title: 5 pooled soldier brains, samples collected from Colony O43

description: single-cell RNA-Sequencing

data_processing:
Aligned to honey bee genome build HAv3.1 and deformed wing virus reference genome with Cell Ranger 3.0 with default settings (expected cells = 3,000). Output for downstream analysis is located in Processed Data Files ("filtered_genes_bc_matricies" folder from Cell Ranger 3.0 output).
Genome_build: HAv3.1
Supplementary_files_format_and_content: processed files are what's included in "filtered_gene_bc_matricies" directory from Cell Ranger 3.0

source_name: 5 pooled brains

growth_protocol: Adult worker honey bees were collected from apiaries at the University of Illinois at Urbana-Champaign Bee Research Facility in Urbana, IL.

extract_protocol:
We followed the "short dissociation protocol" from Davie et al. 2018. Briefly, individual bee brains were dissected in ice-cold Dulbecco's phosphate-buffered saline (DPBS, ThermoFisher, cat. #14190144) and cut into small pieces. Pools of five brains were placed in an Eppendorf tube containing 0.05% trypsin-EDTA (Invitrogen, cat. # 25300054) in DPBS. Brains were dissociated on a shaker (25°C, 1000 rpm) for 15 minutes with gentle pipette mixing every 5 min. Debris was removed and cells were spun down at a 400 rcf in a 4°C centrifuge. We removed the supernatant and replaced it with 1 ml of ice-cold DPBS. We repeated this “washing” process twice but, after the third centrifugation, replaced the supernatant with 400 ul of DPBS containing 0.04% UltraPure BSA (ThermoFisher, cat. #AM2616). Cells were then passed through a 40 um Flowmi Tip Strainer (Bel0Art, cat# H136800040). Cell counting was performed on a Nexcelom Cellometer.
scRNA-Seq libraries were constructed with the Chromium Single Cell 3’ Library and Gel Bead Kit v3 and were sequenced on a 2 x 150nt lane in a NovaSeq6000 (Illumina, San Diego, CA).

treatment_protocol: "Soldiers" were collected by repeatedly striking a colony with a brick for 2 min and selecting bees that stung one of nine 5 cm x 5 cm suede leather patches suspended roughly 21 cm from the colony entrance. Immediately after soldiers were collected, the colony entrance was reduced and exiting bees were sprinkled with Talcum powder for future identification. Within 15-30 min, we collected "foragers," or bees that returned with both a Talcum powder coating and a pollen load. This method allowed us to collect foragers that were in the colony during the mechanical disturbance but did not respond to it, thus allowing us to separate highly aggressive soldiers from returning foragers who experienced but did not respond to the disturbance. For both soldiers and foragers, field-caught bees were rapidly dissected with minutes of being caught.

value: 5 pooled brains

tag: behavioral state

tag: colony

tag: collection date


title: BRO7F-079_PD_WTS

status: Public on May 09 2023

type: SRA

city: Seoul

first: Yeon Hee

last: Park

address: 81 Ilwon-ro, Gangnam-gu

country: South Korea

institute: Samsung Medical Center

description: paired-end sequence reads

library_source: transcriptomic

data_processing:
After trimming poor quality bases from the FASTQ files, reads were aligned to the human reference genome (hg19) with STAR v2.5.2b.
Alignment quality was verified with SAMTOOLS (v 0.1.19).
Estimated gene expression was calculated in terms of Transcripts Per Million (TPM) using RSEM v1.3.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: breast tissue of breast cancer patients

extract_protocol:
Total RNA from fresh-frozen tumor tissues was extracted with an RNeasy Mini Kit (Qiagen) and from FFPE tissues using ReliaPrep™ FFPE Total RNA Miniprep System (Promega) according to the manufacturer’s instructions.
Seqeuncing libraries were prepared using the TruSeq RNA Access Library Prep Kit (Illumina, Inc.) using standard Illumina protocols.

tag: tissue

value: breast

tag: gender

value: female

tag: disease state

value: breast cancer

tag: time

value: PD


title: 5 pooled soldier brains, samples collected from Colony O22

city: Princeton

first: Ian

middle: Michael

last: Traniello

state: NJ

address: Princeton University

department: Lewis-Sigler Insitute for Genomic Biology

country: USA

institute: Princeton University

description: single-cell RNA-Sequencing

organism: Apis mellifera

value: forager


title: K49A-22 dot_2-cell

city: Ann Arbor

first: Qianyi

last: Ma

state: MI

address: 1141 E Catherine St

department: Human Genetics

institute: University of Michigan

description:
Smart-seq2
Sample_5056-LM-32

library_source: transcriptomic single cell

data_processing:
The reads were trimmed using Cutadapt v2.3 (Martin, 2011).
The reads were evaluated with FastQC (Andrews, 2010) (v0.11.8) to determine quality of the data.
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011).
Alignment options followed ENCODE standards for RNA-seq (Dobin).
Assembly: mm10
Supplementary files format and content: Tab-delimited gene expression matrix

organism: Mus musculus

source_name: embryo

extract_protocol:
Two-cell embryos were collected between 26 and 28 hours post fertilization. Each embryo was immediately placed into a single well of a plexWell Rapid Single Cell plate (SmartSeq Platform), which was then frozen until sample prep.
Libraries were generated from 2 cell embryos using Smart Seq2 platform.
Single-embryo RNA sequencing using NovaSeq 6000 Illumina platform

tag: cell type

value: embryo

tag: strain

tag: age

value: 26 - 28 hours post fertilization


title: 5 pooled soldier brains, samples collected from Colony O38

description: single-cell RNA-Sequencing


title: WT-5_2-cell

description:
Smart-seq2
Sample_5056-LM-33


title: BRO7F-079_Baseline_WTS

description: paired-end sequence reads

value: Baseline


title: K49A-16_2-cell

description:
Smart-seq2
Sample_5056-LM-31


title: K49A-11_2-cell

description:
Smart-seq2
Sample_5056-LM-38


title: mtRF1-AAQ mito-monosomes

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

country: Switzerland

institute: UNIL

data_processing:
Reads where trimmed from adapter sequence using cutadapt (version: 3.5; options: --match-read-wildcards --overlap 8 --discard-untrimmed --minimum-length 30) and quality filtered using fastx_toolkit (version: 0.0.14; options: -Q33 -q 24 -p 90)
UMIs were extracted from each read with UMItools (options: extract --extract-method string --bc-pattern NNNNNNNNCCCCC --3prime --filter-cell-barcode –error-correct-cell).
Reads where size-selected for single ribosome using two sizes: 26 to 35 (usual monosome fragments) and 35 to 50 for longer read monosome samples. To estimate rRNA and tRNA contamination, reads were mapped to human and human cytosolic rRNA and tRNA databases using bowtie2 (options: -p 2 -L 15 -k 20 --trim5 2). Reads that failed to map to these, where then mapped to the mitochondrial genome (Ensembl database v. 107).
Assembly: Ensembl genome v107
Supplementary files format and content: BigWig (.bw): mitochondrial genome coverage files separated in plus and minus strand mapping reads
Library strategy: Ribo-seq

source_name: HEK293 EBNA

growth_protocol: HEK293 EBNA cells were grown as suspension culture in serum-free EX-CELL 293 medium (Sigma-Aldrich) at 37° C and 4.5% CO2. For transfection, 1.2 x 109 cells were pelleted at 500 x g for 5 min and resuspended in 60 ml RPMI 1640 medium (Gibco) supplemented with 0.6 ml 10% Pluronic F-68. Next, 1.8 mg plasmid DNA and 3.6 mg PEI Max 40kDa (Polysciences) were added to the cells. After 1h incubation in the shaker the cells were diluted to 1.2 l with EX-CELL 293 medium. The cells were incubated for two days before being harvested by centrifugation at 1,000 x g for 10 min at 4° C. Control cells were not transfected.

extract_protocol:
For ribosome profiling of isolated mitochondria, freshly harvested cells were rinsed with ice-cold 1X PBS pH 7.4. All steps were performed at 4° C or on ice roughly following previously published methods (Aibara et al. 2018; Clayton and Shadel 2014). Cells were resuspended in a hypotonic buffer (10 mM HEPES KOH pH 7.5, 10 mM NaCl, and 1.5 mM MgCl2) left to swell for 10 min and lysed using glass dounce homogenizer. Cell lysate was mixed with 1 volume of 2x MS homogenization buffer (20 mM HEPES KOH pH 7.5, 420 mM mannitol, 140 mM sucrose, 2 mM EDTA), cleared by centrifugation at 1,300 x g for 5 min, with supernatant cleared again at 3,000 x g for 5 min. Mitochondria were pelleted by centrifugation at 9,500 x g for 20 min, resuspended in resuspension buffer (20 mM HEPES KOH pH 7.5, 250 mM sucrose, 1 mM EDTA). Sucrose step gradients were prepared in SW32.1 tubes by layering different concentration of sucrose in gradient buffer (20 mM HEPES KOH pH 7.5, 1 mM EDTA): 1.5 ml 60% (w/v) sucrose on the bottom, 4.5 ml 32% (w/v) sucrose in the middle and 3 ml 23% (w/v) on top. The mitochondria suspension was loaded onto the sucrose step gradients and centrifuged using a SW32.1 rotor (Beckman-Coulter) at 22,000 x g for 70 min. Mitochondria were harvested from the interface between the 32- and 60% sucrose layer and flash-frozen in liquid N2. Mitochondria were lysed in 5 volumes of polysome buffer (150 mM NaCl, 20 mM Tris-HCl pH7.4, 5 mM MgCl2, 5 mM DTT, 100 µg/ ml cycloheximide, complete EDTA-free protease inhibitors (Roche) and 40 U/ml RNasin plus (Promega)) supplemented with 1% Triton X-100 and 0.5% Sodium deoxycholate. Lysates were incubated on ice for 10 min and cleared by centrifugation at 10000g, 4° C for 10 min.
Ribosome footpritnting and library construction was performed as described earlier (Arpat et al. 2020, McGlisny and Ingolia 2017) with few modifications. Libraries were generated from 24-36 nt (monosome footprints) and 36-69 nt (extended range that includes disome footprints) without ribosomal RNA depletion.

tag: cell line

value: HEK293 EBNA

tag: genotype

value: Overexpressed mtRF1-AAQ

tag: treatment


title: K49A-5_2-cell

description:
Smart-seq2
Sample_5056-LM-37


title: BRO7F-074_Baseline_WTS

description: paired-end sequence reads


title: Liver PCLS GFIPO 48h H26

city: Biberach a.d. Riss

first: Eric

last: Simon

address: Birkendorfer Str. 65

country: Germany

institute: Boehringer Ingelheim Pharma GmbH & Co KG

description:
1047_0107
Liver PCLS GFIPO 48h

data_processing:
reads passing quality control filter were mapped against or GRCm38 (mouse data) reference genomes using STAR (v2.5.2b)
Gene expression levels were quantified based on genome annotation files from Ensembl version 86 using RSEM (v1.3.0) and featureCounts (v1.5.1). For additional quality control we used FastQC (v0.11.5), picardmetrics (v0.2.4) and dupRadar (v1.0.0).
Supplementary files format and content: 1047_uReads.txt containts tab delimited normalized read counts per gene (row) for all samples (column).
Supplementary files format and content: 1047_uTPM.txt containts tab delimited normalized TPM per gene (row) for all samples (column).

