title: BrainCell_Enhancer-eHGT_385m_MouseID-651224_Cell-16


title: HALL_06_HR4_GC_GC

status: Public on Jun 26 2024

type: RNA

city: Stirling

first: James

last: Timmons

address: Bridge of Allan

country: United Kingdom

institute: Augur Precision Medicine LTD

description: human skeletal muscle

hyb_protocol: Standard

scan_protocol: Standard

data_processing:
CEL files were GC correct and then processed using IRON (default settings) using custom CDFs and then an SD filter applied to focus on signals above background. The full length transcript probe-set based data are provided along with the custom CDF.
Array probes were aligned to genome reference Grch38 and transcriptome reference gencode43 and a probe-level CDF was created.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: post-training sample

label_protocol: Affymetrix WT kit

extract_protocol: Trizol

tag: tissue

value: vastus lateralis

tag: treatment group and time

value: post-training sample

tag: age

value: young adult


title: HALL_06_UT0_GC_GC

description: human skeletal muscle

source_name: pre-training sample

value: pre-training sample


title: HALL_08_UT0_GC_GC

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_385m_MouseID-651224_Cell-12

type: SRA

city: Seattle

first: John

middle: Kenneth

last: Mich

state: WA

address: 615 Westlake Ave N

country: USA

institute: Allen Institute for Brain Science

library_source: transcriptomic single cell

data_processing:
Base-calling using standard Illumina software.
Alignment with STAR (https://github.com/alexdobin/STAR)
Transformed by counts per million.
Assembly: mm10
Supplementary files format and content: Processed data in counts per million (CPM) format.

molecule: polyA RNA

organism: Mus musculus

source_name: VISp

extract_protocol:
Single SYFP2-expressing cells from mouse brain were flow sorted into individual tubes in SMARTerv4 collection buffer.
SMARTerv4

value: VISp

tag: treatment

tag: genotype


title: HALL_08_HR3_GC_GC

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_385m_MouseID-651224_Cell-11


title: HALL_06_LR4_GC_GC

description: human skeletal muscle


title: HALL_05_UT1_GC_GC

description: human skeletal muscle


title: HALL_04_UT0_GC_GC

description: human skeletal muscle


title: HALL_11_HR3_GC_GC

description: human skeletal muscle


title: HALL_05_HR4_GC_GC

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_385m_MouseID-651224_Cell-10


title: BrainCell_Enhancer-eHGT_385m_MouseID-651224_Cell-9


title: BrainCell_Enhancer-eHGT_385m_MouseID-651224_Cell-8


title: BrainCell_Enhancer-eHGT_385m_MouseID-651224_Cell-7


title: HALL_03_UT0_GC_GC

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_385m_MouseID-651224_Cell-6


title: HALL_04_HR4_GC_GC

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_385m_MouseID-651224_Cell-15


title: HALL_04_LR4_GC_GC

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_385m_MouseID-651224_Cell-5


title: HALL_03_HR4_GC_GC

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_385m_MouseID-651224_Cell-4


title: HALL_02_UT1_GC_GC

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_385m_MouseID-651224_Cell-3


title: BrainCell_Enhancer-eHGT_385m_MouseID-651224_Cell-1


title: HALL_01_UT0_GC_GC

description: human skeletal muscle


title: HALL_01_LR4_GC_GC

description: human skeletal muscle


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-651223_Cell-16


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-651223_Cell-15


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-651223_Cell-14


title: HALL_03_LR4_GC_GC

description: human skeletal muscle


title: S9A_SWOLL

description: human skeletal muscle

source_name: PRE

value: PRE


title: S9B_SWOLL

description: human skeletal muscle

source_name: POST

value: POST


title: BrainCell_Enhancer-eHGT_385m_MouseID-651224_Cell-2


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-651223_Cell-12


title: HALL_02_LR4_GC_GC

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_390h_MouseID-651220_Cell-27


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-651223_Cell-11


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-651223_Cell-13


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-651223_Cell-9


title: S8A_SWOLL

description: human skeletal muscle


title: S8B_SWOLL

description: human skeletal muscle


title: S59B_2_SWOLL

description: human skeletal muscle


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-651223_Cell-7


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-651223_Cell-10


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-651223_Cell-8


title: S7B_SWOLL

description: human skeletal muscle


title: S7A_SWOLL

description: human skeletal muscle


title: S59A_2_SWOLL

description: human skeletal muscle


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-651223_Cell-4


title: S57B_2_SWOLL

description: human skeletal muscle


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-651223_Cell-3


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-651223_Cell-2


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-651223_Cell-6


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-651223_Cell-5


title: BrainCell_Enhancer-eHGT_381h_MouseID-651222_Cell-7

source_name: MB/HB

value: MB/HB


title: S58B_2_SWOLL

description: human skeletal muscle


title: S58A_2_SWOLL

description: human skeletal muscle


title: S52B_2_SWOLL

description: human skeletal muscle


title: S52A_2_SWOLL

description: human skeletal muscle


title: S57A_2_SWOLL

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_381h_MouseID-651222_Cell-6


title: BrainCell_Enhancer-eHGT_381h_MouseID-651222_Cell-4


title: BrainCell_Enhancer-eHGT_381h_MouseID-651222_Cell-3


title: S51B_2_SWOLL

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_381h_MouseID-651222_Cell-2


title: BrainCell_Enhancer-eHGT_381h_MouseID-651222_Cell-1


title: S50B_SWOLL

description: human skeletal muscle


title: S50A_SWOLL

description: human skeletal muscle


title: S49A_SWOLL

description: human skeletal muscle


title: S51A_2_SWOLL

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_381h_MouseID-651222_Cell-5


title: S4B_SWOLL

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_375m_MouseID-651221_Cell-11

source_name: CBX

value: CBX


title: BrainCell_Enhancer-eHGT_375m_MouseID-651221_Cell-8


title: S48A_SWOLL

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_375m_MouseID-651221_Cell-10


title: BrainCell_Enhancer-eHGT_375m_MouseID-651221_Cell-7


title: BrainCell_Enhancer-eHGT_375m_MouseID-651221_Cell-9


title: S4A_SWOLL

description: human skeletal muscle


title: S48B_SWOLL

description: human skeletal muscle


title: S47A_SWOLL

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_375m_MouseID-651221_Cell-6


title: BrainCell_Enhancer-eHGT_375m_MouseID-651221_Cell-5


title: BrainCell_Enhancer-eHGT_375m_MouseID-651221_Cell-4


title: S49B_SWOLL

description: human skeletal muscle


title: S45B_SWOLL

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_375m_MouseID-651221_Cell-3


title: S47B_SWOLL

description: human skeletal muscle


title: S43B_SWOLL

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_375m_MouseID-651221_Cell-2


title: BrainCell_Enhancer-eHGT_375m_MouseID-651221_Cell-1


title: BrainCell_Enhancer-eHGT_390h_MouseID-651220_Cell-15


title: BrainCell_Enhancer-eHGT_390h_MouseID-651220_Cell-14


title: S43A_SWOLL

description: human skeletal muscle


title: S41A_SWOLL

description: human skeletal muscle


title: S41B_SWOLL

description: human skeletal muscle


title: S40A_SWOLL

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_390h_MouseID-651220_Cell-13


title: S39B_SWOLL

description: human skeletal muscle


title: S45A_SWOLL

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_390h_MouseID-651220_Cell-12


title: S39A_SWOLL

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_390h_MouseID-651220_Cell-11


title: S38B_SWOLL

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_390h_MouseID-651220_Cell-8


title: BrainCell_Enhancer-eHGT_390h_MouseID-651220_Cell-9


title: BrainCell_Enhancer-eHGT_390h_MouseID-651220_Cell-7


title: BrainCell_Enhancer-eHGT_390h_MouseID-651220_Cell-10


title: S38A_SWOLL

description: human skeletal muscle


title: S33B_SWOLL

description: human skeletal muscle


title: S35A_SWOLL

description: human skeletal muscle


title: S40B_SWOLL

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_390h_MouseID-651220_Cell-5


title: BrainCell_Enhancer-eHGT_390h_MouseID-651220_Cell-3


title: BrainCell_Enhancer-eHGT_390h_MouseID-651220_Cell-6


title: S33A_SWOLL

description: human skeletal muscle


title: S35B_SWOLL

description: human skeletal muscle


title: S32A_SWOLL

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_390h_MouseID-651220_Cell-2


title: BrainCell_Enhancer-eHGT_390h_MouseID-651220_Cell-1


title: 293_ML60218_rep2

city: Urbana

first: Ruiying

last: Cheng

state: IL

address: B520 Chemical & Life Sciences Laboratory

department: School of Molecular & Cellular Biology

institute: The University of Illinois Urbana-Champaign

library_source: transcriptomic

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina
Reads were first trimmed using TrimGalore
mapped to the hg38 transcriptome and quantified with Salmon43 Differentially expressed genes were determined using DESeq2
Assembly: hg38
Supplementary files format and content: raw counts, and Transcribe per milion in CSV format

source_name: Kidney

growth_protocol: HEK293Tcells were obtained from ATCC (CRL-3216, Batch#70049877) and grown in 10 cm BioLite™   Cell Culture   Treated   Dishes   (Catalog# 12-556-002 Thermo   Scientific)   in Dulbecco’s Modified Eagle Medium, high glucose (Catalog# 11965092, Gibco). HEK293T experiments were conducted on cells between passage 10-25.

extract_protocol:
E.Z.N.A.® Total RNA Kit I (Catalog# R6834-01, Omega), with 100% ethanol instead of 70% at the binding step to enrich small RNA.
Kapa Hyper Stranded mRNA library kit (Roche)

treatment_protocol: siRNA is transfected using Lipofectamine® RNAiMax (cat # 13778150) with standard protocol

value: Kidney

tag: cell line

tag: cell type

value: epithelial


title: 293_ML60218_rep3


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-37


title: S31B_SWOLL

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_390h_MouseID-651220_Cell-4


title: S31A_SWOLL

description: human skeletal muscle


title: S28A_SWOLL

description: human skeletal muscle


title: 293_ML60218_rep1


title: S28B_SWOLL

description: human skeletal muscle


title: 293_DMSO_rep3

value: DMSO


title: 293_DMSO_rep2


title: 293_DMSO_rep1


title: S2B_SWOLL

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-35


title: Hek293T_siPOLR3A_rep3


title: S22B_SWOLL

description: human skeletal muscle


title: S32B_SWOLL

description: human skeletal muscle


title: Hek293T_siPOLR3A_rep2


title: S23B_SWOLL

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-34


title: S22A_SWOLL

description: human skeletal muscle


title: Hek293T_siPOLR3A_rep1


title: S23A_2_SWOLL

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-36


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-33


title: Hek293T_siControl_rep3

value: siControl


title: Hek293T_siControl_rep1


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-32


title: NHBE cells, undifferentiated, rep C

city: Minneapolis

first: Frances

last: Shepherd

state: MN

address: 689 23rd Ave SE

institute: University of Minnesota

description: 150 bp reads

data_processing:
Reads were trimmed of adapter sequences and low-quality bases with Trimmomatic (version 0.39) and mapped to the human reference genome from Ensembl (GRCh38 release 111) with STAR (version 2.7.8a).
Reads per gene were counted with HTSeq (version 1.99.2). Differential expression testing was performed with DESeq2 (version 1.42).
Assembly: GRCh38 release 111
Supplementary files format and content: Tab-separated gene count files from HTSeq

growth_protocol: Normal human bronchial/tracheal epithelial (NHBE) (Lonza Bioscience, CC-2540S) cells, harvested from healthy individuals, were expanded using either Pneumacult-Ex Plus Media (STEMCELL Technologies) and seeded on 6.5mm Transwell 0.4 μm pore polyester inserts (STEMCELL Technologies). Once confluent 2-4 days post-seeding, the ALI cultures were airlifted: apical media was removed to expose cells and basal compartment media was replaced with either Pneumacult-ALI Basal Media (STEMCELL Technologies). Cells were maintained at air-liquid interface (ALI) at 37°C and 5% CO2 in a humidified incubator. Cells were used at 3+ weeks post-ALI.

