus

growth_protocol: HeLa and RAW264.7 cell lines were cultured in DMEM medium (Gibco) supplemented with 10% fetal bovine serum and 1% penicillin/ streptomycin at 37°C under 5% CO2.

extract_protocol:
Cells grown in cell culture dishes at ~90% confluency were incubated with 50 nM photocatalyst in fresh medium at 37°C under 5% CO2 for 30 min, washed with PBS for three times, incubated with 50 µM QMPAB-2 in culture medium for 30 min and washed twice with PBS. After washing, cells were maintained in fresh medium at 37°C under 5% CO2 for 5 min and illuminated with blue LED (4 mW cm-2; λmax ∼460 nm) for 15 min at room temperature. Cells were placed about 5 cm from the light source. After illumination, cells were immediately collected using cell scraper and lysed with TRIzol reagent. Cellular total RNA purification was operated following the manufacture protocol by isopropanol precipitation.Total RNA was extracted using TRIzol reagent(Invitrogen).
RNA libraries were prepared using SMARTer Stranded Total RNA-Seq Kit v2(Takara). Labeled RNA was captured using Dynabeads MyOne Streptavidin C1 (Invitrogen).

value: macrophage

value: WT


title: T47D, PRA, 3D, vehicle treated, rep1

description: Library name: PRA_3D_veh_rep1


title: 1009_1

description:
Sample 17
10x Genomics


title: Translating RNA-seq, rep3,read1

city: Austin

first: Can

last: Cenik

state: Texas

address: 2500 Speedway

department: Department of Molecular Biosciences

institute: University of Texas

description: Library name: AR_3_POLY_RNA

data_processing:
Ribosome profiling data were processed using RiboFlow. We extracted the first 12 nucleotides from the 5’ end of the reads using UMI-tools with the following parameters: 'umi_tools extract -p "^(?P<umi_1>.{12})(?P<discard_1>.{4}).+$" --extract-method=regex'. The four nucleotides downstream of the UMIs are discarded as they are incorporated during the reverse transcription step. We clipped the 3’ adapter AAAAAAAAAACAAAAAAAAAA using cutadapt with the parameters “-a AAAAAAAAAACAAAAAAAAAA --overlap=4 --trimmed-only --maximum-length=56 --minimum-length=31 --quality-cutoff=28”. For RNA-seq  we clipped the 3’ adapter AGATCGGAAGAGCACACGTCTGAACTCCAGTCA using the  cutadapt with the parameters “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --quality-cutoff=28' After UMI extraction and adapter trimming, reads were aligned to ribosomal and transfer RNAs using Bowtie2 with the parameters "-L 15 --no-unal --norc". The unaligned reads were mapped to a manually-curated transcriptome with the parameters "-L 15 --norc --no-unal". We retained alignments with mapping quality greater than 2 followed by deduplication using UMI-tools. As the last step, .ribo files are created using RiboPy
We extracted the first 12 nucleotides from the 5’ end of the reads using UMI-tools with the following parameters: 'umi_tools extract -p "^(?P<umi_1>.{12})(?P<discard_1>.{4}).+$" --extract-method=regex'. The four nucleotides downstream of the UMIs are discarded as they are incorporated during the reverse transcription step.
We clipped the 3’ adapter AAAAAAAAAACAAAAAAAAAA using cutadapt with the parameters “-a AAAAAAAAAACAAAAAAAAAA --overlap=4 --trimmed-only --maximum-length=56 --minimum-length=31 --quality-cutoff=28”.
For RNA-seq  we clipped the 3’ adapter AGATCGGAAGAGCACACGTCTGAACTCCAGTCA using the  cutadapt with the parameters “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --quality-cutoff=28' After UMI extraction and adapter trimming, reads were aligned to ribosomal and transfer RNAs using Bowtie2 with the parameters "-L 15 --no-unal --norc". The unaligned reads were mapped to a manually-curated transcriptome with the parameters "-L 15 --norc --no-unal". We retained alignments with mapping quality greater than 2 followed by deduplication using UMI-tools. As the last step, .ribo files are created using RiboFlow
Assembly: Assembly: A curated transcriptome of primary transcripts was used for alignment. Reference files for use with RiboFlow are located at https://github.com/ribosomeprofiling/references_for_riboflow
Supplementary files format and content: Ribo file

molecule: cytoplasmic RNA

growth_protocol: HEK293T cell lines were obtained from ATCC. HEK293T cell lines were maintained in Dulbecco's modified Eagle's media (DMEM, GIBCO) supplemented with 10% Fetal Bovine Serum (FBS, GeminiBio) and 1% Penicillin and Streptomycin (GIBCO, Life Technologies) at 37°C in 5% CO2 atmosphere.

extract_protocol:
Four replicates of ~8 X10^6 HEK293T cells were plated in 150 cm2 plates. After ~18 h, cells were washed and then scraped with ice cold PBS, followed by centrifugation at 300 g for 5 min. 600 ul Lysis buffer (20 mM Tris, 150 mM NaCl, 5 mM MgCl2, 1mM DTT, Triton and 100 ug/ml of cycloheximide) was added to the cell pellet followed by incubation on ice for 10 min and the lysate was clarified by centrifugation at 1300g for 10 min at 4Â°C. The cleared lysate (50 ul) was directly used for total RNA extraction by adding 700 ul of Trizol (Zymo). 200 ul of the lysate along with 20 ul of the Ribonucleoside Vanadyl Complex was layered on the 1M sucrose cushion and subjected to ultracentrifugation at 38000 rpm for 2.5 h at 4°C. The remaining 350 ul was used for ribosome profiling. The pellet was dislodged in 700 ul of Qiazol and stored -80 °C until use the next day.
Total RNA and translating RNA was extracted using Zymo RNA miniprep kit as per manufacturer's protocol (Zymo). The concentration was estimated using nanodrop and the integrity of the extracted RNA was determined by 2100 Bioanalyzer (RNA 6000 Pico Kit, Agilent). 1μg of the extracted RNA was used for Poly A selection using NEBNext poly(A) mRNA magnetic isolation kit (NEB, E7490S). This was followed by library preparation using NEBNext Ultra II RNA library prep kit for Illumina (NEB, E7770S) as per the manufacturer's protocol using 7 PCR cycles. The quality and concentration of the libraries formed were determined by Bioanlyzer (High sensitivity DNA assay kit, Agilent). Equimolar amounts of the libraries were pooled and sequencing was done using NovaSeqx Plus (2X150 paired end).
For ribosome profiling, RNA was isolated using miRNeasy Mini kit and size-selected by running 1 µg of each sample in a 15% polyacrylamide TBE-UREA gel. 26–34 nt RNA fragments were excised, RNA fragments were extracted and precipitated. Ribosome profiling libraries were prepared using the D-Plex Small RNA-Seq Kit (Diagenode) as previously described. The cDNA was amplified for eleven cycles. Each library was cleaned with AMPure XP beads and eluted with 30 μL of RNase-free water. To completely remove the primer-dimers, size-selection was done using a 12 % polyacrylamide gel followed by excision of the fragment (~200bp). The DNA was extracted by overnight incubation in a buffer (10 mM magnesium acetate tetrahydrate, 0.5 M ammonium acetate, 1 mM EDTA (pH 8.0) at room temperature followed by ethanol precipitation (-20 °C, overnight) to recover the size selected libraries. The resulting libraries were analyzed with the Agilent High Sensitivity DNA Kit (Agilent). Each library was mixed in equimolar proportion for sequencing with the NovaSeqx Plus (2X150 paired end).

treatment_protocol: To validate translational buffering, we attempted to generate a series of knockdowns of buffered genes using the MultiCas12a approach. Briefly, we synthesized a three 10-plex cRNA array targeting 8 buffered and 2 non-buffered genes as double stranded gene fragments (Twist Biosciences). The arrays differed in the gRNA efficiency of their target. A fourth crRNA array targeted the intergenic region to be used as a negative control. Overall, four 10-plex crRNA were cloned in pCH67 into the Bsmb1 cloning site (Addgene, 217667) using NEBuilder HiFi DNA Assembly Master Mix (NEB, E2621). Lentivirus was generated with the cloned pCH67 or pCH45 (multiAsCas12a-KRAB, Agdgene, 217330) along with psPAX2 (Addgene, 12260)and pMD2.G (Addgene ,2259) using lipofectamine 3000 (Invitrogen) as per manufacturer's protocol.The lentivirus was used to infect HEK293T cells followed by selection using puromycin. Following selection, BFP positive cells were sorted using FACS to select for cells that express MultiCas12a. HEK293T cells were then continued to grow for 24 hours followed by plating in 150 cm2 plates to perform ribosome profiling, with matched total and translating RNA sequencing. However the knockdown efficiency was low with this approach,

value: Human embryonic kidney

value: knowkdown

value: CRISPR KD


title: RAW264.7 cells, Sync-label Enrich, Blank, rep1

description:
5_RAW_Sync_label_LPS_VS_Blank_DESeq2_DEG.csv
RAW264.7_Sync-label_LPS_and_Blank_Reads_Count.txt
RAW_Sync_Blank_1


title: sputum, control, rep 15

description:
genexSC-15
10x Genomics Chromium 3' V2

value: control


title: sputum, asthma, rep 14

description:
genexSC-14
10x Genomics Chromium 3' V2


title: RAW264.7 cells, CAT-seq Enrich, LPS 24h, rep2

description:
Dynamic_Change_Upon_LPS_Normalized_FPKM.xlsx
RAW_Single_LPS_24h_2

source_name: wildtype RAW264.7 cells with CAT-seq,LPS stimulation time 24h

value: CAT-seq+,LPS 24h


title: Forebrain MR Wildtype2

city: Research Triangle Park

first: Serena

middle: M

last: Dudek

state: NC

address: 111 TW Alexander Dr.

department: Neurobiology

institute: NIEHS

data_processing:
Raw reads were processed by SpaceRanger with default setting.
Assembly: mm10
Supplementary files format and content: The filtered feature count matrix was generated from SpaceRanger.
Library strategy: Spatial transcriptome

source_name: control mouse brain

extract_protocol:
The frozen sections of mouse mouse brain were placed on 10X genomics Visium spatial transcriptomics slides
RNA libraries were prepared according to the Visium spatial transcriptomic slide manual

value: brain

tag: strain

value: Emx1-Cre negative:MR fl/fl


title: T47D, PRA, 3D, R5020 treated, rep3

description: Library name: PRA_3D_R50_rep3


title: sputum, asthma, rep 13

description:
genexSC-13
10x Genomics Chromium 3' V2

value: sputum

value: primary cells

value: immune cells and bronchial epithelial cells


title: RAW264.7 cells, Sync-label Enrich, LPS, rep1

description:
5_RAW_Sync_label_LPS_VS_Blank_DESeq2_DEG.csv
RAW264.7_Sync-label_LPS_and_Blank_Reads_Count.txt
RAW_Sync_LPS_1