source_name: Liver

extract_protocol:
Three PCLS slides per donor per assay condition have been pooled to ensure to get enough material for RNA Sequencing. After homogenization and lysis using in Qiazol buffer (Qiagen, Venlo, the   Netherlands), samples were mixed with 1/5th volume of chloroform (Sigma) and separated using phase extraction tubes. The RNA was then isolated with the RNeasy Lipid Tissue Mini Kit (Qiagen, Venlo, the  Netherlands) or the FavorPrep TM Tissue Total RNA Mini Kit (Favorgen, Vienna, Austria).  RNA samples were quantitatively and qualitatively assessed using the fluorescence-based Broad Range Quant-iT RNA Assay Kit (ThermoFisher) and the Standard Sensitivity RNA Analysis DNF-471 Kit on a 96-channel Fragment Analyzer (Agilent), respectively.
Total RNA was normalized on the MicroLab STAR automated liquid platform (Hamilton). 100ng input was used for library construction with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina #E7760, together with the QIAseq FastSelect RNA removal Kit (Qiagen) upstream and the NEBNext Multiplex Oligos for Illumina #E7600 downstream (all New England Biolabs). Fragmentation time was set to 15min. A total of 12 PCR cycles was used for the index PCR while the final libraries were eluted in 25 µL. Of note, the only deviation from the manufacturer’s protocol was the use of Ampure XP beads (Beckman Coulter) at the double-stranded cDNA purification step, instead of the recommended SPRIselect Beads. Total RNA sequencing libraries were quantified by the fluorescence dye-based methodology High Sensitivity dsDNA Quanti-iT Assay Kit (ThermoFisher) on a Synergy HTX (BioTek). Library molarity averaged at 100.3 nM. Total RNA libraries were also assessed for size distribution and adapter dimer presence by the High Sensitivity NGS Fragment DNF-474 Kit on a 96-channel Fragment Analyzer (Agilent). Sequencing libraries were normalized on the MicroLab STAR (Hamilton), pooled and spiked in with PhiX Control v3 (Illumina).
The library pool was subsequently clustered on an S2 Flow Cell and sequenced on a NovaSeq 6000 Sequencing System (Illumina) with dual index, paired-end reads at 2x100 bp length (Read parameters: Rd1: 101, Rd2: 8, Rd3: 8, Rd4: 101) reaching a target depth of approximately 60 million Pass-Filter reads per sample (6.5% CV, see).

treatment_protocol: Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: Unknown

tag: donor id

value: Liver

tag: sampling

value: Snap-frozen

value: GFIPOh

tag: timepoint


title: K49A-10_2-cell

description:
Smart-seq2
Sample_5056-LM-30


title: Liver PCLS GFIO 48h H26

description:
1047_0106
Liver PCLS GFIO 48h

value: GFIOh


title: BRO7F-072_Baseline_WTS

description: paired-end sequence reads


title: 5 pooled forager brains, samples collected from Colony O43

description: single-cell RNA-Sequencing

value: soldier


title: BRO7F-070_Baseline_WTS

description: paired-end sequence reads


title: K49A-4_2-cell

description:
Smart-seq2
Sample_5056-LM-29


title: 5 pooled forager brains, samples collected from Colony O38

description: single-cell RNA-Sequencing

value: 5 pooled brains


title: WT-11_2-cell

description:
Smart-seq2
Sample_5056-LM-34


title: Liver PCLS GFI 48h H26

description:
1047_0104
Liver PCLS GFI 48h

value: GFIh


title: WT-22_2-cell

description:
Smart-seq2
Sample_5056-LM-28


title: 5 pooled forager brains, samples collected from Colony O22

description: single-cell RNA-Sequencing


title: BRO7F-068_Baseline_WTS

description: paired-end sequence reads

value: breast

value: female


title: Liver PCLS GF 48h H26

description:
1047_0103
Liver PCLS GF 48h

value: GFh


title: WT-16_2-cell

description:
Smart-seq2
Sample_5056-LM-27


title: Liver PCLS F 48h H26

description:
1047_0102
Liver PCLS F 48h

value: Fh


title: A375, CD58-mid, rep 2

city: New York

first: Patricia

last: Ho

state: NY

address: 650 West 168th Street

country: Canada

institute: Columbia University

description:
CD58_mi_2A_A, CD58_mi_2A_B, CD58_mi_2A_C, CD58_mi_2A_D, CD58_mi_2B_A, CD58_mi_2B_B, CD58_mi_2B_C, CD58_mi_2B_D
all_samples.count.txt
all_samples.count_normalized.txt

library_source: genomic

data_processing:
Raw data was de-multiplexed and converted to fastq files in BaseSpace
MAGeCK (v0.5.9.2): Mageck count command with default parameters was used for count matrix generation.
Supplementary files format and content: Tab-separated values containing table of raw and normalized read counts of sgRNAs
Library strategy: CRISPR screen custom DNA library

molecule: genomic DNA

source_name: Cell Line

growth_protocol: A375 cells were cultured in Dulbecco's Modified Eagle Medium with 10% heat-inactivated fetal bovine serum.

extract_protocol:
Genomic DNA was collected from sorted and unsorted cells using a Qiagen DNeasy Blood and Tissue Kit.
sgRNA sequences were amplified from gDNA by PCR using Ex Taq DNA polymerase (TaKaRa). For each reaction, a maximum of 10 µg gDNA in a final volume of 100 µL was used with primers containing barcodes and Illumina sequencing reactions, 28 cycles of PCR amplification.

treatment_protocol: A375 Cas9-expressing cells were transduced with Brunello sgRNA library virus at an MOI <0.3. At two days post-transduction, cells were put into selection with  0.75 µg/mL puromycin, and cells were continuously expanded up until sorting, keeping in puromycin,  2 µg/mL blasticidin, and 1% penicillin/streptomycin throughout to maintain Cas9 and sgRNA expression. 10 days after transduction, cells were formaldehyde fixed, stained, and sorted by FACS based on CD58 expression.

value: Cell Line

value: Melanoma

tag: day (post-tranduction)

tag: condition

value: CD58-mid sort


title: BRO7F-066_Baseline_WTS

description: paired-end sequence reads

value: breast cancer

value: Baseline


title: 5 pooled soldier brains, samples collected from Colony O2

description: single-cell RNA-Sequencing

tag: behavioral state

value: forager

tag: colony


title: WT-10_2-cell

description:
Smart-seq2
Sample_5056-LM-26

tag: tissue

value: embryo

value: 26 - 28 hours post fertilization


title: WT-4_2-cell

description:
Smart-seq2
Sample_5056-LM-25


title: Liver PCLS G 48h H26

description:
1047_0101
Liver PCLS G 48h

tag: gender

value: Unknown

value: Liver

value: Snap-frozen

value: Gh


title: A375, CD58-mid, rep 1

description:
CD58_mi_1A_A, CD58_mi_1A_B, CD58_mi_1A_C, CD58_mi_1A_D, CD58_mi_1B_A, CD58_mi_1B_B, CD58_mi_1B_C, CD58_mi_1B_D
all_samples.count.txt
all_samples.count_normalized.txt


title: Liver PCLS CTR 48h H26

description:
1047_0100
Liver PCLS CTR 48h

value: CTRh


title: 5 pooled forager brains, samples collected from Colony O2

description: single-cell RNA-Sequencing

value: 5 pooled brains

value: soldier

tag: collection date


title: BRO7F-071_Baseline_WTS

description: paired-end sequence reads

value: breast

value: female

tag: disease state

tag: time


title: BRO7F-066_PD_WTS

description: paired-end sequence reads

value: PD


title: Liver PCLS GFIP 48h H26

description:
1047_0105
Liver PCLS GFIP 48h

value: GFIPh


title: K49A-21_2-cell

description:
Smart-seq2
Sample_5056-LM-24

tag: cell type

tag: strain


title: BRO7F-063_Baseline_WTS

description: paired-end sequence reads


title: A375, CD58-low, rep 2

description:
CD58_lo_2A_A, CD58_lo_2A_B, CD58_lo_2A_C, CD58_lo_2A_D, CD58_lo_2B_A, CD58_lo_2B_B, CD58_lo_2B_C, CD58_lo_2B_D
all_samples.count.txt
all_samples.count_normalized.txt

value: Cell Line

tag: cell line

value: Melanoma

value: CD58-low sort


title: BRO7F-062_Baseline_WTS

description: paired-end sequence reads

value: breast cancer

value: Baseline


title: K49A-15_2-cell

description:
Smart-seq2
Sample_5056-LM-23

value: embryo

tag: age

value: 26 - 28 hours post fertilization


title: Liver PCLS GFIPO 24h H26

description:
1047_0099
Liver PCLS GFIPO 24h

value: Unknown

value: Liver

tag: treatment

value: GFIPOh


title: BRO7F-061_PD_WTS

description: paired-end sequence reads


title: K49A-9_2-cell

description:
Smart-seq2
Sample_5056-LM-22


title: A375, CD58-low, rep 1

description:
CD58_lo_1A_A, CD58_lo_1A_B, CD58_lo_1A_C, CD58_lo_1A_D, CD58_lo_1B_A, CD58_lo_1B_B, CD58_lo_1B_C, CD58_lo_1B_D
all_samples.count.txt
all_samples.count_normalized.txt


title: BRO7F-061_Baseline_WTS

description: paired-end sequence reads


title: A375, Day 10, rep 2

description:
D10_2_A, D10_2_B, D10_2_C, D10_2_D
all_samples.count.txt
all_samples.count_normalized.txt

value: pre-sort


title: K49A-3_2-cell

description:
Smart-seq2
Sample_5056-LM-21


title: Liver PCLS GFIP 24h H26

description:
1047_0097
Liver PCLS GFIP 24h

tag: donor id

value: Snap-frozen


title: A375, Day 10, rep 1

description:
D10_1_A, D10_1_B, D10_1_C, D10_1_D
all_samples.count.txt
all_samples.count_normalized.txt


title: Liver PCLS GFI 24h H26

description:
1047_0096
Liver PCLS GFI 24h

tag: sampling

value: GFIh


title: BRO7F-057_Baseline_WTS

description: paired-end sequence reads

value: breast


title: WT-21_2-cell

description:
Smart-seq2
Sample_5056-LM-20


title: BRO7F-056_Baseline_WTS

description: paired-end sequence reads

value: female


title: A375, Day 6, rep 2

description:
D6_2_A, D6_2_B, D6_2_C, D6_2_D
all_samples.count.txt
all_samples.count_normalized.txt


title: WT-15_2-cell

description:
Smart-seq2
Sample_5056-LM-19


title: A375, Day 6, rep 1

description:
D6_1_A, D6_1_B, D6_1_C, D6_1_D
all_samples.count.txt
all_samples.count_normalized.txt


title: BRO7F-051_Baseline_WTS

description: paired-end sequence reads


title: WT-9_2-cell

description:
Smart-seq2
Sample_5056-LM-18


title: sgRNA virus

description:
D0_2_A, D0_2_B, D0_2_C, D0_2_D
all_samples.count.txt
all_samples.count_normalized.txt

source_name: virus

extract_protocol:
Viral DNA was extracted using the QIAmp Micro DNA kit (Qiagen).
sgRNA sequences were amplified from gDNA by PCR using Ex Taq DNA polymerase (TaKaRa). For each reaction, a maximum of 10 µg gDNA in a final volume of 100 µL was used with primers containing barcodes and Illumina sequencing reactions, 28 cycles of PCR amplification.

value: virus


title: BRO7F-048_Baseline_WTS

description: paired-end sequence reads


title: WT-3_2-cell

description:
Smart-seq2
Sample_5056-LM-17


title: C_SD_POOL1_scATAC_lane2

city: Stanford

first: Benjamin

last: Ober-Reynolds

state: CA

address: 279 Campus Drive West

department: Genetics

institute: Stanford University

description:
10x Genomics
C_SD_POOL_fragments.tsv.gz
C_SD_POOL_fragments.tsv.gz.tbi

library_source: genomic single cell

data_processing:
Raw sequencing data was converted into fastq format using the command ‘cellranger-atac mkfastq’ (10x Genomics, v1.2.0). Resulting fastq files were aligned to the hg38 reference genome (cellranger-atac-GRCh38-1.2.0) and quantified using the command ‘cellranger-atac count’.
For scATAC-seq libraries sequenced on multiple lanes (C_PB1 and C_SD_POOL): after running 'cellranger-atac count', samples that were split onto multiple lanes were combined using the command 'cellranger-atac aggr' to generate an aggregated fragments file which was used for downstream analyses.
Assembly: hg38
Supplementary files format and content: Fragments files and tabix index of fragments files