extract_protocol:
RNA was extracted using the RNeasy Plus Micro Kit (Qiagen)
Library preparation was performed using the SMART-Seq mRNA LP kit (Takara).

value: Unsorted, undifferentiated cells (cells at week 0, prior to ALI culturing)


title: S19B_SWOLL

description: human skeletal muscle


title: S19A_SWOLL

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-31


title: Hek293T_siControl_rep2


title: NHBE cells, undifferentiated, rep A

description: 150 bp reads


title: S2A_SWOLL

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-30


title: NHBE cells, triple negative population, rep C

description: 150 bp reads

value: Triple negative cells (SiR-tubulin-/CD271-/CD66c-)


title: NHBE cells, triple negative population, rep A

description: 150 bp reads


title: NHBE cells, secretory population, rep C

description: 150 bp reads


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-28


title: NHBE cells, secretory population, rep B

description: 150 bp reads


title: S18B_SWOLL

description: human skeletal muscle


title: S18A_SWOLL

description: human skeletal muscle


title: S17b_SWOLL

description: human skeletal muscle


title: NHBE cells, CD66c+ other population, rep C

description: 150 bp reads

value: CD66c+ "other" cells (SiR-tubulin-/CD271 intermediate/CD66c+)


title: NHBE cells, secretory population, rep A

description: 150 bp reads


title: S17A_SWOLL

description: human skeletal muscle


title: S16B_SWOLL

description: human skeletal muscle


title: NHBE cells, undifferentiated, rep B

description: 150 bp reads


title: S16A_SWOLL

description: human skeletal muscle


title: NHBE cells, CD66c+ other population, rep B

description: 150 bp reads


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-27


title: NHBE cells, triple negative population, rep B

description: 150 bp reads


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-29


title: NHBE cells, CD66c+ other population, rep A

description: 150 bp reads


title: NHBE cells, ciliated population, rep B

description: 150 bp reads

value: Ciliated cells (SiR-tubulin+/CD271-)


title: NHBE cells, ciliated population, rep C

description: 150 bp reads


title: NHBE cells, ciliated population, rep A

description: 150 bp reads


title: S13B_2_SWOLL

description: human skeletal muscle

value: vastus lateralis


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-25


title: NHBE cells, basal population, rep C

description: 150 bp reads


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-26


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-24


title: NHBE cells, basal population, rep B

description: 150 bp reads


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-23


title: NHBE cells, basal population, rep A

description: 150 bp reads


title: S13A_2_SWOLL

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-22


title: Male sample, Replicate #3

city: Tsukuba

first: Yuki

last: Yoshida

state: Ibaraki

address: 1-2 Owashi

department: NIAS

country: Japan

institute: NARO

data_processing:
Raw RNA-Seq reads were mapped to the coding sequences and quantified using RSEM v1.3.3. The raw counts were then submitted to statistical testing using DESeq2 v1.38.0 within the run_DE.pl from the Trinity pipeline v2.15.1. Transcripts with FDR values < 0.05 were deemed as differentially expressed genes (DEGs).
Assembly: BHEN00000000.1
Supplementary files format and content: RSEM.isoform.TMM.EXPR.matrix.gz : Normalized expression values for each samples
Supplementary files format and content: RSEM.isoform.counts.matrix.Female_vs_Male.DESeq2.DE_results.gz : Differentially expressed genes detected by DESeq2

organism: Paramacrobiotus metropolitanus

source_name: whole body

extract_protocol:
Total RNA was extracted with Direct-Zol RNA kit (Zymo)
Poly-A selection and sequencing libraries were constructed with NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs)

value: whole body

tag: Sex

value: Male


title: Male sample, Replicate #4


title: Male sample, Replicate #2


title: Male sample, Replicate #1


title: Female sample, Replicate #2

value: Female


title: Female sample, Replicate #1


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-20

value: VISp


title: C459_post

description: human skeletal muscle

value: young adult


title: A584_post

description: human skeletal muscle

value: POST


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-19


title: S10A_SWOLL

description: human skeletal muscle

value: PRE


title: S10B_SWOLL

description: human skeletal muscle


title: HYPAT9B

description: human skeletal muscle


title: Lj-1POAb

city: Cambridge

first: Douglas

middle: S

last: Kwon

state: MA

address: 600 Main ST

institute: Ragon Institute

data_processing:
DESeq2
Since samples were barcoded in library preparation and then pooled for sequencing, reads from each sample were demultiplexed based on their associated barcode sequence using custom scripts. Up to 1 mismatch in the barcode was allowed, provided it did not assign the read a separate barcode included in the sequencing pool. Barcode sequences were trimmed from the first read, as were terminal G’s from the second read that may have been added by SMARTScribe during template switching.
For each sample, reads were aligned to the sample species reference genome (GCF_022455535.1 / ASM2245553v1 for L. crispatus; GCF_022456925.1 / ASM2245692v1 for L. gasseri; GCF_022456915.1 / ASM2245691v1 for L. jensenii) using BWA96 and read counts were assigned to genes and other genomic features using custom scripts. Differential expression analysis was conducted using DESeq246. The Benjamini-Hochberg procedure was used to control the false discovery rate (FDR) with ɑ=0.05.
Assembly: GCF_022455535.1_ASM2245553v1_translated_cds.faa
Assembly: GCF_022456915.1_ASM2245691v1_translated_cds.faa
Assembly: GCF_022456925.1_ASM2245692v1_translated_cds.faa
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Lactobacillus jensenii

growth_protocol: All strain isolates All vaginal bacterial isolates were cultured under anaerobic conditions at 37–40°C using a palladium catalyst-based anaerobic chamber (COY) with an atmosphere of 5% carbon dioxide, 5% hydrogen, and 90% nitrogen (Airgas #X03NI90C3001054). Isolates were revived from frozen 25% glycerol stocks on MRS agar plates (Hardy Diagnostics #89407-144). For cultivation in liquid media, Lactobacillus MRS (MRS+CQ) broth supplemented with L-cysteine (4 mM) and L. glutamine (1.1 mM) in static culture was used. Starter cultures were grown for 48 hours.

extract_protocol:
Trizol-preserved bacterial samples prepared as above were thawed, transferred to 2 mL FastPrep tubes (MP Biomedicals #115065002) containing 500 µL of 0.1 mm Zirconia/Silica beads (BioSpec Products #11079101z), and bead beaten for 90 seconds at 10 m/sec speed using the FastPrep-24 5G (MP Biomedicals #116005500) with a Metal QuickPrep adapter. After bead beating, samples were incubated on ice for 3 min, and 200 µL chloroform was added to each sample and mixed by tube inversion. After 3 min incubation at room temperature, samples were centrifuged (12,000xg, 15 min at 4°C) to form separated phase layers between the organic & aqueous sections. For each sample, 200 µL of the clear aqueous phase was transferred to separate clean tubes, mixed with an equal volume (200 µL) of 100% ethanol by tube inversion, and incubated for 5 min at RT. Using a Direct-zol RNA Purification kit (Zymo Research #R2070), each sample was then transferred to a Direct-zol spin column and centrifuged (16,500xg, 1 min at RT). Columns were washed twice with 400 µL Direct-zol RNA Pre-Wash Buffer, and once with 700 µL Direct-zol RNA Wash Buffer and then centrifuged at max speed for 2 min. To dry the pellet and remove any ethanol carryover, columns were centrifuged with lids open (12,000xg, 1 min at RT). Finally, columns were moved to RNase-free 1.5mL tubes, incubated with 100 µL of nuclease-free water for 5 min, and then eluted by centrifugation (12,000xg, 1 min at RT). Extracted RNA samples were kept on ice for use and QC or stored at –80°C.
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Illumina cDNA libraries were generated using a modified version of the RNAtag-seq protocol94. Briefly, 250 ng of total RNA was fragmented, depleted of genomic DNA, dephosphorylated, and ligated to DNA adapters carrying 5’-AN8-3’ barcodes of known sequence with a 5’ phosphate and a 3’ blocking group (IDT). Barcoded RNA molecules were pooled and depleted of rRNA using the Pan-Bacteria riboPOOL depletion kit (siTOOLs Biotech, Galen Laboratories #dp-K096). Pools of barcoded RNAs were converted to Illumina cDNA libraries in 2 main steps: (i) reverse transcription of the RNA using a primer designed to the constant region of the barcoded adaptor with addition of an adapter to the 3’ end of the cDNA by template switching using SMARTScribe Reverse Transcriptase (Takara ClonTech #639538) as described95; (ii) PCR amplification using primers whose 5’ ends target the constant regions of the 3’ or 5’ adaptors and whose 3’ ends contain the full Illumina P5 or P7 sequences. cDNA libraries were sequenced on the Illumina NovaSeq SP 100 platform to generate paired end reads.

treatment_protocol: Representative strains were grown to exponential phase in MRS broth supplemented with L-cysteine (4 mM) and L. glutamine (1.1 mM), then treated with OA (3.2 mM), LOA (3.2 mM), POA (3.2 mM), or no treatment for 1 hour. Three culture replicates were performed for each condition. After treatment, cultures were pelleted and resuspend in trizol for bulk RNA-sequencing. Bulk RNA-sequencing and DESeq246 analysis identified genes differentially expressed (DE) in each species for each fatty acid treatment compared to no treatment controls. Strains were cultured anaerobically at 37C.