source_name: wildtype RAW264.7 cells with Sync-label and LPS treatment

value: Sync-label+,LPS+


title: T47D, PRA, 3D, vehicle treated, rep2

description: Library name: PRA_3D_veh_rep2


title: RAW264.7 cells, CAT-seq Enrich, LPS 24h, rep1

description:
Dynamic_Change_Upon_LPS_Normalized_FPKM.xlsx
RAW_Single_LPS_24h_1


title: sputum, control, rep 12

description:
genexSC-12
10x Genomics Chromium 3' V2


title: 856_1

description:
Sample 16
10x Genomics

value: Metastatic melanoma


title: T47D, PRB, 2D, R5020 treated, rep3

description: Library name: PRB_2D_R50_rep3

value: ER+ breast cancer

value: B


title: 776_1

description:
Sample 15
10x Genomics


title: T47D, PRB, 2D, R5020 treated, rep2

description: Library name: PRB_2D_R50_rep2


title: sputum, control, rep 11

description:
genexSC-11
10x Genomics Chromium 3' V2


title: RAW264.7 cells, CAT-seq Enrich, LPS 8h, rep2

description:
Dynamic_Change_Upon_LPS_Normalized_FPKM.xlsx
RAW_Single_LPS_8h_2

source_name: wildtype RAW264.7 cells with CAT-seq,LPS stimulation time 8h

value: CAT-seq+,LPS 8h


title: T47D, PRB, 2D, R5020 treated, rep1

description: Library name: PRB_2D_R50_rep1


title: RAW264.7 cells, CAT-seq Enrich, LPS 8h, rep1

description:
Dynamic_Change_Upon_LPS_Normalized_FPKM.xlsx
RAW_Single_LPS_8h_1

value: macrophage


title: 1098_4

description:
Sample 13
10x Genomics


title: T47D, PRB, 2D, vehicle treated, rep3

description: Library name: PRB_2D_veh_rep3

value: vehicle


title: RAW264.7 cells, CAT-seq Enrich, LPS 2h, rep2

description:
Dynamic_Change_Upon_LPS_Normalized_FPKM.xlsx
RAW_Single_LPS_2h_2

source_name: wildtype RAW264.7 cells with CAT-seq,LPS stimulation time 2h

value: WT

value: CAT-seq+,LPS 2h


title: sputum, asthma, rep 9

description:
genexSC-9
10x Genomics Chromium 3' V2

value: asthma


title: 452_2

description:
Sample 12
10x Genomics


title: T47D, PRB, 2D, vehicle treated, rep2

description: Library name: PRB_2D_veh_rep2


title: RAW264.7 cells, CAT-seq Enrich, LPS 0h, rep2

description:
Dynamic_Change_Upon_LPS_Normalized_FPKM.xlsx
RAW_Single_LPS_0h_2

source_name: wildtype RAW264.7 cells with CAT-seq,LPS stimulation time 0h

value: CAT-seq+,LPS 0h


title: sputum, control, rep 8

description:
genexSC-8
10x Genomics Chromium 3' V2

value: control


title: RAW264.7 cells, CAT-seq Enrich, LPS 2h, rep1

description:
Dynamic_Change_Upon_LPS_Normalized_FPKM.xlsx
RAW_Single_LPS_2h_1


title: 509_2

description:
Sample 11
10x Genomics


title: sputum, asthma, rep 7

description:
genexSC-7
10x Genomics Chromium 3' V2


title: T47D, PRA, 2D, R5020 treated, rep3

description: Library name: PRA_2D_R50_rep3

value: A


title: T47D, PRB, 2D, vehicle treated, rep1

description: Library name: PRB_2D_veh_rep1


title: sputum, asthma, rep 6

description:
genexSC-6
10x Genomics Chromium 3' V2


title: 1227_1

description:
Sample 9
10x Genomics


title: T47D, PRA, 2D, R5020 treated, rep2

description: Library name: PRA_2D_R50_rep2


title: RAW264.7 cells, CAT-seq Enrich, LPS, rep2

description:
RAW264.7_CAT-seq_LPS_VS_Blank_Relative_Expression.xls
RAW_Single_LPS_2

source_name: wildtype RAW264.7 cells with CAT-seq and LPS treatment

value: CAT-seq+,LPS+


title: T47D, PRA, 2D, R5020 treated, rep1

description: Library name: PRA_2D_R50_rep1


title: sputum, control, rep 10

description:
genexSC-10
10x Genomics Chromium 3' V2

value: sputum


title: 509_1

description:
Sample 14
10x Genomics


title: 1037_1

description:
Sample 7
10x Genomics


title: RAW264.7 cells, CAT-seq Enrich, LPS, rep1

description:
RAW264.7_CAT-seq_LPS_VS_Blank_Relative_Expression.xls
RAW_Single_LPS_1


title: 1087_1

description:
Sample 10 (Mucosal Sample 5)
10x Genomics


title: RAW264.7 cells, CAT-seq Enrich, LPS 0h, rep1

description:
Dynamic_Change_Upon_LPS_Normalized_FPKM.xlsx
RAW_Single_LPS_0h_1


title: sputum, control, rep 4

description:
genexSC-4
10x Genomics Chromium 3' V2

value: primary cells


title: RAW264.7 cells, CAT-seq Enrich, Blank, rep2

description:
RAW264.7_CAT-seq_LPS_VS_Blank_Relative_Expression.xls
RAW_Single_Blank_2

source_name: wildtype RAW264.7 cells with CAT-seq treatment

value: CAT-seq+,LPS-


title: T47D, PRA, 2D, vehicle treated, rep3

description: Library name: PRA_2D_veh_rep3


title: Bbs8 WT iWAT SVF, p2, rep2

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Demultiplexing was perfomed using bcl2fastq2 v2.20
Fastq files from Seq-Well were loaded into a snakemake-based data pre-processing pipeline (version 0.31, available at https://github.com/Hoohm/dropSeqPipe) that relies on the Drop-seq tools provided by the McCarroll lab (Macosko, Basu et al. 2015)
Alignment was performed using STAR alignment against the murine reference genome mm10.
The scRNA-seq data analysis was conducted using the seurat analysis pipeline (version 4.1.1) unless otherwise specified. To address differences in sequencing depth, the downsampleBatches function from the scuttle package (version 1.0.4) was employed using default parameter setting. Cells expressing fewer than 100 or more than 1000 genes, as well as those with more than 20 percent mitochondrial genes, were removed.
Assembly: mm10
Supplementary files format and content: comma separated files include count data of filtered cells

molecule: polyA RNA

source_name: inguinal white adipose tissue

extract_protocol:
Progenitor cell isolation from the stromal vascular fraction (SVF) was performed as previously described (Sieckmann et al., 2022).Tissues were minced, and digested with collagenase II and DNAse I at 37°C for 30 min. The digestion was quenched by adding AT buffer (0.5% BSA in PBS). The dissociated cells were passed through a 100-μm filter (Corning). The stromal vascular fraction, was resuspended in red blood cell lysis buffer (BioLegend) and further filtered through a 70-μm filter (Corning).
Seq-Well S3 protocol

value: inguinal white adipose tissue

value: Stromal vascular fraction

value: wt


title: RPE_iCut_ABCB1_cr6_24h_Dam_R1-gatc.counts.txt.gz

description:
Library name: 6604_8_pA-DamID_ABCB1_cr6_24h_R1_Dam_ACACAGAA_S32_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"

value: hTERT-immortalized retinal pigment epithelial

value: wildtype


title: sputum, asthma, rep 1

description:
genexSC-1
10x Genomics Chromium 3' V2

value: immune cells and bronchial epithelial cells


title: sputum, asthma, rep 3

description:
genexSC-3
10x Genomics Chromium 3' V2


title: T47D, PRA, 2D, vehicle treated, rep2

description: Library name: PRA_2D_veh_rep2

value: ER+ breast cancer

value: vehicle


title: 854_1

description:
Sample 8
10x Genomics

value: Metastatic melanoma


title: sputum, control, rep 5

description:
genexSC-5
10x Genomics Chromium 3' V2


title: sputum, asthma, rep 2

description:
genexSC-2
10x Genomics Chromium 3' V2

value: asthma


title: T47D, PRA, 2D, vehicle treated, rep1

description: Library name: PRA_2D_veh_rep1


title: RAW264.7 cells, CAT-seq Enrich, Blank, rep1

description:
RAW264.7_CAT-seq_LPS_VS_Blank_Relative_Expression.xls
RAW_Single_Blank_1

value: macrophage

value: WT


title: T47D, PRB, vehicle treated, IGG, rep3

description: Library name: PRB_IGG_rep3

data_processing:
Illumina adapters were removed using Trim-Galore.
For alignment and transcript assembly, the sequencing reads were mapped to hg38 using bowtie2.
Peaks were called over IGG using macs2.
IDR was used to define consensus peak sets.
Assembly: hg38
Supplementary files format and content: narrowPeak files containing consensus peak calls for each condition.
Supplementary files format and content: narrowPeak files containing peak calls for each sample
Library strategy: CUT&Run

extract_protocol:
500,000 cells were collected and used for CUT&RUN. The Epicypher CUT&RUN kit was used per the manufacturer's protocol.
Libraries were built from individual samples with the NEB Next Ultra II FS Library Kit. CUT&RUN libraries were pooled and sequenced on the Illumina NovaSeq X Plus with 50 bp paired-end reads

value: B

tag: cut&run target

value: IGG


title: 1224_3

description:
Sample 4
10x Genomics


title: WT1_MuSCs-K27me3

city: Montreal

first: Vahab

middle: D.

last: Soleimani

state: Quebec

address: 3755 Chem. de la Côte-Sainte-Catherine

department: Lady Davis Institute for Medical Research

country: Canada

institute: Jewish General Hospital

description: Library name: MuSCsWT1H3K27me3_SOL2381A1-1

data_processing:
Illumina BaseSpace software was used for basecalling.
Data was analysed using the GenPipes pipeline v.3.1.5 (https://academic.oup.com/gigascience/article/8/6/giz037/5513895)
Peaks were called using MACS2(v2.1.1)
Assembly: mm10
Supplementary files format and content: The bigWig files are normalized genome-wide signal coverage tracks used for visual inspection of the peaks and comparison between conditions
Library strategy: Cut&Run

source_name: skeletal muscle/ muscle stem cells

extract_protocol:
45 000 Muscle stem cells (ITGA7+/VCAM1+/CD11b-/CD45-/CD31-/Ly6a-) were isolated by Fluorescence Activated Cell Sorting (FACS) into 2%FBS in PBS for the Cut&Run on freshly isolated cells. For the Cut&Run of REST, cells were first  isolated by FACS and cultured in growth media for 1 week and then 100 000K cells were obtained to perform Cut&Run.
Cut&Run of H3K27me3 on MuSCS and Cut&Run of REST  on myoblasts were performed using the commercially available Cut&Run Kit (Epicypher, 14-1048) according to the manufacturer’s guidelines. Libraries were prepared using the Cut&Run Library Prep Kit (Epicypher, 14-1001) according to the manufacturer’s guidelines.

value: skeletal muscle/ muscle stem cells


title: Bbs8 WT iWAT SVF, p2, rep1


title: 406_3

description:
Sample 3
10x Genomics


title: T47D, PRB, vehicle treated, IGG, rep2

description: Library name: PRB_IGG_rep2


title: Bbs8 WT iWAT SVF, p1, rep3


title: 926_1

description:
Sample 2
10x Genomics


title: T47D, PRB, vehicle treated, IGG, rep1

description: Library name: PRB_IGG_rep1


title: COP1SNP [SAM24384939]

city: South San Francisco

first: Rohit

last: Reja

state: CA

address: 1 DNA Way

institute: Genentech

data_processing:
Reads were aligned to the GRCh38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. Supplementary files use Entrez gene IDs, counts and RPKM statistics.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw count and RPKM values for each Sample

source_name: Skin

extract_protocol:
Total RNA was extracted using a RNeasy Mini Kit (Qiagen, cat 74104) and quantified in a NanoDrop 8000 (ThermoFisher).
0.1 μg of total RNA was used for library preparation with a TruSeq Stranded Total RNA Library Prep Kit (Illumina). The libraries were multiplexed and then sequenced on an Illumina HiSeq4000 (Illumina) to generate 30 million single end 50 bp reads.