source_name: scalp

extract_protocol:
Scalp punch biopsies were rinsed with ice cold 1x PBS and then lightly diced into 1-2mm pieces with a sterile razor blade. The diced sample was then dissociated using the Miltenyi Biotec Human While Skin Dissociation Kit (Product no. 130-101-540) according to the manufacturer’s directions. Briefly, samples were incubated in 0.5 mL dissociation solution containing the indicated volumes of Enzymes P, A, and D for 3 h at 37℃. Following incubation, 0.5 mL of ice cold RPMI 1640 w/ 10% FBS was added to each sample and then samples were mechanically dissociated using the gentleMACs dissociator with the ‘h_skin_01’ program. Following dissociation, samples were briefly centrifuged and then filtered through a 70µm cell strainer. The dissociation tube was washed with additional ice cold media and then samples were centrifuged for 10 minutes at 300 x g in a swinging bucket centrifuge. After aspirating the supernatant, samples were either resuspended in 0.1mL BamBanker freezing medium (Wako Chemicals, 302-14681) and cryopreserved at -80℃, or proceeded immediately to staining for FACS. Cells were stained with anti-CD90 PE Cy7 (BD Pharmingen, order no. 561558) for 30 min at 4℃ in FACS staining buffer (PBS with 0.5% BSA), then washed with FACS buffer. Live cells were distinguished using LIVE/DEAD Fixable Aqua Dead Cell Stain Kit (ThermoFisher, order no. L34957) according to the manufacturer’s directions. For cryopreserved samples, cells were thawed at 37℃ for 3 min, resuspended in RPMI + 10% FBS and washed with FACS buffer prior to staining. Aqua negative live cells were sorted as fibroblast (CD90+) and non-fibroblast (CD90-) populations. Sorted cells were counted and the CD90+ population was reduced by half before recombining with the CD90- population for further processing by single cell ATAC-seq and/or single cell RNA-seq.
Following sorting, cell suspensions were centrifuged at 300 x g for 5 minutes at 4℃ and resuspended in 1x PBS with 0.5% BSA. Samples were counted using a hemocytometer and the required volume of cells was aliquoted for generation of single-cell RNA sequencing libraries. Single-cell RNA-seq libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3′ RNA v3.1 protocol, targeting 8,000 cells per sample. After the required number of sorted cells were aliquoted for generation of scRNA-seq libraries, the remaining sample volume was used for generation of single-cell ATAC sequencing libraries. The remaining cell volume was used to prepare nuclei according to the 10x ATAC nuclei isolation protocol for ‘low cell input nuclei isolation’ (CG000169, Rev B). Single cell ATAC-seq libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell ATAC v1.1 protocol, targeting 6,000 cells per sample. Completed scRNA-seq libraries were sequenced on an Illumina NextSeq 550 platform with 28/8/0/91 base pair cycles. Completed scATAC-seq libraries were sequenced on an Illumina NextSeq 550 platform with 33/8/16/33 base pair cycles.

value: scalp

tag: preservation

value: frozen

tag: age (rounded)

value: multiple


title: BRO7F-046_Baseline_WTS

description: paired-end sequence reads


title: Liver PCLS GFIO 24h H26

description:
1047_0098
Liver PCLS GFIO 24h

value: GFIOh

tag: timepoint


title: K49A-20_2-cell

description:
Smart-seq2
Sample_5056-LM-16


title: C_SD_POOL1_scATAC_lane1


title: Liver PCLS G 24h H26

description:
1047_0093
Liver PCLS G 24h

value: Gh


title: Liver PCLS F 24h H26

description:
1047_0094
Liver PCLS F 24h

value: Fh


title: Liver PCLS GF 24h H26

description:
1047_0095
Liver PCLS GF 24h

value: GFh


title: Liver PCLS CTR 24h H26

description:
1047_0092
Liver PCLS CTR 24h

value: CTRh


title: BRO7F-044_Baseline_WTS

description: paired-end sequence reads

value: breast cancer

value: Baseline


title: C_SD3_scATAC

description: 10x Genomics

value: fresh

tag: Sex

value: M


title: K49A-14_2-cell

description:
Smart-seq2
Sample_5056-LM-15

value: embryo

value: 26 - 28 hours post fertilization


title: BRO7F-043_Baseline_WTS

description: paired-end sequence reads

value: breast


title: K49A-8_2-cell

description:
Smart-seq2
Sample_5056-LM-14


title: C_SD2_scATAC

description: 10x Genomics

value: F


title: BRO7F-042_Baseline_WTS

description: paired-end sequence reads

value: female


title: K49A-2_2-cell

description:
Smart-seq2
Sample_5056-LM-13


title: C_SD1_scATAC

description: 10x Genomics

value: scalp


title: BRO7F-040_Baseline_WTS

description: paired-end sequence reads


title: WT-20_2-cell

description:
Smart-seq2
Sample_5056-LM-12


title: Liver PCLS GFI 48h H27

description:
1047_0088
Liver PCLS GFI 48h

value: Unknown

value: Liver

value: Snap-frozen

value: GFIh


title: C_PB3_scATAC

description: 10x Genomics


title: Liver PCLS GFIP 48h H27

description:
1047_0089
Liver PCLS GFIP 48h

value: GFIPh


title: BRO7F-039_Baseline_WTS

description: paired-end sequence reads


title: Liver PCLS GFIO 48h H27

description:
1047_0090
Liver PCLS GFIO 48h

value: GFIOh


title: BRO7F-037_Baseline_WTS

description: paired-end sequence reads


title: C_PB2_scATAC

description: 10x Genomics


title: Liver PCLS GF 48h H27

description:
1047_0087
Liver PCLS GF 48h

value: GFh


title: WT-14_2-cell

description:
Smart-seq2
Sample_5056-LM-11


title: Liver PCLS F 48h H27

description:
1047_0086
Liver PCLS F 48h

value: Fh


title: C_PB1_scATAC_lane2

description:
10x Genomics
C_PB1_fragments.tsv.gz
C_PB1_fragments.tsv.gz.tbi


title: WT-8_2-cell

description:
Smart-seq2
Sample_5056-LM-10


title: Liver PCLS GFIPO 48h H27

description:
1047_0091
Liver PCLS GFIPO 48h

value: GFIPOh


title: BRO7F-032_Baseline_WTS

description: paired-end sequence reads

value: breast cancer

value: Baseline


title: Liver PCLS G 48h H27

description:
1047_0085
Liver PCLS G 48h

value: Gh


title: Liver PCLS GFIPO 24h H27

description:
1047_0083
Liver PCLS GFIPO 24h


title: BRO7F-034_Baseline_WTS

description: paired-end sequence reads


title: K49A-13_2-cell

description:
Smart-seq2
Sample_5056-LM-7

value: embryo

value: 26 - 28 hours post fertilization


title: K49A-19_2-cell

description:
Smart-seq2
Sample_5056-LM-8


title: WT-2_2-cell

description:
Smart-seq2
Sample_5056-LM-9


title: AA4_scATAC

description: 10x Genomics

value: AA

value: fresh

value: F


title: C_PB1_scATAC_lane1

value: scalp

value: M


title: BRO7F-023_Baseline_WTS

description: paired-end sequence reads

value: breast

value: female


title: Liver PCLS CTR 48h H27

description:
1047_0084
Liver PCLS CTR 48h

value: Unknown

value: Liver

value: Snap-frozen

value: CTRh


title: AA7_scATAC

description: 10x Genomics

value: frozen


title: BRO7F-022_Baseline_WTS

description: paired-end sequence reads

value: breast cancer


title: Liver PCLS GFIO 24h H27

description:
1047_0082
Liver PCLS GFIO 24h

value: GFIOh


title: K49A-7_2-cell

description:
Smart-seq2
Sample_5056-LM-6


title: AA2_scATAC

description: 10x Genomics


title: Liver PCLS GFIP 24h H27

description:
1047_0081
Liver PCLS GFIP 24h

value: GFIPh


title: Liver PCLS GFI 24h H27

description:
1047_0080
Liver PCLS GFI 24h

value: GFIh


title: K49A-1_2-cell

description:
Smart-seq2
Sample_5056-LM-5

value: embryo

value: 26 - 28 hours post fertilization


title: BRO7F-021_Baseline_WTS

description: paired-end sequence reads

value: Baseline


title: WT-19_2-cell

description:
Smart-seq2
Sample_5056-LM-4


title: AA1_scATAC

description: 10x Genomics

value: AA

value: fresh

value: F


title: Liver PCLS GF 24h H27

description:
1047_0079
Liver PCLS GF 24h

value: GFh


title: BRO7F-020_PD_WTS

description: paired-end sequence reads

value: breast

value: female

value: PD


title: C_SD3_scRNA

description: 10x Genomics

data_processing:
Raw sequencing data was converted into fastq format using the command ‘cellranger mkfastq’ (10x Genomics, v3.1.0). Resulting fastq files were then aligned to the hg38 reference genome (cellranger-GRCh38-3.0.0) and quantified using the command ‘cellranger count’.
The expression matricies produced from Cell Ranger are included as processed data.
Assembly: hg38
Supplementary files format and content: Expression matricies divided into matrix, barcode, and feature files.

molecule: polyA RNA

value: scalp

value: M


title: BRO7F-021_PD_WTS

description: paired-end sequence reads


title: WT-13_2-cell

description:
Smart-seq2
Sample_5056-LM-3


title: Liver PCLS F 24h H27

description:
1047_0078
Liver PCLS F 24h

value: Unknown

value: Liver

value: Snap-frozen

value: Fh


title: WT-7_2-cell

description:
Smart-seq2
Sample_5056-LM-2


title: BRO7F-020_Baseline_WTS

description: paired-end sequence reads

value: breast cancer


title: Liver PCLS G 24h H27

description:
1047_0077
Liver PCLS G 24h

value: Gh


title: WT-1_2-cell

description:
Smart-seq2
Sample_5056-LM-1

value: embryo

value: 26 - 28 hours post fertilization


title: Liver PCLS CTR 24h H27

description:
1047_0076
Liver PCLS CTR 24h

value: CTRh


title: C_SD1_scRNA

description: 10x Genomics

value: fresh


title: C_SD2_scRNA

description: 10x Genomics

value: F


title: C_PB2_scRNA

description: 10x Genomics


title: C_PB3_scRNA

description: 10x Genomics


title: WT-MNASE-4

description: wild type

data_processing:
CTA and fastQC
BWA-MEM for alignment
Picard MarkDuplicates and Samtools for filtering
MACS2 callpeak
Assembly: mm10
Supplementary files format and content: Bigwig trakc files and tab-delimited broadPeak files

source_name: epididymis and vas deferens

extract_protocol:
Sperm pellets were then centrifuged at 2500xg for 5 minutes and chromatin was then decondensed using 50 mM DTT for 1 hour at room temperature. DTT was then quenched for 30 minutes at room temperature with 100 mM N-ethylmaleimide. Sperm cells were then lysed in buffer containing 0.25% NP-40 and 0.25% DOC for 30 minutes at room temperature prior to addition of 5 U MNase. Samples were digested at 37oC for 5 minutes, centrifuged at 20,000xg for 20 minutes and soluble chromatin was collected. Insoluble chromatin was digested a second time with 15 U of MNase at 37oC for 5 minutes. Samples were then run on a 2% agarose gel and bands corresponding to Mononucleosomes were cut out and purified using a Zymo gel extraction kit for sequencing.
Libraries constructed with the NEBNext Ultra II DNA Library Prep Kit are constructed with UMI adaptors. The unique molecular identifier consists of an 11 base sequence that is located 3’ to the i7 index.  This sequence enables more accurate removal of duplicate reads and error correction through consensus sequence building.  Sequence data containing a UMI read will be recorded as Read 2 in the FASTQ files, with the forward and reverse data being reported as Read 1 and Read 3, respectively. For all paired-end analysis, R1 was used as Forward read and R3 was used as Reverse read.
Mnase-seq using NovaSeq S4 Illumina Sequencing platform

treatment_protocol: 30 million sperm per genotype were treated with 5 µl of 20 mg/ml DNaseI for 15 minutes at 37°C. Sperm pellets were then washed several times in PBS and subsequently treated with 0.5% Triton and 0.05% L-alpha-phosphatidylcholine for 15 minutes on ice.

value: epididymis and vas deferens

value: sperm

tag: genotype

value: wild type

value: MNASE digestion


title: BY4742 eIF4E-AID strain, 8 hour DMSO, rnaseq, biol rep 2

city: Berkeley

first: Paige

middle: D

last: Diamond

address: Barker Hall

department: MCB

institute: University of California - Berkeley

data_processing:
Ribosome profiling reads were first trimmed using Cutadapt to remove adapter sequences.
Reads from ribosome profiling were processed as detailed in (McGlincy and Ingolia 2017). Ribosome profiling and RNA-seq reads were aligned using STAR (Dobin et al. 2013) to the S288C reference genome R64.1.
Assembly: R64-sacCer3
Supplementary files format and content: Tab-delimited text file containing raw, unnormalized read counts for each sample.