value: bacterial isolate

value: WT

value: 3.2 mM Palmitoleic acid

tag: time

value: 1 hour


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-18


title: Lj-1POAa


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-21


title: Female sample, Replicate #3


title: Lj-1LOAc

value: 3.2 mM Linoleic acid


title: Lj-1LOAb


title: HYPAT9A

description: human skeletal muscle


title: Lj-1LOAa


title: Lj-1POAc


title: HYPAT8B

description: human skeletal muscle


title: Lj-1OAc

value: 3.2 mM Oleic acid


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-17


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-16


title: Lj-1OAb


title: HYPAT7B

description: human skeletal muscle


title: HYPAT8A

description: human skeletal muscle


title: Lj-1OAa


title: HYPAT7A

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-15


title: Lj-1CTRLb

value: No treatment control


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-14


title: Lj-1CTRLa


title: Lg-1POAc

organism: Lactobacillus gasseri


title: Lg-1POAb


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-13


title: HYPAT6B

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-12


title: Lg-1LOAb


title: Lg-1POAa


title: Lg-1OAc


title: Lg-1LOAa


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-10


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-11


title: HYPAT6A

description: human skeletal muscle


title: HYPAT4B

description: human skeletal muscle


title: Lj-1CTRLc


title: Lg-1OAb


title: Lg-1LOAc


title: Lg-1OAa


title: Lg-1CTRLc


title: Lg-1CTRLb


title: Lg-1CTRLa


title: HYPAT4A

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-7


title: Lc-12POAc

organism: Lactobacillus crispatus


title: Lc-12POAb


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-6


title: Lc-12LOAb


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-8


title: HYPAT2A

description: human skeletal muscle


title: Lc-12LOAa


title: HYPAT14B

description: human skeletal muscle


title: HYPAT1A

description: human skeletal muscle


title: HYPAT2B

description: human skeletal muscle


title: HYPAT1B

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-4


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-9


title: Lc-12OAa


title: Lc-12CTRLc


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-45


title: Lc-12CTRLb


title: Lc-12LOAc


title: Lc-12CTRLa


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-44


title: HYPAT13A

description: human skeletal muscle


title: HYPAT13B

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-5


title: HYPAT14A

description: human skeletal muscle


title: Lc-12OAc


title: Lc-12OAb


title: HYPAT12B

description: human skeletal muscle


title: HYPAT12A

description: human skeletal muscle


title: RIP_MouseIgG_01

city: Milan

first: Edoardo

last: Pedrini

state: Lombardy

address: Via Olgettina 60

department: Division of Neuroscience

country: Italy

institute: Hospital San Raffaele

data_processing:
Reads have been trimmed with Cutadapt for adapter sequences and quality and Aligned to the reference genome with STAR
Bam files were counted against the Genecode V31 human GTF annoation of genes (exon and gene_name) using featureCount
Assembly: hg38
Supplementary files format and content: raw count matrices from featureCount with multimapping fractional counts

source_name: ECFCs

growth_protocol: human ECFCs were grown in ECM-2 media supplemented with 10% FBS.

extract_protocol:
For each RIP, 1.2x10^6 of replicative senescent ECFCs were used. Immunoprecipitation was performed with anti-RIG-I antibody (MABF297, Merck) and anti-SNRP70 (SAB2102255, Merck) which served as a positive control.  Corresponding IgG control was also used as the negative control. RNA from immunoprecipitated fraction was extracted using TRI reagent.
The library prep was done with the KAPA RNA HyperPrep kit, without ribosomal depletion. The input was 5-10 ng per sample for RIG-I RIP samples, and < 1ng for SNRP70 and IgG control samples. Nine PCR cycles were performed for library amplification. Samples were sequenced and the paired end reads were generated on NextSeq 2000.

treatment_protocol: ECFCs were cultured with regular passaging until they reached replicative senescence.

value: ECFCs

tag: replicate

value: endothelial cells


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-43


title: RIP_SNRP70_01


title: RIP_RIGI_04


title: HYPAT11B

description: human skeletal muscle

value: vastus lateralis


title: RIP_RIGI_03


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-42


title: HYPAT11A

description: human skeletal muscle


title: RIP_RIGI_02


title: HYPAT10B

description: human skeletal muscle


title: RIP_RIGI_01


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-39


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-41


title: lexA3 sspA∆, AZT-treated biol rep 1

city: Waltham

first: Susan

middle: T

last: Lovett

address: 415 South St.

department: Rosenstiel Center

institute: Brandeis University

description:
raw_counts_09_23_data.tsv
normalized_counts_09_23_data.tsv
lexA_sspA_azt_1

data_processing:
The Cutadapt tool was used to demultiplex samples and to trim reads and remove the r1adapter.
Reads were mapped to the E. coli MG1655 reference genome (GenBank U00096.3) using the STAR RNAseq aligner v2.7.11a.
Differential expression analysis was conducted using the R Bioconductor package, DESeq2, yielding the log2 fold change. Significance (p-value) was determined via the Wald test embedded within DESeq2. Normalized counts (median ratios) were calculated through DESeq2 and normalized counts (RPKM) were derived from R package EdgeR.
Assembly: GenBank U00096.3
Supplementary files format and content: tab-delimited text files with gene, raw counts for each sample
Supplementary files format and content: tab-delimited text files with gene, gene id,  normalized counts, RPKM and Median Ratio, summing biological replicates.

organism: Escherichia coli K-12

growth_protocol: Cultures were prepared in LB growth medium, Lennox formulation. Cultures were grown with aeration at 37° after 1:100 dilution until they reached an OD of 0.3. Cultures were split at this time and treated with AZT or not. After 1 hr of continued growth, cells were harvested by centrifugation, washed with Tris-sucrose and resuspended in 50 mM Tris pH 7.5 10% sucrose  and flash-frozen in dry ice-ethanol bath and stored at -20° C.

extract_protocol:
Total RNA was extracted using the Split RNA Extraction Kit (Lexogen) followed by RiboCop rRNA Depletion for Gram - Bacteria (Lexogen).
Library preparation employed the CORALL2 library kit  and protocol (Lexogen).
SIRV and ERCC RNA Spike-In Mix 1 (ThermoFisher) were added for quality control.  Unique Molecular Identifiers were employed to allow removal of PCR duplicates during read processing.

treatment_protocol: Cultures were treated or not with azidothymidine (AZT) at 100 ng/ml for 1 hr.

value: rph+ lexA3 sspAdeltaFRT kan malG::Tn10

value: 100 ng/ml AZT, 1 hr


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-38


title: lexA3 sspA∆, untreated biol rep 2

description:
raw_counts_09_23_data.tsv
normalized_counts_09_23_data.tsv
lexA_sspA_un_2

value: untreated


title: sspA∆, AZT-treated biol rep 1

description:
raw_counts_09_23_data.tsv
normalized_counts_09_23_data.tsv
sspA_azt_1

value: rph+ sspAdeltaFRT kan


title: lexA3 sspA∆, untreated biol rep 1

description:
raw_counts_09_23_data.tsv
normalized_counts_09_23_data.tsv
lexA_sspA_un_1


title: sspA∆, AZT-treated biol rep 2

description:
raw_counts_09_23_data.tsv
normalized_counts_09_23_data.tsv
sspA_azt_2


title: lexA3 sspA∆, AZT-treated biol rep 2

description:
raw_counts_09_23_data.tsv
normalized_counts_09_23_data.tsv
lexA_sspA_azt_2


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-40

value: VISp


title: HYPAT10A

description: human skeletal muscle

value: young adult


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-37


title: sspA∆, untreated biol rep 1

description:
raw_counts_09_23_data.tsv
normalized_counts_09_23_data.tsv
sspA_un_1


title: lexA3, AZT-treated biol rep 2

description:
raw_counts_09_23_data.tsv
normalized_counts_09_23_data.tsv
lexA_azt_2

value: rph+ lexA3 malG::Tn10


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-36


title: lexA3, AZT-treated biol rep 1

description:
raw_counts_09_23_data.tsv
normalized_counts_09_23_data.tsv
lexA_azt_1

value: rph+ lexA3 malG::Tn10 kan


title: lexA3, untreated biol rep 1

description:
raw_counts_09_23_data.tsv
normalized_counts_09_23_data.tsv
lexA_un_1


title: Lc-12POAa

value: bacterial isolate

value: WT


title: C576

description: human skeletal muscle

value: POST


title: C600

description: human skeletal muscle


title: lexA3, untreated biol rep 2

description:
raw_counts_09_23_data.tsv
normalized_counts_09_23_data.tsv
lexA_un_2


title: C582

description: human skeletal muscle

value: middle aged adult


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-35


title: wild-type, AZT-treated biol rep 1

description:
raw_counts_09_23_data.tsv
normalized_counts_09_23_data.tsv
wt_azt_1

value: rph+


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-34


title: C573

description: human skeletal muscle


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-33


title: wild-type, AZT-treated biol rep 2

description:
raw_counts_09_23_data.tsv
normalized_counts_09_23_data.tsv
wt_azt_2


title: sspA∆, untreated biol rep 2

description:
raw_counts_09_23_data.tsv
normalized_counts_09_23_data.tsv
sspA_un_2


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-32


title: wild-type, untreated biol rep 2

description:
raw_counts_09_23_data.tsv
normalized_counts_09_23_data.tsv
wt_un_2


title: XL_St11_5_NPB_Ctl_ChIP_rep3

city: Evanston

first: Carole

last: LaBonne

address: 2220 Campus Drive

department: Molecular Biosciences

institute: Northwestern University

library_source: genomic

data_processing:
fastq files were trimmed using fastp and aligned using botwie2. Samtools was used to generate bam files. Picard was used to deduplicate bam files.
Genrich was used for peak calling on namesorted bam files  (-t Sox3 samples -c Ctl samples -v -e MT -a 20.0 )
Assembly: Xenopus laevis 9.2
Supplementary files format and content: annotated bedfiles of Sox3 peaks (annoated using HOMER)

molecule: genomic DNA

organism: Xenopus laevis

source_name: animal pole explant

extract_protocol:
Animal pole explants were crosslinked for 15 minutes (10% formaldehyde (methanol-free)) and the fixation was quenched (125 mM glycine in PBSTr). Samples were lysed and sonicated and incbated with antibody overnight. Protein G Dynabeads were applied to sample for 1 hr and then washed in EDTA-free wash buffer before being tagemented with Tn5 transposase (40 min at 37C). Following tagmentation, samples were washed and reverse crosslinked. Qiagen MinElulte Reaction Clean Up kit was used to purify samples
Nextera primers and NEBNext Q5 master mix were used for library construction

value: animal pole explant

value: Stage 11.5

value: neural plate border

value: wild type

value: Wnt8a +Chordin mRNA


title: wild-type, untreated biol rep 1

description:
raw_counts_09_23_data.tsv
normalized_counts_09_23_data.tsv
wt_un_1


title: C561

description: human skeletal muscle

value: vastus lateralis


title: XL_St11_5_NPB_Ctl_ChIP_rep2


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-31


title: XL_St11_5_NPB_Sox3_ChIP_rep3

value: Sox3 + Wnt8a +Chordin mRNA


title: C558

description: human skeletal muscle

value: PRE


title: XL_St11_5_NPB_Sox3_ChIP_rep2


title: XL_St11_5_NPB_Sox3_ChIP_rep1


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-30

value: VISp


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-29


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-28


title: Naive_IgG_1

city: West Lafayette

first: Majid

last: Kazemian

state: IN

address: 201 S. University Steet

department: Biochemistry and Computer Science

institute: Purdue University

data_processing:
Bowtie2 (v2.5.1) was used to align reads to the mm10 genome build.
The BAM files were sorted using SAMtools (v1.17), and duplicate reads were marked using Picard MarkDuplicates (v3.1.1).
DeepTools (v3.5.1) was used to create BigWig using CPM normalization.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: prostate

growth_protocol: Freshly sorted cells without any in vitro culture

extract_protocol:
Minced prostate tissues from naïve or inflamed POET3 mice were digested with collagenase followed by trypsinization. Dissociated cells were passed through 20G needles and 40 µm cell strainers to eliminate aggregates, followed by removal of red blood cells by ACK buffer. Isolated cells were stained with fluorescence-conjugated specific antibodies for CD45, CD31, Sca-1 and CD49f. CD45-CD31-Sca-1+CD49f+ basal stem cells were sorted on theBD FACSAriaunder sterile conditions. Stem cells from 9 naïve prostates and 4 inflamed prostates were pooled for each naïve and inflamed replicate, respectively.
Cleavage Under Targets and Tagmentation (CUT&Tag) was performed as per the published protocol (https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3). Barcoded i5 and i7 primers from Diagenode (24UDI for Tagmented libraries Set I) were used for the library preparation along with NEBNext Ultra II Q5 Master Mix. Libraries were amplified for 13 cycles on the thermal cycler followed by bead purication and validation using Agilent D1000 on a Agilent TAPE Station

treatment_protocol: Prostate inflammation was induced in POET3 (Prostate Ovalbumin Expressing Transgenic 3) mice by adoptive transfer of pre-activated splenocytes from OT-1 mice and was allowed to develop for 7 days before prostate harvest.

