title: AGS-5

city: shenzhen

first: xinghan

last: jin

address: No. 628, Zhenyuan Road, Xinhu street

institute: The seventh Affiliated Hospital of Sun Yat sen University

description: 5 μM GR127935

data_processing:
CLC Genomics Workbench v11.01
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomics benchwork(parameter-Quality limit:0.05)
Read count extraction and normallization were performed using CLC genomics benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: stomach

growth_protocol: AGS cells were cultured in DMEM/F12 supplemented with 10% fetal bovine serum (FBS; Cellmax), SGC7901 cells were cultured in RPMI-1640 supplemented with 10% FBS

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: AGS and SGC7901 were treated by 2 different drug concentrations5 μM or 0 μM

value: stomach

tag: cell line

value: AGS

value: gastrc cancer


title: Leukemic B-cell progenitors_Vav3-/-_H2aK119Ub-Rep1

status: Public on Apr 16 2022

type: SRA

city: cincinnati

first: Ramesh

middle: C

last: Nayak

state: OH

address: 3333 Burnet Ave

country: USA

institute: Cincinnati Children's

description: CUT&RUN assay for maping  H2aK119Ub

library_source: genomic

data_processing:
Data analysis was performed in Scientific Data Analyses platform “SciDAP” (https://scidap.com, Datirium, LLC) using “TrimGalore Chip-Seq PE” pipeline. This and other containerized CWL pipelines used in analysis are available at https://github.com/datirium/workflows. Briefly, adapters were trimmed from raw reads  with Trim Galore and the reads were aligned to the mm10 reference genome with BowTie. Maximum 3 mismatches per read were allowed. Only uniquely mapped reads were reported. In the next step, all PCR duplicates were removed by Samtools. For peak calling MACS281 was run with the FDR of 0.05.
Differentially Bmi1, Ring1b and H2AK119Ub bound sites between WT and Vav3-/- leukemic B-cell progenitors (n=2/group) were identified by using Diffbind- Differential Binding Analysis of ChIP-Seq Peak Data - 1.0.082 pipeline attached to SciDAP platform, using “Deseq2” analyses method. Only significant differentially bound sites with p-value ≤ 0.05 and with a minimum of 2 fold change (Log2Fold Change ≥ 1 and ≤ -1)  were reported. Based on this, all differential peaks were divided into two groups: 1) Log2FC ≥ 1, 2) Log2FC ≤ -1. Each peak group was cleaned from duplicates based on the peak start and end coordinates and centered by peak center. Re-centered peaks were used for generating tag-density plots within 20kb radius from peak center with “Homer”. For gene TSS-centered tag density plots, each peak was assigned to the nearest gene within 20kb radius from TSS. The resulted two groups of genes were deduplicated and intersected based on the gene names thus obtaining three groups of genes. Genes from every group were re-centered on the TSS and used for generating tag-density heatmap within 20kb radius from gene TSS with Homer. The tag density maps were generated using https://software.broadinstitute.org/morpheus/. The representative genome browser map of specific loci was obtained from IGV browser in “SciDAP” platform.

molecule: genomic DNA

organism: Mus musculus

source_name: BM marrow

growth_protocol: Leukemic B-cell progenitors (FSChiB220+IgM-CD43+CD19+) were sorted from the the BM of WT and Vav3-/- leuekmic B-cell progenitors derived from bone maarow of WT and Vav3-/- leukmeic chimeric mice.

extract_protocol:
Sorted leukemic B-cell progenitors were washed twice with wash buffer [20 mM HEPES; PH-7.5, 150mM NaCl, 0.5mM spermidine] containing protease inhibitor cocktail (Roche, Catalog. 11873580001). Cells were bound to Concanavalin A magnetic beads (Bangs Laboratories, Inc. Catalog. BP531) followed by permeabilization and antibody binding (Bmi1 Ab, Cell signaling technologies, Catalog-5856; Ring1b Ab, Cell Signaling technolgies, Catalog. 5694; H2aK119Ub Ab, Cell Signaling Technologies, Catalog. 8240) at 1:50 dilution in wash buffer containing 0.025% digitonin. Antibody bound cells were treated with proteinA-MNase (700 ng/mL) for 1h at 40C followed by targeted digestion in presence of CaCl2 at 00C for 30 min. The digestion reaction was stopped by adding STOP buffer containing 20 mM EDTA and 4mM EGTA.  The MNase digested DNA fragments were released at 370C, and extracted using QIAGEN MinElute Reaction Cleanup kits (Catalog. 28204), and used for DNA library preparation.
The CUT&RUNseq libraries were prepared by using NEBNext Ultra II DNA library preparation kit for Illumina (Catalog. E7103S) and NEBNext multiplex Oligoes for Illumina (Catalog. E7335S). The libraries were run on Illumina sequencer NextSeq500 and NovaSeq6000 with paired end sequencing.
CUT&RUNseq

tag: cell type

value: B-cell progenitor

tag: strain

tag: genotype


title: SGC7901-5

country: China

description: 5 μM GR127935

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

value: WT

tag: treatment


title: SGC7901-0

description: 0 μM GR127935


title: AGS-0

description: 0 μM GR127935


title: OR-3

type: RNA

city: Hiroshima

first: Kentaro

last: Tokumo

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

department: Molecular and Internal Medicine

country: Japan

institute: Hiroshima University

hyb_protocol: 2.3 µg of single-strand DNA was incubated in GeneChip® Hybridization Oven 645 (Affymeterix) using the GeneChip™ Hybridization, Wash, and Stain Kit (Thermo Fisher). Hybridized with Clariom S Array, human (Termo Fisher).

scan_protocol: The arrays were then stained and washed in a GeneChip® Fluidics Station 450 (Affymetrix) and scanned in a GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: A CEL file is automatically created after scanning. CELL files were analyzed with Transcriptome Analysis Console (TAC) ver. 4.0 to create a text file of expression levels.

label: biotin

source_name: EGFR mutation-positive lung adenocarcinoma cell line H1975, after 3 week of osimertinib treatment

label_protocol: Using the GeneChip™ WT PLUS Reagent Kit (Thermo Fisher), 250 ng of total RNA to cRNA was processed into biotin-labeled single-stranded DNA.

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, penicillin, and streptomycin (100 U/mL and 100 µg/mL, respectively) in a humidified 5% CO2 atmosphere at 37°C in an incubator. Cells were seeded at a density of 1 × 105 cells/well in six-well plates

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions

treatment_protocol: After 24 h of incubation, the medium of the plates was replaced with a medium containing 0.5 µM osimertinib. Starting from this time point as day 1, the medium was changed every 3 days (day 4, day 7), and the surviving cells on day 8 were determined to be EGFR-TKI-tolerant cells

value: osimertinib-tolerant cells


title: Leukemic B-cell progenitors_WT_Bmi1-Rep1

description: CUT&RUN assay for maping Bmi1


title: Leukemic B-cell progenitors_WT_H2aK119Ub-Rep1

description: CUT&RUN assay for maping  H2aK119Ub


title: C-2

source_name: EGFR mutation-positive lung adenocarcinoma cell line H1975, naive cells cultured for 2 week

value: normal cells


title: OR-2

source_name: EGFR mutation-positive lung adenocarcinoma cell line H1975, after 2 week of osimertinib treatment


title: OR-1

source_name: EGFR mutation-positive lung adenocarcinoma cell line H1975, after 1 week of osimertinib treatment


title: Wnt+ adipocytes, without LF3 treatment, rep1

status: Public on Apr 15 2022

city: NEW ORLEANS

first: Zhi

last: Liu

state: United States

address: 2734 CALHOUN

institute: Tulane

data_processing:
HISAT2, mapping
featureCounts, quantification
DESeq2, differential gene expression analysis
Assembly: mm10
Supplementary files format and content: DEGs

source_name: immortalized stromal cells derived from iBAT

extract_protocol:
Total RNA was extracted from tissue or cells according to protocol for the RNeasy Lipid Tissue Mini Kit (Qiagen, 74804) or RNeasy Mini Kit (Qiagen, 27106) accordingly.
Libraries were prepared using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEW ENGLAND BioLabs) according to the manufacturer’s instruction.

value: adipogenic differentiation


title: Wnt+ adipocytes, with LF3 treatment, rep1

value: immortalized stromal cells derived from iBAT


title: Wnt+ adipocytes, without LF3 treatment, rep2


title: Wnt+ adipocytes, without LF3 treatment, rep3


title: Wnt+ adipocytes, with LF3 treatment, rep3


title: pk87gr53 RA (ID 3161)

city: San Francisco

first: Michael

last: Brainard

state: CA

address: 675 Nelson Rising Ln

institute: University of California, San Francisco

data_processing:
Sequencing reads were first trimmed for adaptor sequences using trim_galore (https://github.com/FelixKrueger/TrimGalore, --quality 20, --paired, --overlap 10, adaptors AAAAAAAAAA and GTACTCTGCGTTGATACCACTGCTTCCGCGGACAGGCGTGTAGATCT). We first generated an initial alignment to the Bengalese finch genome (lonStrDom2, GCF_005870125.1) using STAR v2.7.8a (STARsolo mode, default parameters, --outFilterIntronMotifs RemoveNoncanonical) (Dobin et al., 2013). To better annotate the 3’ UTRs of Bengalese finch gene models, we identified transcript 3’ ends by assembling transcripts using these initial alignments and the RNA-seq assembler Stringtie (Kovaka et al., 2019) (--fr -m 100). These Stringtie models were then intersected with the NCBI Bengalese finch transcriptome (lonStrDom2, GCF_005870125.1). New Stringtie exons were filtered by same-strandedness to the intersected references gene, minimal expression level (at least 10% of expression max for a given gene), and at least within 10 kilobases from the 3’ end of the gene. 3’UTRs of the reference transcriptome were extended out to these new exons. Reads were then re-aligned to this extended transcriptome using the ‘bus’ subcommand from kallisto v0.46.1 (Bray et al., 2016; Melsted et al., 2021) followed by barcode error correction using bustools v0.39.3 ‘correct’, sorting using ‘sort’, and read counting using ‘count’.
Gene filtering: genes were kept if they were expressed in at least 1/8 of the total number of samples (8 brain regions were assayed)
Sample filtering: samples were removed if the number of detected genes in the sample was less than 30% of the total number of genes
Assembly: lonStrDom2, GCF_005870125.1
Supplementary files format and content: dat_filtered.csv - Gene (rows) by samples (columns) matrix of unique molecular identifier counts. Column names correspond to ‘id’ column in ‘metadata.csv’
Supplementary files format and content: metadata.csv – Sample-, animal-level metadata for dat_filtered.csv