organism: Saccharomyces cerevisiae

growth_protocol: Cells were treated with 500 µM indole-3-acetic acid (IAA) (Sigma-Aldrich #12886) or DMSO for either 1 or 8 hours and grown at 30C  to mid-log phase (typically 150 mL cultures at OD600 0.6 – 1.0) in YPD.

extract_protocol:
30ug of RNA for ribosome profiling was harvested by TRIzol extraction; 1ug of RNA for RNA-seq was harvested by phenol-chloroform extraction.
Ribosome profiling was conducted as detailed in (McGlincy and Ingolia 2017) for 1-hour eIF4E depletion samples and corresponding DMSO controls. Adjustments were made to (McGlincy and Ingolia 2017) for the 8-hour eIF4E depletion samples and their corresponding DMSO control samples as follows. Reverse transcription was performed with primer PD1131. rRNA depletion was achieved via subtractive hybridization was performed using complementary oligos PD1043-1046 as described in (Ingolia et al. 2012 p. 20). Circularization was performed with CircLigase I (Epicentre #CL4111K) instead of CircLigase II, following the manufacturer’s protocol recommendations.   Total RNA for RNA-sequencing was isolated from cell lysates using acid phenol extraction (Ares 2012). For 1-hour eIF4E depletion samples and corresponding DMSO controls, poly(A) enrichment was performed using DynabeadsTM oligo(dT)25 (Thermo Scientific #61002) according to the manufacturer instructions. For 8-hour eIF4E depletion samples and corresponding DMSO controls, rRNA depletion was performed using QIAseq FastSelect -rRNA yeast kit (Qiagen #334215) according to the manufacturer instructions. All libraries were generated with NEBNext Ultra II Directional RNA library prep kit (NEB #E7760).

tag: time point

tag: agent

value: DMSO


title: MT-MNASE-2

tag: tissue


title: C_PB1_scRNA

description: 10x Genomics

value: scalp

tag: disease state

value: M


title: Liver PCLS GFIPO 48h H29

description:
1047_0075
Liver PCLS GFIPO 48h

tag: gender

value: Unknown

value: Liver

value: GFIPOh


title: BY4742 eIF4E-AID strain, 8 hour IAA, rnaseq, biol rep 2

value: 500microM IAA


title: Liver PCLS GFIO 48h H29

description:
1047_0074
Liver PCLS GFIO 48h

value: Snap-frozen

value: GFIOh


title: WT-MNASE-3

description: wild type

tag: cell type


title: Liver PCLS GFIP 48h H29

description:
1047_0073
Liver PCLS GFIP 48h

value: GFIPh


title: BY4742 eIF4E-AID strain, 8 hour IAA, ribo profiling, biol rep 2


title: AA8_scRNA

description: 10x Genomics

value: AA

value: frozen


title: WT-MNASE-2

description: wild type


title: BY4742 eIF4E-AID strain, 8 hour IAA, ribo profiling, biol rep 1


title: MT-MNASE-1


title: AA7_scRNA

description: 10x Genomics

value: F


title: Liver PCLS GF 48h H29

description:
1047_0071
Liver PCLS GF 48h

value: GFh


title: BY4742 eIF4E-AID strain, 8 hour IAA, rnaseq, biol rep 1


title: Liver PCLS GFI 48h H29

description:
1047_0072
Liver PCLS GFI 48h

value: GFIh


title: BY4742 eIF4E-AID strain, 8 hour DMSO, ribo profiling, biol rep 2


title: AA4_scRNA

description: 10x Genomics

value: fresh


title: WT-MNASE-1

description: wild type

value: epididymis and vas deferens

value: sperm

value: wild type

value: MNASE digestion


title: OC shST3GAL3 tumors-3

city: Shanghai

first: Haiou

last: Liu

address: No.128, Shengyang road, Yangpu distinct, Shanghai, P. R. China.

country: China

institute: Fudan University

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp ).
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
The expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited txt files include TPM values for each sample.

source_name: tumor tissue

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: tumor tissue

value: murine ovarian cancer cell

value: ST3GAL3 knockdown


title: BY4742 eIF4E-AID strain, 8 hour DMSO, ribo profiling, biol rep 1

value: DMSO


title: Liver PCLS F 48h H29

description:
1047_0070
Liver PCLS F 48h

value: Unknown

value: Liver

value: Snap-frozen

value: Fh


title: AA2_scRNA

description: 10x Genomics

value: scalp

value: AA

value: M


title: OC shST3GAL3 tumors-2


title: Liver PCLS CTR 48h H29

description:
1047_0068
Liver PCLS CTR 48h

value: CTRh


title: OC shST3GAL3 tumors-1


title: WT, untreated, MPP8, irCLIP, replicate 2

first: Tomek

last: Swigut

address: 265 Campus Dr

department: Chemical and Systems Biology

description: MPP8 irCLIP-seq

data_processing:
RT stops were called utilizing the improved FAST-iCLIP pipeline as previously described (Zarnegar et al., 2016).
Duplicates were removed with fastx-collapser, 5’ barcodes and 3’ adaptors were trimmed
STAR was used to align to the mm10 genome build
Assembly: mm10

source_name: R1 WT

growth_protocol: R1 mESCs were grown in monolayer in 2i + LIF medium

extract_protocol:
Whole-cell lysates were generated in CLIP lysis buffer (50 mM HEPES, 200 mM NaCl, 1 mM EDTA, 10% glycerol, 0.1% NP-40, 0.2% Triton X-100 and 0.5% N-lauroylsarcosine) and briefly sonicated using a probe-tip Branson sonicator to solubilize the chromatin.
Library were constructed as previously described (Zarnegar et al., 2016).
irCLIP-seq

treatment_protocol: Protein-RNA interactions were fixed with UV crosslinking to a total of 0.35 J cm−2.

value: R1 WT

value: ESC

value: untreated


title: WT, untreated, MPP8, irCLIP, replicate 1

description: MPP8 irCLIP-seq


title: BY4742 eIF4E-AID strain, 8 hour DMSO, rnaseq, biol rep 1


title: Liver PCLS G 48h H29

description:
1047_0069
Liver PCLS G 48h

value: Gh


title: Liver PCLS GFIPO 24h H29

description:
1047_0067
Liver PCLS GFIPO 24h

value: GFIPOh


title: PCL5-P2A-ZEM CiBER, pοst-gRNA induction, gcn4Δ, pΖ barcodes, biol rep 1

description:
pcl5_gcn4_post_pZ_a
pcl5_screen_gcn4_barcode_counts.txt

data_processing:
Sequencing data was first subjected to processing using Cutadapt (Martin 2011) to trim adapter sequences and deconvolve multiplexed libraries based on embedded nucleotide indices.
Trimmed barcodes were then counted as described in (Muller et al. 2020).
Assembly: Custom dual barcoded gRNA plasmid library
Supplementary files format and content: Tab-delimited text file containing raw, unnormalized read counts for each sample.
Library strategy: Amplicon sequencing

source_name: dual barcode plasmid library

growth_protocol: Yeast populations transformed with plasmid libraries were inoculated in a custom turbidostat (McGeachy et al. 2019) and maintained in SCD -URA media with 10 nM beta-estradiol at a density corresponding to OD600 of 0.6. After a period of six doublings (9 hours), a sample of 50 mL was taken prior to the induction of gRNAs.

extract_protocol:
RNA was extracted by phenol-chloroform extraction.
Barcode library preparations were performed as previously described (Muller et al. 2020, 2022). The cDNA products were amplified with PD780 and RM810 for P(Z)-mScarlet libraries, and RM810 and RM511 for P(TFC1)-citrine libraries.

treatment_protocol: The induction was carried out by adding anyhydrotetracycline (Abcam Biochemicals #ab145350) to both the growth chamber and the turbidostat media reservoir, in order to achieve a final concentration of 250 ng/ml. Following another six doublings, which took another 9 hours, a post-induction sample of 50 mL was collected.

value: dual barcode plasmid library

value: pZ barcode

value: gcn4delta PCL5-P2A-ZEM

value: post-anyhydrotetracycline


title: PCL5-P2A-ZEM CiBER, post-gRNA induction, gcn4Δ, pΖ barcodes, biol rep 2

description:
pcl5_gcn4_post_pZ_b
pcl5_screen_gcn4_barcode_counts.txt


title: PCL5-P2A-ZEM CiBER, pοst-gRNA induction, gcn4Δ, pTFC1 barcodes, biol rep 2

description:
pcl5_gcn4_post_pTFC1_b
pcl5_screen_gcn4_barcode_counts.txt

value: pTFC1 barcode


title: PCL5-P2A-ZEM CiBER, pοst-gRNA induction, gcn4Δ, pTFC1 barcodes, biol rep 1

description:
pcl5_gcn4_post_pTFC1_a
pcl5_screen_gcn4_barcode_counts.txt


title: OC shControl tumors-2

value: tumor tissue

value: murine ovarian cancer cell

value: wild type


title: PCL5-P2A-ZEM CiBER, pre-gRNA induction, gcn4Δ, pΖ barcodes, biol rep 2

description:
pcl5_gcn4_pre_pZ_b
pcl5_screen_gcn4_barcode_counts.txt

value: pre-anyhydrotetracycline


title: OC shControl tumors-1


title: Liver PCLS GFI 24h H29

description:
1047_0064
Liver PCLS GFI 24h

value: Unknown

value: Liver

value: Snap-frozen

value: GFIh


title: shST3GAL3 tumors-3

source_name: ST3GAL3 knockdown tumor tissues

value: ST3GAL3 knockdown


title: MPP8-AGH, auxin, 2 day, replicate 2

description: rna-seq following mpp8 depletion

data_processing:
Visualization tracks were generated with bedtools genomecov (−bg −scale) with scaling factor being 106 per number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).
Assembly: mm10

source_name: R1 MPP8-AGH

extract_protocol:
Total RNA was extracted with TRIzol. rRNA-depletion was performed with the Ribo Minus Eukaryote kit (V2). RNA was fragmented using the RNA fragmentation kit from Ambion.
Ovation RNA-seq FFPE kit

value: R1 MPP8-AGH

value: ESC

value: auxin, 500uM, 2d

tag: time

value: 2 day


title: MPP8-AGH, untreated, 7 day, replicate 1

description: rna-seq following mpp8 depletion

tag: cell line

value: untreated

value: 7 day


title: MPP8-AGH, auxin, 7 day, replicate 1

description: rna-seq following mpp8 depletion


title: MPP8-AGH, auxin, 2 day, replicate 1

description: rna-seq following mpp8 depletion


title: Liver PCLS GF 24h H29

description:
1047_0063
Liver PCLS GF 24h

value: GFh


title: PCL5-P2A-ZEM CiBER, pre-gRNA induction, gcn4Δ, pTFC1 barcodes, biol rep 2

description:
pcl5_gcn4_pre_pTFC1_b
pcl5_screen_gcn4_barcode_counts.txt

value: dual barcode plasmid library

value: pTFC1 barcode

value: gcn4delta PCL5-P2A-ZEM


title: shST3GAL3 tumors-1

value: tumor tissue

value: murine ovarian cancer cell


title: PCL5-P2A-ZEM CiBER, pre-gRNA induction, gcn4Δ, pTFC1 barcodes, biol rep 1

description:
pcl5_gcn4_pre_pTFC1_a
pcl5_screen_gcn4_barcode_counts.txt

value: pre-anyhydrotetracycline


title: PCL5-P2A-ZEM CiBER, post-gRNA induction, GCN4, pZ barcodes, biol rep 2

description:
pcl5_post_pZ_b
pcl5_screen_wt_barcode_counts.txt

value: pZ barcode

value: GCN4 PCL5-P2A-ZEM

value: post-anyhydrotetracycline


title: MPP8-AGH, untreated, 2 day, replicate 2

description: rna-seq following mpp8 depletion


title: OC shControl tumors-3

value: wild type


title: PCL5-P2A-ZEM CiBER, pre-gRNA induction, gcn4Δ, pΖ barcodes, biol rep 1

description:
pcl5_gcn4_pre_pZ_a
pcl5_screen_gcn4_barcode_counts.txt


title: shST3GAL3 tumors-2

value: ST3GAL3 knockdown


title: MPP8-AGH, auxin, 7 day, replicate 2

description: rna-seq following mpp8 depletion

value: R1 MPP8-AGH

value: ESC


title: Liver PCLS F 24h H29

description:
1047_0062
Liver PCLS F 24h

value: Unknown

value: Liver

value: Snap-frozen

value: Fh


title: MPP8-AGH, untreated, 2 day, replicate 1

description: rna-seq following mpp8 depletion

value: untreated

value: 2 day


title: Liver PCLS GFIO 24h H29

description:
1047_0066
Liver PCLS GFIO 24h

value: GFIOh


title: shControl tumors-3

source_name: Tumor tissues

value: tumor tissue


title: Liver PCLS CTR 24h H29

description:
1047_0060
Liver PCLS CTR 24h

value: CTRh


title: PCL5-P2A-ZEM CiBER, post-gRNA induction, GCN4, pZ barcodes, biol rep 1

description:
pcl5_post_pZ_a
pcl5_screen_wt_barcode_counts.txt

value: dual barcode plasmid library


title: Liver PCLS GFIP 24h H29

description:
1047_0065
Liver PCLS GFIP 24h

value: GFIPh


title: TASOR-AGH, auxin, TASOR (GFP) 3

description: tasor (gfp) ChIP-seq with or without auxin degration

data_processing:
ChIP-seq fastq files were aligned to the mm10 assembly with BWA MEM.
Peak calls were performed with macs3 callpeak function with --broad option, mouse genome effective size and corresponding background reads.
Visualization tracks were generated with bedtools genomecov (−bg −scale) with scaling factor being 106 per number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).
Assembly: mm10