value: prostate

value: basal stem cells

value: control


title: C546

description: human skeletal muscle

value: young adult


title: XL_St11_5_NPB_Ctl_ChIP_rep1


title: Inflamed_IgG_2

value: inflamed


title: C549

description: human skeletal muscle

value: POST


title: C543

description: human skeletal muscle


title: Naive_AR_1

value: WT


title: C534

description: human skeletal muscle


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-27


title: C540

description: human skeletal muscle


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-26


title: Inflamed_H3k27ac_1


title: Inflamed_H3k27ac_2


title: C528

description: human skeletal muscle

value: middle aged adult


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-25


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-24


title: Inflamed_AR_2


title: Inflamed_AR_1


title: Naive_H3K27ac_1


title: C510

description: human skeletal muscle


title: LLC knockdown cell

city: Miaoli County

first: Jingxing

last: Yang

address: 35, Keyan Road, Zhunan Town

department: Immunology Research Center

country: Taiwan

institute: National Health Research Institutes

description: Gene expression data from LLC-shPDLIM2 cells

hyb_protocol: Samples were hybridized with Clariom™ S Assay, mouse Arrays (Applied Biosystems) and scanned at the NHRI Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Applied Biosystems).

data_processing: The data were analyzed using Transcriptome Analysis Console (TAC) Software default analysis settings. Expression values were processed with Signal Space Transformation (SST) and Robust Multichip Average method, which included log2 transformation and quantile normalization.

source_name: LLC cells were infected with virus supernatant containing shPDLIM2 shRNA

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Plus cDNA Synthesis Kit (Applied Biosystems) and then fragmented and labeled with the WT Terminal Labeling Kit (Applied Biosystems).

growth_protocol: Murine Lewis lung carcinoma (LLC) cells were maintained in DMEM containing 10% FBS, 2 mM L-glutamine, 1% antibiotic-antimycotic, and 10 mM HEPES.

extract_protocol: RNA was extracted from LLC cells using the Qiagen RNeasy Plus Mini kit, following the manufacturer’s instructions.

treatment_protocol: LLC cells were infected in the presence of viral supernatants (containing PDLIM2 shRNA) and 8 mg/ml polybrene, and stable cell lines were selected using puromycin (3 ng/ml).

tag: strain

value: Lewis lung carcinoma (LLC) cells


title: Young_1

description:
Young
10X Genomics
PN0372_0001

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files, gzipped

source_name: retina enriched sample

growth_protocol: Mouse retinal tissue was digested and endothelial cell enrichment carried out with CD31 antibody and autoMACS

extract_protocol:
Retinas were digested using the Neurosphere dissociation kit (Miltenyi Biotec),  vascular structures were pelleted down, supernatant discarded and the pellet digested again and triturated by pipetting. Cell suspension was then washed with HBSS/1% BSA (wt/vol)/0.1% D-glucose (wt/vol), and filtered through a 40um strainer. CD31+ cells were enriched using CD31 microbeads and the autoMACS Pro-separator (Miltenyi Biotec) for magnetic separation. Sorted cells were then washed, counted, and a suspension of 1000 cells/ul was loaded onto the microfluidic chip and libraries prepared using the 10x Genomics v3.1 kit.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriately sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Retinas from 3, 12, and 23 month aged mice

value: retina enriched sample

value: retinal cells

value: 3 months


title: WT_R2_LRS

city: New Haven

first: Jackson

last: Gordon

state: CT

address: 333 Cedar St

department: MB&B

institute: Yale University

data_processing:
PacBio: Reads were trimmed with cutadapt (settings: --cores=14 --discard-untrimmed --no-indels --revcomp -e 0.2)
PacBio: Deduplication was carried out with PrinSeq-lite (settings: settings -derep 2 -out_format 3), then again (settings: -trim_left 5 -out_format 3)
PacBio: Reads were mapped with minimap2 to GRCh38/hg38 genome (ammended to also contain exogenous WT PABPN1 sequence) (settings: -x splice:hq –secondary no -t 12 -a -u f).
PacBio: Samtools sort was used to sort reads by genomic position. Samtools view (settings -S -b) was used to convert .sam files to .bam files. Samtools index was used to generate index files corresponding to each .bam file. Samtools view was also used to separate reads mapping to hg38 from those mapping to the plasmid sequence. Bedtools bamtobed (setting -bed12) was used to generate bed12 files from .bam files.
PacBio: The flair software suite (https://flair.readthedocs.io/en/latest/) was used to assign reads to splice isoforms, quantify isoform usage between samples, and mark isoforms with retained introns.
PacBio: Poly(A) tail lengths were counted using a custom script that counts soft-clipped bases on 3′ ends of reads.
RNA-seq: Illumina adapters were trimmed using fastp.
RNA-seq: Reads were mapped with STAR to GRCh38/hg38 genome (ammended to also contain exogenous WT PABPN1 sequence) (settings: --runMode alignReads --outSAMtype BAM SortedByCoordinate --outFilterMismatchNmax 2 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000).
RNA-seq: Samtools sort was used to sort reads by genomic position. Samtools view (settings -S -b) was used to convert .sam files to .bam files. Samtools index was used to generate index files corresponding to each .bam file. Samtools view was also used to separate reads mapping to hg38 from those mapping to the plasmid sequence.
RNA-seq: Read coverage for each sample was quantified using salmon (settings: -l A --validateMappings –gcBias).
RNA-seq: Differential expression between conditions was quantified using DESeq2.
TimeLapse-seq: Reads were filtered for unique sequences using FastUniq v.1.1
TimeLapse-seq: Reads were trimmed trimmed of adaptor sequences with Cutadapt v3.2
TimeLapse-seq: Reads were aligned to GRCh38/hg38 genome with HISAT-3N
TimeLapse-seq: Reads aligning to annotated transcripts were quantified with HTSeq htseq-count
TimeLapse-seq: SAMtools v.1.539 was used to collect only uniquely mapped read pairs (SAM flag = 83/163 or 99/147).
TimeLapse-seq: Mutation calling and cB file generation was carried out with bam2bakR (https://github.com/simonlabcode/bam2bakR)
TimeLapse-seq: RNA synthsis and degradation kinetics were assessed using the BakR software suite (https://github.com/simonlabcode/bakR).
TimeLapse-seq: Differential expression between conditions was quantified using DESeq2.
Assembly: GRCh38/hg38
Supplementary files format and content: For long-read sequencing: Tab-delimited files containing poly(A) tail lengths for each read, mapped to either genome or transcriptome.
Supplementary files format and content: For Illumina sequencing: Tab-delimited files include transcripts per million (TPM) values for each sample.
Supplementary files format and content: For TimeLapse-seq: Tab-delimited file includes T to C mutation counts for each sample.

growth_protocol: HEK293T cells capable of expressing PABPN1 mutants (Empty Vector, Wild-Type, S19/S150/S197/S304 to A, S19/S150/S197/S304 to A) were maintained at 37°C and 5% CO2 in DMEM + Glutamax medium (GIBCO) containing 100 U/ml penicillin, 100 μg/ml streptomycin (GIBCO), and 10% tetracycline-free fetal bovine serum (GIBCO).

extract_protocol:
Cells were harvested by scraping or rinsing in ice cold PBS followed by centrifugation at 270 x g for 10 minutes. Cell pellets were washed twice in ice cold PBS and either used immediately or flash frozen in liquid nitrogen and stored at -80°C. RNA was extracted using TRIzol (Invitrogen)
For long read sequencing: RNA was then reverse transcribed with TGIRT-III reverse transcriptase (InGex). Following reverse transcription, RNA was digested with RNase H (New England Biolabs) to remove any bound TGIRT-III and cDNA purified with the Qiagen MinElute kit. To prepare the 5′ adapter, single stranded DNA adapter oligo was treated with Mnth ligase (New England Biolabs). The prepared adapter was then ligated to the cDNA pool using Thermostable 5´ App DNA/RNA Ligase (New England Biolabs) and again purified with the Qiagen MinElute kit. PCR amplification of cDNA library was carried out with Advantage PCR kit with primers that anneal to the 5 and 3′ adapter sequences. Samples were barcoded with overhanging reverse primers and amplified to PCR 18 cycles. DNA purification was carried out using AMPure beads (Beckman Coulter) and pooled at equimolar ratios. The PacBio SMRTbell prep kit was used for final library preparation according to the manufacturer (Pacific Biosciences) and sequenced on a PacBio Sequel II Long-Read Sequencer. Replicates 1 and 2 were sequenced on separate flow cells (1 flow cell each).
For RNA seq: Extracted RNA was used to prepare RNA-seq libraries using the KAPA mRNA HyperPrep Kit (Kapa Biosystems). The RNA-seq library was sequenced on the Illumina Novaseq 6000 platform generating ~25 million paired-end reads per sample.
For TimeLapse-seq: RNA was precipitated in isopropanol supplemented with 1 mM DTT and 20 μg glycogen and washed with freshly prepared 75% ethanol. Dried pellets were resuspended in nuclease-free water. Turbo DNase was used to deplete any remaining genomic DNA. RNAclean beads were used to isolate the RNA, which was then subjected to TimeLapse chemistry (2,2,2-trifluoroethylamine and mCPBA) and further purified with RNAclean beads. This recoded RNA was prepared for sequencing using the mammalian pico-input SMARTer stranded Total RNA-Seq kit v2 according to the manufacturer. The RNA-seq library was sequenced on the Illumina Novaseq 6000 platform generating ~30 million paired-end reads per sample.

treatment_protocol: For induction of PABPN1 mutant expression, cells were treated with 1 µg/mL Doxycycline Hyclate (ThermoFisher) for 3 days. For TimeLapse-seq experiments: During the last two hours of Doxycycline induction, 100 μM s4U was added to all samples (200 μM s4U for empty vector samples). A single replicate of each cell line received DMSO (no s4U).