organism: Lonchura striata

source_name: Brain

extract_protocol:
A fast Nissl staining procedure was developed to quickly stain cryosections before laser capture microdissection. Anhydrous 100% ethanol solution was prepared by adding 15 g of molecular sieve beads (Sigma 208582, 3 Å, 8-12 mesh) to 500 mL 100% molecular grade ethanol (Sigma E7023). Cresyl violet staining solution was prepared as by dissolving cresyl violet powder (Sigma) to 4% wt/vol in 75% ethanol (75% molecular grade ethanol, 25% nuclease-free water), stirring for two days, then filtering through a 0.22 μm filter. Before staining, a series of 95%, 75%, 50% ethanol solutions were prepared. To stain, each slide was thawed at room temperature on a bench for 20 seconds then transferred to 95% ethanol for 30 seconds, 75% ethanol for 30 seconds, and 50% ethanol for 30 seconds. 400 μL of cresyl violet staining solution was then applied to the slide for 30 seconds. Slides were destained and dehydrated by transferring to 50% ethanol for 30 seconds, 75% ethanol for 30 seconds, 95% ethanol for 30 seconds, then two rounds of 100% ethanol for 30 seconds each. Slides were then allowed to air dry. Time series experiments indicated that RNA quality was maintained for up to 45 minutes following staining.  After staining, slides were loaded onto a Leica LMD7000. Song nuclei were identified by anatomical landmarks (such as lamina and position relative to brain surfaces) and their higher intensity Nissl staining relative to surrounding regions. Sections cut from the surrounding tissue (power 45, aperture 50,  speed 10, specimen balance 0, head 90%, pulse 92, offset 15) into 8-well strip caps containing 31.5 μL of RNA Lysis Buffer/PK (see SPRI RNA purification). After filling each cap with a section, the strip was placed onto a 96-well plate pre-chilled on ice and covered with an ice pack. Once a plate was filled, it was vortexed, spun down at 3,250 x g for 5 minutes at 4 °C, then transferred to dry ice. For long-term storage, plates were stored at -80 °C. The following solutions were prepared before LCM section collection: 50% guanidinium thiocyanate (Sigma) in nuclease-free water, 5X CN buffer (250 mM sodium citrate pH 7.0 (Sigma), 5% NP-40 (Sigma)), and RNA Lysis Buffer (20% guanidine thiocyanate, 1X CN buffer). The following solutions were prepared before RNA purification: RNA Wash Buffer (25 mM sodium citrate pH 7.0, 15% guanidinium thiocyanate, 40% isopropanol) and solid phase reversible immobilization (SPRI) bead solution. SPRI bead solution was prepared by first vortexing Sera-Mag SpeedBeads™ Carboxyl Magnetic Beads, hydrophobic (Fisher) until fully suspended transferring 1 mL beads to a 1.5 mL tube. Beads were washed  by placing the tube on a tube magnet, waiting until solution cleared, removing the solution, adding 1 mL of TE Buffer (10 mM UltraPure Tris HCl, pH 8.0 (ThermoFisher), 1 mM EDTA pH 8 (ThermoFisher)), and pipetting to mix. This wash was repeated once more, then the beads were resuspended in 1 mL TE Buffer. Separately, 9 g polyethylene glycol 8000 (Amresco), 10 mL 5 M NaCl, 500 μL 1 M UltraPure Tris HCl pH 8.0 (ThermoFisher), 100 μL 0.5 M EDTA pH 8.0 (ThermoFisher), and 500 μL 2% sodium azide (Sigma) were combined and brought to ~49 mL using nuclease-free water. Solution was mixed by inversion until PEG 8000 went into solution. Then, 137.5 μL of 20% Tween-20 and 1 mL of beads/TE were added and mixed by inversion. This SPRI bead solution was then stored at 4 °C.   Just before LCM collection, 31.5 μL of RNA Lysis Buffer/PK (1.5 μL of Proteinase K (Ambion), 30 μL of RNA Lysis Buffer) was prepared for each well. To purify RNA following LCM section collection, samples were first allowed to thaw on ice if stored at -80 °C. SPRI bead solution was allowed to come to room temperature, then 40 uL SPRI bead solution was mixed with 47.5 uL isopropanol for each sample. Samples were then lysed by incubating at 42 °C for 30 minutes in a thermocycler then placed at room temperature. 87.5 uL of SPRI/isopropanol solution was added to each sample then mixed 10x by pipetting. Samples were incubated for 5 minutes at room temperature then transferred to a magnetic plate stand. After 3 minutes, the solution was removed, the plate was removed from the magnetic stand, 100 uL of RNA Wash Buffer was added, and beads were resuspended by pipetting. The plate was immediately transferred back to the magnetic plate stand and held there for 2 minutes until the solution cleared. The solution was removed, and the plate was removed from the stand. 100 uL of 70% ethanol was added, beads were resuspended by pipetting 10 times, the plate was returned to the magnetic stand, the solution was allowed to clear for 2 minutes, the solution was removed. This step was repeated for two total ethanol washes. Following the final wash, the beads were allowed to dry for 10 minutes while the plate remained on the stand. Residual ethanol was removed by pipetting. The elute RNA, the plate was removed from the magnet, 15 uL of nuclease-free water was added to each sample, and beads were resuspended by pipetting 10 times. Samples were incubated at room temperature for 5 minutes, then the plate was transferred to a low-elution volume magnetic stand. After 2 minutes or until the solution cleared, 10-12 μL eluted RNA was transferred to new 96-well plates on ice. Plates were sealed using foil adhesive, frozen on dry ice, then transferred to -80 °C for long-term storage.
The SLCR-seq library preparation was adapted from several low input and single-cell RNA-sequencing library protocols (Islam et al., 2014, 2012; Kivioja et al., 2012; Macosko et al., 2015; Picelli et al., 2014, 2013). Barcoded unique molecular identifier (UMI) reverse transcription (RT) primers were prepared in advance in a 96-well plate (RT/TSO/dNTP mix). Each well contained 10 μM barcoded reverse transcription primer (RT_primer, IDT), 10 μM template-switching oligonucleotide with lock nucleic acids (TSO_LNA, Exiqon), and 10 mM dNTPs. Plates were sealed with foil adhesive and stored at -80 °C. Two RT primers were used in this study: one for the initial 18 bird deafening dataset (RT_primer_v1, 25 base UMI, 6 base barcode), and another for the 10 bird unilateral LMAN dataset (RT_primer_v2, 14 base UMI, 12 base barcode). RT_primer_v1 and RT_primer_v2 sets consisted of 24 and 48 barcodes, respectively (Supplemental Table 1). Barcodes were at least one edit distance away from all other barcodes in the set. For library preparation, total RNA prepared from SPRI RNA purification was thawed on ice, then 4 μL total RNA was placed into a well of a 96-well plate chilled on ice. 1 μL RT/TSO/dNTP mix was added and mixed 10 times by pipetting. Plates were sealed with foil adhesive, incubated at 72 °C for 3 minutes, then snap-cooled in ice for at least 2 minutes. An RT Master Mix was prepared containing 1x Enzscript RT buffer (Enzymatics), 5 mM dithiothreitol, 1 mM betaine, 12 mM MgCl2, 0.25 μL Recombinant Ribonuclease Inhibitor (Takara), and 10 U/μL Enzscript Moloney-Murine Leukemia Virus Reverse Transcriptase (Enzymatics). 5 μL of RT Master Mix was added to each sample and mixed by pipetting 10x times. Plates were sealed with foil adhesive and incubated in a thermocycler: 42 °C for 90 minutes, 70 °C for 15 minutes, 4 °C hold. Reactions were then pooled within a barcode set (e.g. barcodes 1-48 from RT_primer_v2 were combined into one tube). To purify cDNA, 0.6x volume of Ampure XP bead solution was added to each pooled sample and mixed by pipetting 10 times. Samples were incubated for 5 minutes and transferred to a tube magnet. After the beads cleared from the solution, the solution was removed, and the beads were washed in 400 μL freshly prepared 80% ethanol for 30 seconds. This step was repeated for a total of two washes. After the second wash, the ethanol solution was removed, and the beads were allowed to dry for 5-10 minutes. Beads were then resuspended in 22 μL of nuclease-free water and incubated for 2 minutes. 20 μL eluted cDNA was transferred to new 1.5 mL LoBind tubes or 96-well plates and either stored at -20 °C or amplified immediately. During the purification a 40 μL cDNA Amplification Master Mix was prepared containing 10 μL KAPA HiFi 5x Buffer, 1 μL 10 mM dNTPs, 4 μL 10 mM TSO_PCR primer, 0.5 μL 1 U/μL KAPA HiFi Hotstart DNA polymerase, and 24.5 μL nuclease-free water. 10 μL of purified cDNA was added to this master mix, pipetted 10x to mix, then amplified under the following cycling parameters: 95 °C for  minutes, then 4 cycles of 98 °C for 30 seconds, 65 °C for 45 seconds, and 72 °C for 3 minutes. Reactions were then placed on ice. During this initial amplification, a second master mix was prepared to determine the target number of amplification cycles by quantitative PCR. This mix contained 3 μL KAPA HiFi 5x Buffer, 0.3 μL 10 mM dNTPs, 1.2 μL 10 mM TSO_PCR primer, 0.15 μL 1 U/μL KAPA HiFi Hotstart DNA polymerase, 0.75 μL 20x EvaGreen (Biotium), and 4.6 μL nuclease-free water. 5 μL of preamplified cDNA was added to this mix and amplified in a real-time PCR machine: 98 °C for 3 minutes, followed by 24 cycles of 98 °C for 20 seconds, 67 °C  for 20 seconds, and 72 °C  for 3 minutes, followed by 72 °C  for 5 minutes. The target number of additional cycles was determined by identifying the Ct at 20% of the max fluorescence then subtracting 5 cycles from this number. This number was generally between 5-7 additional cycles. The remaining 45 μL was placed back into the thermocycler and cycled for 98 °C for 30 seconds, the number of additional cycles at 98 °C for 20 seconds, 67 °C  for 20 seconds, and 72 °C  for 3 minutes, followed by 72 °C for 5 minutes. To purify the amplified cDNA, 0.6x volume of Ampure XP bead solution was added to each reaction and mixed by pipetting 10 times. Samples were incubated for 5 minutes and transferred to a tube magnet. After the beads cleared from the solution, the solution was removed, and the beads were washed in 200 μL freshly prepared 80% ethanol for 30 seconds. This step was repeated for a total of two washes. After the second wash, the ethanol solution was removed, and the beads were allowed to dry for 5 minutes. Beads were then resuspended in 22 μL of nuclease-free water and incubated for 2 minutes. 20 μL eluted cDNA was transferred to new 1.5 mL LoBind tubes or 96-well plates and stored at -20 °C. Sample concentration was quantified using Qubit dSDNA High Sensitivity kit (ThermoFisher), then sample concentrations were standardized to 100 pg/μL. To prepare tagmented DNA, 4 μL (400 pg) of amplified cDNA was added to 10  μL Tagmentation Buffer (Buffer TD from the Nextera XT DNA Sample Prep Kit, Illumina), 1 μL nuclease-free water, and 5 μL ATM (Nextera XT). Reactions were mixed by pipetting 10 times the incubated at 55 °C for 5 minutes. 5 μL of Buffer NT was then added, then the reactions were incubated for 5 minutes at room temperature. Final libraries were constructed by first preparing a PCR master mix containing 20 μL KAPA HiFi 5x Buffer, 2 μL 10 mM dNTPs, 5 μL 10 mM P5-TSO_Hybrid primer, 5 μL 10 mM PCR2 primer, 1 μL 1 U/μL KAPA HiFi Hotstart DNA polymerase, and 42 μL nuclease-free water. PCR2 contains an i7 index (Supplemental Table 1). The 25 μL tagmentation reaction was then added directly to the mix, and mixed by pipetting 10 times. Samples were amplified using 72 °C for 3 minutes; 95 °C for 3 minutes; followed by 16 cycles of 98 °C for 10 seconds, 55 °C for 30 seconds, and 72 °C for 30 seconds; followed by 72 °C for 5 minutes. Samples were then purified by adding 1.2x volumes of Ampure XP, incubating for 5 minutes, then transferring to a tube magnet. After the beads cleared from the solution, the solution was removed, and the beads were washed in 200 μL freshly prepared 80% ethanol for 30 seconds. This step was repeated for a total of two washes. After the second wash, the ethanol solution was removed, and the beads were allowed to dry for 5 minutes. Beads were then resuspended in 22 μL of Low Elution Buffer (10 mM Tris HCl pH 8.0, 0.1 mM EDTA, 0.05% Tween-20) and incubated for 2 minutes. 20 μL eluted cD`NA was transferred to new 1.5 mL LoBind tubes and stored at -20 °C. Library size distributions were assessed using a Bioanalyzer High Sensitivity DNA Chip (Agilent), and library concentrations were determined using the KAPA Library Quantification Kit (Illumina Complete Kit, Roche). Samples were pooled at equal concentrations then size selected using a BluePippin and 2% BluePippin gels. DNA from 180 to 500 bp was selected then purified using the MinElute kit (Qiagen) with two rounds of 10 μL elution in Low Elution Buffer. Samples were stored at -20 °C.