source_name: R1 TASOR-AGH

extract_protocol:
Cells were fixed on plate in 1% formaldehyde (in PBS) at room temperature for 10 mins with agitation. Glycine at a final concentration of 0.125M was added to quench fixation. After cell lysis, chromatin was sheared using the Covaris for 5 minutes per sample.
NEBNext library prep

value: R1 TASOR-AGH

value: auxin, 500uM, 12h

tag: chip antibody

value: GFP (Thermo Fisher Scientific, A-11122)


title: MPP8-AGH, untreated, 7 day, replicate 2

description: rna-seq following mpp8 depletion

tag: treatment

value: 7 day


title: Liver PCLS GFIPO 48h TX25

description:
1047_0059
Liver PCLS GFIPO 48h

tag: donor id

value: GFIPOh


title: shControl tumors-1

value: murine ovarian cancer cell

value: wild type


title: PCL5-P2A-ZEM CiBER, post-gRNA induction, GCN4, pTFC1 barcodes, biol rep 2

description:
pcl5_post_pTFC1_b
pcl5_screen_wt_barcode_counts.txt

value: pTFC1 barcode

value: GCN4 PCL5-P2A-ZEM

value: post-anyhydrotetracycline


title: TASOR-AGH, auxin, TASOR (GFP) 2

value: ESC


title: Liver PCLS G 24h H29

description:
1047_0061
Liver PCLS G 24h

value: Unknown

value: Liver

tag: sampling

value: Snap-frozen

value: Gh


title: Liver PCLS GFIP 48h TX25

description:
1047_0058
Liver PCLS GFIP 48h


title: HM1-shST3GAL3-3

source_name: HM1 cells, ST3GAL3 knockdown

value: cell line

value: ST3GAL3 knockdown


title: PCL5-P2A-ZEM CiBER, post-gRNA induction, GCN4, pTFC1 barcodes, biol rep 1

description:
pcl5_post_pTFC1_a
pcl5_screen_wt_barcode_counts.txt

value: dual barcode plasmid library


title: HM1-shST3GAL3-2


title: Liver PCLS GF 48h TX25

description:
1047_0056
Liver PCLS GF 48h

value: GFh


title: PCL5-P2A-ZEM CiBER, pre-gRNA induction, GCN4, pZ barcodes, biol rep 1

description:
pcl5_pre_pZ_a
pcl5_screen_wt_barcode_counts.txt

value: pZ barcode

value: pre-anyhydrotetracycline


title: Liver PCLS GFI 48h TX25

description:
1047_0057
Liver PCLS GFI 48h

value: GFIh


title: TASOR-AGH, untreated, TASOR (GFP) 3

value: R1 TASOR-AGH

value: untreated

value: GFP (Thermo Fisher Scientific, A-11122)


title: PCL5-P2A-ZEM CiBER, pre-gRNA induction, GCN4, pZ barcodes, biol rep 2

description:
pcl5_pre_pZ_b
pcl5_screen_wt_barcode_counts.txt

value: GCN4 PCL5-P2A-ZEM


title: shControl tumors-2

value: tumor tissue

value: murine ovarian cancer cell

value: wild type


title: HM1-shControl-3

source_name: HM1 cells


title: TASOR-AGH, untreated, TASOR (GFP) 2

value: ESC


title: HM1-shST3GAL3-1


title: HM1-shControl-2


title: TASOR-AGH, untreated, TASOR (GFP) 1


title: Liver PCLS F 48h TX25

description:
1047_0055
Liver PCLS F 48h

value: Unknown

value: Liver

value: Snap-frozen

value: Fh


title: Liver PCLS GFIP 24h TX25

description:
1047_0051
Liver PCLS GFIP 24h

value: GFIPh


title: Liver PCLS CTR 48h TX25

description:
1047_0053
Liver PCLS CTR 48h

value: CTRh


title: PCL5-P2A-ZEM CiBER, pre-gRNA induction, GCN4, pTFC1 barcodes, biol rep 1

description:
pcl5_pre_pTFC1_a
pcl5_screen_wt_barcode_counts.txt

value: dual barcode plasmid library

value: pTFC1 barcode


title: HM1-shControl-1

value: cell line


title: ARO10-P2A-ZEM CiBER, post-gRNA induction, pZ barcodes, biol rep 1

value: pZ barcode

value: post-anyhydrotetracycline


title: CPSF3-AGH, 12h auxin, MPP8,  replicate 3

description: cpsf3 auxin inducible degron

source_name: R1 CPSF3-AGH

value: R1 CPSF3-AGH

value: auxin, 500uM, 12h

value: MPP8 (Proteintech, 16796-1)


title: CPSF3-AGH, 12h auxin, MPP8,  replicate 2

description: cpsf3 auxin inducible degron


title: ARO10-P2A-ZEM CiBER, post-gRNA induction, pZ barcodes, biol rep 2


title: Sox2-1kb MPP8 KO clone M16, untreated, PRO-seq

description: PRO-seq to assess nascent transcription upon WDR82 or MPP8 KO

data_processing:
none provided by the submitter
Assembly: mm10

source_name: Sox2-1kb, MPP8 KO clone M16

extract_protocol:
Nuclear run-on assays were performed essentially as described in Reimer et al. [K. A. Reimer, C. A. Mimoso, K. Adelman, K. M. Neugebauer, Molecular Cell (2021)] with modifications noted: 2X nuclear run-on buffer consisted of (10 mM Tris (pH 8), 10 mM MgCl2, 1 mM DTT, 300mM KCl, 20uM/ea biotin-11-NTPs (Perkin Elmer), 0.8U/uL SuperaseIN (Thermo), 1% sarkosyl).
Library construction was performed as described in Reimer et al. [K. A. Reimer, C. A. Mimoso, K. Adelman, K. M. Neugebauer, Molecular Cell (2021)]
PRO-seq

value: Sox2-1kb, MPP8 KO clone M16

value: untreated


title: CPSF3-AGH, 12h auxin, MPP8,  replicate 1

description: cpsf3 auxin inducible degron

value: ESC


title: Liver PCLS GF 24h TX25

description:
1047_0049
Liver PCLS GF 24h

value: Unknown

value: GFh


title: Liver PCLS GFI 24h TX25

description:
1047_0050
Liver PCLS GFI 24h

value: Liver

value: Snap-frozen

value: GFIh


title: ARO10-P2A-ZEM CiBER, post-gRNA induction, pTFC1 barcodes, biol rep 2


title: Sox2-1kb MPP8 KO clone M1, untreated, PRO-seq

source_name: Sox2-1kb, MPP8 KO clone M1

value: Sox2-1kb, MPP8 KO clone M1


title: CPSF3-AGH, untreated, MPP8,  replicate 3

description: cpsf3 auxin inducible degron


title: PCL5-P2A-ZEM CiBER, pre-gRNA induction, GCN4, pTFC1 barcodes, biol rep 2

description:
pcl5_pre_pTFC1_b
pcl5_screen_wt_barcode_counts.txt

value: dual barcode plasmid library

value: GCN4 PCL5-P2A-ZEM

value: pre-anyhydrotetracycline


title: TASOR-AGH, auxin, TASOR (GFP) 1

value: R1 TASOR-AGH

value: GFP (Thermo Fisher Scientific, A-11122)


title: Liver PCLS F 24h TX25

description:
1047_0048
Liver PCLS F 24h

source_name: Liver

value: Fh


title: Sox2-1kb, untreated, PRO-seq


title: CPSF3-AGH, untreated, MPP8,  replicate 1

description: cpsf3 auxin inducible degron

value: R1 CPSF3-AGH


title: CPSF3-AGH, untreated, MPP8,  replicate 2

description: cpsf3 auxin inducible degron

value: MPP8 (Proteintech, 16796-1)


title: WDR82 KO clone W8, untreated, PRO-seq

source_name: WDR82 KO clone W8

value: WDR82 KO clone W8


title: Liver PCLS G 24h TX25

description:
1047_0047
Liver PCLS G 24h

value: Gh


title: ARO10-P2A-ZEM CiBER, pre-gRNA induction, pZ barcodes, biol rep 2

value: pZ barcode


title: Liver PCLS GFIO 48h TX06

description:
1047_0045
Liver PCLS GFIO 48h

value: Unknown

value: GFIOh


title: CPSF3-AGH, 12h auxin, H3K9me3,  replicate 2

description: cpsf3 auxin inducible degron

value: ESC

value: auxin, 500uM, 12h

value: H3K9me3 (Abcam, ab8898)


title: WDR82 KO clone W5, untreated, PRO-seq

source_name: WDR82 KO clone W5

value: WDR82 KO clone W5

value: untreated


title: Liver PCLS CTR 24h TX25

description:
1047_0046
Liver PCLS CTR 24h

value: Liver

value: Snap-frozen

value: CTRh


title: WDR82 KO clone W4, untreated, PRO-seq

source_name: WDR82 KO clone W4

value: WDR82 KO clone W4


title: ARO10-P2A-ZEM CiBER, pre-gRNA induction, pTFC1 barcodes, biol rep 2

value: dual barcode plasmid library

value: pTFC1 barcode

value: pre-anyhydrotetracycline


title: CPSF3-AGH, untreated, H3K9me3,  replicate 2

description: cpsf3 auxin inducible degron

value: R1 CPSF3-AGH


title: WT, untreated, PRO-seq

source_name: WT

value: WT


title: Liver PCLS CTR 48h TX06

description:
1047_0039
Liver PCLS CTR 48h


title: CPSF3-AGH, untreated, H3K9me3,  replicate 1

description: cpsf3 auxin inducible degron


title: TASOR-AGH, untreated, WDR82

description: endogenous wdr82 or k4me3 ChIP-seq

value: R1 TASOR-AGH


title: CPSF3-AGH, 12h auxin, H3K9me3,  replicate 1

description: cpsf3 auxin inducible degron


title: Liver PCLS GFIP 24h TX06

description:
1047_0037
Liver PCLS GFIP 24h

value: Unknown

value: GFIPh


title: ARO10-P2A-ZEM CiBER, pre-gRNA induction, pTFC1 barcodes, biol rep 1


title: ARO10-P2A-ZEM CiBER, post-gRNA induction, pTFC1 barcodes, biol rep 1

value: post-anyhydrotetracycline


title: Liver PCLS GFI 24h TX06

description:
1047_0036
Liver PCLS GFI 24h

value: GFIh


title: Liver PCLS GFIP 48h TX06

description:
1047_0044
Liver PCLS GFIP 48h


title: no-tag_FLAG_control ChIP

first: Eliana

middle: Rose

last: Bondra

state: California

address: 440 Barker Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

data_processing:
FASTQ generation using Illumina Casava v2.2.
Raw reads were mapped to SacCer3 genome modified to include the mutant promoter site where applicable, and mat∆hmr∆ or hml∆mat∆, using Bowtie2 with following options: --local --soft-clipped-unmapped-tlen --no-unal --no-mixed --no-discordant
PCR duplicates were removed using, sequentially, SAMtools -fixmate -sort -markdup
bedgraph files were generated that included reads between 0-500bp (average fragment size from sonication) and normalized to the genome-wide median (median excluded subtelomeres, chromosome III, and rDNA)
Assembly: SacCer3 (modified)
Supplementary files format and content: bedgraph (normalized to genome-wide median)