tag: group

value: PacBio (long-read sequencing)

value: Human embryonic Kidney

value: WT + wild-type PABPN1

value: Doxycycline induction, 3 days


title: Old_1

description:
Old
10X Genomics
PN0372_0003

value: 23 months


title: 4SD_R1_LRS

value: WT + 4SD PABPN1


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-22

value: VISp


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-21


title: 4SA_R1_LRS

value: WT + 4SA PABPN1


title: 4SD_R2_LRS


title: 4SA_R2_LRS


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-23


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-20


title: WT_R1_LRS


title: EV_R2_LRS

value: WT + Empty Vector


title: Adult_1

description:
Adult
10X Genomics
PN0372_0002

value: 12 months


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-19


title: EV_R1_LRS


title: spleen APAP-30h

city: Frankfurt

first: Malte

last: Bachmann

address: Theodor Stern Kai 7

department: General Pharmacology

country: Germany

institute: University Hospital Frankfurt

data_processing:
Performed using MACE kit v.2 (GenXPro, Frankfurt, Germany)
Poly(A) mRNA underwent poly-A specific reverse transcription and template -switched based second strand synthesisi followed by competitive PCR
Duplicate reads verified by implemented unique molecular identifiers (TrueQuant IDs) were eliminated from raw dataset
Low quality sequence-bases were eliminated (htpps://gthub.com/marcelm/cutadept/)
Poly(A)-tails were clipped by in-house Phyton-Script; transcripts were quantified by HTSeq. Differengtially expressed genes were identified by DESeq2
Assembly: mm10
Supplementary files format and content: all-merged txt file include log2normalized values for each sample

source_name: spleen

extract_protocol:
splenic RNA was isolated by trizol and Dnase I digested
Library preparation was done with MACE-kit v.2 (GenXPro, Frankfurt, Germany)

treatment_protocol: 0.9% NaCl-solution or 300mg/kg APAP i.p.

value: spleen


title: C498

description: human skeletal muscle

value: vastus lateralis

value: PRE


title: LLC control cell

description: Gene expression data from LLC-shEmpty cells

source_name: LLC cells were infected with virus supernatant containing shEmpty shRNA

value: Lewis lung carcinoma (LLC) cells


title: C459

description: human skeletal muscle

value: young adult


title: C402

description: human skeletal muscle


title: APAP-30h

data_processing:
Performed using Rapid MACE kit (GenXPro, Frankfurt, Germany)
Poly(A) mRNA underwent poly-A specific reverse transcription and template -switched based second strand synthesisi followed by competitive PCR
Duplicate reads verified by implemented unique molecular identifiers (TrueQuant IDs) were eliminated from raw dataset
Low quality sequence-bases were eliminated (htpps://gthub.com/marcelm/cutadept/)
Poly(A)-tails were clipped by in-house Phyton-Script; transcripts were quantified by HTSeq. Differengtially expressed genes were identified by DESeq2
Assembly: mm10
Supplementary files format and content: all-merged txt file include log2normalized values for each sample

source_name: liver

extract_protocol:
hepatic RNA was isolated by trizol and Dnase I digested
Library preparation was done with MACE-kit v.2 (GenXPro, Frankfurt, Germany)

treatment_protocol: 300mg/kg APAP i.p./ 5mg/kg AZD7986: -12h, 0h, 12h, 24h (p.o.) + APAP at time point 0h

value: liver


title: C375

description: human skeletal muscle

value: POST

value: middle aged adult


title: C378

description: human skeletal muscle


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-16


title: Kidney, Old-JQ1, rep3

city: Kumamoto

first: Mitsuyoshi

last: Nakao

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

data_processing:
Basecalls and conversion to FASTQ files were performed using BaseSpace Onsite (Illumina)
Adaptor trimming and QC were done using Trim galore (v0.5.0).
Mapping of the trimmed reads on the reference genome was done using rsem-calculate-expression (RSEM v1.3.1).
Expression quantification was done using rsem-calculate-expression (RSEM v1.3.1).
Differentially expressed gene (DEG) analysis was done using RNAseqChef (Etoh K et al., 2023)
Assembly: hg19 or mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: tab-delimited text file includes TPM values for each sample.

growth_protocol: (Cell lines) IMR-90 ER:Ras cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 200 mM L-glutamine, 1 mM sodium pyruvate, 10% (v/v) heat-inactivated fetal bovine serum (FBS), and penicillin/streptomycin.  (Mouse) Animal experiments were approved by the Animal Care and Use Committee of Kumamoto University (A2019-098), and conducted in accordance with its guidelines.

extract_protocol:
(Cell lines) Total RNA was extracted using RNeasy Mini Kit (QIAGEN).  (Mouse) Total RNA was extracted using Trizol reagent.
Messenger RNA was purified using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Libraries were synthesized using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: (Cell lines) To induce quiescence, IMR-90 ER:Ras cells were cultured with the above medium containing 0.1% FBS for 2 days. To induce oncogene-induced senescence, IMR-90 ER:Ras cells were treated with 100 nM 4-Hydroxytamoxifen (4-OHT) for 6 days or 8 days. Transfection of siRNA was performed using RNAiMAX (Invitrogen). (Mouse) Young (8–9 weeks old) and aged (89–90 weeks old) male C57BL/6J mice (JAXON LABORATORY JAPAN) were intraperitoneally injected with 10,11-Dehydrocurvularin (DCV; 10 mg/kg/ 200 l), JQ1 (50 mg/kg/ 200 l), or vehicle control (200 l corn oil) two or three times a week for 1 month, and the liver and kidney tissue was then collected.

value: Kidney

value: 50 mg/kg JQ1


title: C330

description: human skeletal muscle


title: APAP-AZD7986-30h


title: Kidney, Old-JQ1, rep4


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-18


title: Kidney, Old-JQ1, rep2


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-15


title: Kidney, Old-JQ1, rep1


title: Kidney, Old-DCV, rep4

value: 10 mg/kg DCV


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-17


title: Kidney, Old-DCV, rep3


title: C354

description: human skeletal muscle


title: C297

description: human skeletal muscle


title: C321

description: human skeletal muscle


title: C486

description: human skeletal muscle


title: spleen Kontr-30h


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-14


title: Kidney, Old-DCV, rep1


title: Kidney, Old-veh, rep3

value: Veh.


title: Kidney, Old-veh, rep4


title: C237

description: human skeletal muscle


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-13


title: Kidney, Old-DCV, rep2


title: Kidney, Old-veh, rep1


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-11


title: Kidney, Young-veh, rep4


title: C282

description: human skeletal muscle


title: C222

description: human skeletal muscle


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-10


title: Kidney, Young-veh, rep3


title: Kidney, Young-veh, rep2


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-9


title: Kidney, Young-veh, rep1


title: Kidney, Old-veh, rep2


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-12


title: Liver, Old-JQ1, rep4

source_name: Liver

value: Liver


title: C504

description: human skeletal muscle


title: C168

description: human skeletal muscle


title: Liver, Old-JQ1, rep3


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-8

value: VISp


title: C570

description: human skeletal muscle


title: Liver, Old-JQ1, rep2


title: Liver, Old-JQ1, rep1


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-7


title: Liver, Old-DCV, rep4


title: C165

description: human skeletal muscle


title: C141

description: human skeletal muscle


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-6


title: C126

description: human skeletal muscle


title: Liver, Old-DCV, rep1


title: Liver, Old-veh, rep4


title: Liver, Old-veh, rep2


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-3


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-5


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-4


title: Liver, Old-veh, rep3


title: Liver, Old-veh, rep1


title: Liver, Young-veh, rep4


title: Liver, Old-DCV, rep2


title: Liver, Young-veh, rep2


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-2


title: C117

description: human skeletal muscle


title: Liver, Old-DCV, rep3


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-630480_Cell-1


title: C120

description: human skeletal muscle


title: C102

description: human skeletal muscle


title: C99

description: human skeletal muscle


title: 53371_cre (JAK1 KO)

city: Detroit

first: Kay-Uwe

last: Wagner

state: MI

address: 421 East Canfield, EL01TM

department: Department of Oncology

institute: Barbara Ann Karmanos Cancer Institute  Wayne State University School of Medicine

data_processing:
The quality of sequenced reads was evaluated using FastQC (v0.11.9).
For the differential expression analysis between parental and Jak1 knockout samples, the 75 or 150 base paired-end reads were aligned to the GRCm38/mm10 mouse reference genome (UCSC) via Rsubread (v2.0.0).
Transcript abundance was determined using the featureCounts function of the Rsburead package, and low abundance gene transcripts (cpm < 5 in more than half of the samples) were omitted in further downstream analyses.
The edgeR package was used for the paired sample differential expression analysis between wildtype parental cells and isogenic Jak1 KO cells. Genes that passed the threshold of an FDR (False Discovery Rate) below 0.05 were considered as significantly deregulated.
To visualize the differential expression of select deregulated genes, the gene counts were log2 transformed and scaled to highlight differences in isogenic cell line pairs and were subsequently plotted as a heatmap using the R-function heatmap.2 (package: gplots v3.0.3).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files that contain gene Entrez IDs and corresponding normalized or normalized and log2 transformed  values of gene counts for each sample.

growth_protocol: Mouse PDAC cells  were maintained in DMEM medium supplemented with 10% FBS, L-glutamine, and nonessential amino acids as well as 10 µg/ml penicillin/ streptomycin and 50 µg/ml gentamicin.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). Total RNA was extracted from flash-frozen cultured cancer cells using the RNeasy Mini Kit (QIAGEN). QIAGEN's protocol was followed to extract the total RNA. The concentration of the RNA was determined on a NanoDrop spectrophotometer, and the integrity of the RNA was validated using gel electrophoresis. Quality and quantity of the total RNA was re-confirmed by Novogene. Only high quality RNA was used for library prepration.   1.3 ug of total RNA was used for the construction of sequencing libraries.
Library construction was performed by Novogene  with the following procedure: After the QC, mRNA was enriched using oligo(dT) beads. Next, the mRNA was fragmented randomly by adding fragmentation buffer, followed by cDNA was synthesis using mRNA template and random hexamer primers. Next a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. After a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment. The quality of the library was confirmed via: (1) Qubit 2.0: tests the library concentration preliminarily. (2) Agilent 2100: tests the insert size. (3) Q-PCR: quantifies the library effective concentration precisely.

treatment_protocol: To generate isogenic cell lines that are deficient in JAK1, the parental lines were infected with pBabe-Cre-puro retroviral particles and selected with increasing concentrations of puromycin (2, 4, and 7 µg/ml).

value: Pancreatic Ductal Adenocarcinoma cell line

value: JAK1 Knockout


title: Liver, Young-veh, rep3


title: 53371 (WT)

value: Wildtype


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-43


title: 53369_cre (JAK1 KO)


title: C54

description: human skeletal muscle

data_processing:
CEL files were GC correct and then processed using IRON (default settings) using custom CDFs and then an SD filter applied to focus on signals above background. The full length transcript probe-set based data are provided along with the custom CDF.
Array probes were aligned to genome reference Grch38 and transcriptome reference gencode43 and a probe-level CDF was created.

extract_protocol: Trizol


title: 52424_cre (JAK1 KO)


title: C57

description: human skeletal muscle


title: C81

description: human skeletal muscle


title: C78

description: human skeletal muscle


title: 53369 (WT)


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-42

data_processing:
Base-calling using standard Illumina software.
Alignment with STAR (https://github.com/alexdobin/STAR)
Transformed by counts per million.
Assembly: mm10
Supplementary files format and content: Processed data in counts per million (CPM) format.

extract_protocol:
Single SYFP2-expressing cells from mouse brain were flow sorted into individual tubes in SMARTerv4 collection buffer.
SMARTerv4


title: 52424 (WT)


title: C51

description: human skeletal muscle


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-40


title: Liver, Young-veh, rep1


title: 52419 (WT)


title: 52205 (WT)