value: Brain

tag: region

value: RA

tag: ID

tag: nest

tag: Sex

value: male

tag: reference

value: posterior

value: intact

tag: library


title: pk90gr56 RA (ID 3169)

value: deaf


title: pk90gr56 RA (ID 3153)


title: pk87gr53 LMAN (ID 3133)

value: LMAN

value: anterior


title: pk87gr53 NC (ID 3190)

value: NC


title: pk90gr56 Area X (ID 3141)

value: Area X


title: pk90gr56 Stri (ID 4174)

value: Stri


title: pk87gr53 NR (ID 3134)

value: NR


title: pk90gr56 Arco (ID 3170)

value: Arco


title: pk87gr53 Arco (ID 3162)


title: pk87gr53 LMAN (ID 3117)


title: pk90gr56 Arco (ID 3154)


title: pk90gr56 Stri (ID 3142)


title: pk90gr56 Area X (ID 4173)


title: pk87gr53 NR (ID 3118)


title: Wnt+ adipocytes, with LF3 treatment, rep2


title: bu22wh42 RA (ID 3083)


title: bu22wh42 Stri (ID 3075)


title: pk87gr53 RA (ID 3177)


title: bu21wh41 NC (ID 3059)


title: pk87gr53 LMAN (ID 3145)


title: bu21wh41 HVC (ID 3051)

value: HVC


title: C57 mouse retina, non-treated, P28, rep1

city: Qingyuan

first: le

last: li

address: B24 Yinquan South Road, Qingyuan 511518, Guang Dong, China

institute: the Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (parameter- removing reads containing adapters;removing reads containing more than 10% of unknown nucleotides(N);removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.)
Trimmed sequence reads were mapped to ribosome RNA (rRNA) database using Bowtie2 ,The rRNA mapped reads then will be removed.
The remaining clean reads were mapped to Ensembl_release103 using HISAT2. 2.4  (parameters- -rna-strandness RF and other parameters set as a default)
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: Ensembl_release103
Supplementary files format and content: tab-delimited xls files include FPKM values and counts for each Sample

source_name: retina

growth_protocol: MSC-EVs (MSC-Exo) or NS were injected into the vitreous of rd10 mice at postnatal day 14 (P14) and P21

extract_protocol:
RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA). Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, A base added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified

treatment_protocol: 1 μL MSC-EVs (1× 1010 in 1 μL) or NS was intravenously injected into both eyes of the animal

value: retina

value: C57 BL/6J mouse

value: non-treated


title: bu21wh41 RA (ID 3035)

value: Brain


title: bu22wh42 NC (ID 3108)


title: bu21wh41 HVC (ID 3052)


title: bu21wh41 NC (ID 3060)


title: bu22wh42 NR (ID 3076)


title: bu21wh41 NR (ID 3027)


title: bu22wh42 Area X (ID 3067)


title: bu21wh41 Stri (ID 3028)


title: bu21wh41 RA (ID 3036)

value: RA


title: bu22wh42 Arco (ID 3091)

value: male


title: bu22wh42 NC (ID 3106)

value: posterior


title: bu22wh42 NC (ID 3107)


title: bu21wh41 LMAN (ID 3019)

value: intact


title: bu22wh42 HVC (ID 3098)

value: deaf


title: bu21wh41 Arco (ID 3041)


title: bu21wh41 Area X (ID 3020)


title: bu22wh42 NR (ID 3073)


title: bu22wh42 RA (ID 3081)


title: bu21wh41 NC (ID 3057)


title: bu22wh42 NR (ID 3074)


title: bu21wh41 RA (ID 3033)


title: bu22wh42 LMAN (ID 3065)

value: LMAN


title: bu21wh41 NC (ID 3058)


title: bu21wh41 HVC (ID 3050)


title: bu21wh41 NR (ID 3025)

value: anterior


title: bu22wh42 HVC (ID 3100)


title: bu21wh41 Stri (ID 3026)


title: bu21wh41 RA (ID 3034)


title: bu22wh42 NC (ID 3105)

value: NC


title: bu22wh42 Stri (ID 3071)


title: bu22wh42 Area X (ID 3079)

value: Area X


title: bu21wh41 HVC (ID 3047)


title: bu22wh42 Area X (ID 3063)


title: bu22wh42 Arco (ID 3089)


title: bu21wh41 LMAN (ID 3017)


title: bu21wh41 Stri (ID 3039)

value: Stri


title: bu21wh41 Area X (ID 3031)


title: bu21wh41 Arco (ID 3042)


title: bu22wh42 HVC (ID 3096)


title: bu21wh41 HVC (ID 3048)


title: bu22wh42 NC (ID 3103)


title: bu22wh42 Area X (ID 3064)


title: bu21wh41 NC (ID 3056)


title: bu22wh42 Stri (ID 3072)


title: bu22wh42 Stri (ID 3088)


title: bu22wh42 Area X (ID 3080)


title: bu22wh42 NR (ID 3069)

value: NR


title: bu22wh42 Area X (ID 3077)


title: bu21wh41 Stri (ID 3024)


title: bu22wh42 Stri (ID 3087)


title: bu22wh42 LMAN (ID 3061)


title: bu21wh41 Arco (ID 3053)

value: Arco


title: bu21wh41 LMAN (ID 3015)


title: bu21wh41 RA (ID 3045)


title: bu22wh42 NC (ID 3104)


title: bu21wh41 LMAN (ID 3029)


title: bu22wh42 Arco (ID 3102)


title: bu21wh41 NR (ID 3037)


title: bu22wh42 RA (ID 3094)


title: bu22wh42 NR (ID 3070)


title: bu22wh42 NR (ID 3086)


title: bu21wh41 Area X (ID 3032)


title: bu21wh41 NR (ID 3021)


title: bu22wh42 LMAN (ID 3062)


title: bu21wh41 Arco (ID 3054)


title: bu21wh41 RA (ID 3046)


title: bu21wh41 NR (ID 3038)


title: bu21wh41 Stri (ID 3022)


title: bu21wh41 LMAN (ID 3030)


title: bu22wh42 Stri (ID 3085)


title: bu21wh41 Area X (ID 3014)


title: bk27bk53 Arco (ID 2991)


title: bk27bk53 NC (ID 3008)


title: or74pu64 HVC (ID 2975)

value: HVC


title: or74pu64 Arco (ID 2959)


title: or74pu64 RA (ID 2951)


title: bk27bk53 Arco (ID 2992)


title: bk27bk53 RA (ID 2984)


title: bk27bk53 HVC (ID 3000)


title: or74pu64 HVC (ID 2976)


title: or74pu64 LMAN (ID 2944)


title: or74pu64 HVC (ID 2968)


title: bk27bk53 NC (ID 3007)


title: or74pu64 Arco (ID 2973)


title: bk27bk53 RA (ID 2981)


title: bk27bk53 Arco (ID 2989)


title: bk27bk53 HVC (ID 2997)


title: or74pu64 RA (ID 2965)


title: or74pu64 HVC (ID 2967)


title: bk27bk53 RA (ID 2983)


title: or74pu64 Area X (ID 2957)


title: or74pu64 Stri (ID 2949)


title: bk27bk53 NC (ID 3006)


title: or74pu64 HVC (ID 2974)


title: or74pu64 RA (ID 2958)


title: bk27bk53 RA (ID 2982)


title: or74pu64 Arco (ID 2966)


title: bk27bk53 Arco (ID 2990)


title: or74pu64 Stri (ID 2950)


title: pu37bk12 LMAN (ID 4259)


title: pu37bk12 RA (ID 4275)


title: wh32br40 Area X (ID 4221)

value: Inbrd. Cag


title: or74pu64 LMAN (ID 2934)


title: bk27bk53 NC (ID 3005)


title: wh32br40 HVC (ID 4251)


title: wh32br40 RA (ID 4227)


title: pu37bk12 Arco (ID 4284)


title: wh32br40 NC (ID 4243)


title: wh32br40 NR (ID 4219)


title: wh32br40 Arco (ID 4236)


title: pu37bk12 RA (ID 4276)


title: wh32br40 RA (ID 4228)


title: wh32br40 NR (ID 4220)


title: pu37bk12 Arco (ID 4283)


title: wh32br40 HVC (ID 4249)


title: pu37bk12 NR (ID 4265)


title: wh32br40 LMAN (ID 4211)


title: pu37bk12 NR (ID 4268)


title: wh32br40 HVC (ID 4241)


title: pu37bk12 LMAN (ID 4257)


title: pu37bk12 RA (ID 4273)


title: wh32br40 Arco (ID 4225)


title: pu37bk12 HVC (ID 4298)


title: pu37bk12 HVC (ID 4290)


title: pu37bk12 HVC (ID 4297)


title: wh32br40 RA (ID 4226)


title: pu37bk12 LMAN (ID 4258)


title: pu37bk12 RA (ID 4274)


title: pu37bk12 NR (ID 4266)


title: pu37bk12 NR (ID 4263)


title: wh32br40 NR (ID 4217)


title: wh32br40 HVC (ID 4250)


title: pu37bk12 HVC (ID 4299)


title: wh32br40 Arco (ID 4231)


title: pu37bk12 LMAN (ID 4255)


title: wh32br40 Arco (ID 4223)


title: pu37bk12 RA (ID 4288)


title: pu37bk12 NR (ID 4264)


title: pu37bk12 Arco (ID 4296)


title: wh32br40 LMAN (ID 4208)


title: pu37bk12 Arco (ID 4280)


title: wh32br40 Arco (ID 4233)


title: wh32br40 HVC (ID 4248)


title: wh32br40 RA (ID 4224)


title: pu37bk12 Arco (ID 4295)


title: or37pu44 Area X (ID 3389)


title: or38pu45 NR (ID 3402)


title: or37pu44 RA (ID 3409)


title: or37pu44 NC (ID 3442)


title: pu37bk12 Arco (ID 4279)


title: or38pu45 LMAN (ID 3401)


title: or38pu45 Stri (ID 4202)


title: or38pu45 Area X (ID 4193)


title: or37pu44 HVC (ID 3423)


title: or38pu45 RA (ID 3415)


title: or38pu45 Arco (ID 3418)


title: wh32br40 Arco (ID 4232)


title: or38pu45 HVC (ID 3449)


title: or37pu44 NC (ID 3440)


title: or38pu45 HVC (ID 3433)


title: or37pu44 RA (ID 3407)


title: or37pu44 Stri (ID 3390)


title: or37pu44 LMAN (ID 3395)


title: or38pu45 LMAN (ID 4191)


title: or38pu45 NC (ID 3432)


title: or38pu45 LMAN (ID 4199)


title: or37pu44 NR (ID 3396)


title: or38pu45 NR (ID 4200)


title: or38pu45 Stri (ID 4194)


title: or38pu45 HVC (ID 3447)


title: or37pu44 Stri (ID 3388)


title: or38pu45 NR (ID 4192)


title: or38pu45 HVC (ID 3431)


title: or37pu44 Area X (ID 3387)


title: or37pu44 Arco (ID 3408)


title: or38pu45 Stri (ID 3400)


title: or38pu45 RA (ID 3413)


title: or38pu45 Area X (ID 4205)


title: or37pu44 RA (ID 3405)


title: or37pu44 Area X (ID 3393)


title: or37pu44 NC (ID 3438)