treatment_protocol: No treatment

value: Skin


title: Bbs8 WT iWAT SVF, p1, rep2


title: 1232_1

description:
Sample 6 (Mucosal Sample 4)
10x Genomics


title: 1098_5

description:
Sample 5
10x Genomics


title: iPSC-derived motor neuron cultures, sporadic ALS, line 8FF6, 2D (plate) format, batch 3

city: Los Angeles

first: Shaughn

last: Bell

address: 8700 Beverly Blvd

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

description: 10x Genomics

data_processing:
Sample demultiplexing was performed by the Cedars-Sinai Applied Genomics, Computation and Translational Core.  Raw data were delivered as multiple gzipped fastq files.
Demultiplexed fastq files were run via CellRanger v6.1.2 using the "cellranger count" command with the "--include-introns" option using the precompiled CellRanger human reference sequence “v2020-A” provided on the 10x Genomics website.
CellRanger output “filtered_feature_bc_matrix files” (barcodes.tsv.gz, features.tsv.gz & matrix.mtx.gz) were loaded into R (v4.2.1) via Rstudio (v2022.07.1, Build 554) and combined into one matrix file per sample with genes as rows (with both gene symbol and Ensmbl ID) and cells (nuclei) as columns. Each matrix file was then processed by summing all Ensmbl IDs with the same gene symbol to the gene symbol level via standard R matrix processing functions.
Assembly: hg38
Supplementary files format and content: Comma separated count matricies with gene symbols as rows and cell IDs as columns

molecule: nuclear RNA

source_name: frozen cell pellet

extract_protocol:
All steps were performed on ice.  Wide-bore Rainin LTS pipette tips were used exclusively throughout. Frozen cell pellets were thawed on ice, resuspended in cold homogenization buffer (5mM MgCl2, 3mM Mg(Ac)2, 10mM Tris pH7.8, 0.017 mM PMSF, 0.17 mM b-mercaptoethanol, 320 mM Sucrose, 0.1 mM EDTA, 0.1% NP40, RNAse inhibitors, and Protease inhibitors), and transferred to a 2 ml glass dounce.  The tissue was manually lysed with 50 strokes each of the "A" and "B" pestles.  Homogenate was filtered using 70 um Flowmi pipette tip filters and gently mixed 1:1 with a 50% Iodixanol solution (5mM MgCl2, 3mM Mg(Ac)2, 10mM Tris pH7.8, 0.017 mM PMSF, 0.17 mM b-mercaptoethanol, RNAse inhibitors, Protease inhibitors, and 50% Iodixanol).  A centrifugation gradient was set up using 600 ul 40% Iodixanol solution (5mM MgCl2, 3mM Mg(Ac)2, 10mM Tris pH7.8, 0.017 mM PMSF, 0.17 mM b-mercaptoethanol, RNAse inhibitors, Protease inhibitors, 160 mM Sucrose, 0.2 ug/ul OrangeG, and 40% Iodixanol), 600 ul 29% Iodixanol solution (5mM MgCl2, 3mM Mg(Ac)2, 10mM Tris pH7.8, 0.017 mM PMSF, 0.17 mM b-mercaptoethanol, RNAse inhibitors, Protease inhibitors, 160 mM Sucrose, and 29% Iodixanol) and 800 ul of the 50% Iodixanol + Sample mixture (25% Iodixanol final concentration).  This was centrifuged at 3000 x g for 1 hour with the breaks disengaged.  Any debris on the top surface was removed, and 200 ul of the thin cloudy layer containing the nuclei was extracted, mixed with 1.8 ml PBS + 1% BSA solution, and centrifuged at 500 x g for 10 minutes with breaks engaged.  1.8 ml supernatant was removed and the remaining 200 ul plus nuclei pellet was resuspended in 1.8 ml PBS + 1% BSA solution.  The nuclei suspension was counted via hemocytometer and checked for nucleus quality.  A portion of this suspension was then diluted to achieve the correct nuclei concentration for the 10x Chromium NextGEM 3' protocol with a target of ~4,000 nuclei per sample.
Standard 10x protocol found in "Chromium NextGEM Single Cell 3' Reagent Kits v3.1 User Guide, Rev D" (single index)

value: frozen cell pellet

value: iPSC-derived motor neuron cultures

value: ALS

value: Batch 3


title: COP1SNP [SAM24384938]


title: T47D, PRB, R5020 treated, PR CUT&RUN, rep3

description: Library name: PRB_PR_R50_rep3

value: PR


title: WT [SAM24335534]


title: Bbs8 WT iWAT SVF, p1, rep1

value: inguinal white adipose tissue

value: Stromal vascular fraction

value: wt


title: WT [SAM24335533]


title: COP1SNP [SAM24384940]


title: Bbs8 KO iWAT SVF, p2, rep 3

value: ko


title: T47D, PRB, R5020 treated, PR CUT&RUN, rep2

description: Library name: PRB_PR_R50_rep2

value: ER+ breast cancer


title: Bbs8 KO iWAT SVF, p2, rep 2


title: T47D, PRB, vehicle treated, PR CUT&RUN, rep2

description: Library name: PRB_PR_veh_rep2

value: vehicle


title: WT [SAM24335532]


title: iPSC-derived motor neuron cultures, normal control, line 6DHM, 2D (plate) format, batch 3

description: 10x Genomics

value: CTL


title: iPSC-derived motor neuron cultures, normal control, line 2NK3, 2D (plate) format, batch 3

description: 10x Genomics


title: Bbs8 KO iWAT SVF, p2, rep 1


title: MTF_Cre+_4

city: Providence

first: Geongoo

last: Han

address: 171 Meeting St.

institute: Brown University

description: Library name: sv_ry_mtf1_ko_si_rna8

data_processing:
Adapter and low-quality sequences were trimmed from the raw sequence reads using Trimmomatic (v0.36)
Trimmed sequences were aligned to the mm10 mouse genome and reads per gene was counted using STAR (v2.7.3a)
Gene count was normalized in DESeq2 v1.38.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file raw counts for all samples
Supplementary files format and content: tab-delimited text file normalized counts by DESeq2 for all samples

source_name: small intestine

extract_protocol:
RNA from small intestine tissue was extracted using the RNeasy Mini Kit (Qiagen).
The RNA library was prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs)

value: small intestine

value: KO


title: T47D, PRB, vehicle treated, PR CUT&RUN, rep1

description: Library name: PRB_PR_veh_rep1

value: B


title: T47D, PRB, R5020 treated, PR CUT&RUN, rep1

description: Library name: PRB_PR_R50_rep1


title: MTF_Cre+_3

description: Library name: sv_ry_mtf1_ko_si_rna7


title: H3K27ac-H2WT-Rep3__PXU005

city: Suzhou

first: Peng

last: Xu

state: Jiangsu

address: Office3625 Building703, RENAI ROAD No.199, INDUSTRIAL PARK DISTRICT

department: Suzhou Medical College

institute: Soochow University

description: Library name: sample 6

data_processing:
BWA (default parameter) was used to align reads to human genome hg19. Duplicated reads were marked by Picard, and uniquely mapped reads were retained by samtools (parameter “-q 1 -F 1024”).We confirmed quality control results were good following the ENCODE guideline for CHIPSEQ, reads were then extend to the estimated fragment size(by SPP) and converted to bigwig files. We observed clear peaks observed by inspection on Integrated Genomics Viewer (Broad Institute) and there was high consistency among replicates.Free pipeline to run with DNAnexus available at https://www.stjude.cloud/tools.html. Source code of ChIP-Seq pipeline to deposit on DNAnexus were also available at https://github.com/stjude/ChIP-Seq
Assembly: hg19
Supplementary files format and content: bigwig

source_name: Human bone marrow

growth_protocol: Cells were expanded in StemSpan serum-free expansion medium (SFEM; Stem Cell Technologies) supplemented with 1 µM dexamethasone, 1 µg/mL doxycycline, 50 ng/mL human stem cell factor (SCF), 3 units/mL erythropoietin (EPO), and 1% penicillin–streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Human bone marrow

value: erythroblast cells

value: WILD TYPE

value: H3K27ac(Abcam, ab4729)


title: iPSC-derived motor neuron cultures, sporadic ALS, line 7TN6, 3D (chip) format, batch 3

description: 10x Genomics

value: frozen cell pellet

value: iPSC-derived motor neuron cultures

value: ALS


title: Bbs8 KO iWAT SVF, p1, rep2

value: inguinal white adipose tissue


title: Bbs8 KO iWAT SVF, p1, rep1

value: Stromal vascular fraction


title: MTF_Cre+_2

description: Library name: sv_ry_mtf1_ko_si_rna6


title: T47D, PRA, vehicle treated, IGG, rep3

description: Library name: PRA_IGG_rep3

value: A

value: IGG


title: iPSC-derived motor neuron cultures, sporadic ALS, line 7TN6, 2D (plate) format, batch 3

description: 10x Genomics

value: Batch 3


title: T47D, PRA, vehicle treated, IGG, rep2

description: Library name: PRA_IGG_rep2

value: ER+ breast cancer

value: vehicle


title: Bbs8 WT iWAT, APC P3, n3

data_processing:
Demultiplexing was perfomed using bcl2fastq2 v2.20
nf-core RNA-seq v1.4.2 (Ewels et al., 2020) pipeline using STAR (Dobin et al., 2013) for alignment
library strandedness parameter was set to forward
Assembly: mm10
Supplementary files format and content: Gene x sample matrix of read counts before filtering

extract_protocol:
Progenitor cell isolation from the stromal vascular fraction (SVF) was performed as previously described (Sieckmann et al., 2022).Tissues were minced and digested with collagenase II and DNAse I at 37°C for 30 min. The digestion was quenched by adding AT buffer (0.5% BSA in PBS). The dissociated cells were passed through a 100-μm filter (Corning). The stromal vascular fraction was resuspended in red blood cell lysis buffer (BioLegend). Isolated cells were then further subjected to antibody staining. Flow sorting of cell was done by gating to isolate single cells distinct from debris, doublets, and dead cells. The cells were further gated to exclude the lineage (CD31, CD45, TER119) and to enrich for CD29 and Sca1 to isolate pre-adipocytes. Subpopulations were sorted by CD26 and CD55 for the P1 population, CD54 for P2 subpopulation, and CD142 for P3. After sorting, cells were stored in Trizol. Total RNA was extracted using the miRNeasy Micro kit (Qiagen) according to manufacturer’s protocol.
Smart‐seq02 (Picelli et al. 2014)

value: APC P3

value: wt


title: T47D, PRA, vehicle treated, IGG, rep1

description: Library name: PRA_IGG_rep1


title: MTF_Cre+_1

description: Library name: sv_ry_mtf1_ko_si_rna5

value: small intestine

value: KO


title: iPSC-derived motor neuron cultures, normal control, line 2NK3, 3D (chip) format, batch 3

description: 10x Genomics

value: CTL


title: iPSC-derived motor neuron cultures, sporadic ALS, line 8FF6, 3D (chip) format, batch 3

description: 10x Genomics


title: Bbs8 WT iWAT, APC P2, n3

value: APC P2


title: iPSC-derived motor neuron cultures, sporadic ALS, line 9FP9, 2D (plate) format, batch 2

description: 10x Genomics

value: Batch 2


title: MTF_Cre-_4

description: Library name: sv_ry_mtf1_ko_si_rna4

value: WT


title: MTF_Cre-_3

description: Library name: sv_ry_mtf1_ko_si_rna3


title: iPSC-derived motor neuron cultures, normal control, line EDi029-A, 2D (plate) format, batch 2

description: 10x Genomics

value: frozen cell pellet

value: iPSC-derived motor neuron cultures


title: Bbs8 WT iWAT, APC P1, n3

value: inguinal white adipose tissue

value: APC P1


title: iPSC-derived motor neuron cultures, sporadic ALS, line 9FP9, 3D (chip) format, batch 2