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-41


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-39


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-38


title: wing disc with Zelda-GFP damaged rep 1

first: Rachel

last: Smith-Bolton

state: Illinois

address: 601 S.Goodwin Ave

department: Cell and Developmental biology

institute: University of Illinois at Urbana Champaign

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software
Paired end reads were aligned using bowtie2
Aligned reads were sorted by coordinates using SAMtools
PCR duplicates were removed using MarkDuplicates, part of Picard
Coverage file was obtained by using BAMcoverage, part of deeptools. Samples were normalized to 1x
Peaks were called using MACS2 software
Supplementary files format and content: .bigwig, .bed and .narrowPeak
Assembly: dm6
Library strategy: CUT&RUN

organism: Drosophila melanogaster

source_name: wing disc

extract_protocol:
Discs were dissected and chromatin was released in accordance to CUT&Run protocol as per Ki (Cell Signaling  #86652)
libraries were constructed using UltraLow Input Library construction kit from Tecan

value: wing disc

tag: cut&run antibody

value: Rabbit anti-GFP (#ab290)


title: wing disc with Zelda-GFP damaged rep2


title: C48

description: human skeletal muscle

value: vastus lateralis


title: 52205-cre (JAK1 KO)


title: 52419-cre (JAK1 KO)


title: wing disc with Zelda-GFP undamaged rep 1


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-37

source_name: VISp


title: wild type wing disc damaged rep 1


title: wild type wing disc undamaged rep2


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-36


title: wild type wing disc undamaged rep 1


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-35


title: 44h APF eyes, mCherryRNAi, rep4

city: Ann Arbor

first: Laura

last: Buttitta

address: 1105 N University Ave

department: Molecular, Cellular and Developmental Biology

institute: University of Michigan

description:
half males, half females
S4 300 cycle

data_processing:
Raw sequencing file quality was assessed with FastQC
Reads were trimmed using Cutadapt 1.18 with Python 3.7.3
Reads were aligned to dm6 genome using STAR 2.7.6a
Assembly: dm6
Supplementary files format and content: BigWig

source_name: pupa eye

extract_protocol:
Pupal eyes were dissected in 1X PBS and transferred to Trizol for RNA extraction
Total RNA (ribo-depeletion) for Mi-2DN, Mi-2WT, Mi-2RNAi and w1118 samples; PolyA RNA for E93RNAi and mCherryRNAi samples

value: pupa eye

tag: developmental stage

value: 44h APF

value: pooled male and female

value: GMR-P35/w; GMR-Gal4/+; UAS-mCherry RNAi/+


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-34


title: wild type wing disc damaged rep2


title: 44h APF eyes, mCherryRNAi, rep2

description:
half males, half females
S4 300 cycle


title: C39

first: James

last: Timmons

address: Bridge of Allan

institute: Augur Precision Medicine LTD

description: human skeletal muscle

source_name: POST

value: POST

value: young adult


title: C195

description: human skeletal muscle

value: middle aged adult


title: C27

description: human skeletal muscle


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-33

first: John

last: Mich

address: 615 Westlake Ave N

institute: Allen Institute for Brain Science


title: C30

description: human skeletal muscle

source_name: PRE

value: PRE


title: C15

description: human skeletal muscle


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-32


title: 44h APF eyes, mCherryRNAi, rep1

description:
half males, half females
S4 300 cycle


title: 44h APF eyes, E93RNAi, rep4

description:
half males, half females
S4 300 cycle

value: GMR-P35/w; GMR-Gal4/UAS-E93 RNAi; +


title: 44h APF eyes, mCherryRNAi, rep3

description:
half males, half females
S4 300 cycle


title: 44h APF eyes, E93RNAi, rep3

description:
half males, half females
S4 300 cycle


title: wing disc with Zelda-GFP undamaged rep2


title: C6

description: human skeletal muscle


title: 44h APF eyes, E93RNAi, rep1

description:
half males, half females
S4 300 cycle


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-31


title: 24h APF eyes, w1118, rep3

description:
half males, half females
S4 300 cycle

value: 24h APF


title: B589

description: human skeletal muscle


title: 24h APF eyes, w1118, rep2

description:
half males, half females
S4 300 cycle


title: B595

description: human skeletal muscle


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-30

value: VISp


title: 24h APF eyes, w1118, rep1

description:
half males, half females
S4 300 cycle


title: B586

description: human skeletal muscle


title: 24h APF eyes, Mi-2RNAi, rep1

description:
half males, half females
S4 300 cycle

value: GMR-P35/w; GMR-Gal4/+; UAS-Mi-2 RNAi/+


title: 24h APF eyes, Mi-2RNAi, rep3

description:
half males, half females
S4 300 cycle


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-28


title: 24h APF eyes, Mi-2WT, rep3

description:
half males, half females
S4 300 cycle

value: GMR-P35/w; GMR-Gal4/+; UAS-Mi-2-WT/+


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-29


title: B574

description: human skeletal muscle


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-27


title: 24h APF eyes, Mi-2RNAi, rep2

description:
half males, half females
S4 300 cycle


title: 44h APF eyes, E93RNAi, rep2

description:
half males, half females
S4 300 cycle


title: 24h APF eyes, Mi-2DN, rep3

description:
half males, half females
S4 300 cycle

value: GMR-P35/w; GMR-Gal4/+; UAS-Mi-2-DN/+


title: 24h APF eyes, Mi-2WT, rep1

description:
half males, half females
S4 300 cycle


title: B565

description: human skeletal muscle


title: 24h APF eyes, Mi-2DN, rep2

description:
half males, half females
S4 300 cycle


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-26


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-25


title: 24h APF eyes, Mi-2DN, rep1

description:
half males, half females
S4 300 cycle


title: B559

description: human skeletal muscle


title: 44h APF eyes, w1118, rep3

description:
half males, half females
S4 300 cycle


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-24


title: 44h APF eyes, w1118, rep2

description:
half males, half females
S4 300 cycle


title: 44h APF eyes, w1118, rep1

description:
half males, half females
S4 300 cycle


title: 44h APF eyes, Mi-2RNAi, rep3

description:
half males, half females
S4 300 cycle


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-23


title: 44h APF eyes, Mi-2RNAi, rep1

description:
half males, half females
S4 300 cycle


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-22


title: C9

description: human skeletal muscle


title: 44h APF eyes, Mi-2WT, rep3

description:
half males, half females
S4 300 cycle


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-21


title: 44h APF eyes, Mi-2WT, rep2

description:
half males, half females
S4 300 cycle


title: 44h APF eyes, Mi-2WT, rep1

description:
half males, half females
S4 300 cycle


title: B547

description: human skeletal muscle


title: B556

description: human skeletal muscle


title: 44h APF eyes, Mi-2DN, rep3

description:
half males, half females
S4 300 cycle


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-20


title: 44h APF eyes, Mi-2DN, rep2

description:
half males, half females
S4 300 cycle


title: 44h APF eyes, Mi-2DN, rep1

description:
half males, half females
S4 300 cycle


title: B499

description: human skeletal muscle


title: B466

description: human skeletal muscle


title: B538

description: human skeletal muscle


title: B550

description: human skeletal muscle


title: ATAC_24h APF eyes, w1118, rep2

description:
half males, half females
S4 300 cycle

data_processing:
Raw sequencing files assessed using FastQC
Trimmomatic-0.39 used to trim adaptors and low-quality bases
Reads aligned to dm6 genome using Bowtie2.4.1 with --local --very-sensitive parameters. Max fragment size set to 1000.
Duplicates marked using picard-tools2.8.1 MarkDuplicates, and BAM files generated using samtools1.5.
Peaks called using macs2 version 2.1.2. Bigwigs and heatmaps generated using DeepTools.
Assembly: dm6
Supplementary files format and content: BigWig

extract_protocol:
Tissues were dissected in CUT&RUN wash buffer, then dissociated in collagenase/dispase solution for 40 minutes
Libraries were prepared using Nextera PCR primers and NEBNext High-Fidelity 2x PCR Master Mix. Libraries were amplified using 8-10 PCR cycles, then cleaned up using AMPure XP beads from Beckman Coulter. Library quality was assessed using an Agilent Tape Station.


title: 44h APF eyes, Mi-2RNAi, rep2

description:
half males, half females
S4 300 cycle


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-18


title: B424

description: human skeletal muscle


title: ATAC_24h APF eyes, Mi-2RNAi, rep3

description:
half males, half females
S4 300 cycle


title: ATAC_24h APF eyes, w1118, rep1

description:
half males, half females
S4 300 cycle


title: ATAC_24h APF eyes, Mi-2RNAi, rep2

description:
half males, half females
S4 300 cycle


title: B376

description: human skeletal muscle


title: B325

description: human skeletal muscle


title: ATAC_24h APF eyes, Mi-2RNAi, rep1

description:
half males, half females
S4 300 cycle


title: ATAC_24h APF eyes, Mi-2WT, rep3

description:
half males, half females
S4 300 cycle


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-17


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-16


title: ATAC_24h APF eyes, Mi-2WT, rep2

description:
half males, half females
S4 300 cycle


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-19


title: B313

description: human skeletal muscle


title: ATAC_24h APF eyes, Mi-2WT, rep1

description:
half males, half females
S4 300 cycle


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-15


title: ATAC_24h APF eyes, Mi-2DN, rep2

description:
half males, half females
S4 300 cycle


title: ATAC_24h APF eyes, Mi-2DN, rep1

description:
half males, half females
S4 300 cycle


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-13


title: ATAC_44h APF eyes, Mi-2RNAi, rep3

description:
half males, half females
S4 300 cycle


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-14


title: B298

description: human skeletal muscle


title: ATAC_44h APF eyes, Mi-2RNAi, rep2

description:
half males, half females
S4 300 cycle


title: B361

description: human skeletal muscle


title: B274

description: human skeletal muscle


title: ATAC_44h APF eyes, w1118, rep1

description:
half males, half females
S4 300 cycle


title: ATAC_44h APF eyes, w1118, rep2

description:
half males, half females
S4 300 cycle


title: B295

description: human skeletal muscle


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-12


title: ATAC_44h APF eyes, Mi-2WT, rep1

description:
half males, half females
S4 300 cycle


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-11


title: ATAC_44h APF eyes, Mi-2WT, rep2

description:
half males, half females
S4 300 cycle


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-10


title: B244

description: human skeletal muscle


title: ATAC_44h APF eyes, Mi-2WT, rep3

description:
half males, half females
S4 300 cycle


title: ATAC_44h APF eyes, Mi-2RNAi, rep1

description:
half males, half females
S4 300 cycle


title: ATAC_44h APF eyes, Mi-2DN, rep1

description:
half males, half females
S4 300 cycle


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-9


title: XL_St9_Ctl_ChIP_rep3

value: animal pole explant

value: Stage 9

value: blastula animal pole

value: wild type


title: XL_St9_Ctl_ChIP_rep2


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-8


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-7


title: XL_St9_Ctl_ChIP_rep1


title: B220

description: human skeletal muscle

value: vastus lateralis


title: XL_St9_Sox3_ChIP_rep3

value: Sox3 mRNA


title: B196

description: human skeletal muscle


title: B202

description: human skeletal muscle


title: ATAC_44h APF eyes, Mi-2DN, rep2

description:
half males, half females
S4 300 cycle

value: pupa eye

value: 44h APF

value: pooled male and female


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-6


title: XL_St11_5_NPB_WT_RNA_rep3

description:
NPB_11_5_counts.txt
NPB_11_5_TPMs.txt

data_processing:
fastq files were trimmed using fastp. Rsem/botwie2 was used to generate TPMs ( --estimate-rspd \ --append-names\ --output-genome-bam\ --forward-prob 0)
Read counts were genrated using STAR (--outSAMstrandField intronMotif --outSAMtype BAM \ SortedByCoordinate --twopassMode Basic --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.03 \ --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3) and Htseq (-r pos -f bam -s reverse -m union)
DeSeq was used to determine differential expression from read counts (design = ~ Replicate + Treatment; lowly expressed genes (TPM <3) were filtered out)
Assembly: Xenopus Laevis 9.2
Supplementary files format and content: DESeq output in txt format
Supplementary files format and content: TPM data with each column being a different replicate in txt format