source_name: Saccharomyces cerevisiae

extract_protocol:
Cells were lysed by mechanical disruption in a bead beater. Chromatin was fragmented by sonication. IPs were performed using 5mL mouse monoclonal anti-FLAG® M2 antibody (MilliporeSigma, product no F1804) and 50uL DynaBeads Protein G magnetic beads (ThermoFisher Scientific catalog number 10003D).   DNA was purified using Qiagen spin column kit
NEB Ultra II library prep kit

value: Saccharomyces cerevisiae

value: matdelta::klLEU2 ADE2, lys2, TRP1, hml@2delta::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal; hmrdelta::NatMX

value: anti-FLAG® M2 antibody (MilliporeSigma, product F1804) and DynaBeads Protein G magnetic beads (ThermoFisher Scientific catalog number 10003D)


title: sir4∆_wtpromoter_Sua7FLAG input rep1

value: ADE2, lys2, TRP1, hml@2delta::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal; sir4delta::k.l.URA3; hmrdelta::HygMX; matdelta::k.l.LEU2; SUA7-3xFLAG-Kanmx


title: ARO10-P2A-ZEM CiBER, pre-gRNA induction, pZ barcodes, biol rep 1

value: pZ barcode


title: CPSF3-AGH, untreated, input,  replicate 1

description: cpsf3 auxin inducible degron

value: ESC

value: untreated


title: sir4∆_mutpromoter_Sua7FLAG input rep1

value: ADE2, lys2, TRP1, hml@2delta*Rap1bs-mutation::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal ; sir4delta::k.l.URA3; hmrdelta::HygMX; matdelta::k.l.LEU2; SUA7-3xFLAGKanmX


title: WDR82 KO W4, untreated, WDR82

description: endogenous wdr82 or k4me3 ChIP-seq

source_name: R1 WDR82 KO clone W4

value: R1 WDR82 KO clone W4


title: CPSF3-AGH, 12h auxin, input,  replicate 1

description: cpsf3 auxin inducible degron

value: auxin, 500uM, 12h


title: WT, untreated, H3K4me3

description: endogenous wdr82 or k4me3 ChIP-seq

source_name: R1 WT

value: R1 WT

value: H3K4me3 (Abcam, ab8580)


title: HBEC2 siLATS-rep3

city: BOSTON

first: Boting

last: Ning

state: Massachusetts

address: 72 E Concord St

institute: BOSTON UNIVERSITY

description: Gene expression data from human bronchial epithelial treated with LATS targeting siRNA.

data_processing:
FASTQ files were demultiplexed and created by Illumina BaseSpace. The quality of the FASTQ files was examined with FastQC v0.11.3. The samples were aligned to the build version hg19 of the human genome using STAR 2-pass alignment (v2.5.3a). RSEM v1.3.0 was then used the quantify the gene and transcript counts using Ensembl v75 annotation, and RSeQC was used to calculate the quality metrics.
Assembly: hg19

source_name: Human Bronchial Epithelial Cells

growth_protocol: Human bronchial epithelial cells were cultured in PneumaCult-Ex Plus.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
Sequencing libraries were prepared from total RNA samples using Illumina TruSeq RNA Sample Preparation Kit v2. The libraries from individual samples were pooled sequencing. HBEC samples were sequenced on the Illumina HiSeq 2500 platform to generate single end 50bp reads.

treatment_protocol: HBECs were transfected with control,  pan-TEAD targeting, TP63 targeting and LATS1/2 targeting siRNAs and RNA was extracted for quality assessment and library prep for RNA-sequencing. 3 unique siRNA control sequences were used, and all siRNA transfected samples were collected in triplicate, 48hours after transfection.

tag: sirna

value: LATS siRNA


title: no-tag_FLAG_control input


title: Liver PCLS F 24h TX06

description:
1047_0034
Liver PCLS F 24h

value: Unknown

value: Liver

value: Snap-frozen

value: Fh


title: HBEC2 siLATS-rep2


title: Liver PCLS GF 24h TX06

description:
1047_0035
Liver PCLS GF 24h

value: GFh


title: WT, untreated, WDR82

description: endogenous wdr82 or k4me3 ChIP-seq


title: Liver PCLS GFIO 24h TX06

description:
1047_0038
Liver PCLS GFIO 24h

value: GFIOh


title: Liver PCLS G 24h TX06

description:
1047_0033
Liver PCLS G 24h

value: Gh


title: HBEC2 siLATS-rep1


title: WDR82 KO W4, untreated, input 2

description: endogenous wdr82 or k4me3 ChIP-seq


title: Liver PCLS CTR 24h TX06

description:
1047_0032
Liver PCLS CTR 24h

value: CTRh


title: SIR_mutpromoter_Sua7FLAG input rep2

value: Saccharomyces cerevisiae

value: ADE2, lys2, TRP1, hmlalpha2delta*Rap1bs-mutation::CRE, ura3-1; 3xV5_Rap1-N-terminal ; hmrdelta::HygMX; matdelta::k.l.LEU2; SUA7-3xFLAGKanMX


title: HBEC1 siLATS-rep3


title: TASOR-AGH WDR82 KO T5, untreated, TASOR (GFP)

description: wdr82 ko in wt or tasor tagged backgrounds

source_name: R1 TASOR-AGH WDR82 KO clone T5

value: R1 TASOR-AGH WDR82 KO clone T5

value: ESC

value: untreated

value: GFP (Thermo Fisher Scientific, A-11122)


title: SIR_mutpromoter_Sua7FLAG ChIP rep1

value: anti-FLAG® M2 antibody (MilliporeSigma, product F1804) and DynaBeads Protein G magnetic beads (ThermoFisher Scientific catalog number 10003D)


title: SIR_mutpromoter_Sua7FLAG input rep1


title: SIR_wtpromoter_Sua7FLAG input rep2

value: matdelta::klLEU2 ADE2, lys2, TRP1, hml@2delta::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal; hmrdelta::NatMX; SUA7-3xFLAGKanMX


title: SIR_mutpromoter_Sua7FLAG ChIP rep2


title: WT, untreated, input 2

description: endogenous wdr82 or k4me3 ChIP-seq

value: R1 WT


title: SIR_wtpromoter_Sua7FLAG input rep1


title: Liver PCLS GFIO 48h H1

description:
1047_0030
Liver PCLS GFIO 48h

value: Unknown


title: CPSF3-AGH, untreated, input,  replicate 2

description: cpsf3 auxin inducible degron

value: R1 CPSF3-AGH


title: Liver PCLS GFIP 48h H1

description:
1047_0029
Liver PCLS GFIP 48h

value: Liver

value: Snap-frozen

value: GFIPh


title: WDR82 KO W4, untreated, H3K4me3

description: endogenous wdr82 or k4me3 ChIP-seq

value: R1 WDR82 KO clone W4

value: H3K4me3 (Abcam, ab8580)


title: Liver PCLS GFIPO 48h H1

description:
1047_0031
Liver PCLS GFIPO 48h

value: GFIPOh


title: TASOR-AGH, untreated, TASOR (GFP)

value: R1 TASOR-AGH


title: TASOR-AGH WDR82 KO T1, untreated, TASOR (GFP)

source_name: R1 TASOR-AGH WDR82 KO clone T1

value: R1 TASOR-AGH WDR82 KO clone T1


title: SIR_wtpromoter_Sua7FLAG ChIP rep2

value: Saccharomyces cerevisiae


title: Liver PCLS GFI 48h H1

description:
1047_0028
Liver PCLS GFI 48h

value: GFIh


title: WDR82 KO W8, untreated, MPP8

source_name: R1 WDR82 KO clone W8

value: R1 WDR82 KO clone W8

value: ESC

value: untreated

value: MPP8 (Proteintech, 16796-1)


title: Liver PCLS GF 48h H1

description:
1047_0027
Liver PCLS GF 48h

value: GFh


title: HBEC2 siTEAD-rep3

description: Gene expression data from human bronchial epithelial treated with TEAD targeting siRNA.

value: TEAD siRNA


title: Liver PCLS F 48h H1

description:
1047_0026
Liver PCLS F 48h

value: Unknown

value: Fh


title: TASOR-AGH WDR82 KO T1, untreated, WDR82

description: endogenous wdr82 or k4me3 ChIP-seq


title: HBEC2 siTEAD-rep2


title: HBEC2 siTEAD-rep1


title: sir4∆_mutpromoter_Elf1FLAG ChIP rep2

value: ADE2, lys2, TRP1, hml@2delta*Rap1bs-mutation::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal ; sir4delta::k.l.URA3; hmrdelta::HygMX; matdelta::k.l.LEU2; ELF1-3xFLAGKanmX

value: anti-FLAG® M2 antibody (MilliporeSigma, product F1804) and DynaBeads Protein G magnetic beads (ThermoFisher Scientific catalog number 10003D)


title: WT, untreated, MPP8

value: R1 WT


title: WDR82 KO W4, untreated, MPP8

value: R1 WDR82 KO clone W4


title: SIR_wtpromoter_Sua7FLAG ChIP rep1

value: matdelta::klLEU2 ADE2, lys2, TRP1, hml@2delta::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal; hmrdelta::NatMX; SUA7-3xFLAGKanMX


title: HBEC1 siLATS-rep2

value: LATS siRNA


title: Liver PCLS G 48h H1

description:
1047_0025
Liver PCLS G 48h

value: Liver

value: Snap-frozen

value: Gh


title: sir4∆_mutpromoter_Elf1FLAG input rep1

value: Saccharomyces cerevisiae


title: Liver PCLS GFIPO 24h H1

description:
1047_0024
Liver PCLS GFIPO 24h

value: GFIPOh


title: WDR82 KO W8, untreated, H3K9me3

value: R1 WDR82 KO clone W8

value: ESC

value: untreated

value: H3K9me3 (Abcam, ab8898)


title: HBEC1 siTEAD-rep3

value: TEAD siRNA


title: HBEC1 siLATS-rep1


title: WDR82 KO W4, untreated, H3K9me3


title: HBEC1 siTEAD-rep2


title: sir4∆_wtpromoter_Elf1FLAG input rep2

value: ADE2, lys2, TRP1, hml@2delta::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal; sir4delta::k.l.URA3; hmrdelta::HygMX; matdelta::k.l.LEU2; ELF1-3xFLAG-Kanmx


title: Liver PCLS GFIP 24h H1

description:
1047_0022
Liver PCLS GFIP 24h

value: Unknown

value: GFIPh


title: WT, untreated, H3K9me3

value: R1 WT


title: HBEC1 siTEAD-rep1


title: Liver PCLS GFI 24h H1

description:
1047_0021
Liver PCLS GFI 24h

value: GFIh


title: sir4∆_wtpromoter_Elf1FLAG ChIP rep2

value: anti-FLAG® M2 antibody (MilliporeSigma, product F1804) and DynaBeads Protein G magnetic beads (ThermoFisher Scientific catalog number 10003D)


title: TASOR-AGH WDR82 KO T5, untreated, input

value: R1 TASOR-AGH WDR82 KO clone T5


title: sir4∆_mutpromoter_Elf1FLAG input rep2

value: ADE2, lys2, TRP1, hml@2delta*Rap1bs-mutation::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal ; sir4delta::k.l.URA3; hmrdelta::HygMX; matdelta::k.l.LEU2; ELF1-3xFLAGKanmX


title: HBEC2 siTP63-rep3

description: Gene expression data from human bronchial epithelial treated with TP63 targeting siRNA.