description: 10x Genomics

value: ALS


title: MTF_Cre-_1

description: Library name: sv_ry_mtf1_ko_si_rna1


title: MTF_Cre-_2

description: Library name: sv_ry_mtf1_ko_si_rna2


title: T47D, PRA, R5020 treated, PR CUT&RUN, rep2

description: Library name: PRA_PR_R50_rep2

value: A

value: PR


title: T47D, PRA, R5020 treated, PR CUT&RUN, rep1

description: Library name: PRA_PR_R50_rep1

value: ER+ breast cancer


title: T47D, PRA, R5020 treated, PR CUT&RUN, rep3

description: Library name: PRA_PR_R50_rep3


title: Bbs8 KO iWAT, APC P1, n3

value: ko


title: ETV1ETV4ETV5 KO [SAM24359733]

data_processing:
Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. Supplementary files use Entrez gene IDs, counts and RPKM statistics.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw count and RPKM values for each Sample

value: Skin

value: Primary melanocytes

value: ETV1ETV4ETV5 KO


title: iPSC-derived motor neuron cultures, normal control, line 9DE2, 3D (chip) format, batch 2

description: 10x Genomics


title: T47D, PRA, vehicle treated, PR CUT&RUN, rep3

description: Library name: PRA_PR_veh_rep3

value: vehicle


title: iPSC-derived motor neuron cultures, normal control, line 6DHM, 3D (chip) format, batch 3

description: 10x Genomics

value: CTL

value: Batch 3


title: Bbs8 KO iWAT, APC P2, n3

value: APC P2


title: iPSC-derived motor neuron cultures, sporadic ALS, line 7FRQ, 3D (chip) format, batch 2

description: 10x Genomics

value: Batch 2


title: T47D, PRA, vehicle treated, PR CUT&RUN, rep2

description: Library name: PRA_PR_veh_rep2


title: Bbs8 KO iWAT, APC P3, n2

value: APC P3


title: T47D, PRA, vehicle treated, PR CUT&RUN, rep1

description: Library name: PRA_PR_veh_rep1


title: iPSC-derived motor neuron cultures, normal control, line 2NK3, 3D (chip) format, batch 2

description: 10x Genomics

value: frozen cell pellet

value: iPSC-derived motor neuron cultures


title: ETV1ETV4ETV5 KO [SAM24359732]


title: Bbs8 KO iWAT, APC P2, n2

value: inguinal white adipose tissue


title: LCC3131

city: Pittsburgh

first: Rebekah

last: Dadey

state: PA

address: 5115 Centre Avenue

department: Hematology/Oncology

institute: University of Pittsburgh

description: Library name: LCC3131

data_processing:
Following sequencing of UPitt scRNAseq cohort, we demultiplexed utilizing bcl2fastq and utilized 10x Genomics CellRanger (v7.0) to align to human reference sequence (GRCh38) to create feature barcode matrices. We utilized Seurat for downstream analysis
Assembly: GRCh38
Supplementary files format and content: Upitt_scRNAseq_count.txt.gz which contains counts from single cell gene expression
Supplementary files format and content: Upitt_scRNAseq_metadata.txt.gz which contains metadata

source_name: Primary Tumor

extract_protocol:
Single cell suspensions were generated from tumor (n=6) specimens from patients confirmed with hepatocellular carcinoma (HCC). After initial isolation, specimens were placed on ice in Militenyi Storage Solution for a maximum of 1.5 hours (Cat#130-100-008). Tissues were then cut into small pieces by mechanical disruption and dissociated with the Militenyi Human Tumor Dissociation kit (Cat#130-095-929) and gentleMACS Dissociator (Cat#130-093-235) following the manufacturer’s instructions. After dissociation samples were quenched with cRPMI and red blood cell lysed with BD Pharm Lyse (Cat #BDB555899) following manufacturer’s instructions. If necessary, samples were indexed by Biolegend TotalSeq C anti-human Hash tag antibodies (Cat# 394661, 394663). Briefly, cells were Fc blocked by Biolegend Human TruStain FcX Fc Blocking reagent (Cat# 322301) and Hash antibodies were stained at 1ug/1x10^6 cells for 30 minutes. Cells were washed 3X with FACS buffer (Biolegend, Cat #420201) and resuspended in cRPMI for 10X 5’ GEX library prep. All samples were processed as soon as possible following surgery.
Single-cell(sc) RNAseq libraries were generated utilizing the Chromium Single Cell 5’ Reagent with a targeted depth of 50,000 reads/cell. Briefly, cells were counted using the Cellometer Auto2000 (Nexcelom). Cells were passed through the 10X Chromium controller and library preparation for gene expression and feature barcode (FTBO) was performed following the manufacturer’s instructions. Final library concentration was determined by Qubit Analyzer and Tapestation and sequenced on either a NovaSeq at UPMC Genome Core or a NovaSeq X Plus at Novogene.

value: Primary Tumor

tag: tumor

value: Hepatocellular Carcinoma


title: ETV1ETV4ETV5 KO [SAM24359731]


title: LCC3068

description: Library name: LCC3068


title: iPSC-derived motor neuron cultures, sporadic ALS, line 1BR2, 3D (chip) format, batch 2

description: 10x Genomics

value: ALS


title: iPSC-derived motor neuron cultures, sporadic ALS, line 3CA9, 3D (chip) format, batch 1

description: 10x Genomics

value: Batch 1


title: Bbs8 KO iWAT, APC P1, n2

value: APC P1

value: ko


title: Bbs8 KO iWAT, APC P3, n3


title: Bbs8 WT iWAT, APC P3, n2

value: wt


title: ETV5 KO [SAM24359729]

value: Skin

value: Primary melanocytes

value: ETV5 KO


title: LCC3031

description: Library name: LCC3031


title: ETV5 KO [SAM24359728]


title: iPSC-derived motor neuron cultures, control, line EDi043-A, 96 Well, experiment 5.4

data_processing:
Demultiplexed FASTQ files were quantified using Salmon v1.1.0
Salmon outputs were loaded into R via the tximeta package
Assembly: GRCh38, GENCODE version 30
Supplementary files format and content: A matrix of pseudocounts from Salmon collapsed to the gene level via tximeta with genes as rows and samples as columns exported to a comma separated values (csv) file.

extract_protocol:
RNA integrity was analyzed on the 2100 Bioanalyzer using the Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA) and RNA quantified using the Qubit RNA HS Assay Kit (ThermoFisher Scientific, Waltham, MA).  Total RNA-Seq library construction was performed using the IDT xGen Broad-Range RNA Library Prep Kit (Integrated DNA Technologies, Coralville, IA), following rRNA depletion using Lexogen RiboCop Depletion Kit Human/Mouse/Rat v2 (Lexogen Inc., Greenland, NH).  Final library concentration was measured via the Qubit 1X dsDNA HS Assay kit (ThermoFisher Scientific) and library size was evaluated on the 4200 TapeStation using the Agilent D1000 ScreenTape System (Agilent Technologies).  Multiplexed libraries were sequenced on a NovaSeq 6000 (Illumina, San Diego, CA) using 75bp single-end sequencing.  On average, about 50 million reads were generated from each sample.
The top channel of chip samples or a well from a 96 well plate were incubated with cold Accutase (STEMCELL Technologies) for 20 minutes at 37°C, then cells were extracted by flushing and washing with cold phosphate buffered saline (PBS), pelleted by centrifuge at 350 rcf, and frozen at -80°C. RNA was extracted from pellets using the RNeasy Micro Kit (Qiagen).
Various methods:  see SAMPLES "library construction protocol" section

value: CTR

value: Flow


title: iPSC-derived motor neuron cultures, normal control, line EDi029-A, 3D (chip) format, batch 1

description: 10x Genomics

value: CTL


title: Bbs8 WT iWAT, APC P2, n2

value: APC P2


title: LCC3027

description: Library name: LCC3027


title: iPSC-derived motor neuron cultures, control, line EDi043-A, Chip, Flow, rep 3, experiment 5.4


title: Bbs8 WT iWAT, APC P3, n1

value: APC P3


title: ETV1 KO [SAM24359726]

value: ETV1 KO


title: Bbs8 WT iWAT, APC P1, n2

value: inguinal white adipose tissue


title: LCC2134

description: Library name: LCC2134

value: Primary Tumor


title: iPSC-derived motor neuron cultures, control, line EDi043-A, Chip, Flow, rep 1, experiment 5.4

value: iPSC-derived motor neuron cultures


title: ETV1 KO [SAM24359725]


title: Bbs8 WT iWAT, APC P1, n1


title: iPSC-derived motor neuron cultures, control, line EDi029-A, Chip, Flow, rep 3, experiment 5.4


title: ETV5 KO [SAM24359730]


title: WT [SAM24359723]

value: WT


title: Bbs8 KO iWAT, APC P3, n1


title: Bbs8 KO iWAT, APC P1, n1


title: iPSC-derived motor neuron cultures, control, line EDi028-A, 96 Well, experiment 5.4


title: WT [SAM24359722]


title: ETV1 KO [SAM24359727]


title: Bbs8 KO iWAT, APC P2, n1


title: LCC3063

description: Library name: LCC3063

value: Hepatocellular Carcinoma


title: iPSC-derived motor neuron cultures, control, line EDi029-A, Chip, Flow, rep 2, experiment 5.4


title: Choroid plexus, THX2

city: Nouzilly

first: Hugues

last: Dardente

address: INRA

department: INRAE - Centre Val de Loire

country: France

institute: INRAE

data_processing:
Image analyses and base calling were performed using the NovaSeq Control Software and Real-Time Analysis component (Illumina). Demultiplexing and adapter trimming were performed using Illumina's conversion software bcl2fastq (v2.20, default parameters). The quality of the raw data was assessed using FastQC (v0.11.8) and summarized using MultiQC (v1.9) from the Babraham Institute.
TopHat2 (v2.1.1), a splice junction mapper, was used to align the RNA-Seq reads to the Ovis aries genome (NCBI Oar_Rambouillet_v1.0) with a set of gene model annotations (gff file downloaded from NCBI on April 6, 2021). Aligments were processed using samtools (v1.9) and raw gene counts were obtained using FeatureCounts (v2.0.0, with the parameters “-s 2“ to take into account read orientation).
Assembly: Genome assembly Oar_Rambouillet_v1.0
Supplementary files format and content: tab-delimited text file include raw gene counts for every gene (NCBI GeneID|Symbol) and every sample

organism: Ovis aries

source_name: Choroid plexus

extract_protocol:
TriReagent
cDNA Libraries were prepared using Illumina’s Stranded mRNA Prep Ligation kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions

value: Choroid plexus

value: thyroidectomy

tag: rearing condition

value: Long days


title: KO_DOX_1

city: Shanghai

first: Fei

state: Shanghai

address: 1609 Xietu Road

institute: Zhongshan Hospital, Fudan University

description: KO_DOX_1 (biological replicate 1)

data_processing:
We performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
Sequence and primary analysis:  Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100). And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: heart

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).
The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

value: heart

value: KO

value: DOX


title: Bbs8 WT iWAT, APC P2, n1

value: wt


title: iPSC-derived motor neuron cultures, control, line EDi028-A, Chip, Flow, rep 3, experiment 5.4

value: CTR

value: Flow


title: iPSC-derived motor neuron cultures, control, line EDi028-A, Chip, Flow, rep 2, experiment 5.4


title: KO1

city: Freiburg

first: Maximilian

last: Frosch

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

description: Library name: KO1

data_processing:
Image analysis and base calling were done by the Real Time Analysis Software (RTA) v3.9.25. The resulting .cbcl files were converted into .fastq files with the bcl2fastq v2.20 software. Fastq files were quality controlled using FastQC v0.73 and trimmed with Trim Galore! v0.6.7. Reads were mapped to the GRCm39 mouse genome using the RNA STAR aligner v2.7.8.
Assembly: GRCm39
Supplementary files format and content: fastq files

source_name: brain - sorted microglia

extract_protocol:
Microglia were FACS-sorted from whole brains, into a collection tube and then total RNA was extracted using PicoPure RNA Isolation Kit (KIT0204, Life Technologies) according to manufacturer’s protocol.
Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). Thereby 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step 1:5 dilutions of the unique dual indexing (i7 and I5) adapters were used. The libraries were quantified using the KAPA Library Quantification Kit - Illumina/ABI Prism User Guide (Roche Sequencing Solutions, Inc., Pleasanton, CA, USA).