extract_protocol:
RNA was extracted from animal pole explants using trizol and LiCl was used to precipitate RNA.
Ultra™ II Directional RNA Library Prep Kit for Illumina was used to generate libraries

value: Stage 11.5

value: neural plate border

value: Wnt8a +Chordin mRNA


title: XL_St9_Sox3_ChIP_rep1


title: XL_St9_Sox3_ChIP_rep2


title: B193

description: human skeletal muscle

value: PRE

value: middle aged adult


title: B190

description: human skeletal muscle

value: POST

value: young adult


title: B187

description: human skeletal muscle


title: XL_St11_5_NPB_WT_RNA_rep1

description:
NPB_11_5_counts.txt
NPB_11_5_TPMs.txt


title: XL_St11_5_NPB_WT_RNA_rep2

description:
NPB_11_5_counts.txt
NPB_11_5_TPMs.txt


title: B181

description: human skeletal muscle


title: 24h APF eyes, Mi-2WT, rep2

description:
half males, half females
S4 300 cycle

value: 24h APF

value: GMR-P35/w; GMR-Gal4/+; UAS-Mi-2-WT/+


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-4

value: VISp


title: XL_St9_WT_RNA_rep3

description:
SoxB1_MO_St9_counts.txt
WT_vs_SoxB1_MOs_DESeq.txt

value: animal pole explant

value: Stage 9

value: blastula animal pole


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-5


title: XL_St9_WT_RNA_rep2

value: wild type


title: XL_St9_WT_RNA_rep1


title: XL_St9_B1MOs_RNA_rep2

value: soxb1 morpholinos


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-2


title: IMR-90, Sen-siRb/p53, rep3

value: senescent fibroblast

value: siRb/p53, 100 nM 4-OHT for 8 days


title: IMR-90, Sen-siRb/p53, rep2


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-43


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-44


title: B136

description: human skeletal muscle

value: vastus lateralis


title: B130

description: human skeletal muscle


title: B166

description: human skeletal muscle


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-1


title: B175

description: human skeletal muscle


title: IMR-90, Sen-siRb/p53, rep1


title: H3K27ac, INPUT, Pano

city: Bethesda

first: Varun

last: Sood

state: Maryland

address: 41 Medlars Drive

department: Laboratory of receptor biology and gene expression

institute: National Institues of Health, National Cancer Institute, Center for Cancer Research

description: Input

data_processing:
Single-end reads were aligned to the genome sequence of concatenated human (hg38) and spike-in Drosophila (dm6) genomes using Bowtie 2 (Langmead and Salzberg, 2012) with following specified options “–no-mixed” and “–no-discordant”
PCR duplicates and reads mapped more than once were removed with SAMTools
The mapped hg38 reads were down sampled by multiplying the ratio of minimum dm6 reads between all samples to the mapped dm6 reads for respective samples. The maximum value for the donwsampling factor thus equals 1 for sample with lowest dm6 reads and its hg38 count remains unchanged. Read counts for rest of the samples were downsampled based on the ratio described above
Read coverage and reproducibility across replicates was analyzed using multiBamSummary and plotCorrelation functions from deepTools suite
Genome coverage tracks were generated using the pileup function from MACS2
Assembly: Hg38 and dm6
Supplementary files format and content: bigWig

source_name: HBEC

growth_protocol: Human bronchial epithelial cells (HBECs) were grown in Keratinocyte-SFM medium (Gibco, 17005-042) supplemented with Penicillin/Strep (100units/mL Penicillin, 100micrograms/mL Streptomycin)

extract_protocol:
107cells were fixed on plate with 1% paraformaldehyde for 15min and neutralized with 125mM glycine.  Fixed cells were washed twice with ice-cold PBS and scraped off in ice-cold PBS containing Protease Inhibitor Cocktail (Sigma–Aldrich #P2714). Cells were pelleted and then resuspended in ChIP Lysis Buffer (0.5% (w/v) sodium dodecyl sulfate (SDS), 8 mM EDTA, 40 mM Tris-HCl (pH 8), protease inhibitor cocktail). Cells were kept on ice for one hour before sonication at 4°C (Bioruptor, Diagenode) to an average DNA length of 200–500 bp by 15 pulses of 10 secs on and 10 secs off at high intensity. Cell debris was removed by centrifugation at top speed for 20 min and chromatin concentration recorded using OD260. Samples were diluted to a final concentration of 200mg/ml in ChIP dilution buffer (0.01% (w/v) SDS, 1.2 mM EDTA, 16.7 mM Tris-HCl (pH 8), 1.1% (v/v) Triton X-100, 167 mM NaCl, protease inhibitor cocktail) and 600mg chromatin was used for each immunoprecipitation. 4 mg of anti-H3K27Ac coupled to 50 ml Pierce™ Protein A/G Magnetic Beads was added to each sample and rotated overnight at 4°C. For spike-in normalization 4 mg of drosophila chromatin (Active motif # 53083) and 2 ml spike-in antibody (Active motif # 61686) were added per sample. The beads were harvested by magnets and washed once for 10 min in the cold room by rotation with 1 ml of ChIP Low Salt Wash Buffer (0.01% (w/v) SDS, 2 mM EDTA, 20 mM Tris-HCl (pH 8), 1% (v/v) Triton X-100, 150 mM NaCl), 1 ml of ChIP High Salt Wash Buffer (0.01% (w/v) SDS, 2 mM EDTA, 20 mM Tris-HCl (pH 8), 1% (v/v) Triton X-100, 500 mM NaCl), and 1 ml of ChIP LiCl Wash Buffer (250 mM LiCl, 1% (w/v) IGEPAL, 1% (w/v) sodium deoxycholate, 10 mM Tris-HCl (pH 8), 1 mM EDTA). Finally, the beads were washed twice for 2 min in the cold room by rotation with 1 ml of TE buffer (1 mM EDTA, 10 mM Tris-HCl (pH 8)). Antibody-bound chromatin fragments were digested and crosslinks reversed with Reversal Buffer (0.0075% (w/v) SDS, 200 mM NaCl, 10 mM EDTA, 50 mM Tris-HCl (pH 7.5), 25 µg proteinase K (Thermo Fisher Scientific) by incubating at 50°C for two hours with shaking and subsequently seven hours at 65°C. ChIP DNA samples were purified with phenol-chloroform extraction and ethanol precipitation with glycogen (Thermo Fisher Scientific) as carrier.
ChIP-seq libraries were generated using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB # E7645S) following the manufacturer’s protocol.

treatment_protocol: Cell were treated with 1uM Panobinostat for 4 hours and DMSO alone was used as control

value: HBEC

value: Human Brinchial epithelial cell

value: Wild-type

value: DMSO


title: BrainCell_Enhancer-GFAP_promoter_MouseID-630479_Cell-3


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-45


title: H3K27ac, INPUT, DMSO

description: Input

value: Panobinostat


title: H3K27ac, ChIP, DMSO_1

description: ChIP with ab4729


title: H3K27ac, ChIP, Pano_3

description: ChIP with ab4729


title: H3K27ac, ChIP, Pano_2

description: ChIP with ab4729


title: XL_St9_B1MOs_RNA_rep1


title: B163

city: Stirling

description: human skeletal muscle

value: PRE

value: young adult


title: H3K27ac, ChIP, DMSO_2

description: ChIP with ab4729


title: B127

description: human skeletal muscle

value: middle aged adult


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-42

city: Seattle

value: VISp


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-41


title: IgG_rep3

city: Heidelberg

first: Thileepan

last: Sekaran

address: Mayerhoffstarsse

institute: EMBL

description: Isotype matched Immunoprecipitation sample

library_source: other

data_processing:
The UMI barcode ligaged during library preparation, was appended to the read name using UMI tools extract and trimmed for adapter using cutadapt.
Trimmed reads were mapped to human genome using STAR and the PCR duplicated reads were discarded using UMI tools dedup.
The deduplicated reads were processed using htseq-clip suite to quantify the total cross-link sites per sliding-windows per gene.
DEWseq was used to compute the differentially enriched sliding-windows in IP samples over SMI samples
Assembly: hg38
Supplementary files format and content: tab delimited text file that includes the cross-link counts per sliding-windows per gene
Library strategy: eCLIP-Seq

molecule: other

growth_protocol: Huh7 cells were maintained in a 37°C incubator with 5% CO2, with Dulbecco's modified Eagle's medium (DMEM) growth media (reconstituted from Sigma D5523) supplemented with supplemented with 1 g/L D-glucose (Sigma), 10% heat inactivated FBS (Thermo Fischer Scientific 10270106), 2 mM L-glutamine Thermo Fischer Scientific 25030081), and 100 U/ml Penicillin-streptomycin (Thermo Fischer Scientific 15140122).

extract_protocol:
Cells were UV-crosslinked and lysed in RIPA buffer. The lysates were sonicated for 10 cycles (30sec on/off) (Diagenode Bioruptor). 500 μg precleared cell protein lysate was treated with 1 U RNase I (Ambion AM2294) for 5 min at 37°C. After addition of 4 μl of RNAsin Plus ribonuclease inhibitor (Promega N2611), the samples were spun down, transferred to a new tube and used for immunoprecipitation (IP) with the antibody coupled beads. The IP eluates were purified after SDS-PAGE electrophoresis and transfer to nitrocellulose membrane, followed by protease digestion and library preparation steps.
Libraries were constructed according to Van Nostrand et. al, 2016. The final libraries were prepared following 14 PCR cycles for MDH2 IP and IgG IP and 9 PCR cycles for SMI. The libraries were gel purified, replicates were pooled and analyzed using Agilent Bioanalyzer High-Sensitivity DNA kit and library concentrations were estimated with Qubit.