value: TP63 siRNA


title: Liver PCLS GF 24h H1

description:
1047_0020
Liver PCLS GF 24h

value: Liver

value: Snap-frozen

value: GFh


title: HBEC2 siTP63-rep2


title: TASOR-AGH WDR82 KO T1, untreated, input

value: R1 TASOR-AGH WDR82 KO clone T1


title: sir4∆_wtpromoter_Elf1FLAG input rep1

value: Saccharomyces cerevisiae


title: Liver PCLS F 24h H1

description:
1047_0019
Liver PCLS F 24h

value: Fh


title: HBEC2 siTP63-rep1


title: Liver PCLS G 24h H1

description:
1047_0018
Liver PCLS G 24h

value: Gh


title: TASOR-AGH, untreated, input

source_name: R1 TASOR-AGH

value: R1 TASOR-AGH

value: ESC

value: untreated


title: WDR82 KO W8, untreated, input

value: R1 WDR82 KO clone W8


title: HBEC1 siTP63-rep3


title: Liver PCLS CTR 24h H1

description:
1047_0017
Liver PCLS CTR 24h

value: Unknown

value: CTRh


title: SIR_mutpromoter_Elf1FLAG input rep2

value: ADE2, lys2, TRP1, hmlalpha2delta*Rap1bs-mutation::CRE, ura3-1; 3xV5_Rap1-N-terminal ; hmrdelta::HygMX; matdelta::k.l.LEU2; ELF1-3xFLAGKanMX


title: sir4∆_mutpromoter_Elf1FLAG ChIP rep1

value: anti-FLAG® M2 antibody (MilliporeSigma, product F1804) and DynaBeads Protein G magnetic beads (ThermoFisher Scientific catalog number 10003D)


title: HBEC1 siTP63-rep2


title: WDR82 KO W4, untreated, input 1

value: R1 WDR82 KO clone W4


title: Liver PCLS GFIPO 48h TX08

description:
1047_0016
Liver PCLS GFIPO 48h

value: Male

value: GFIPOh


title: WT, untreated, input 1

value: R1 WT


title: SIR_mutpromoter_Elf1FLAG ChIP rep1


title: SIR_mutpromoter_Elf1FLAG input rep1


title: HBEC1 siTP63-rep1

value: TP63 siRNA


title: SIR_wtpromoter_Elf1FLAG input rep2

value: matdelta::klLEU2 ADE2, lys2, TRP1, hml@2delta::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal; hmrdelta::NatMX; ELF1-3xFLAGKanMX


title: Liver PCLS GFIO 48h TX08

description:
1047_0015
Liver PCLS GFIO 48h

value: Liver

value: Snap-frozen

value: GFIOh


title: day 128_bone marrow plasma cells

city: Melbourne

first: Zhoujie

last: Ding

state: VIC

address: 89 Commercial Road

country: Australia

institute: Monash University

description: single cell RNA seq

data_processing:
Raw sequences were processed on the SevenBridges platform (SevenBridges, Boston, MA, USA) to identify sample tags and reads per cell (aligned to the GRCm38 build of the mouse reference genome). De-multiplexing and downstream analysis was performed by Seqgeq (BD)
Assembly: GRCm38 build
Supplementary files format and content: Combined_ZD_MR_cartridge2_RSEC_MolsPerCell.csv is a matrix table (CSV) with normalised counts of molecules per cell for every gene and every cell of samples
Supplementary files format and content: ZD_MR_cartridge2_Sample_Tag_Calls.csv is a matrix table (CSV) with information for sample tags needed to de-multiplex samples in the Combined_ZD_MR_cartridge2_RSEC_MolsPerCell.csv file by Seqgeq software

source_name: plasma cells from bone marrow

extract_protocol:
human CD4+ and humna CD4- plasma cells were sorted from bone marrow and spleen of BLTcre.mcl1fl/+ mice. Purified populations were labelled with sample tags according to the manufacturer’s instructions (WTA kit, BD Biosciences).
Single-cell capture, cDNA synthesis and library preparation were performed using the BD Rhapsody Single-Cell Analysis System (BD Biosciences) for whole transcriptome analysis, according to the manufacturer’s instructions.

value: bone marrow

tag: strain


title: Zfp661 KO mESCs (replicate 2), ChIP Input

city: Bethesda

first: Jinpu

last: Jin

address: Building 6B, Room 2B-211, 6 Center Drive

institute: NICHD

description: ChIP-seq

data_processing:
Raw fastq reads were cleaned using Trimmomatic (v0.38) to remove sequencing adaptors and low-quality bases from both ends with the parameters “LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25”. The resulting clean reads were mapped onto the mouse genome (mm10) using BWA with default parameters, and only uniquely mapped reads (with tag X0:i:1) were retained for downstream analyses.
MACS2 (v2.2.7.1) was used to call peaks with one duplicated tag kept, fragment length 200bp for single-end reads, and the threshold q ≤ 0.01. Peaks that overlapped (overlap represents any bases of a peak sharing with other peaks/regions) with the regions on ENCODE blacklist (Amemiya et al. 2019) were filtered out. During peak calling, ChIP inputs were used as controls for all factors except for ZFP661. For ZFP661 in ZFP661-3HA OE mESCs, ChIP input and the corresponding ChIP in EV control mESCs using anti-HA antibodies (referred to as HA-ChIP) were used as controls to detect peaks (referred to as input-peaks and HA-peaks), respectively. Only HA-peaks that overlapped with input-peaks were retained as reliable peaks for downstream analyses. For ZFP661 in endogenous tagged ZFP661-3HA mESCs, HA-ChIP in un-tagged mESCs were used as ChIP input to detect peaks. For H3K9me3, the peak regions from MACS2 output were used directly. For other factors, the 50 bp flanking regions of ChIP summits (i.e., summits ± 50 bp) were used as refined peak regions for downstream analyses.
To generate high-quality and consistent ChIP peak lists, peaks from two biological replicates in the same condition (i.e., WT or Zfp661 KO, EV control or ZFP661-3HA OE) were combined by retaining peaks in replicate 1 that overlapped with peaks in replicate 2. As ZFP661 expressed at low level in mESCs, the following steps were employed to generate a high-quality peak list for ZFP661 in ZFP661-3HA mESC: ZFP661 peaks in ZFP661-3HA mESCs were detected using a relatively loose threshold (q ≤ 0.1), and only peaks that overlapped with consistent ZFP661 peaks in ZFP661-3HA OE mESCs were retained. To generate consistent ChIP signal (i.e., bigwig) files, deepTools (v3.5.1) was used with the parameters “--normalizeUsing CPM --binSize 10 –extendReads” (CPM represents counts per million) and with chrM and regions on ENCODE blacklist excluded. The ChIP signals were normalized by subtracting the ChIP input in each biological replicate (for ZFP661, subtracted by HA-ChIP), and then the two biological replicates were averaged to generate a consistent bigwig file for each factor.
Assembly: mm10
Supplementary files format and content: bigwig signal files (.bw), MACS2 peak files (.NarrowPeak), tar of consistent bigwig files (.tar), and tar of consistent peak files (.tar).

source_name: R1 mESCs

growth_protocol: Cells were cultured in a 37 °C humidified incubator with 5% CO2.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min and quenched with 0.4M glycine for 5 min.
ChIP assays were performed according to the ENCODE protocol with modifications. 20M cells/ChIP were used for ZFP661-3HA (anti-HA: Abcam, ab9110), CTCF (anti-CTCF: Millipore, 07-729), RAD21 (Anti-RAD21: Abcam, ab992) and KAP1 (anti-KAP1: Abcam, ab22553), and 10M cells/ChIP were used for H3K9me3 (anti-H3K9me3: Abcam, ab8898). 5 μg of antibodies were used for each ChIP. ChIP DNA was purified, and 10 μl (or up to 50 ng) of ChIP DNA was used as input to construct ChIP library using ThruPLEX DNA-Seq Kit (Takara, R400676). The ChIP inputs from the same biological replicate were evenly sampled and pooled together to construct the corresponding ChIP input library.

value: R1 mESCs

value: mouse embryonic stem cells

value: Zfp661 KO

value: Input control


title: GFIPO_48h_m5

description:
1048_0080
1048_0080

data_processing:
reads passing quality control filter were mapped against or GRCm38 (mouse data) reference genomes using STAR (v2.5.2b)
Gene expression levels were quantified based on genome annotation files from Ensembl version 86 using RSEM (v1.3.0) and featureCounts (v1.5.1). For additional quality control we used FastQC (v0.11.5), picardmetrics (v0.2.4) and dupRadar (v1.0.0).
Assembly: GRCm38 (mouse data)
Supplementary files format and content: 1048_uReads.txt containts tab delimited normalized read counts per gene (row) for all samples (column).
Supplementary files format and content: 1048_uTPM.txt containts tab delimited normalized TPM per gene (row) for all samples (column).

treatment_protocol:
Glucose_48h_36mM_Fructose_48h_Insulin_48h_Palmitic Acid_48h_Oleic Acid_48h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

tag: animal id

value: GFIPO

tag: timepoint


title: Liver PCLS GFIP 48h TX08

description:
1047_0014
Liver PCLS GFIP 48h

data_processing:
reads passing quality control filter were mapped against or GRCm38 (mouse data) reference genomes using STAR (v2.5.2b)
Gene expression levels were quantified based on genome annotation files from Ensembl version 86 using RSEM (v1.3.0) and featureCounts (v1.5.1). For additional quality control we used FastQC (v0.11.5), picardmetrics (v0.2.4) and dupRadar (v1.0.0).
Supplementary files format and content: 1047_uReads.txt containts tab delimited normalized read counts per gene (row) for all samples (column).
Supplementary files format and content: 1047_uTPM.txt containts tab delimited normalized TPM per gene (row) for all samples (column).

value: GFIPh


title: sir4∆_wtpromoter_Elf1FLAG ChIP rep1

value: Saccharomyces cerevisiae

tag: genotype

value: ADE2, lys2, TRP1, hml@2delta::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal; sir4delta::k.l.URA3; hmrdelta::HygMX; matdelta::k.l.LEU2; ELF1-3xFLAG-Kanmx

value: anti-FLAG® M2 antibody (MilliporeSigma, product F1804) and DynaBeads Protein G magnetic beads (ThermoFisher Scientific catalog number 10003D)


title: Liver PCLS F 48h TX08

description:
1047_0011
Liver PCLS F 48h

value: Male

value: Fh


title: Liver PCLS GFI 48h TX08

description:
1047_0013
Liver PCLS GFI 48h

value: GFIh


title: WT mESCs (replicate 1), ChIP Input

description: ChIP-seq

value: WT


title: SIR_wtpromoter_Elf1FLAG ChIP rep1

value: matdelta::klLEU2 ADE2, lys2, TRP1, hml@2delta::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal; hmrdelta::NatMX; ELF1-3xFLAGKanMX


title: Liver PCLS GF 48h TX08

description:
1047_0012
Liver PCLS GF 48h

value: Liver

value: Snap-frozen

value: GFh


title: Zfp661 KO mESCs (replicate 1), ChIP Input

description: ChIP-seq

value: R1 mESCs


title: SIR_wtpromoter_Elf1FLAG input rep1


title: GF_48h_m5

description:
1048_0076
1048_0076

treatment_protocol:
Glucose_48h_36mM_Fructose_48h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: GF


title: GFIO_48h_m5

description:
1048_0079
1048_0079

treatment_protocol:
Glucose_48h_36mM_Fructose_48h_Insulin_48h_Oleic Acid_48h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: GFIO


title: WT mESCs (replicate 2), ChIP Input

description: ChIP-seq

value: mouse embryonic stem cells

value: Input control


title: WT mESCs (replicate 2), RAD21 ChIP

description: ChIP-seq

value: RAD21 (Abcam, ab992)


title: GFIP_48h_m5

description:
1048_0078
1048_0078

treatment_protocol:
Glucose_48h_36mM_Fructose_48h_Insulin_48h_Palmitic Acid_48h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: GFIP


title: SIR_mutpromoter_Elf1FLAG ChIP rep2

value: Saccharomyces cerevisiae

value: ADE2, lys2, TRP1, hmlalpha2delta*Rap1bs-mutation::CRE, ura3-1; 3xV5_Rap1-N-terminal ; hmrdelta::HygMX; matdelta::k.l.LEU2; ELF1-3xFLAGKanMX


title: Liver PCLS CTR 48h TX08

description:
1047_0009
Liver PCLS CTR 48h

value: Male

value: CTRh


title: GFI_48h_m5

description:
1048_0077
1048_0077

treatment_protocol:
Glucose_48h_36mM_Fructose_48h_Insulin_48h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: GFI