value: brain - sorted microglia


title: KO_DOX_2

description: KO_DOX_2 (biological replicate 2)


title: KO3

description: Library name: KO3


title: Choroid plexus, THX1


title: KO2

description: Library name: KO2


title: KO_PBS_2

description: KO_PBS_2 (biological replicate 2)

value: PBS


title: Choroid plexus, Long2

value: control


title: Het4

description: Library name: Het4


title: iPSC-derived motor neuron cultures, control, line EDi022-A, 96 Well, experiment 5.4


title: KO_PBS_1

description: KO_PBS_1 (biological replicate 1)


title: Het2

description: Library name: Het2


title: Choroid plexus, Short2

value: Short days


title: WT_DOX_2

description: WT_DOX_2 (biological replicate 2)


title: iPSC-derived motor neuron cultures, control, line EDi022-A, Chip, Flow, rep 3, experiment 5.4


title: iPSC-derived motor neuron cultures, control, line EDi022-A, Chip, Flow, rep 1, experiment 5.4


title: Choroid plexus, Short1


title: iPSC-derived motor neuron cultures, control, line EDi022-A, Chip, Flow, rep 2, experiment 5.4


title: WT_DOX_1

description: WT_DOX_1 (biological replicate 1)


title: iPSC-derived motor neuron cultures, sporadic ALS, line 9FP9iALS, 96 Well, experiment 5.4

value: ALS


title: WT_PBS_2

description: WT_PBS_2 (biological replicate 2)


title: WT1

description: Library name: WT1


title: Choroid plexus, Long1


title: WT2

description: Library name: WT2


title: Tha14

description: Library name: Tha14

data_processing:
Fastq files were further processed using the Cell Ranger v7.1.0 pipeline (10x Genomics) for demultiplexing, read alignment
Assembly: GRCm38, mm10
Supplementary files format and content: Fastq files, filtered feature-barcode matrices, Seurat objects

source_name: brain

extract_protocol:
snRNA-seq using 10x was conducted on nuclei extracted from frozen brain specimen
cDNA amplification and library preparation were conducted following the manufacturer’s instructions (Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics)).

value: brain

value: Knockout


title: Tha15

description: Library name: Tha15

value: Hetero


title: Tha13

description: Library name: Tha13


title: iPSC-derived motor neuron cultures, sporadic ALS, line 9FP9iALS, Chip, Flow, rep 1, experiment 5.4

value: iPSC-derived motor neuron cultures


title: Tha12

description: Library name: Tha12


title: Tha9

description: Library name: Tha9


title: iPSC-derived motor neuron cultures, control, line EDi028-A, Chip, Flow, rep 1, experiment 5.4


title: iPSC-derived motor neuron cultures, sporadic ALS, line 9FP9iALS, Chip, Flow, rep 3, experiment 5.4


title: ventral iSP (viSP)

city: Kuamomoto

first: Shunsuke

last: Tanigawa

state: Kumamoto

address: 2-2-1 Chuou-ku honjyo

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

description: 10x Genomics

data_processing:
10x library equencing was performed on Illumina HiSeq X. Sequencing data were analyzed using Illumina bcl2fastq software (version 2.20.0) and converted to FASTQ format files. Subsequently, alignment was performed using the cellranger count function of Cell Ranger Single Cell software (version 7.1.0, 10x Genomics) with using STAR aligner 2.7.2a. The GRCm38 mouse reference genome, mm10 r102  was used.
Assembly: GRCm38
Supplementary files format and content: Tab-separated value files and matrix files

source_name: stromal progenitor from mouse ESC

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium. Reverse transcription was performed in droplet.
library construction was performed by using Chromium Single Cell 3ʹ Reagent Kits v2.

value: stromal progenitor from mouse ESC


title: reconstituted ureter

description: 10x Genomics

source_name: mouse embryonic ureteral epithelium ×mouse ESC-derived ventral iSPs


title: WT_PBS_1

description: WT_PBS_1 (biological replicate 1)

value: WT


title: Tha10

description: Library name: Tha10


title: iPSC-derived motor neuron cultures, sporadic ALS, line 9FP9iALS, Chip, Flow, rep 2, experiment 5.4


title: Tha11

description: Library name: Tha11


title: WT4

description: Library name: WT4


title: Het1

description: Library name: Het1


title: dorsal iSP (diSP)

description: 10x Genomics


title: EGC, PBS, KO, SI, 24hr, rep4

city: Stanford

first: Julia

last: Kaltschmidt

address: 288 Campus Drive

department: Neurosurgery

institute: Stanford University

data_processing:
Raw sequence reads were trimmed to remove adaptor contamination and poor-quality reads using Trim Galore! (v.0.4.4, parameters: --paired --length 20 --phred33 --q 30). Trimmed sequences were aligned using STAR (v.2.5.3, default parameters). Multi-mapped reads were filtered.
Data visualization and analysis were performed using custom Rstudio scripts and the following Bioconductor packages: Deseq2 (Love at al. 2014), topGO, destiny and org.Mm.eg.db. Finally, we excluded pseudogenes and predicted genes from the count matrix to focus predominantly on well-annotated, protein-coding genes. In total, all the following analyses were performed on the same set of 21,076 genes.
Read quality control and counting were performed as previously described by Hahn et al (2023).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file including raw counts for each sample

source_name: EGC

extract_protocol:
RNA was isolated for sequencing using RNeasy Plus Micro Kit (Cat# 74034).
cDNA and library sytheses were performed in house using the Smart-seq2 protocol as described by Schaum et al (2020) and Iram et al (2022).

treatment_protocol: Lipopolysaccharide (LPS) from E. coli O111:B4 (Cat #tlrl-eblps) was purchased from Invivogen (San Diego, CA) and was reconstituted to 5mg/ml by homogenizing in 1ml of endotoxin-free water. Mice were randomly divided into a control group (phosphate-buffered saline - PBS), and treatment group (LPS), and received either a single IP injection of LPS (2mg/kg body weight) in PBS, or PBS alone. Mice were sacrificed 2 or 24 hours following PBS or LPS injection

tag: tissue (region)

value: Small Intestine

tag: tissue (layer)

value: Myenteric Plexus

value: EGC

value: Gpr37-/-; Plp1eGFP

tag: Sex

value: Female


title: Tha8

description: Library name: Tha8

tag: tissue


title: EGC, PBS, KO, SI, 24hr, rep3

tag: cell type

tag: mouse id


title: MK P7.

description: 10x Genomics

source_name: Kidney

value: Kidney


title: iPSC-derived motor neuron cultures, sporadic ALS, line 5XVDiALS, 96 Well, experiment 5.4

tag: cell line

tag: genotype

value: Flow


title: iPSC-derived motor neuron cultures, sporadic ALS, line 5XVDiALS, Chip, Flow, rep 3, experiment 5.4


title: Tha7

description: Library name: Tha7


title: iPSC-derived motor neuron cultures, sporadic ALS, line 5XVDiALS, Chip, Flow, rep 2, experiment 5.4


title: iPSC-derived motor neuron cultures, sporadic ALS, line 5XVDiALS, Chip, Flow, rep 1, experiment 5.4


title: iPSC-derived motor neuron cultures, sporadic ALS, line 3CA9iALS, 96 Well, experiment 5.4


title: MEK E17.5.

description: 10x Genomics

source_name: Embryonic kidney

value: Embryonic kidney


title: EGC, PBS, KO, SI, 24hr, rep1

value: Male

value: PBS

tag: timepoint


title: 90Tha

description: Library name: 90Tha


title: EGC, PBS, WT, SI, 24hr, rep6

value: Gpr37WT; Plp1eGFP

tag: treatment


title: Tha6

description: Library name: Tha6

value: brain


title: MEK E15.5.

description: 10x Genomics


title: iPSC-derived motor neuron cultures, sporadic ALS, line 3CA9iALS, Chip, Flow, rep 3, experiment 5.4

value: ALS


title: MEK E11.5.

description: 10x Genomics


title: MEK E13.5.

description: 10x Genomics


title: 154Tha

description: Library name: 154Tha

value: Knockout


title: EGC, PBS, WT, SI, 24hr, rep4


title: iPSC-derived motor neuron cultures, sporadic ALS, line 2XWCiALS, 96 Well, experiment 5.4

value: iPSC-derived motor neuron cultures


title: Corrected-Aicar-3

city: Philadelphia

first: Michael

last: Beers

address: 3450 Hamilton Walk

institute: University of Pennsylvania

description: Library name: Corrected-Aicar-3

data_processing:
RNA-SEQ Fastq files from paired end reads were trimmed, processed and evaluated for quality control using fastp. Resulting files were aligned against the mouse genome (mm10) using bowtie2 and quantified via featureCounts. Duplicate reads and chimeric fragments were flagged and excluded from the analysis.
scRNA-seq Fastq files were aligned to the mm10 reference genome using STARSolo
Downstream processing was performed using Seurat v3
Assembly: mm10
Supplementary files format and content: tab seperated files

source_name: iPSC

extract_protocol: scRNASeq Libraries were prepared using Illumina stranded total RNA accordine to manufacture instructions.  Total RNA for RNA-Seq was processed from cell pellets using the RNAeasy kit from Qiagen following manufacture instructions.

treatment_protocol: For scRNA-seq single cell suspensions were prepared by physical and enzymatic dissociation (Collagenase, DNase, Dispase) followed by MACS sorting by LS columns with CD45+ and CD31 cell removal using CD45 and CD31 micobeads. For flow cytometery RNA-seq single cell suspension were stainined with an antibody mix to identify AT2 cells and transitional AT2 cells. AT2 cells were identified as CD45-CD31-Epcam+CD104-MHCII hiCD51- and transitional At2 cells  CD45-CD31-Epcam+CD104-MHCII hiCD51+. Dead cells were excluded by Dapi staining. iAT2s were collected from matrigel dropplets via enzymatic digestion followed by immediate freezing of the cell pellets

value: iPSC

value: tdt/WT

value: Aicar


title: 1385Tha

description: Library name: 1385Tha


title: MK P0.