title: or38pu45 Arco (ID 3430)


title: or37pu44 Arco (ID 3422)


title: or38pu45 Arco (ID 3414)


title: or37pu44 Arco (ID 3406)


title: or37pu44 Stri (ID 3386)


title: or38pu45 Stri (ID 4190)


title: or38pu45 Stri (ID 4206)


title: or38pu45 HVC (ID 3445)


title: or37pu44 NR (ID 3378)


title: or38pu45 RA (ID 3429)


title: or37pu44 RA (ID 3421)


title: or37pu44 Area X (ID 3385)


title: or37pu44 RA (ID 3419)


title: or37pu44 LMAN (ID 3377)


title: or38pu45 RA (ID 3411)


title: or38pu45 Area X (ID 4197)


title: or38pu45 Area X (ID 4189)


title: or38pu45 NC (ID 3444)


title: or38pu45 LMAN (ID 4203)


title: or37pu44 NC (ID 3436)


title: or37pu44 LMAN (ID 3391)


title: or38pu45 Arco (ID 3428)


title: or37pu44 Stri (ID 3394)


title: or38pu45 NR (ID 4204)


title: or38pu45 NR (ID 4196)


title: or37pu44 Arco (ID 3420)


title: or37pu44 NR (ID 3392)


title: or38pu45 LMAN (ID 4187)


title: or38pu45 NR (ID 4188)


title: or38pu45 Arco (ID 3412)


title: or37pu44 NR (ID 3376)


title: or37pu44 NR (ID 3384)


title: or38pu45 LMAN (ID 4195)


title: gr56gr57 HVC (ID 3349)


title: gr56gr57 RA (ID 3333)


title: gr58gr59 RA (ID 3341)


title: or38pu45 RA (ID 3427)


title: gr58gr59 Area X (ID 3325)


title: gr56gr57 LMAN (ID 3317)


title: gr58gr59 NC (ID 3374)


title: gr58gr59 NC (ID 3358)


title: or37pu44 Arco (ID 3404)


title: gr56gr57 Area X (ID 3303)


title: gr56gr57 NC (ID 3350)


title: gr58gr59 Arco (ID 3342)


title: gr56gr57 Arco (ID 3334)


title: gr58gr59 Stri (ID 3326)


title: gr56gr57 Stri (ID 3288)


title: gr58gr59 NR (ID 3296)


title: or38pu45 HVC (ID 3443)


title: gr56gr57 Area X (ID 3287)


title: gr58gr59 HVC (ID 3373)


title: bk27bk53 Stri (ID 2987)


title: bk27bk53 RA (ID 2995)


title: bk27bk53 Area X (ID 2979)


title: or74pu64 Arco (ID 2971)


title: bk27bk53 Area X (ID 2980)


title: or74pu64 RA (ID 2963)


title: gr56gr57 HVC (ID 3347)


title: or74pu64 Area X (ID 2948)


title: or74pu64 RA (ID 2964)


title: bk27bk53 Arco (ID 3004)


title: gr58gr59 RA (ID 3339)


title: or74pu64 Area X (ID 2956)


title: or74pu64 Stri (ID 2931)


title: gr56gr57 Stri (ID 3304)


title: gr56gr57 RA (ID 3331)


title: gr56gr57 Area X (ID 3301)


title: gr58gr59 Area X (ID 3309)


title: gr58gr59 NC (ID 3372)


title: gr58gr59 Arco (ID 3340)


title: gr58gr59 Area X (ID 3323)


title: gr56gr57 NC (ID 3348)


title: gr58gr59 NC (ID 3356)


title: gr56gr57 Arco (ID 3332)


title: or74pu64 Arco (ID 2972)


title: or74pu64 NR (ID 2940)


title: gr58gr59 Stri (ID 3310)


title: gr58gr59 HVC (ID 3371)


title: gr58gr59 NR (ID 3324)


title: gr56gr57 Stri (ID 3316)


title: gr56gr57 Stri (ID 3302)


title: gr56gr57 RA (ID 3345)


title: gr56gr57 Area X (ID 3315)


title: gr58gr59 RA (ID 3337)


title: gr58gr59 NR (ID 3294)


title: gr56gr57 NC (ID 3362)


title: gr58gr59 Arco (ID 3354)


title: gr58gr59 Arco (ID 3338)


title: gr56gr57 Area X (ID 3313)


title: gr56gr57 RA (ID 3329)


title: gr58gr59 HVC (ID 3355)


title: gr56gr57 LMAN (ID 3299)


title: gr56gr57 Arco (ID 3330)


title: gr56gr57 Arco (ID 3346)


title: gr56gr57 NR (ID 3300)


title: FPC diet HA-nSREBP-1c ChIP-seq: Control+1c Input

city: Philadelphia

first: Bridget

last: Gosis

state: PA

address: 1819 Montrose St.

department: Perelman School of Medicine

institute: University of Pennsylvania

data_processing:
Trimmomatic (v0.36) was used to trim the adaptors and remove low-quality sequencing reads in FASTQ files.
Reads were aligned to the mm9 reference genome using Bowtie2 (v2.2.6).
The bam files were sorted and duplicates were consequently removed via Samtools (v0.1.19)
Bam files were then converted to bed files by bedtools; reads aligning to blacklist regions and to chrM were also removed.
Tag directories were then generated for each sample using HOMER (v4.4)
The HOMER program getDifferentialPeaksReplicates.pl (v4.11) was used to call peaks (using default settings: at least a fold-change of 4 and FDR of 0.001) over input and the HA ChIP samples done in the Control or LiFKO samples (not injected with HA-nSREBP-1c virus).
The HOMER program makeUCSCfile and the UCSC program bedGraphToBigWig were then used to make bigWig files from tag directories, normalized to 1e7 reads.
Specific data processing steps applicable to different samples, as indicated for each sample.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: Normalized expression values csv file
Supplementary_files_format_and_content: ChIP-seq: bigWig files indicating strength of binding
Supplementary_files_format_and_content: ChIP-seq: peak text files

source_name: Liver tissue

growth_protocol: Flcnlox/lox mice on normal chow were given either AAV8-TBG-GFP (control mice given control virus, referred to as “control”), AAV8-TBG-Cre (LiFKO mice given control virus, referred to as “LiFKO”), AAV8-TBG-GFP in combination with AAV8-ApoE/AAT-nSREBP-1c (control mice given nSREBP-1c virus, referred to as “control+1c”), or  AAV8-TBG-Cre in combination with AAV8-ApoE/AAT-nSREBP-1c (LiFKO mice given nSREBP-1c virus, referred to as “LiFKO+1c”).

extract_protocol:
Mice were then sacrificed ad lib and livers were harvested. Nuclei lysates were then fixed and sonicated. Chromatin was then saved for input or subject to immunoprecipitation (ChIP) with HA beads. DNA was then isolated for both input and ChIP samples.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina with NEBNext set 1 and 2 indexes. Sequencing was then done on an Illumina NextSeq 550, via single-read sequencing (75 cycles).

treatment_protocol: About a week after virus injection, mice were fed 9 days of FPC diet regimen.

tag: diet intervention

value: 9 days FPC diet

tag: aav8 injection

value: GFP (1.5e11 GC) + HA-nSREBP-1c (1.0e11 GC)

tag: feeding state when sacrificed

value: Ad lib

tag: chip antibody

tag: chip or input sample

value: Input


title: gr58gr59 Area X (ID 3291)

value: Brain

value: male


title: gr58gr59 Stri (ID 3322)


title: gr56gr57 LMAN (ID 3285)

value: intact


title: gr56gr57 Stri (ID 3314)


title: gr58gr59 HVC (ID 3369)

value: posterior

value: deaf


title: gr58gr59 RA (ID 3353)

value: RA


title: gr58gr59 Stri (ID 3292)

value: anterior


title: gr58gr59 NR (ID 3308)


title: FPC diet HA-nSREBP-1c ChIP-seq: Control ChIP

data_processing:
Trimmomatic (v0.36) was used to trim the adaptors and remove low-quality sequencing reads in FASTQ files.
Reads were aligned to the mm9 reference genome using Bowtie2 (v2.2.6).
The bam files were sorted and duplicates were consequently removed via Samtools (v0.1.19)
Bam files were then converted to bed files by bedtools; reads aligning to blacklist regions and to chrM were also removed.
Tag directories were then generated for each sample using HOMER (v4.4)
The HOMER program getDifferentialPeaksReplicates.pl (v4.11) was used to call peaks (using default settings: at least a fold-change of 4 and FDR of 0.001) over input and the HA ChIP samples done in the Control or LiFKO samples (not injected with HA-nSREBP-1c virus).
The HOMER program makeUCSCfile and the UCSC program bedGraphToBigWig were then used to make bigWig files from tag directories, normalized to 1e7 reads, and in certain circumstances normalized to input.
Specific data processing steps applicable to different samples, as indicated for each sample.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: Normalized expression values csv file
Supplementary_files_format_and_content: ChIP-seq: bigWig files indicating strength of binding
Supplementary_files_format_and_content: ChIP-seq: peak text files

value: Control

value: Anti-HA Agarose beads (Sigma A2095)

value: ChIP


title: gr56gr57 NR (ID 3284)

value: NR


title: gr56gr57 LMAN (ID 4185)

value: LMAN


title: FPC diet HA-nSREBP-1c ChIP-seq: LiFKO+1c Input

value: Cre (1.5e11 GC) + HA-nSREBP-1c (1.0e11 GC)


title: gr58gr59 Area X (ID 3321)

value: Area X


title: FPC diet HA-nSREBP-1c ChIP-seq: Control+1c rep3 ChIP

description: FPC_HA-nSREBP-1c_ChIP-seq_Control_with_1c_peakset.txt

value: 9 days FPC diet

value: GFP (1.5e11 GC) + HA-nSREBP-1c (1.0e11 GC)


title: gr58gr59 NC (ID 3368)

value: NC


title: gr56gr57 RA (ID 3343)

value: Brain


title: gr58gr59 Arco (ID 3352)

value: Arco

value: male


title: gr58gr59 RA (ID 3335)

value: posterior


title: FPC diet HA-nSREBP-1c ChIP-seq: LiFKO ChIP

value: LiFKO

value: Ad lib


title: gr56gr57 Arco (ID 3344)

value: intact


title: gr56gr57 RA (ID 3327)

value: RA


title: FPC diet HA-nSREBP-1c ChIP-seq: LiFKO+1c rep3 ChIP

description: FPC_HA-nSREBP-1c_ChIP-seq_LiFKO_with_1c_peakset.txt

value: Anti-HA Agarose beads (Sigma A2095)


title: FPC diet HA-nSREBP-1c ChIP-seq: LiFKO+1c rep2 ChIP

value: ChIP


title: FPC diet HA-nSREBP-1c ChIP-seq: LiFKO+1c rep1 ChIP


title: gr56gr57 Arco (ID 3328)


title: gr58gr59 Area X (ID 3289)

value: anterior

value: deaf


title: FPC diet TFE3 ChIP-seq: Control Input

data_processing:
Trimmomatic (v0.36) was used to trim the adaptors and remove low-quality sequencing reads in FASTQ files.
Reads were aligned to the mm9 reference genome using Bowtie2 (v2.2.6).
The bam files were sorted and duplicates were consequently removed via Samtools (v0.1.19)
Bam files were then converted to bed files by bedtools; reads aligning to blacklist regions and to chrM were also removed.
Tag directories were then generated for each sample using HOMER (v4.4)
The HOMER program getDifferentialPeaksReplicates.pl (v4.11) was used to call peaks (using default settings: at least a fold-change of 4 and FDR of 0.001) over input and the TFE3 ChIP samples done in the Tfe3 KO genotype.
The HOMER program makeUCSCfile and the UCSC program bedGraphToBigWig were then used to make bigWig files from tag directories, normalized to 1e7 reads.
Specific data processing steps applicable to different samples, as indicated for each sample.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: Normalized expression values csv file
Supplementary_files_format_and_content: ChIP-seq: bigWig files indicating strength of binding
Supplementary_files_format_and_content: ChIP-seq: peak text files

extract_protocol:
Mice were then sacrificed ad lib and livers were harvested. Nuclei lysates were then fixed and sonicated. Chromatin was then saved for input or subject to immunoprecipitation (ChIP) with TFE3 antibody. DNA was then isolated for both input and ChIP samples.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina with NEBNext set 1 and 2 indexes. Sequencing was then done on an Illumina NextSeq 550, via single-read sequencing (75 cycles).