title: Liver PCLS GFIO 24h TX08

description:
1047_0007
Liver PCLS GFIO 24h

value: GFIOh


title: Zfp661 KO mESCs (replicate 2), RAD21 ChIP

description: ChIP-seq

value: Zfp661 KO


title: Liver PCLS G 48h TX08

description:
1047_0010
Liver PCLS G 48h

value: Liver

value: Gh


title: G_48h_m5

description:
1048_0074
1048_0074

treatment_protocol:
Glucose_48h_36mM
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: G


title: MAT_wtpromoter_Rpb3FLAG input rep2

value: ADE2, lys2, TRP1, hmldelta::NatMX, hmrdelta::HygMX, 3xV5-Rap1;  RPB3-3xFLAG-KanMX


title: Liver PCLS GFIP 24h TX08

description:
1047_0006
Liver PCLS GFIP 24h

value: Snap-frozen

value: GFIPh


title: WT mESCs (replicate 1), RAD21 ChIP

description: ChIP-seq

value: R1 mESCs

value: mouse embryonic stem cells

value: WT


title: MAT_wtpromoter_Rpb3FLAG input rep1


title: F_48h_m5

description:
1048_0075
1048_0075

treatment_protocol:
Fructose_48h_Glucose_48h_25mM
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: F


title: MAT_wtpromoter_Rpb3FLAG ChIP rep2

value: Saccharomyces cerevisiae

value: anti-FLAG® M2 antibody (MilliporeSigma, product F1804) and DynaBeads Protein G magnetic beads (ThermoFisher Scientific catalog number 10003D)


title: SIR_wtpromoter_Elf1FLAG ChIP rep2

value: matdelta::klLEU2 ADE2, lys2, TRP1, hml@2delta::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal; hmrdelta::NatMX; ELF1-3xFLAGKanMX


title: Liver PCLS GFI 24h TX08

description:
1047_0005
Liver PCLS GFI 24h

value: Male

value: GFIh


title: Zfp661 KO mESCs (replicate 1), RAD21 ChIP

description: ChIP-seq

value: RAD21 (Abcam, ab992)


title: GFIPO_24h_m5

description:
1048_0072
1048_0072

treatment_protocol:
Glucose_24h_36mM_Fructose_24h_Insulin_24h_Palmitic Acid_24h_Oleic Acid_24h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: GFIPO


title: Liver PCLS GF 24h TX08

description:
1047_0004
Liver PCLS GF 24h

value: Liver

value: GFh


title: WT mESCs (replicate 2), CTCF ChIP

description: ChIP-seq

value: CTCF (Millipore, 07-729)


title: CTR_48h_m5

description:
1048_0073
1048_0073

treatment_protocol:
Glucose_48h_25mM
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: CTR


title: Zfp661 KO mESCs (replicate 2), CTCF ChIP

description: ChIP-seq

value: Zfp661 KO


title: MAT_mutpromoter_Rpb3FLAG input rep2

value: ADE2, lys2, TRP1, hmldelta::NatMX, hmrdelta::HygMX, 3xV5-Rap1; MATalpha-Rap1*bs; RPB3-3xFLAG-KanMX


title: Liver PCLS G 24h TX08

description:
1047_0002
Liver PCLS G 24h

value: Snap-frozen

value: Gh


title: MAT_mutpromoter_Rpb3FLAG ChIP rep1


title: Liver PCLS F 24h TX08

description:
1047_0003
Liver PCLS F 24h

value: Fh


title: Zfp661 KO mESCs (replicate 1), CTCF ChIP

description: ChIP-seq

value: R1 mESCs

value: mouse embryonic stem cells


title: MAT_wtpromoter_Rpb3FLAG ChIP rep1

value: Saccharomyces cerevisiae

value: ADE2, lys2, TRP1, hmldelta::NatMX, hmrdelta::HygMX, 3xV5-Rap1;  RPB3-3xFLAG-KanMX

value: anti-FLAG® M2 antibody (MilliporeSigma, product F1804) and DynaBeads Protein G magnetic beads (ThermoFisher Scientific catalog number 10003D)


title: MAT_mutpromoter_Rpb3FLAG input rep1


title: GFIO_24h_m5

description:
1048_0071
1048_0071

treatment_protocol:
Glucose_24h_36mM_Fructose_24h_Insulin_24h_Oleic Acid_24h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: Male

value: GFIO


title: GFIP_24h_m5

description:
1048_0070
1048_0070

treatment_protocol:
Glucose_24h_36mM_Fructose_24h_Insulin_24h_Palmitic Acid_24h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: GFIP


title: WT mESCs (replicate 1), CTCF ChIP

description: ChIP-seq

value: WT


title: S33_WT4 IR

city: Tel-Aviv

first: Amit

last: Levon

address: Ramat Aviv

country: Israel

institute: Tel-Aviv University

description: S33_FKDL202582263-1a-GB05-AK690_H7YKLDSXY_L4

data_processing:
Adaptor clipping and leading and trailing low quality or N bases trimming was done using Trimmomatic v0.36 in paired-end mode.
The processed reads were aligned to the human genome (hg19) using Rsubread v2.0.0 ‘align’ function (sortReadsByCoordinates=True, detectSV=False) in paired-end mode, with the human UCSC refseq genes (hg19) GTF as an external annotation file.
Split samples S18-S28 were merged into one bam file, using the Samtools v1.3.1 ‘merge’ command.
Gene expression was calculated using Rsubread ‘featureCounts’ (countMultiMappingReads=False) in paired end mode to count the number of reads that map to each gene, with the GENCODE GRCh37 (hg19) v25 GTF as an external annotation file.
The reads were then normalized by TPM (Transcripts Per Kilobase Million) using the total exonic length acquired from the same GENCODE database.
In order to remain with only genes that have been robustly expressed in the samples, we continued only with genes that have a value of at least 1.0 TPM in all replicates of at least one biological condition in the dataset.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample (txt file).
Supplementary_files_format_and_content: Matrix table with TPM normalized gene counts for every gene and every sample (txt file).
Supplementary_files_format_and_content: Matrix table with TPM normalized gene counts only for genes that have a value of at least 1.0 TPM in all replicates of at least one biological condition in the dataset (txt file).

source_name: Skin primary fibroblasts

growth_protocol: Cells were grown in complete Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 1% (v/v) penicillin/streptomycin and 1% (v/v) L-glutamine. The cultures were maintained at 37°C in a humidified atmosphere with 5% CO2 and 3% O2

extract_protocol:
Total RNA was isolated using Qiazol Lysis Reagent (QIAGEN) and purified with the MiRNeasy Kit (QIAGEN), according to the manufacturer’s protocol. The RNA purity (260/230 and 280/260) was measured by nanodop.  RNA concentration was measured by Qbit and the integrity was measured using the Tapstation instrument. The purified RNA was used for subsequent library preparation and sequencing.
Library preparation was performed Using the mRNA Tecan Genomics Universal Plus mRNA-Seq with NuQuant (includes UDI-UMI) kit.

treatment_protocol: For IR-induced senescence, cells were exposed to 10Gy X-rays using the Faxitron (X-ray) cabinet providing 0.5 Gy/min, and harvested 10 days later .

value: Human-derived skin fibroblasts

tag: genotype/variation

value: IR (10 Gy)


title: GF_24h_m5

description:
1048_0068
1048_0068

extract_protocol:
Three PCLS slides per donor per assay condition have been pooled to ensure to get enough material for RNA Sequencing. After homogenization and lysis using in Qiazol buffer (Qiagen, Venlo, the   Netherlands), samples were mixed with 1/5th volume of chloroform (Sigma) and separated using phase extraction tubes. The RNA was then isolated with the RNeasy Lipid Tissue Mini Kit (Qiagen, Venlo, the  Netherlands) or the FavorPrep TM Tissue Total RNA Mini Kit (Favorgen, Vienna, Austria).  RNA samples were quantitatively and qualitatively assessed using the fluorescence-based Broad Range Quant-iT RNA Assay Kit (ThermoFisher) and the Standard Sensitivity RNA Analysis DNF-471 Kit on a 96-channel Fragment Analyzer (Agilent), respectively.
Total RNA was normalized on the MicroLab STAR automated liquid platform (Hamilton). 100ng input was used for library construction with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina #E7760, together with the QIAseq FastSelect RNA removal Kit (Qiagen) upstream and the NEBNext Multiplex Oligos for Illumina #E7600 downstream (all New England Biolabs). Fragmentation time was set to 15min. A total of 12 PCR cycles was used for the index PCR while the final libraries were eluted in 25 µL. Of note, the only deviation from the manufacturer’s protocol was the use of Ampure XP beads (Beckman Coulter) at the double-stranded cDNA purification step, instead of the recommended SPRIselect Beads. Total RNA sequencing libraries were quantified by the fluorescence dye-based methodology High Sensitivity dsDNA Quanti-iT Assay Kit (ThermoFisher) on a Synergy HTX (BioTek). Library molarity averaged at 100.3 nM. Total RNA libraries were also assessed for size distribution and adapter dimer presence by the High Sensitivity NGS Fragment DNF-474 Kit on a 96-channel Fragment Analyzer (Agilent). Sequencing libraries were normalized on the MicroLab STAR (Hamilton), pooled and spiked in with PhiX Control v3 (Illumina).
The library pool was subsequently clustered on an S2 Flow Cell and sequenced on a NovaSeq 6000 Sequencing System (Illumina) with dual index, paired-end reads at 2x100 bp length (Read parameters: Rd1: 101, Rd2: 8, Rd3: 8, Rd4: 101) reaching a target depth of approximately 60 million Pass-Filter reads per sample (6.5% CV, see).

treatment_protocol:
Glucose_24h_36mM_Fructose_24h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: Liver

value: GF


title: F_24h_m5

description:
1048_0067
1048_0067

treatment_protocol:
Fructose_24h_Glucose_24h_25mM
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: F


title: GFI_24h_m5

description:
1048_0069
1048_0069

treatment_protocol:
Glucose_24h_36mM_Fructose_24h_Insulin_24h
Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: GFI


title: Day 60 human CD4+_3

data_processing:
Reads were aligned  with  package rnasik 1.5.4 and used iGenomes, GRCm38 build as reference
Gene read counts were converted to log 2 counts per million, quantile normalized and precision weighted with the Voom function of the Limma package through Degust
Genes were filtered from downstream analysis if they did not have a CPM (counts per million mapped reads) value of at least 2 in at least 3 sample libraries. Immunoglobulin genes were excluded from expression analysis.
Genome_build: GRCm38 build
Supplementary_files_format_and_content: CountMatrix_hierarchical_clustering.csv is Matrix table (CSV) with normalised counts for genes with FDR<0.05 across all samples
Supplementary_files_format_and_content: Day60negative_vs_Day60positive.csv is matrix table (CSV) with normalised counts comparing samples that are Day 60 human CD4+ with Day 60 human CD4-
Supplementary_files_format_and_content: Day60negative_vs_Day270positive.csv matrix table (CSV) with normalised counts comparing samples that are Day 270 human CD4+ with Day 60 human CD4-

extract_protocol:
RNA was isolated from cells with Qiagen RNeasy Micro Kits according to the manufacturer’s instructions.
TruSeq RNA Library Prep Kit

value: bone marrow

value: plasma


title: Endogenously tagged ZFP661-3HA mESCs, ChIP anti-HA

description: ChIP-seq

source_name: JM8.F6 mESCs

value: JM8.F6 mESCs

value: Endogenously tagged ZFP661-3HA

value: HA (Abcam, ab9110)


title: Liver PCLS CTR 24h TX08

description:
1047_0001
Liver PCLS CTR 24h

source_name: Liver

treatment_protocol: Biopsies (6 mm diameter) were made from liver tissues, and sliced using a Krumdieck tissue slicer (Alabama Research and Development, Munford, USA) according to the protocol described by de Graaf et al (Nature protocols paper). Precision-cut liver slices (PCLSs) had a wet weight of ~5 mg. PCLSs were cultured at 37degC under 80% O2 and 5% CO2, as previously described9. Culture lasted 24 or 48 hours and the culture medium was refreshed every 24 hours. Different culture media were used to mimic metabolic abnormalities. The control medium consisted of Williams medium E with Glutamax (Invitrogen, Bleiswijk, The Netherlands), 50mg/mL gentamycin (Invitrogen), and 25mM glucose (Merck, Darmstadt, Germany). Hyperglycemia was simulated by addition of 36mM glucose or 5mM fructose (Merck).

value: Snap-frozen

value: CTRh