value: hepatocyte derived cellular carcinoma

value: IgG control IP


title: H3K27ac, ChIP, Pano_1

description: ChIP with ab4729


title: B43

description: human skeletal muscle


title: B106

description: human skeletal muscle

value: POST


title: IgG_rep1


title: IgG_rep2


title: IP_rep3

description: Immunoprecipitation sample

value: MDH2 Ab IP


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-40


title: IP_rep2

description: Immunoprecipitation sample


title: SMI_rep3

description: Size Matched Input sample

value: input control


title: SMI_rep2

description: Size Matched Input sample


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-37


title: B19

description: human skeletal muscle


title: B103

description: human skeletal muscle


title: SMI_rep1

description: Size Matched Input sample


title: B31

description: human skeletal muscle


title: B85

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-38


title: hiPSC2_d24_replica2_plate2

city: Nijmegen

first: Jo Huiqing

last: Zhou

address: Geert Grooteplein 26/28

country: Netherlands

institute: Radboud University

description:
hiPSC2_d24_replica2_plate2
scRNA_barcodes_384.tab

data_processing:
For the matrix files, preprocessing of reads was done automatically with workflow tool seq2science v0.9.2 using the scrna-seq workflow, Single-end reads were trimmed with fastp v0.20.1 with default options. Genome assembly GRCh38.p13 was downloaded with genomepy 0.12.0. The genome and gene annotations was extended with custom regions. Reads were aligned and transformed to bus format with kb-python v0.26.4, a python wrapper for kallisto and bustools.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include gene count values for each plate, for each sample a .mtx matrix file with the reads, a .genes.txt file with the genes corresponding the the matrix file, and a .barcodes.txt file containing the barcodes linked to the matrix file

growth_protocol: Corneal differentiation of hPSCs was performed with a previously established protocol  (Hongisto et al., 2017, 2018). Briefly, hPSCs cultured in Essential 8™ Flex medium (ThermoFisher) on recombinant laminin 521 (L521; Biolamina) were induced towards the surface ectoderm in a 4-day suspension culture, which involved the formation of embryoid bodies with 5 µM Blebbistatin overnight, followed by one day supplementation with bFGF (50 ng/ml) and SB-505124 (10 μM) and two-day supplementation with BMP4 (25 ng/ml).  Adherent differentiation from D4 onwards was carried out in CnT-30 medium (CELLnTEC) on Collagen IV (Col IV; Sigma, 5.0 µg/cm2) and L521 (0.5 µg/cm2) combination matrix

extract_protocol:
A single-cell suspension was made using trypsin. After which cells were filtered using a 40uM filter to remove cell clumps. Cells were stained with 7-AAD.
Live cells were selected for and FACs-sorted onto 384-well plates containing primers with unique molecular identifiers, according to the SORT-Seq protocol.  Plates were spun down (1200 × g, 1 min, 4 °C) and ERCC spike‐in mix (1:50,000) was dispensed by a Nanodrop into each well. 150 nl of the Reverse Transcription (RT) mix was similarly dispensed into each well. Thermal cycling conditions were set at 4 °C 5 min; 25 °C 10 min; 42 °C 1 h; 70 °C 10 min. Each plate their library was pooled together and the cDNA was purified using AmpureXP beads. Overnight In vitro transcription was carried out at 16 °C, with the lid set at 70 °C. An exonuclease digestion step was performed thereafter for 20 min at 37 °C, followed by fragmentation of the RNA samples. After a beads cleanup, the samples were subjected to library RT and amplification to tag the RNA molecules with specific and unique sample indexes, followed by a final beads cleanup (1:0.8, reaction mix: beads), and the sample cDNA libraries were eluted with DNAse free water. Libraries were quantified using the KAPPA quantification kit following manufacturers protocol after which the plates were sequenced on the Illumina NextSeq 500 for 25 million reads per plate.

value: differentiating hiPSC


title: hiPSC2_d24_replica3_plate1

description:
hiPSC2_d24_replica3_plate1
scRNA_barcodes_384.tab


title: B7

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-36


title: A590

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-35


title: hiPSC2_d11_replica2_plate2

description:
hiPSC2_d11_replica2_plate2
scRNA_barcodes_384.tab


title: hiPSC2_d11_replica3_plate1

description:
hiPSC2_d11_replica3_plate1
scRNA_barcodes_384.tab


title: hiPSC2_d0_replica3_plate1

description:
hiPSC2_d0_replica3_plate1
scRNA_barcodes_384.tab

value: hiPSC


title: hiPSC2_d0_replica2_plate2

description:
hiPSC2_d0_replica2_plate2
scRNA_barcodes_384.tab


title: hiPSC1_d24_replica2_plate2

description:
hiPSC1_d24_replica2_plate2
scRNA_barcodes_384.tab


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-34


title: hiPSC1_d24_replica1_plate1

description:
hiPSC1_d24_replica1_plate1
scRNA_barcodes_384.tab


title: A584

description: human skeletal muscle

value: vastus lateralis


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-33


title: A587

description: human skeletal muscle


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-32


title: hiPSC1_d11_replica1_plate1

description:
hiPSC1_d11_replica1_plate1
scRNA_barcodes_384.tab


title: A566

description: human skeletal muscle


title: hiPSC1_d0_replica2_plate2

description:
hiPSC1_d0_replica2_plate2
scRNA_barcodes_384.tab


title: A548

description: human skeletal muscle


title: hESC_d24_replica3_plate1

description:
hESC_d24_replica3_plate1
scRNA_barcodes_384.tab

value: differentiating hESCs


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-34


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-31


title: hESC_d11_replica3_plate1

description:
hESC_d11_replica3_plate1
scRNA_barcodes_384.tab


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-40


title: hiPSC1_FACS_rep2

data_processing:
Preprocessing of reads was done automatically with workflow tool seq2science v0.7.1
Paired-end reads were trimmed with fastp v0.20.1 with default options. Genome assembly GRCh38.p13 was downloaded with genomepy 0.11.1. The effective genome size was estimated per sample by khmer v2.0 by calculating the number of unique kmers with k being the average read length per sample. Reads of RNAseq samples were aligned with STAR v2.7.6a with default options. Afterwards, duplicate reads were marked with Picard MarkDuplicates v2.23.8. General alignment statistics were collected by samtools stats v1.14. Mapped reads were removed if they did not have a minimum mapping quality of 30, were a (secondary) multimapper or aligned inside the ENCODE blacklist. RNAseq sample counting and summarizing to gene-level was performed on filtered bam using HTSeq-count v0.12. Sample sequencing strandedness was inferred using RSeQC v4.0.0 order to improve quantification accuracy.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include gene count values for each Sample

extract_protocol:
Total RNA was isolated using the  Qiagen RNeasy® Plus Kit, according to the manufacturer’s protocol. RNA concentrations were measured using the the DeNovix DS-11FX spectrometer.
500 ng of RNA was was prepared for sequencing using the KAPA RNA HyperPrep Kit with. Libraries were sequenced on the Illumina NextSeq 500, generating an average of 15–20 million reads per sample.

treatment_protocol: Induced LSCs were selected via FACS for AREG+, ITGA6+ PODXL-, and cultured an additional 15 days in CNT30 medium.

value: induced LSCs

value: WT


title: hESC_d0_replica3_plate1

description:
hESC_d0_replica3_plate1
scRNA_barcodes_384.tab

value: hESCs


title: IP_rep1

description: Immunoprecipitation sample


title: hiPSC1_FACS_rep1


title: hESC_FACS_rep2


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-39


title: hiPSC1_d0_replica1_plate1

description:
hiPSC1_d0_replica1_plate1
scRNA_barcodes_384.tab


title: hESC_FACS_rep1


title: IMR-90, Sen-siACLY#2, rep3

value: senescent fibroblast

value: siACLY#2+ 4-OHT for 6 days


title: A530

description: human skeletal muscle

value: PRE

value: young adult


title: A524

description: human skeletal muscle


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-38

value: VISp


title: A503

description: human skeletal muscle


title: A500

description: human skeletal muscle


title: IMR-90, Sen-siACLY#2, rep2


title: A494

description: human skeletal muscle


title: A485

description: human skeletal muscle


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-37


title: IMR-90, Sen-siACLY#2, rep1


title: IMR-90, Sen-siACLY#1, rep3

value: siACLY#1+ 4-OHT for 6 days


title: A455

description: human skeletal muscle


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-36


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-35


title: IMR-90, Sen-siACLY#1, rep1


title: IMR-90, Sen-Ctrl, rep3

value: siCtrl + 4-OHT for 6 days


title: IMR-90, Sen-Ctrl, rep2


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-34


title: IMR-90, Pro-Ctrl, rep3

value: proliferative fibroblast

value: siCtrl


title: IMR-90, Sen-siACLY#1, rep2


title: IMR-90, Sen-Ctrl, rep1


title: IMR-90, Pro-Ctrl, rep2


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-33


title: IMR-90, Pro-Ctrl, rep1


title: IMR-90, Sen, rep3

value: siCtrl, 100 nM 4-OHT for 8 days


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-32


title: IMR-90, Sen, rep1


title: IMR-90, Sen, rep2


title: IMR-90, Qui, rep3

value: quiescent fibroblast

value: siCtrl, 0.1% FBS for 2 days


title: XL_St9_B1MOs_RNA_rep3

value: animal pole explant

value: Stage 9

value: blastula animal pole

value: wild type

value: soxb1 morpholinos


title: IMR-90, Qui, rep2


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-30


title: IMR-90, Qui, rep1


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-29


title: A437

description: human skeletal muscle

value: vastus lateralis

value: POST

value: middle aged adult


title: A395

description: human skeletal muscle

value: PRE

value: young adult


title: A377

description: human skeletal muscle


title: IMR-90, Pro, rep3


title: IMR-90, Pro, rep2


title: A347

description: human skeletal muscle


title: A536

description: human skeletal muscle


title: IMR-90, Sen-siACLY, H3K27Ac ChIP

data_processing:
Basecalls and conversion to FASTQ files were performed using BaseSpace Onsite (Illumina)
The sequenced reads were mapped to the human reference genome (hg19) using Bowtie2 version 2.3.4.1.
Uniquely mapped reads were extracted using samtools version 1.9. PCR duplicates and repeat regions (defined by hg19.RepeatMasker.20130422) were filtered outusing samtools version 1.9. and bedtools version 2.17.0.
BigWig files normalized by counts per million (CPM) are generated using bamCoverage 3.1.1.
BedGraph (.bdg) files normalized by the appropriate input sample for the ChIP sample are created using the "peakcall" function of macs2 version 2.1.1.
Assembly: hg19
Supplementary files format and content: BigWig files for input samples.
Supplementary files format and content: BedGraph (.bdg) files normalized by the appropriate input sample for the ChIP sample.

growth_protocol: IMR-90 ER:Ras cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 200 mM L-glutamine, 1 mM sodium pyruvate, 10% (v/v) heat-inactivated fetal bovine serum (FBS), and penicillin/streptomycin.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Following cell lysis, cells were treated with 10 U of Micrococcal nuclease per 1 × 10^6 nuclei at 37℃ for 20 min and then sonicated by Picoruptor (Diagenode) for 2 min. Chromatin fragments were incubated at 4℃ overnight with the appropriate antibodies, followed by a pull-down assay using M-280 sheep anti-rabbit IgG (Thermo Fisher Scientific). After decrosslinking, the DNA was purified using a QIAquick PCR Purification Kit (Qiagen).
The ChIP-seq library was prepared using a NEBNext Ultra DNA Library Prep Kit and sequenced using the Illumina NextSeq 500/550 system (Illumina), according to the manufacturer’s protocol.

treatment_protocol: To induce oncogene-induced senescence, IMR-90 ER:Ras cells were treated with 100 nM 4-Hydroxytamoxifen (4-OHT) for 6 days.Transfection of siRNA was performed using RNAiMAX (Invitrogen).

value: senescent fibroblast

tag: chip antibody

value: anti-H3K27Ac (abcam, ab4729)

value: siACLY, 100 nM 4OHT for 6 days


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-28

value: VISp


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-39


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-27


title: IMR-90, Pro, rep1

value: proliferative fibroblast

value: siCtrl


title: A326

description: human skeletal muscle