value: Control

value: Input


title: FPC diet TFE3 ChIP-seq: Tfe3 KO ChIP

data_processing:
Trimmomatic (v0.36) was used to trim the adaptors and remove low-quality sequencing reads in FASTQ files.
Reads were aligned to the mm9 reference genome using Bowtie2 (v2.2.6).
The bam files were sorted and duplicates were consequently removed via Samtools (v0.1.19)
Bam files were then converted to bed files by bedtools; reads aligning to blacklist regions and to chrM were also removed.
Tag directories were then generated for each sample using HOMER (v4.4)
The HOMER program getDifferentialPeaksReplicates.pl (v4.11) was used to call peaks (using default settings: at least a fold-change of 4 and FDR of 0.001) over input and the TFE3 ChIP samples done in the Tfe3 KO genotype.
The HOMER program makeUCSCfile and the UCSC program bedGraphToBigWig were then used to make bigWig files from tag directories, normalized to 1e7 reads, and in certain circumstances normalized to input.
Specific data processing steps applicable to different samples, as indicated for each sample.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: Normalized expression values csv file
Supplementary_files_format_and_content: ChIP-seq: bigWig files indicating strength of binding
Supplementary_files_format_and_content: ChIP-seq: peak text files

value: 9 days FPC diet

value: TFE3 (Sigma HPA023881)


title: FPC diet TFE3 ChIP-seq: LiFKO Input


title: FPC diet HA-nSREBP-1c ChIP-seq: Control+1c rep2 ChIP

value: GFP (1.5e11 GC) + HA-nSREBP-1c (1.0e11 GC)


title: gr56gr57 Area X (ID 3297)

value: Brain

value: Area X


title: FPC diet HA-nSREBP-1c ChIP-seq: Control+1c rep1 ChIP


title: FPC diet TFE3 ChIP-seq: LiFKO+1c Input

value: Cre (1.5e11 GC) + HA-nSREBP-1c (1.0e11 GC)


title: gr58gr59 Arco (ID 3336)

value: Arco

value: male

value: posterior


title: gr58gr59 Stri (ID 3306)

value: Stri


title: FPC diet TFE3 ChIP-seq: LiFKO+1c rep3 ChIP

description: FPC_TFE3_ChIP-seq_LiFKO_with_1c_peakset.txt

value: Ad lib


title: FPC diet TFE3 ChIP-seq: Control+1c Input


title: gr58gr59 Area X (ID 3305)


title: gr58gr59 NR (ID 3320)

value: NR


title: FPC diet TFE3 ChIP-seq: LiFKO+1c rep1 ChIP

value: ChIP


title: FPC diet TFE3 ChIP-seq: Control+1c rep3 ChIP

description: FPC_TFE3_ChIP-seq_Control_with_1c_peakset.txt


title: gr56gr57 NR (ID 4186)

value: anterior

value: intact


title: gr56gr57 NR (ID 3282)


title: gr56gr57 Stri (ID 3298)


title: FPC diet TFE3 ChIP-seq: LiFKO rep3 ChIP

value: LiFKO


title: gr56gr57 LMAN (ID 3281)

value: LMAN


title: FPC diet TFE3 ChIP-seq: Control+1c rep2 ChIP

value: 9 days FPC diet


title: wh21pk76 RA (ID 3259)

value: RA


title: gr58gr59 HVC (ID 3367)

value: HVC

value: deaf


title: FPC diet TFE3 ChIP-seq: Control rep3 ChIP

value: Control

value: TFE3 (Sigma HPA023881)


title: FPC diet TFE3 ChIP-seq: Control rep2 ChIP


title: gr58gr59 Stri (ID 3290)

value: Brain


title: FPC diet TFE3 ChIP-seq: Control+1c rep1 ChIP

value: GFP (1.5e11 GC) + HA-nSREBP-1c (1.0e11 GC)


title: FPC diet TFE3 ChIP-seq: LiFKO rep1 ChIP


title: gr38gr1 RA (ID 3251)

value: male

value: posterior


title: gr38gr1 Area X (ID 3219)

value: Area X


title: FPC diet TFE3 ChIP-seq: LiFKO rep2 ChIP

value: Ad lib


title: Normal chow TFE3 ChIP-seq: LiFKO Input

data_processing:
Trimmomatic (v0.32) was used to trim the adaptors and remove low-quality sequencing reads in FASTQ files.
Reads were aligned to the mm9 reference genome using Bowtie2 (v2.2.8).
The bam files were sorted and duplicates were consequently removed via Samtools (v1.7).
Bam files were then converted to bed files by bedtools; reads aligning to blacklist regions and to chrM were also removed.
Tag directories were then generated for each sample using HOMER (v4.11)
The HOMER program getDifferentialPeaksReplicates.pl (v4.11) was used to call peaks (using default settings: at least a fold-change of 4 and FDR of 0.001) over input and the TFE3 ChIP samples done in the Tfe3 KO genotype.
The HOMER program makeUCSCfile and the UCSC program bedGraphToBigWig were then used to make bigWig files from tag directories, normalized to 1e7 reads.
Specific data processing steps applicable to different samples, as indicated for each sample.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: Normalized expression values csv file
Supplementary_files_format_and_content: ChIP-seq: bigWig files indicating strength of binding
Supplementary_files_format_and_content: ChIP-seq: peak text files

growth_protocol: Flcnlox/lox mice on normal chow were injected with either AAV8-TBG-GFP or -Cre to yield Control and LiFKO mice. Flcnlox/lox; Tfe3-/Y (a whole body deletion of Tfe3) mice were also injected with AAV8-TBG-GFP to yield Tfe3 KO mice.

extract_protocol:
A week or more after injection, mice were sacrificed ad lib, and livers were harvested. Nuclei lysates were then fixed and sonicated. Chromatin was then saved for input or subject to immunoprecipitation (ChIP) with TFE3 antibody. DNA was then isolated for both input and ChIP samples.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina with NEBNext set 1 indexes. Sequencing was then done on an Illumina NextSeq 550, via single-read sequencing (75 cycles).

value: Normal chow

value: Input


title: FPC diet TFE3 ChIP-seq: Control rep1 ChIP

value: ChIP


title: wh21pk76 NC (ID 3272)

value: NC

value: intact


title: FPC diet TFE3 ChIP-seq: LiFKO+1c rep2 ChIP

value: 9 days FPC diet

value: Cre (1.5e11 GC) + HA-nSREBP-1c (1.0e11 GC)


title: wh21pk76 Area X (ID 3243)

value: anterior


title: Normal chow TFE3 ChIP-seq: Control Input


title: gr58gr59 RA (ID 3351)

value: RA

value: deaf


title: gr38gr1 Stri (ID 3220)

value: Stri


title: Normal chow TFE3 ChIP-seq: Tfe3KO rep2 ChIP

data_processing:
Trimmomatic (v0.32) was used to trim the adaptors and remove low-quality sequencing reads in FASTQ files.
Reads were aligned to the mm9 reference genome using Bowtie2 (v2.2.8).
The bam files were sorted and duplicates were consequently removed via Samtools (v1.7).
Bam files were then converted to bed files by bedtools; reads aligning to blacklist regions and to chrM were also removed.
Tag directories were then generated for each sample using HOMER (v4.11)
The HOMER program getDifferentialPeaksReplicates.pl (v4.11) was used to call peaks (using default settings: at least a fold-change of 4 and FDR of 0.001) over input and the TFE3 ChIP samples done in the Tfe3 KO genotype.
The HOMER program makeUCSCfile and the UCSC program bedGraphToBigWig were then used to make bigWig files from tag directories, normalized to 1e7 reads, and in certain circumstances normalized to input.
Specific data processing steps applicable to different samples, as indicated for each sample.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: Normalized expression values csv file
Supplementary_files_format_and_content: ChIP-seq: bigWig files indicating strength of binding
Supplementary_files_format_and_content: ChIP-seq: peak text files

value: TFE3 (Sigma HPA023881)


title: Normal chow TFE3 ChIP-seq: Tfe3KO rep1 ChIP


title: wh21pk76 HVC (ID 3279)

value: Brain

value: HVC


title: wh21pk76 Arco (ID 3260)

value: Arco

value: male

value: posterior


title: wh21pk76 HVC (ID 3271)


title: gr38gr1 Area X (ID 3203)

value: Area X


title: wh21pk76 NR (ID 3212)

value: NR


title: Normal chow TFE3 ChIP-seq: LiFKO rep4 ChIP

description: Normal_chow_TFE3_ChIP-seq_LiFKO_peakset.txt

value: Normal chow

value: LiFKO

value: Ad lib

value: ChIP


title: Normal chow TFE3 ChIP-seq: LiFKO rep2 ChIP


title: Normal chow TFE3 ChIP-seq: LiFKO rep3 ChIP


title: wh21pk76 RA (ID 3257)

value: intact


title: Normal chow TFE3 ChIP-seq: LiFKO rep1 ChIP


title: wh21pk76 Area X (ID 3241)

value: anterior


title: Normal chow TFE3 ChIP-seq: Control rep3 ChIP

description: Normal_chow_TFE3_ChIP-seq_Control_peakset.txt

value: Control


title: gr38gr1 Area X (ID 3233)

value: deaf


title: Normal chow TFE3 ChIP-seq: Control rep2 ChIP


title: Normal chow TFE3 ChIP-seq: Control rep1 ChIP


title: gr38gr1 Arco (ID 3250)


title: Kli-5-1

city: Wuhan

first: Zhou

last: Jian

address: Wuhan China

institute: AJBK

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic-0.36 with parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20
To evaluate the quality of clean reads , fastqc was used  with default parameters
Trinity was used to assemble the transcriptome and calculate the TMM with default parameters
Genome_build: Trinity.fasta
Supplementary_files_format_and_content: tab-delimited text files include FPKM values  for each Sample and tab-delimited text files include read  counts  for each Sample and transcriptome fasta file

organism: Carex littledalei

source_name: Leaf

growth_protocol: Kobresia plants (Kobresia littledalei) were randomly picked from natural field grounds in Tibet and afterwards transplanted into a nursery bed for recovery,the grass patches were grown in pots for 7 days in a 25℃ greenhouse

extract_protocol:
Leaves were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. MGIEasy mRNA Library Prep Kit(85-05536-01) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard BGI-seq protocols.