description: 10x Genomics


title: Corrected-Aicar-2

description: Library name: Corrected-Aicar-2


title: iPSC-derived motor neuron cultures, sporadic ALS, line 2XWCiALS, Chip, Flow, rep 3, experiment 5.4


title: EGC, PBS, WT, SI, 24hr, rep3

value: Small Intestine

value: Myenteric Plexus


title: iPSC-derived motor neuron cultures, sporadic ALS, line 2XWCiALS, Chip, Flow, rep 2, experiment 5.4


title: EGC, PBS, KO, SI, 24hr, rep2

value: EGC

value: Gpr37-/-; Plp1eGFP


title: 854Tha

description: Library name: 854Tha

value: Hetero


title: EGC, PBS, WT, SI, 24hr, rep1

value: Female


title: iPSC-derived motor neuron cultures, control, line 0002iCTR, Chip, Flow, rep 3, experiment 5.4

value: CTR

value: Flow


title: Corrected-3

description: Library name: Corrected-3

value: Vehicle


title: 1384Tha

description: Library name: 1384Tha


title: EGC, PBS, WT, SI, 24hr, rep2

value: Gpr37WT; Plp1eGFP

value: PBS


title: 43Tha

description: Library name: 43Tha

value: brain


title: Corrected-Aicar-1

description: Library name: Corrected-Aicar-1


title: 155Tha

description: Library name: 155Tha

value: Knockout


title: Corrected-2

description: Library name: Corrected-2


title: 44Tha

description: Library name: 44Tha


title: iPSC-derived motor neuron cultures, control, line EDi043-A, Chip, Flow, rep 3, experiment 5.3

extract_protocol:
The SMART-Seq V4 Ultra Low RNA Input Kit for Sequencing (Takara Bio USA, Inc., Mountain View, CA) was used for reverse transcription and generation of double stranded cDNA for subsequent library preparation using the Nextera XT Library Preparation kit (Illumina, San Diego, CA).  An input of 10 ng RNA was used for oligo(dT)-primed reverse transcription, followed by cDNA amplification and cleanup.  Quantification of cDNA was performed using Qubit (Thermo Fisher Scientific).  cDNA normalized to 80 pg/l was fragmented and sequencing primers added simultaneously.  A limiting-cycle PCR added Index 1 (i7) adapters, Index 2 (i5) adapters, and sequences required for cluster formation on the sequencing flow cell.  Indexed libraries were pooled and cleaned up, and the pooled library size was verified on the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and quantified via Qubit.  Libraries were sequenced on a NovaSeq 6000 (Illumina) using with a 1x75 bp read length and coverage of over 30M reads/sample.
The top channel of chip samples or a well from a 96 well plate were incubated with cold Accutase (STEMCELL Technologies) for 20 minutes at 37°C, then cells were extracted by flushing and washing with cold phosphate buffered saline (PBS), pelleted by centrifuge at 350 rcf, and frozen at -80°C. RNA was extracted from pellets using the RNeasy Micro Kit (Qiagen).
Various methods:  see SAMPLES "library construction protocol" section

value: iPSC-derived motor neuron cultures


title: iPSC-derived motor neuron cultures, control, line EDi043-A, Chip, Flow, rep 2, experiment 5.4


title: EGC, PBS, KO, Colon, 24hr, rep5

value: Colon


title: iPSC-derived motor neuron cultures, control, line EDi043-A, Chip, Flow, rep 2, experiment 5.3


title: iPSC-derived motor neuron cultures, control, line 0002iCTR, Chip, Flow, rep 1, experiment 5.4


title: Mutant-Aicar-3

description: Library name: Mutant-Aicar-3

value: iPSC


title: EGC, PBS, KO, Colon, 24hr, rep4


title: 41Tha

description: Library name: 41Tha


title: 42Tha

description: Library name: 42Tha


title: EGC, PBS, KO, Colon, 24hr, rep2

value: Male


title: iPSC-derived motor neuron cultures, control, line EDi043-A, Chip, Flow, rep 1, experiment 5.3


title: Mutant-Aicar-2

description: Library name: Mutant-Aicar-2

value: Aicar


title: EGC, PBS, KO, Colon, 24hr, rep1

value: Myenteric Plexus


title: iPSC-derived motor neuron cultures, control, line EDi029-A, Chip, Flow, rep 1, experiment 5.3


title: 38Tha

description: Library name: 38Tha


title: iPSC-derived motor neuron cultures, control, line EDi028-A, Chip, Flow, rep 3, experiment 5.3


title: Mutant-3

description: Library name: Mutant-3


title: Hexb-KO-T GEX

description: Library name: Hexb-KO-T GEX

source_name: Brain

extract_protocol:
snRNA-seq using 10x was conducted on nuclei extracted from frozen brain specimen
cDNA amplification and library preparation were conducted following the manufacturer’s instructions (Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics))

value: Brain


title: Corrected-1

description: Library name: Corrected-1

value: tdt/WT


title: EGC, PBS, KO, Colon, 24hr, rep3

value: EGC

value: Gpr37-/-; Plp1eGFP


title: EGC, PBS, WT, Colon, 24hr, rep3

value: Female


title: Mutant-2

description: Library name: Mutant-2


title: iPSC-derived motor neuron cultures, control, line EDi028-A, Chip, Flow, rep 2, experiment 5.3

value: CTR

value: Flow


title: EGC, PBS, WT, Colon, 24hr, rep2

value: Gpr37WT; Plp1eGFP


title: iPSC-derived motor neuron cultures, control, line EDi022-A, Chip, Flow, rep 3, experiment 5.3


title: Hexb-KO GEX

description: Library name: Hexb-KO GEX


title: iPSC-derived motor neuron cultures, control, line EDi022-A, Chip, Flow, rep 2, experiment 5.3


title: Mutant-1

description: Library name: Mutant-1

value: Vehicle


title: EGC, PBS, WT, Colon, 24hr, rep1

value: PBS


title: Hexb-KO-T CMO

description: Library name: Hexb-KO-T CMO


title: 39Tha

description: Library name: 39Tha

value: brain

value: Knockout


title: Hexb-KO CMO

description: Library name: Hexb-KO CMO


title: Hexb-Het-T CMO

description: Library name: Hexb-Het-T CMO


title: EGC, LPS, KO, SI, 24hr, rep4

value: Small Intestine

value: LPS


title: Mutant-Aicar-1

description: Library name: Mutant-Aicar-1

value: iPSC


title: Hexb-Het-T GEX

description: Library name: Hexb-Het-T GEX


title: iPSC-derived motor neuron cultures, control, line EDi022-A, Chip, Flow, rep 1, experiment 5.3

value: iPSC-derived motor neuron cultures


title: iPSC-derived motor neuron cultures, sporadic ALS, line9FP9iALS, Chip, Flow, rep 3, experiment 5.3

value: ALS


title: EGC, PBS, WT, Colon, 24hr, rep4

value: Colon

value: Myenteric Plexus

value: Male


title: iPSC-derived motor neuron cultures, sporadic ALS, line5XVDiALS, Chip, Flow, rep 3, experiment 5.3


title: Hexb-Het CMO

description: Library name: Hexb-Het CMO

value: Brain


title: EGC, LPS, KO, SI, 24hr, rep3

value: EGC

value: Gpr37-/-; Plp1eGFP


title: Hexb-Het GEX

description: Library name: Hexb-Het GEX


title: EGC, LPS, KO, SI, 24hr, rep2


title: EGC, LPS, KO, SI, 24hr, rep1


title: iPSC-derived motor neuron cultures, sporadic ALS, line3CA9iALS, Chip, Flow, rep 2, experiment 5.3

value: Flow


title: EGC, LPS, WT, SI, 24hr, rep3

value: Gpr37WT; Plp1eGFP

value: Female


title: EGC, LPS, WT, SI, 24hr, rep2


title: iPSC-derived motor neuron cultures, sporadic ALS, line 2XWCiALS, Chip, Flow, rep 3, experiment 5.3


title: iPSC-derived motor neuron cultures, sporadic ALS, line3CA9iALS, Chip, Flow, rep 3, experiment 5.3


title: EGC, LPS, WT, SI, 24hr, rep4


title: APEX_WT_1 biological replicate 1

city: Brno

first: Jan

last: Hejatko

address: Kamenice 5

country: Czech Republic

institute: CEITEC

description: Library name: APEX_WT_1

data_processing:
Adapters were trimmed using Cutadapt. Reads were mapped to the TAIR10 Arabidopsis thaliana reference genome using TopHat2 (v2.0.8) with minimum intron length 20 bp, maximum intron length 4,000 bp, and splice junctions guided by TAIR10 GFF annotation.
Expression levels were quantified using Cuffdiff 2.2.1 with default settings and FDR threshold 0.05. Transcript abundances were reported as FPKM values.
Differentially expressed genes were identified between genotypes and between apical vs. basal internodes. Genes with absolute log2 fold change ≥1.1 and consistent or opposing trends were selected as biologically relevant.
Gene ontology enrichment analysis was performed using GOrilla with FDR ≤ 0.001.
Gene-level expression summaries and differential expression tables were exported as text files.
Assembly: TAIR10 (Arabidopsis thaliana reference genome and annotation)
Supplementary files format and content: Tab-delimited text files containing gene-level FPKM values and differential expression results (log2 fold change, p-value, FDR) generated by Cuffdiff.
Supplementary files format and content: Files include FPKM matrices with rows as gene/transcript IDs and columns as sample IDs, and contrast-wise differential expression tables.

organism: Arabidopsis thaliana

source_name: wild-type – inflorescence stem (apical internode)

growth_protocol: Arabidopsis thaliana Col-0 and various mutant and overexpression lines (ahk2,3; arr1,10; arr1,12; arr10,12; arr1,10,12; ipt3,5,7; ipt1,3,5,7; ahp1,2,3,4,5; p35S:CKX2; p35S:CKX3) were grown in soil (compost [TS-3], perlite, and sand in 12:3:4 ratio) in a growth chamber under long-day conditions (16 h light at 21 °C / 8 h dark at 19 °C), at 60% humidity, and 100 µmol m⁻² s⁻¹ light intensity. Stem tissues were harvested at developmental stage 1 (first elongated silique).

extract_protocol:
Apical and basal internodes of inflorescence stems were harvested, flash-frozen in liquid nitrogen, and ground to powder using mortar and pestle. Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.
RNA-seq libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit and sequenced by GATC Biotech AG (Konstanz, Germany).

treatment_protocol: No treatment was applied for RNA-seq samples. (BAP treatment and GUS staining were performed on proNST3:NST3-GUS plants for histological analysis, but not for RNA-seq.)

value: inflorescence stem (apical internode)

value: wild-type

tag: batch


title: iPSC-derived motor neuron cultures, sporadic ALS, line3CA9iALS, Chip, Flow, rep 1, experiment 5.3


title: APEX_ahk23_1 biological replicate 1

description: Library name: APEX_ahk23_1

source_name: ahk2 ahk3 – inflorescence stem (apical internode)

value: ahk2 ahk3


title: APEX_ahk23_3 biological replicate 3

description: Library name: APEX_ahk23_3


title: APEX_ahk23_2 biological replicate 2

description: Library name: APEX_ahk23_2


title: RNA-Seq, dissected germline, ESC332, RPOA-2 depletion via 1 mM IAA, rep 4

first: Elif

last: Sarinay Cenik

state: TX

department: Molecular Biosciences

institute: University of Texas at Austin

description: Library name: ESC-HSl-608

data_processing:
Read trimming: Trim Galore! v0.6.10 used with default parameters.
Genome indexing: HISAT2 v2.2.1 used to build WBcel235 genome index with hisat2-build --seed 40.
Read mapping: HISAT2 v2.2.1 used with hisat2 --seed 40 and default parameters.
Alignment sorting: Picard SortSam v3.1.1 used with -SORT_ORDER coordinate --CREATE_INDEX true.
Feature quantification: featureCounts v2.0.6 used with -t exon -g gene_id -p.
Gene filtering: Retained 19,985 protein-coding genes from WBcel235 annotation and removed genes with fewer than 5 counts across 3 biological replicates.
Assembly: WBcel235
Supplementary files format and content: Comma-delimited file containing filtered raw counts of reads within 19,985 protein coding genes (Wormbase identifiers from WBcel235) across all samples. Note that genes with fewer than 5 counts across 3 biological replicates were filtered out.

organism: Caenorhabditis elegans

source_name: dissected germline

growth_protocol: Maintained and treated at 20°C on non-enriched plated seeded with OP50.

extract_protocol:
Dissected gonads were transferred to 1 mL of TRIzol, vortexed, then incubated for 5 minutes at room temperature. RNA was extracted by adding 200 µL of chloroform to the lysate, spinning for 10 minutes at 15,000 rpm, and isolating the supernatant. The isolated RNA was precipitated overnight at −20°C using 50 mM sodium acetate, 5 mM MgCl2, 15 mg/mL GlycoBlue™ Coprecipitant, and isopropanol.
RNA pellets were washed in 80% ethanol and processed with the SMARTer Stranded RNA-Seq kit. RNA was fragmented, converted to cDNA, and PCR amplified (1 min at 94°C; 15-17 cycles of 15 sec at 98°C, 15 sec at 55°C, 30 sec at 68°C). Libraries were purified using Agencourt AMPure XP beads, quantified with the Qubit™ dsDNA HS Assay Kit, and sequenced on a NovaSeq 6000 v1.5 SP flow cell.