treatment_protocol: The grass pots were sub-divided into 6 batches and moved to a -5℃ cryogenic treatment room; where each grass pot (Kli-0 to Kli5) was exposed to different cold treatment timelines that ranged from 0hours to 48 hours

value: Leaf

value: -5 degreeC

tag: time point (hour)


title: Normal chow TFE3 ChIP-seq: Control rep4 ChIP

value: TFE3 (Sigma HPA023881)


title: wh21pk76 Area X (ID 3225)

value: Brain


title: Kli-5-2


title: wh21pk76 NC (ID 3278)

value: NC


title: Kli-4-3


title: Kli-4-1


title: wh21pk76 Arco (ID 3258)

value: Arco

value: male


title: wh21pk76 NC (ID 3270)

value: posterior


title: wh21pk76 LMAN (ID 3209)

value: LMAN


title: wh21pk76 Stri (ID 3242)

value: Stri


title: Kli-4-2


title: gr38gr1 Stri (ID 3234)


title: Kli-5-3


title: gr38gr1 RA (ID 3249)

value: RA


title: wh21pk76 Stri (ID 3226)


title: wh21pk76 NR (ID 3210)

value: NR


title: Kli-3-1


title: Kli-3-2


title: Kli-3-3


title: gr38gr1 NR (ID 3218)


title: Kli-2-2


title: Kli-1-3


title: wh21pk76 LMAN (ID 3211)


title: wh21pk76 HVC (ID 3277)

value: HVC


title: Kli-2-1


title: gr38gr1 NR (ID 3202)


title: Kli-0-1


title: Kli-1-1


title: wh21pk76 HVC (ID 3269)

value: intact


title: gr38gr1 RA (ID 3247)


title: gr38gr1 RA (ID 3263)


title: wh21pk76 RA (ID 3255)


title: Kli-0-2


title: Kli-2-3


title: Kli-0-3


title: wh21pk76 LMAN (ID 3239)

value: anterior


title: Kli-1-2


title: wh21pk76 Area X (ID 3223)

value: Area X


title: wh21pk76 Arco (ID 3268)


title: mRNA-seq: H9NSC try2 HOXA as2 expressing vector

city: Clermont-Ferrand

first: franck

last: court

address: 28 Place Henri Dunant

country: France

institute: GReD CNRS

data_processing:
RNA-seq were mapped to the human genome (hg19) using tophat2 (version 2.1.0) with a transcript annotation file from Gencode (Release 19).
The reads count per gene were obtained with the HTseq-count script on properly paired reads and Genecode V19 transcript annotation file.
Differential expression analysis between groups was based on reads count using edgeR R packages.
Assembly: hg19 (GRCh37)
Supplementary files format and content: counts_gencode_V19.txt: Tab-delimited text file includes count values for each Sample.

molecule: polyA RNA

source_name: Human Neural Stem Cells

growth_protocol:
Glioblastoma stem cells were cultured in Neurobasal Medium supplemented with B27 1%; N2 0.5%; bFGF 0.05% and EGF 0.005% at 37°C in 5% CO2 humidified incubator. Culture medium was replaced twice a week and when spheres became large and numerous, they were enzymatically dissociated with accutase. Glioblastoma stem cell cultures were characterized by assessing self renewal, differentiation and tumorigenic ability as well as their expression of stemness markers (CD133, SOX2). Finally, all cultures were also classified according to Verhaak's classification of glioblastomas using the method of classification to nearest centroids (ClaNC) with a 840 gene signature.
Human Neural Stem Cells (hNSCs) derived from H9 hESCs were cultivated according to the manufacturer’s recommendations. Cells were maintained in KnockOut D-EM/F12 (Gibco-Thermo Fisher Scientific, Illkirch France ) media supplemented with 2 mM Glutamax® (Gibco-Thermo Fisher Scientific), 1, 20 ng/mL b-FGF (Peprotech, France) and 20 ng/mL EGF (Peprotech, France ) in a T75 flask coated with Geltrex® (Gibco-Thermo Fisher Scientific ) in a humidified incubator at 37 °C and with 5% CO2. Culture medium was replaced twice a week.

extract_protocol:
The total RNA were extracted using the RNeasy Mini Kit (Qiagen, 74104) following the manufacturer's protocol. RNA samples were quality-checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies).
TruSeq Stranded mRNA library preparation and sequencing on Illumina HiSeq4000 were performed by Integragen, SA (Evry, France), according to the manufacturer's protocol.

treatment_protocol: For glioblastoma stem cells, SMART vector targeting HOXA-AS2 (V3SH11246-245316977 or V3SH11246-245298993) was purchased from GE Healthcare (Little Chalfont, UK). Viral particles were produced and concentrated by the Vectorology platform of Montpellier (Biocampus, Montpellier, France). GSCs were infected using a multiplicity of infection of 10 and processed 120 h later for RNA-seq analysis. For H9NSC, Empty and HOXA-AS2 transcript containing pcDNA3.1 (+) vector (Invitrogen V79020, Illkrich, France) were transfected with Fugene HD (Promega, France) according manufacturer’s recommendations and stable integration selection made by adding geneticin in the culture medium (50ul/ml during 24h and then 200ul/ml).

tag: cell type

value: Human Neural Stem Cells:H9NSC

value: HOXA as2 expressing vector


title: mRNA-seq: H9NSC try2 empty vector

value: empty vector


title: mRNA-seq: H9NSC try1 empty vector


title: gr38gr1 Arco (ID 3264)

value: deaf


title: mRNA-seq: H9NSC try1 HOXA as2 expressing vector


title: gr38gr1 Arco (ID 3248)

value: Brain


title: wh21pk76 LMAN (ID 3207)


title: wh21pk76 Arco (ID 3256)


title: mRNA-seq: GSC6 sh3 HOXA as2

source_name: Glioblastoma stem cell

value: Glioblastoma stem cells:GSC6


title: mRNA-seq: GSC11 sh2 HOXA as2

value: Glioblastoma stem cells:GSC11


title: mRNA-seq: GSC6 sh2 HOXA as2


title: mRNA-seq: GSC11 sh3 HOXA as2


title: wh21pk76 NR (ID 3240)

value: male


title: wh21pk76 NC (ID 3276)

value: NC

value: posterior


title: gr38gr1 Stri (ID 3216)

value: Stri


title: gr38gr1 NR (ID 3232)


title: wh21pk76 NR (ID 3208)


title: C365_Ctrl_gRNA_CART19

city: Rochester

first: Saad

last: Kenderian

state: MN

address: 200 First Street SW

department: Hematology Research

institute: Mayo Clinic

data_processing:
Binary base call data converted to fastq using Illumina bcl2fastq software
Check quality with FastQC, trim adapters with trimmomatic, and re-check quality with FastQC
Latest human reference genome GRCh38 was downloaded from NCBI and indexed using STAR
Paired end reads were mapped to the genome, and HTSeq was used to generate expression counts for each gene
DeSeq2 was used to calculate differential expression
Assembly: CRCh38
Supplementary files format and content: tab-delimited text files contain the gene expression counts for each sample or DeSeq2 dataset

source_name: CART cells

extract_protocol:
RNA was isolated using miRNeasy Micro kit (Qiagen, Gaithersburg, MD, USA) and treated with RNase-Free DNase Set (Qiagen, Gaithersburg, MD, USA).
TruSeq RNA Library Prep Kit v2
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CART19, GM-CSF KO CART19, and Ctrl gRNA CART19 were produced on 3 biological replicates of normal donor T cells and total RNA was isolated.

value: CART cells

tag: genotype/condition

value: Ctrl gRNA CART19


title: C365_GM-CSF_KO_CART19

value: GM-CSF KO CART19


title: gr38gr1 Stri (ID 3200)


title: wh21pk76 Stri (ID 3224)

value: intact


title: C365_CART19


title: C364_GM-CSF_KO_CART19


title: C350_GM-CSF_KO_CART19


title: C364_Ctrl_gRNA_CART19


title: gr38gr1 LMAN (ID 3229)

value: LMAN

value: anterior


title: gr38gr1 RA (ID 3245)

value: RA


title: wh21pk76 RA (ID 3253)


title: C350_CART19


title: GBM_149_CT

city: Columbus

first: Maciej

last: Pietrzak

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

institute: Ohio State University

data_processing:
Illumina BaseCalling pipeline
RNA-Seq reads were first mapped to the human genome GRCh38 using Hierarchical Indexing for Spliced Alignment of Transcripts (HISAT2).
Raw read counts for each gene were quantified by using featureCounts software. Then RNA-seq counts were obtained by using GENCODE v.27 Gene Transfer Format (GTF) file as a transcript reference (GENCODE annotation).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw read counts

source_name: Human GBM tissue

growth_protocol: Cells grown in medium+FBS+ DMSO (vehicle)

extract_protocol:
Qiagen Rneasy prep kit
Illumina - performed by Genomics core at OSU

treatment_protocol: AT13387 (dissolved in DMSO) for 24h

value: Human Glioma tissue

value: Vehicle treated Control


title: wh21pk76 RA (ID 3267)


title: gr38gr1 Area X (ID 3199)

value: Area X

value: deaf


title: C350_Ctrl_gRNA_CART19


title: GS_262_DMSO

value: Human-brain derived glioma stem cells


title: GS_262_AT_24H

value: Treatment HSP90 inhibtor (AT13387)


title: wh21pk76 NC (ID 3274)

value: Brain

value: male


title: gr38gr1 LMAN (ID 3213)


title: wh21pk76 Arco (ID 3266)

value: Arco

value: posterior


title: gr38gr1 Arco (ID 3246)


title: C364_CART19

value: CART cells


title: wh21pk76 NR (ID 3238)

value: NR


title: GS_811_AT_24H


title: gr38gr1 NR (ID 3230)


title: wh21pk76 NR (ID 3206)


title: gr38gr1 NR (ID 3198)


title: gr38gr1 NR (ID 3214)


title: GBM_149_AT


title: wh21pk76 HVC (ID 3273)

value: HVC


title: wh21pk76 RA (ID 3265)

value: intact


title: gr38gr1 LMAN (ID 3197)

value: LMAN


title: GS_811_DMSO


title: pk87gr53 RA (ID 3167)


title: pk90gr56 RA (ID 3159)


title: pk87gr53 Stri (ID 3151)

value: Stri

value: anterior


title: pk87gr53 Stri (ID 3139)


title: pk87gr53 NC (ID 3196)

value: NC


title: wh21pk76 Stri (ID 3222)


title: pk90gr56 Stri (ID 3131)


title: Glomerular_566_MN

city: Ann Arbor

first: Sean

last: Eddy

state: MI

address: 1150 West Medical Center Drive

institute: University of Michigan

description: Gene expression data from glomerular compartment of human kidney biopsy

hyb_protocol: According to manufacturer's protocols.

scan_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

data_processing: The data were analyzed using RMA method and Human Entrez Gene custom CDF annotation version 19 (Brainarray) on three individual batches. Each of the hybridizations was normalized seperately and expression matrix contains the batch corrected data using Combat.

source_name: Glomerular RNA from kidney biopsy from patient with membranous nephropathy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: total RNA

value: Glomeruli


title: pk90gr56 NC (ID 3176)


title: Glomerular_570_Other

source_name: Glomerular RNA from kidney biopsy from patient with glomerular disease, other


title: Glomerular_568_MN


title: pk87gr53 Arco (ID 3168)


title: pk87gr53 Stri (ID 3123)


title: Glomerular_572_Other


title: Glomerular_569_MN


title: Glomerular_252_Other


title: Glomerular_571_MN


title: Glomerular_6_MCD

source_name: Glomerular RNA from kidney biopsy from patient with minimal change disease


title: Glomerular_567_MN


title: Glomerular_573_Other


title: pk87gr53 Stri (ID 3152)


title: pk90gr56 Arco (ID 3160)


title: Glomerular_42_Other


title: Glomerular_21_FSGS

source_name: Glomerular RNA from kidney biopsy from patient with focal segmental glomeruloscelrosis


title: Glomerular_220_Other


title: pk87gr53 Stri (ID 3140)


title: Glomerular_38_MN


title: pk90gr56 Stri (ID 3132)


title: Glomerular_212_Other


title: pk87gr53 Stri (ID 3124)


title: Glomerular_214_Other


title: Glomerular_287_Other


title: Glomerular_238_Other


title: Glomerular_207_Other


title: Glomerular_126_MCD


title: pk90gr56 HVC (ID 3173)


title: pk87gr53 RA (ID 3165)

value: RA


title: pk87gr53 Area X (ID 3149)

value: Area X


title: pk90gr56 RA (ID 3157)

value: deaf


title: pk90gr56 Area X (ID 3129)


title: pk87gr53 NC (ID 3182)


title: pk87gr53 Arco (ID 3166)


title: pk87gr53 NC (ID 3194)


title: pk87gr53 Stri (ID 3150)


title: pk87gr53 LMAN (ID 3121)


title: Glomerular_149_MCD


title: pk87gr53 HVC (ID 3183)


title: Glomerular_31_FSGS


title: pk87gr53 NR (ID 3122)


title: Glomerular_90_MN


title: Glomerular_140_MCD


title: Glomerular_181_Other


title: pk90gr56 Stri (ID 3130)


title: pk87gr53 NR (ID 3138)


title: Glomerular_67_FSGS


title: Glomerular_106_MCD


title: Glomerular_80_FSGS


title: Glomerular_135_MN


title: Glomerular_234_MCD


title: Glomerular_290_Other


title: pk87gr53 HVC (ID 3193)


title: pk90gr56 RA (ID 3171)


title: pk87gr53 LMAN (ID 3147)


title: pk90gr56 RA (ID 3155)


title: pk87gr53 HVC (ID 3181)


title: pk90gr56 Area X (ID 3143)


title: pk87gr53 Arco (ID 3180)


title: pk90gr56 NC (ID 3188)


title: pk87gr53 Area X (ID 3135)


title: Glomerular_272_FSGS


title: pk87gr53 Area X (ID 3119)


title: pk90gr56 Arco (ID 3156)


title: Glomerular_291_Other


title: pk87gr53 NR (ID 3148)


title: pk90gr56 Arco (ID 3172)


title: Glomerular_134_MN


title: Glomerular_288_MN


title: Glomerular_29_FSGS


title: Glomerular_110_MN


title: Glomerular_65_FSGS


title: Glomerular_281_Other


title: Glomerular_160_MCD


title: Glomerular_143_MCD


title: Glomerular_40_MN


title: Glomerular_26_FSGS


title: Glomerular_240_Other


title: Glomerular_70_FSGS


title: Glomerular_146_MN


title: Glomerular_257_Other


title: pk90gr56 Stri (ID 3144)


title: Glomerular_117_MCD


title: pk90gr56 LMAN (ID 4175)


title: pk87gr53 Stri (ID 3136)


title: bk27bk53 Stri (ID 2985)


title: bk27bk53 RA (ID 2993)


title: bk27bk53 Area X (ID 2977)


title: pk90gr56 NR (ID 4176)


title: pk87gr53 HVC (ID 3191)


title: pk87gr53 Stri (ID 3120)


title: Glomerular_545_MCD


title: Glomerular_85_FSGS


title: Glomerular_62_FSGS


title: Glomerular_223_Other


title: or74pu64 RA (ID 2961)


title: or74pu64 NR (ID 2945)


title: or74pu64 NR (ID 2953)


title: Glomerular_37_MN


title: bk27bk53 HVC (ID 3010)


title: bk27bk53 RA (ID 2994)


title: or74pu64 Arco (ID 2969)


title: Glomerular_152_MN


title: or74pu64 Arco (ID 2970)


title: Glomerular_109_MN


title: or74pu64 RA (ID 2962)


title: Glomerular_98_MN


title: Glomerular_36_MN


title: bk27bk53 NC (ID 3012)


title: Glomerular_157_MCD


title: or74pu64 Area X (ID 2946)


title: Glomerular_129_MN


title: or74pu64 Area X (ID 2954)


title: Glomerular_425_Other


title: Glomerular_39_MN


title: Glomerular_150_MCD


title: or74pu64 LMAN (ID 2930)


title: Glomerular_69_FSGS


title: bk27bk53 Arco (ID 3001)


title: Glomerular_99_MN


title: Glomerular_66_FSGS


title: or74pu64 LMAN (ID 2938)


title: Glomerular_519_Other


title: Glomerular_72_FSGS


title: Glomerular_148_MN


title: Glomerular_19_FSGS


title: Glomerular_118_MN


title: Glomerular_6_Living donor

source_name: Glomerular RNA from kidney biopsy from healthy Living donor


title: Glomerular_144_MCD


title: rd88rd70 Arco (ID 4470)

data_processing:
Sequencing reads were first trimmed for adaptor sequences using trim_galore (https://github.com/FelixKrueger/TrimGalore, --quality 20, --paired, --overlap 10, adaptors AAAAAAAAAA and GTACTCTGCGTTGATACCACTGCTTCCGCGGACAGGCGTGTAGATCT). We first generated an initial alignment to the Bengalese finch genome (lonStrDom2, GCF_005870125.1) using STAR v2.7.8a (STARsolo mode, default parameters, --outFilterIntronMotifs RemoveNoncanonical) (Dobin et al., 2013). To better annotate the 3’ UTRs of Bengalese finch gene models, we identified transcript 3’ ends by assembling transcripts using these initial alignments and the RNA-seq assembler Stringtie (Kovaka et al., 2019) (--fr -m 100). These Stringtie models were then intersected with the NCBI Bengalese finch transcriptome (lonStrDom2, GCF_005870125.1). New Stringtie exons were filtered by same-strandedness to the intersected references gene, minimal expression level (at least 10% of expression max for a given gene), and at least within 10 kilobases from the 3’ end of the gene. 3’UTRs of the reference transcriptome were extended out to these new exons. Reads were then re-aligned to this extended transcriptome using the ‘bus’ subcommand from kallisto v0.46.1 (Bray et al., 2016; Melsted et al., 2021) followed by barcode error correction using bustools v0.39.3 ‘correct’, sorting using ‘sort’, and read counting using ‘count’.
Gene filtering: genes were kept if they were expressed in at least 1/5 of the total number of samples (5 brain regions were assayed)
Sample filtering: samples were removed if the number of detected genes in the sample was less than 30% of the total number of genes
Assembly: lonStrDom2, GCF_005870125.1
Supplementary files format and content: dat_filtered.csv - Gene (rows) by samples (columns) matrix of unique molecular identifier counts. Column names correspond to ‘id’ column in ‘metadata.csv’
Supplementary files format and content: metadata.csv – Sample-, animal-level metadata for dat_filtered.csv

value: contra


title: rd88rd70 RA (ID 4469)

value: Brain


title: bk27bk53 NC (ID 3011)

value: male


title: rd88rd70 Field L (ID 4498)

value: Field L

value: ipsi


title: Glomerular_123_MN


title: rd88rd70 Arco (ID 4468)

value: Arco

value: posterior


title: Glomerular_5_Living donor


title: rd88rd70 RA (ID 4467)


title: rd88rd70 Arco (ID 4466)


title: rd88rd70 Field L (ID 4496)


title: rd88rd70 NC (ID 4486)


title: Glomerular_1_Living donor


title: rd88rd70 Field L (ID 4495)


title: Glomerular_4_Living donor


title: Glomerular_3_Living donor


title: rd88rd70 RA (ID 4465)


title: Glomerular_229_MN


title: rd88rd70 HVC (ID 4483)

value: HVC


title: rd88rd70 NC (ID 4484)


title: rd88rd70 HVC (ID 4485)


title: Glomerular_215_Other


title: Glomerular_2_Living donor


title: Glomerular_1_FSGS


title: rd88rd70 Arco (ID 4464)


title: rd88rd70 NC (ID 4480)


title: rd88rd70 NC (ID 4482)


title: rd88rd70 Field L (ID 4497)


title: rd88rd70 HVC (ID 4481)


title: rd88rd70 HVC (ID 4479)


title: Glomerular_127_MN


title: pk63gr79 NC (ID 4434)


title: Glomerular_154_MN


title: pk63gr79 NC (ID 4432)


title: Glomerular_217_Other


title: rd88rd70 RA (ID 4463)


title: pk63gr79 HVC (ID 4433)


title: Glomerular_103_MN


title: Glomerular_179_Other


title: Glomerular_108_MCD


title: Glomerular_105_MN


title: Glomerular_11_MN


title: Glomerular_101_MN


title: pk63gr79 Field L (ID 4457)


title: pk63gr79 Field L (ID 4458)


title: Glomerular_158_MCD


title: Glomerular_196_Other


title: Glomerular_107_MN


title: pk63gr79 Field L (ID 4456)


title: Glomerular_189_Other


title: rd19gr79 Field L (ID 4454)


title: Glomerular_5_FSGS


title: rd19gr79 Field L (ID 4453)


title: Glomerular_71_FSGS


title: pk63gr79 HVC (ID 4455)


title: Glomerular_512_Other


title: Glomerular_87_FSGS


title: rd19gr79 NC (ID 4426)


title: rd19gr79 Field L (ID 4451)


title: rd19gr79 Field L (ID 4452)


title: rd19gr79 RA (ID 4395)


title: Glomerular_95_FSGS


title: rd19gr79 NC (ID 4424)


title: Glomerular_185_Other


title: Glomerular_124_MN


title: rd19gr79 HVC (ID 4425)


title: rd19gr79 NC (ID 4430)


title: rd19gr79 HVC (ID 4429)


title: rd19gr79 NC (ID 4428)


title: rd19gr79 HVC (ID 4427)


title: Glomerular_262_Other


title: Glomerular_139_MCD


title: Glomerular_91_MN


title: pk63gr79 Arco (ID 4402)


title: Glomerular_4_MCD


title: Glomerular_73_FSGS


title: Glomerular_244_Other


title: pk63gr79 RA (ID 4401)


title: rd19gr79 HVC (ID 4423)


title: pk63gr79 RA (ID 4399)


title: pk63gr79 RA (ID 4405)


title: Glomerular_294_Other


title: Glomerular_17_Other


title: Glomerular_293_Other


title: Glomerular_13_MN


title: pk63gr79 Arco (ID 4400)


title: Glomerular_14_MN


title: Glomerular_245_Other


title: Glomerular_128_MCD


title: rd19gr79 Arco (ID 4394)


title: Glomerular_12_MN


title: Glomerular_265_Other


title: Glomerular_156_MN


title: rd19gr79 RA (ID 4391)


title: rd19gr79 Arco (ID 4392)


title: Glomerular_180_Other


title: pk63gr79 Arco (ID 4406)


title: Glomerular_119_MN


title: Glomerular_213_Other


title: pk63gr79 RA (ID 4403)


title: Glomerular_145_MCD


title: pk63gr79 Arco (ID 4404)


title: pk92gr50 Field L (ID 4381)


title: rd19gr79 Arco (ID 4398)


title: pk92gr50 Field L (ID 4382)


title: Glomerular_183_Other


title: pk92gr50 Field L (ID 4380)


title: pk92gr50 Field L (ID 4379)


title: rd19gr79 RA (ID 4393)


title: Glomerular_138_MN


title: rd19gr79 RA (ID 4397)


title: pk92gr50 HVC (ID 4359)


title: or82or75 Field L (ID 4374)


title: or82or75 Field L (ID 4373)


title: rd19gr79 Arco (ID 4396)


title: Glomerular_113_MN


title: or82or75 Field L (ID 4372)


title: or82or75 Field L (ID 4371)


title: Glomerular_452_Other


title: Glomerular_209_Other


title: Glomerular_247_Other


title: pk92gr50 HVC (ID 4361)


title: pk92gr50 NC (ID 4360)


title: Glomerular_136_MN


title: Glomerular_2_FSGS


title: Glomerular_88_FSGS


title: Glomerular_141_MN


title: Glomerular_97_MN


title: Glomerular_159_MN


title: or82or75 NC (ID 4348)