treatment_protocol: Auxin (IAA) plates were prepared by diluting Alfa Aesar (#A10556) to 1 mM in NGM agar, while control plates contained an equivalent EtOH volume. Plates were poured, solidified, seeded with OP50, and incubated at 20°C overnight. Synchronized late L4 worms were transferred to control or auxin plates for 18 hours at 20°C.

value: dissected germline

tag: developmental stage

value: young adult

value: hermaphrodite

value: 1 mM auxin (IAA)


title: EGC, LPS, KO, Colon, 24hr, rep4

value: LPS


title: EGC, LPS, WT, SI, 24hr, rep1

value: Small Intestine


title: APEX_WT_2 biological replicate 2

description: Library name: APEX_WT_2


title: iPSC-derived motor neuron cultures, sporadic ALS, line 2XWCiALS, Chip, Flow, rep 2, experiment 5.3

value: iPSC-derived motor neuron cultures

value: ALS


title: iPSC-derived motor neuron cultures, sporadic ALS, line5XVDiALS, Chip, Flow, rep 2, experiment 5.3


title: iPSC-derived motor neuron cultures, control, line 0002iCTR, Chip, Flow, rep 3, experiment 5.3

value: CTR


title: APEX_WT_3 biological replicate 3

description: Library name: APEX_WT_3


title: EGC, LPS, KO, Colon, 24hr, rep3

value: Colon

value: Myenteric Plexus

value: EGC

value: Male


title: RNA-Seq, dissected germline, ESC332, RPOA-2 control, rep 4

description: Library name: ESC-HSl-607

value: EtOH control


title: iPSC-derived motor neuron cultures, control, line 0002iCTR, Chip, Flow, rep 2, experiment 5.3

value: Flow


title: BASE_WT_3 biological replicate 3

description: Library name: BASE_WT_3

source_name: wild-type – inflorescence stem (basal internode)

value: inflorescence stem (basal internode)

value: wild-type


title: EGC, LPS, KO, Colon, 24hr, rep2

value: Gpr37-/-; Plp1eGFP


title: iPSC-derived motor neuron cultures, control, line EDi028-A, Chip, Flow, rep 3, experiment 5.1

extract_protocol:
Total RNA samples were assessed for concentration using a Qubit fluorometer (ThermoFisher Scientific, Waltham, MA) and for quality using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Up to one µg of total RNA was purified for mRNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolab Inc, Ipswich, MA).  Stranded RNA-Seq library construction was performed using the IDT xGen Broad-Range RNA Library Prep Kit (Integrated DNA Technologies, Coralville, IA).  Library concentration was measured with a Qubit fluorometer and library size on an Agilent 4200 TapeStation (Agilent Technologies). Libraries were multiplexed and sequenced on a NovaSeq 6000 (Illumina, San Diego, CA) using 75bp single-end sequencing. On average, approximately 30 million reads were generated from each sample.
The top channel of chip samples or a well from a 96 well plate were incubated with cold Accutase (STEMCELL Technologies) for 20 minutes at 37°C, then cells were extracted by flushing and washing with cold phosphate buffered saline (PBS), pelleted by centrifuge at 350 rcf, and frozen at -80°C. RNA was extracted from pellets using the RNeasy Micro Kit (Qiagen).
Various methods:  see SAMPLES "library construction protocol" section


title: WT [SAM24359724]

source_name: Skin

extract_protocol:
Total RNA was extracted using a RNeasy Mini Kit (Qiagen, cat 74104) and quantified in a NanoDrop 8000 (ThermoFisher).
0.1 μg of total RNA was used for library preparation with a TruSeq Stranded Total RNA Library Prep Kit (Illumina). The libraries were multiplexed and then sequenced on an Illumina HiSeq4000 (Illumina) to generate 30 million single end 50 bp reads.

value: Skin

value: Primary melanocytes

value: WT


title: BASE_WT_2 biological replicate 2

description: Library name: BASE_WT_2


title: EGC, LPS, KO, Colon, 24hr, rep1

value: LPS


title: iPSC-derived motor neuron cultures, control, line EDi028-A, Chip, Flow, rep 2, experiment 5.1


title: BASE_WT_1 biological replicate 1

description: Library name: BASE_WT_1


title: EGC, LPS, WT, Colon,  24hr, rep5

value: Gpr37WT; Plp1eGFP

value: Female


title: iPSC-derived motor neuron cultures, control, line EDi028-A, Chip, Flow, rep 1, experiment 5.1

value: iPSC-derived motor neuron cultures


title: dissected germline, ESC422, GRWD-1 depletion via 1 mM IAA, rep 3

description:
Library name: ESC-HSL-591
Column name in peak_count_matrix_with_coordinates.csv: ESC422_1mM_auxin_rep3

data_processing:
SRAtac v0.5.0 pipeline was used with parameter `--genome WBcel235` for trimming, alignment, decontamination, QC, peak calling and merging, and counting reads within peaks (https://doi.org/10.1186/s12864-023-09576-y).
Assembly: WBcel235
Supplementary files format and content: Comma-delimited file containing a header line, peak genomic coordinates (PeakID, Chr, Start, End, Length), and raw counts of reads within peaks per sample.

extract_protocol:
Dissected gonads were stained with DAPI (5 ng/µL in PBS) and loaded onto a hemocytometer for nuclei counting. A volume containing 50,000 nuclei was mixed with 2.5 μL TDE1 tagmentase. The tagmentation reaction was incubated at 37°C for 30 minutes on a shaker. Immediately after, reactions were cleaned using the Zymo DNA Clean & Concentrator-5 kit.
Tagmented DNA was amplified with Nextera i5/i7 adapters using NEBNext® High-Fidelity 2X PCR Master Mix with 18-19 cycles (98°C for 10 sec, 63°C for 30 sec, 72°C for 1 min) following initial (72°C for 5 min) and final (72°C for 10 min) extensions. PCR products were cleaned with the Zymo DNA Clean & Concentrator-5 kit, and library quality was assessed via nucleosome banding on a gel. Passing libraries were further purified with Agencourt AMPure XP beads, quantified with the Qubit™ dsDNA HS Assay Kit, and sequenced on a NovaSeq 6000 v1.5 SP flow cell.

treatment_protocol: Auxin (IAA) plates were prepared by diluting to 1 mM in NGM agar, while control plates contained an equivalent EtOH volume. Plates were poured, solidified, seeded with OP50, and incubated at 20°C overnight. Synchronized L4 worms were transferred to control or auxin plates for 18 hours at 20°C.

value: dissected germline

value: young adult

value: hermaphrodite

value: 1 mM auxin (IAA)


title: BASE_ahk23_3 biological replicate 3

description: Library name: BASE_ahk23_3

source_name: ahk2 ahk3 – inflorescence stem (basal internode)

value: ahk2 ahk3


title: EGC, LPS, KO, SI, 24hr, rep5

value: Small Intestine

value: Myenteric Plexus

value: EGC


title: iPSC-derived motor neuron cultures, control, line EDi022-A, Chip, Flow, rep 2, experiment 5.1

value: CTR

value: Flow


title: BASE_ahk23_1 biological replicate 1

description: Library name: BASE_ahk23_1

value: inflorescence stem (basal internode)


title: dissected germline, ESC422, GRWD-1 depletion via 1 mM IAA, rep 2

description:
Library name: ESC-HSL-522
Column name in peak_count_matrix_with_coordinates.csv: ESC422_1mM_auxin_rep2


title: EGC, LPS, WT, Colon, 24hr, rep2

value: Colon


title: iPSC-derived motor neuron cultures, control, line EDi022-A, Chip, Flow, rep 3, experiment 5.1


title: EGC, LPS, WT, Colon, 24hr, rep4

value: Male


title: EGC, LPS, WT, Colon, 24hr, rep3

value: LPS


title: BASE_ahk23_2 biological replicate 2

description: Library name: BASE_ahk23_2


title: dissected germline, ESC422, GRWD-1 depletion via 1 mM IAA, rep 1

description:
Library name: ESC-HSL-497
Column name in peak_count_matrix_with_coordinates.csv: ESC422_1mM_auxin_rep1


title: EGC, LPS, WT, Colon, 24hr, rep1

value: Gpr37WT; Plp1eGFP


title: iPSC-derived motor neuron cultures, sporadic ALS, line 5XVDiALS, Chip, Flow, rep 2, experiment 5.1

value: ALS


title: HBV_iATR_Rep2

city: Madison

first: Kinjal

last: Majumder

state: WI

address: 1525 Linden Drive

department: Oncology

institute: University of Wisconsin

description:
Library name: HBV + iATR V3C-seq Replicate 2
hbv_iatr_average.bedgraph

data_processing:
Reads were aligned to the human hg38 genome using Minimap2.
Aligned V3C-seq samples were sorted using Samtools, and the resulting aligned and sorted Bam files were converted to Bedgraph files using Bedtools.
Biological replicates of the samples were determined using Bedtools.
Assembly: Human hg38
Supplementary files format and content: bedgraph

source_name: Liver

growth_protocol: Human HepG2-NTCP cells were propagated in 5% Serum Plus (Sigma Aldrich) containing DMEM/F-12 media (Gibco) supplemented with Penicillin/Streptomycin at 37oC and 5% carbon dioxide. HBV infection was carried out at a genome equivalent (GEQ) of 20 and cells were harvested at 120h. Samples were processed for Chromatin immunoprecipitation (ChIP-seq) or Chromosome Conformation Capture (V3C-seq) assays.

extract_protocol:
For Viral Chromosome Conformation Capture assays, HBV infected cells were crosslinked in 2 percent formaldehyde for 10 minutes, quenched in 0.125 M glycine for 5 minutes, collected and lysed in NP-40 lysis buffer for 10 minutes on ice, before resuspending the nuclei in restriction enzyme buffer (Cutsmart Buffer). Samples were permeabilized in 0.3% SDS for 1 hour on a 37oC shaker, sequestered in 2% Triton X-100 for 1 hour on a 37oC shaker. 1 ul of T5 Exonuclease (New England BioLabs) was added to the samples for 1 hr on a 37oC shaker. Samples were inactivated with 8 ul of 0.25 M EDTA before centrifuging at 5000 RPM for 5 minutes. Pellet was resuspended in restriction enzyme buffer (Buffer 3.1) and digested overnight in 400 U of BglII enzyme. Restriction enzyme was inactivated and samples were subjected to intramolecular ligation with T4 DNA Ligase at room temperature. Samples were then reverse crosslinked and purified, before digesting in secondary restriction enzyme, BglII. BglII was heat inactivated, samples were purified by phenol:chloroform purification, and circularized using T4 DNA Ligase. Samples were purified using a PCR Purification Kit (Qiagen), and equivalent amounts of DNA was used to perform inverse PCR with primers complementary to the HBV genome. Inverse PCR samples were diluted 1:100 in TE, before being used as templates for nested-inverse PCR reactions. 8 independent nested-inverse PCR reactions were pooled, PCR purified using a Qiagen kit and submitted for library preparation and high-throughput sequencing.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (cat # E7645L) according to manufacturer's instructions. Eight samples were pooled per run and samples were analyzed by 75 bp paired-end sequencing on the NextSeq 500 (Illumina).

treatment_protocol: HepG2-NTCP cells were seeded into 6-well plates with DMEM/F-12 and incubated in 5% carbon dioxide at 37 degrees C for 4 hrs. Fresh Spinoculum was made (DMEM/F-12 supplemented with 3% Serum Plus, 2% DMSO, 1% NEAA, and 4% PEG 8000). Solution was then filtered sterilized with 0.22um filter (Corning) Medium and was switched with Spinoculum medium and HBV stock was added to 20 GEQ. Plates were then wrapped with parafilm and then centrifuged at 1000xg at 37 degrees C for 1 hr. Parafilm was removed and plates were incubated in 5% Carbon dioxide at 37oC for 5 days.

value: Liver

value: Hepatocyte


title: dissected germline, ESC422, GRWD-1 control, rep 3

city: Austin

address: 2500 Speedway

description:
Library name: ESC-HSL-529
Column name in peak_count_matrix_with_coordinates.csv: ESC422_0mM_auxin_rep3

value: dissected germline

value: young adult

value: EtOH control


title: iPSC-derived motor neuron cultures, sporadic ALS, line 3CA9iALS, Chip, Flow, rep 3, experiment 5.1

value: iPSC-derived motor neuron cultures


title: EGC, LPS, SI_MP, 2hr, rep4

value: Small Intestine


title: HBV_iATR_Rep1

description:
Library name: HBV + iATR V3C-seq Replicate 1
hbv_iatr_average.bedgraph


title: dissected germline, ESC422, GRWD-1 control, rep 2

description:
Library name: ESC-HSL-521
Column name in peak_count_matrix_with_coordinates.csv: ESC422_0mM_auxin_rep2

value: hermaphrodite


title: iPSC-derived motor neuron cultures, sporadic ALS, line 3CA9iALS, Chip, Flow, rep 1, experiment 5.1


title: HBV_T5_Rep2

description:
Library name: HBV V3C-T5-seq Replicate 2
hbv_t5_average.bedgraph


title: HBV_T5_Rep1

description:
Library name: HBV V3C-T5-seq Replicate 1
hbv_t5_average.bedgraph


title: dissected germline, ESC422, GRWD-1 control, rep 1

description:
Library name: ESC-HSL-496
Column name in peak_count_matrix_with_coordinates.csv: ESC422_0mM_auxin_rep1


title: iPSC-derived motor neuron cultures, sporadic ALS, line 2XWCiALS, Chip, Flow, rep 3, experiment 5.1


title: HBV_Rep2

description:
Library name: HBV V3C-seq Replicate 2
hbv_average.bedgraph


title: dissected germline, ESC332, RPOA-2 depletion via 1 mM IAA, rep 4

description:
Library name: ESC-HSL-589
Column name in peak_count_matrix_with_coordinates.csv: ESC332_1mM_auxin_rep4

value: 1 mM auxin (IAA)


title: EGC, LPS, SI_MP, 2hr, rep2

value: Myenteric Plexus

value: EGC


title: iPSC-derived motor neuron cultures, sporadic ALS, line 5XVDiALS, Chip, Flow, rep 3, experiment 5.1

value: Flow


title: dissected germline, ESC422, GRWD-1 control, rep 4

description:
Library name: ESC-HSL-590
Column name in peak_count_matrix_with_coordinates.csv: ESC422_0mM_auxin_rep4


title: HBV_Rep1

description:
Library name: HBV V3C-seq Replicate 1
hbv_average.bedgraph


title: iPSC-derived motor neuron cultures, sporadic ALS, line 2XWCiALS, Chip, Flow, rep 2, experiment 5.1


title: dissected germline, ESC332, RPOA-2 depletion via 1 mM IAA, rep 3

description:
Library name: ESC-HSL-528
Column name in peak_count_matrix_with_coordinates.csv: ESC332_1mM_auxin_rep3


title: EGC, LPS, Colon_MP,  2hr, rep4

value: Colon


title: Caco2_DMEM_16hr_Butyrate_rep3

city: Cleveland

first: Leah

last: Gates

state: OH

address: 10900 Euclid Avenue

institute: Case Western Reserve University

description: Library name: Sample 37

data_processing:
Transcript Quantification with Salmon (version 0.8.2)
Alignment of ChIPseq reads was done with Rsubread (version 1.30.6)
Normalization and rlog transformation of raw read counts in genes were performed using DESeq2 (version 1.20.0)
Assembly: BSgenome.Hsapiens.UCSC.hg19 (version 1.4.3) and TxDb.Hsapiens.UCSC.hg19.knownGene (version 3.4.0)
Assembly: hg19
Supplementary files format and content: counts, bigwigs

growth_protocol: HCT-116 cells were grown in DMEM medium or human plasma like media (HPLM) with 10% fetal bovine serum and 1% penicillin/streptomycin. When cells were grown in HPLM, cells were washed in PBS and cultured in HPLM for at least three days prior to experiments. Caco-2 cells were grown in Eagle's Minimum Essential Medium supplemented with 2 mM GlutaMAX, 1 mM sodium pyruvate, 20% FBS, and 1% penicillin/streptomycin.

extract_protocol:
RNA was harvested using RNA isolation kits and genomic DNA was isolated following immunoprecipitation of sonicated chromatin.
Libraries were generated using NEBNext Ultra II kits following the manufacturer's protocol.

treatment_protocol: HCT-116 and Caco-2 cells were treated with different short chain fatty acids (SCFAs) or inhibitors for 6 or 24 hours prior to RNA isolation. For ChIP-seq experiments, cells were treated with 5 mM butyrate or 5 mM propionate for 24 hours prior to fixation.

value: Colorectal adenocarcinoma

value: Wild type

value: 5 mM butyrate for 16 hours


title: EGC, LPS, SI_MP, 2hr, rep3

value: Female

value: LPS


title: iPSC-derived motor neuron cultures, control, line EDi028-A, Chip, Flow, rep 5, experiment 1.3

value: CTR


title: EGC, LPS, Colon_MP,  2hr, rep2

value: Male


title: iPSC-derived motor neuron cultures, control, line EDi028-A, Chip, Flow, rep 4, experiment 1.3


title: Caco2_DMEM_16hr_Butyrate_rep1

description: Library name: Sample 35


title: EGC, LPS, Colon_MP,  2hr, rep1


title: Caco2_DMEM_16hr_Vehicle_rep3

description: Library name: Sample 34

value: Equal volume sterile water for 16 hours


title: iPSC-derived motor neuron cultures, control, line EDi028-A, Chip, Static, rep 3, experiment 1.3

value: Static


title: dissected germline, ESC332, RPOA-2 control, rep 3

description:
Library name: ESC-HSL-527
Column name in peak_count_matrix_with_coordinates.csv: ESC332_0mM_auxin_rep3

value: dissected germline

value: young adult

value: EtOH control


title: EGC, LPS, SI_MP, 2hr, rep1

value: Small Intestine


title: EGC, PBS, SI_MP, 2hr, rep4

value: Myenteric Plexus

value: PBS


title: dissected germline, ESC332, RPOA-2 depletion via 1 mM IAA, rep 1

description:
Library name: ESC-HSL-495
Column name in peak_count_matrix_with_coordinates.csv: ESC332_1mM_auxin_rep1

value: hermaphrodite

value: 1 mM auxin (IAA)


title: iPSC-derived motor neuron cultures, control, line EDi028-A, Chip, Static, rep 2, experiment 1.3

value: iPSC-derived motor neuron cultures


title: Caco2_DMEM_16hr_Vehicle_rep2

description: Library name: Sample 33

value: Colorectal adenocarcinoma

value: Wild type


title: Caco2_DMEM_16hr_Vehicle_rep1

description: Library name: Sample 32


title: EGC, LPS, Colon_MP,  2hr, rep3

value: Colon

value: EGC

value: Female


title: dissected germline, ESC332, RPOA-2 control, rep 4

description:
Library name: ESC-HSL-588
Column name in peak_count_matrix_with_coordinates.csv: ESC332_0mM_auxin_rep4


title: EGC, PBS, SI_MP, 2hr, rep3


title: dissected germline, ESC332, RPOA-2 control, rep 2

description:
Library name: ESC-HSL-519
Column name in peak_count_matrix_with_coordinates.csv: ESC332_0mM_auxin_rep2


title: iPSC-derived motor neuron cultures, control, line EDi028-A, Chip, Static, rep 1, experiment 1.3

value: CTR


title: EGC, PBS, SI_MP, 2hr, rep2

value: Male


title: iPSC-derived motor neuron cultures, control, line EDi028-A, Chip, Flow, rep 6, experiment 1.3

value: Flow


title: whole animal, control strain exposed to DMSO, replicate 3

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

country: United Kingdom

institute: King's College London

data_processing:
Raw data: original image data  from the high-throughput sequencing platform were transformed to sequenced reads ( Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contained sequences of reads and corresponding base quality.
Quality control: The sequencing error rate, the Qphred, the quality score (Phred) were calculated and the corresponding relationship between sequencing quality and Phred score in the base calling  was listed.
Sequencing Data Filtration:  Raw reades were removed if they paired reads contained adapter contaminations,  when they contained uncertain nucleotides in excess of 10% and / or the quality of nucleotides was poor (Q eqaul or less than 5).
Sequence Alignment : The sequencing data was aligned to the reference genome through BWA software and the mapping rate and coverage counted according to the alignment results.
Assembly: WBcel235
Supplementary files format and content: SNP detection was performed via ANNOVAR, including gene based annotation, region based annotation , filter based annotation etc.  SNP mutant frequency, InDel percentage in CDS and genome and SV annotations were also determined.

source_name: whole animal

growth_protocol: Parent population (P0) maintained at 20 ºC on standard nematode growth media (NGM) plates using Escherichia coli OP50 as food source. A synchronous L1 culture was generated by standard bleach preparation and grown to L4 stage in the presence or absence of benzo[a]pyrene.

extract_protocol:
Genomic DNA was extracted with QIAGEN genomic-tips (20/G) following the manufacturer’s protocol. The DNA quantity was measured using the Qubit 2.0 (Thermo Fisher) coupled with Qubit dsDNA HS assay kit (Thermo Fisher). The quality was assessed by gel electrophoresis loading 150 ng of sample into each well and separated for 40 minutes at 100 V.
Whole genome resequencing was based on  SBS (sequencing by synthesis) to identify the genetic variations in individual strains . The genomic DNA was randomly sheared into short fragments. The obtained fragments were end repaired, A-tailed and further ligated with Illumina adapter. The fragments with adapters were PCR amplified, size selected, and purified.The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries  were sequenced on the Illumina platform, according to the library concentration.
Whole Genome Sequencing
Illumina NovaSeq PE150

treatment_protocol: L1 stage animals were exposed 48 hours at 20 ºC to benzo[a]pyrene supplemented to both the agar medium and the food source (E. coli OP50).

value: whole animal

value: control

value: DMSO


title: dissected germline, ESC332, RPOA-2 depletion via 1 mM IAA, rep 2

description:
Library name: ESC-HSL-520
Column name in peak_count_matrix_with_coordinates.csv: ESC332_1mM_auxin_rep2

value: dissected germline

value: young adult


title: Caco2_DMEM_16hr_Butyrate_rep2

description: Library name: Sample 36

value: 5 mM butyrate for 16 hours


title: dissected germline, ESC332, RPOA-2 control, rep 1

description:
Library name: ESC-HSL-494
Column name in peak_count_matrix_with_coordinates.csv: ESC332_0mM_auxin_rep1

value: hermaphrodite

value: EtOH control


title: EGC, PBS, SI_MP, 2hr, rep1

value: Small Intestine

value: Myenteric Plexus

value: PBS


title: iPSC-derived motor neuron cultures, control, line EDi022-A, Chip, Flow, rep 4, experiment 1.3

value: iPSC-derived motor neuron cultures


title: iPSC-derived motor neuron cultures, control, line EDi022-A, Chip, Flow, rep 5, experiment 1.3