title: Glomerular_115_MN


title: or82or75 NC (ID 4350)


title: or82or75 HVC (ID 4349)


title: pk92gr50 NC (ID 4362)


title: Glomerular_78_FSGS


title: Glomerular_77_FSGS


title: or82or75 HVC (ID 4347)


title: or82or75 RA (ID 4311)


title: Glomerular_1030_Other


title: or82or75 NC (ID 4346)


title: Glomerular_93_MN


title: or82or75 NC (ID 4344)


title: Glomerular_68_FSGS


title: Glomerular_551_Other


title: Glomerular_64_FSGS


title: Glomerular_75_FSGS


title: or82or75 HVC (ID 4345)


title: pk92gr50 RA (ID 4331)


title: or82or75 HVC (ID 4343)


title: Glomerular_211_Other


title: pk92gr50 Arco (ID 4334)


title: Glomerular_133_MN


title: Glomerular_102_MN


title: Glomerular_507_Other


title: Glomerular_111_MN


title: Glomerular_83_FSGS


title: pk92gr50 RA (ID 4333)


title: pk92gr50 RA (ID 4327)


title: pk92gr50 Arco (ID 4330)


title: or82or75 Arco (ID 4318)


title: Glomerular_82_FSGS


title: pk92gr50 RA (ID 4329)


title: or82or75 Arco (ID 4316)


title: Glomerular_210_Other

source_name: Glomerular RNA from kidney biopsyfrom glomerular disease, other


title: 584_FSGS

description: Gene Expression data from the tubulointerstitial compartment of human Glomerular Disease (Other)

source_name: Tubulointerstitial RNA from kidney biopsy of patient with Focal Segmental Glomerulosclerosis

value: Tubulointerstitial compartment from kidney biopsy


title: Glomerular_719_Other


title: or82or75 RA (ID 4315)


title: pk92gr50 Arco (ID 4332)


title: Glomerular_94_MN


title: pk92gr50 Arco (ID 4328)


title: or82or75 Arco (ID 4312)


title: or82or75 RA (ID 4313)


title: or82or75 RA (ID 4317)


title: 586_MCD

source_name: Tubulointerstitial RNA from kidney biopsy of patient with Minimal Change Disease


title: 582_FSGS


title: or82or75 Arco (ID 4314)


title: bk89 NC (ID 4668)

value: magnolia

value: intact


title: bk101 HVC (ID 4675)


title: bk89 HVC (ID 4667)


title: bk89 Arco (ID 4652)


title: 721_FSGS


title: bk89 NC (ID 4686)


title: Glomerular_81_FSGS

source_name: Glomerular RNA from kidney biopsy from patient with focal segmental glomerulosclerosis


title: bk101 RA (ID 4659)

source_name: Brain


title: 572_Other

source_name: Tubulointerstitial RNA from kidney biopsy of patient with Other Glomerular Disease


title: bk101 Arco (ID 4660)


title: bk89 NC (ID 4670)


title: bk101 NC (ID 4678)


title: bk89 Arco (ID 4654)


title: bk101 NC (ID 4694)


title: bk101 HVC (ID 4693)


title: bk89 HVC (ID 4683)


title: 580_MCD


title: 722_MCD


title: bk89 HVC (ID 4685)


title: 575_MCD


title: 581_FSGS


title: 571_MN

source_name: Tubulointerstitial RNA from kidney biopsy of patient with Membranous Nephropathy


title: bk89 HVC (ID 4669)


title: 577_MCD


title: 723_FSGS


title: 64_FSGS


title: 570_Other


title: 585_MCD


title: 576_FSGS


title: 719_Other


title: 573_Other


title: bk89 RA (ID 4653)


title: 115_MN


title: 578_MCD


title: bk101 NC (ID 4692)


title: 579_FSGS


title: 583_MN


title: 214_Other


title: bk101 NC (ID 4676)


title: bk101 RA (ID 4661)


title: bk101 Stri (ID 4612)

value: Stri

value: anterior


title: bk89 RA (ID 4651)


title: 12_FSGS


title: 21_FSGS


title: 574_MCD


title: bk89 NR (ID 4604)

value: NR


title: 220_Other


title: 192_Other


title: bk89 Area X (ID 4635)


title: 139_MCD


title: bk101 LMAN (ID 4627)

value: LMAN


title: 287_Other


title: 212_Other


title: 96_FSGS


title: bk89 LMAN (ID 4619)


title: bk89 Stri (ID 4638)


title: 38_MN


title: 207_Other


title: bk101 NR (ID 4614)


title: 149_MCD


title: 238_Other


title: 181_Other


title: 20_FSGS


title: 106_MCD


title: 234_MCD


title: bk101 NR (ID 4628)


title: 290_Other


title: bk101 Area X (ID 4629)

value: Area X


title: bk101 Arco (ID 4658)

value: deaf


title: bk89 RA (ID 4663)

value: RA


title: bk101 Stri (ID 4630)

value: Brain


title: bk101 Area X (ID 4611)

value: male


title: 135_MN


title: bk89 Arco (ID 4666)


title: bk89 Area X (ID 4621)


title: 80_FSGS


title: bk101 HVC (ID 4689)


title: 126_MCD


title: bk89 Arco (ID 4664)


title: 31_FSGS


title: 288_MN


title: bk89 Arco (ID 4650)


title: 140_MCD


title: 278_Other


title: 291_Other


title: 142_FSGS


title: bk89 Area X (ID 4637)


title: 289_Other


title: 134_MN


title: bk101 NR (ID 4608)


title: 240_Other


title: 29_FSGS


title: 160_MCD


title: 65_FSGS


title: bk89 NC (ID 4682)

value: NC


title: 281_Other


title: bk101 NC (ID 4690)


title: bk89 Stri (ID 4616)


title: bk101 LMAN (ID 4613)


title: 26_FSGS


title: bk89 Area X (ID 4615)


title: 70_FSGS


title: 143_MCD


title: 67_FSGS


title: bk89 Stri (ID 4634)


title: bk101 Stri (ID 4642)


title: 166_Other


title: bk89 Arco (ID 4648)


title: bk89 RA (ID 4665)


title: bk101 Arco (ID 4674)


title: bk101 LMAN (ID 4639)


title: bk89 NR (ID 4618)


title: 40_MN


title: bk101 RA (ID 4673)


title: 223_Other


title: bk101 LMAN (ID 4607)


title: 272_FSGS


title: bk89 Area X (ID 4631)


title: bk89 RA (ID 4649)


title: 110_MN


title: bk101 RA (ID 4655)


title: bk101 LMAN (ID 4623)


title: bk89 Area X (ID 4633)


title: bk101 Area X (ID 4625)


title: bk101 Stri (ID 4626)


title: 37_MN


title: bk101 NR (ID 4624)


title: bk101 NR (ID 4610)


title: bk89 NR (ID 4602)


title: bk101 Area X (ID 4641)


title: 85_FSGS


title: 62_FSGS


title: bk89 LMAN (ID 4617)


title: 257_Other


title: bk101 NR (ID 4640)


title: 69_FSGS


title: 66_FSGS


title: bk89 LMAN (ID 4599)


title: 146_MN


title: 152_MN


title: 157_MCD


title: 130_MCD


title: 117_MCD


title: bk88 NC (ID 4572)


title: bk88 HVC (ID 4587)


title: bk98 Arco (ID 4564)


title: 36_MN


title: 129_MN


title: bk98 HVC (ID 4579)


title: bk88 Arco (ID 4556)


title: 109_MN


title: 200_Other


title: bk98 HVC (ID 4595)


title: 112_FSGS


title: bk88 NC (ID 4590)


title: bk98 NC (ID 4598)


title: bk88 HVC (ID 4571)


title: 150_MCD


title: bk88 NC (ID 4574)


title: bk98 RA (ID 4563)


title: bk88 Arco (ID 4558)


title: bk98 HVC (ID 4597)


title: bk98 Arco (ID 4566)


title: 99_MN


title: bk88 HVC (ID 4589)


title: 148_MN


title: bk98 NC (ID 4582)


title: bk98 HVC (ID 4581)


title: 39_MN


title: bk88 HVC (ID 4573)


title: bk98 RA (ID 4565)


title: bk98 NC (ID 4580)


title: 33_MCD


title: bk88 RA (ID 4557)


title: bk88 RA (ID 4555)


title: 123_MN


title: 72_FSGS


title: 144_MCD


title: 2_LivingDonor

source_name: Tubulointerstitial RNA from kidney biopsy of patient with LivingDonor


title: 19_FSGS


title: 1_LivingDonor


title: 118_MN


title: 3_LivingDonor


title: 229_MN


title: 6_LivingDonor


title: 132_MCD


title: 7_LivingDonor


title: 215_Other


title: bk88 NR (ID 4508)


title: 51_FSGS


title: bk98 Area X (ID 4547)


title: 179_Other


title: bk98 LMAN (ID 4531)


title: 1_FSGS


title: bk98 Stri (ID 4534)


title: bk88 NR (ID 4542)


title: 6_MCD


title: bk88 Stri (ID 4524)


title: bk98 Stri (ID 4550)


title: 11_MN


title: bk98 Area X (ID 4515)


title: bk88 LMAN (ID 4541)


title: 127_MN


title: bk88 Area X (ID 4509)


title: bk98 Stri (ID 4548)


title: 71_FSGS


title: bk88 NR (ID 4526)


title: bk98 NR (ID 4532)


title: 103_MN


title: 105_MN


title: bk98 LMAN (ID 4517)


title: bk98 Arco (ID 4560)


title: bk88 Arco (ID 4568)


title: bk98 Area X (ID 4533)


title: 107_MN


title: 154_MN


title: bk88 Arco (ID 4552)


title: 217_Other


title: 108_MCD


title: bk88 RA (ID 4567)


title: 92_FSGS


title: 196_Other


title: 189_Other


title: bk98 Area X (ID 4549)


title: 158_MCD


title: bk98 NC (ID 4594)


title: 5_FSGS


title: bk88 NC (ID 4586)


title: bk88 Stri (ID 4510)


title: bk98 Arco (ID 4578)


title: 87_FSGS


title: bk98 Arco (ID 4562)


title: bk98 RA (ID 4559)


title: 185_Other


title: bk88 Arco (ID 4554)


title: 147_MN


title: 124_MN


title: 78_FSGS


title: bk98 HVC (ID 4593)


title: bk98 RA (ID 4577)


title: bk88 HVC (ID 4585)


title: bk98 RA (ID 4561)


title: 237_Other


title: bk88 RA (ID 4569)


title: 95_FSGS


title: 57_Other


title: 170_Other


title: bk88 RA (ID 4553)


title: 252_Other


title: bk88 Arco (ID 4570)


title: bk98 NR (ID 4512)


title: 104_FSGS


title: 47_FSGS


title: 294_Other


title: 262_Other


title: 121_FSGS


title: bk98 Stri (ID 4546)


title: bk98 LMAN (ID 4527)


title: bk98 LMAN (ID 4543)


title: bk98 Stri (ID 4530)


title: 4_MCD


title: 244_Other


title: bk98 NR (ID 4514)


title: bk98 Area X (ID 4529)


title: 131_MN


title: 122_MCD


title: bk88 LMAN (ID 4521)


title: bk88 Stri (ID 4506)


title: bk98 LMAN (ID 4511)


title: bk98 LMAN (ID 4513)


title: bk88 Area X (ID 4505)


title: 101_MN


title: 14_MN


title: 119_MN


title: 245_Other


title: 293_Other


title: bk98 NR (ID 4544)


title: bk88 LMAN (ID 4503)


title: M12_repA_PROseq

city: Storrs

first: Luke

middle: A

last: Wojenski

state: CT

address: 181 Auditorium Drive unit 3197  ESB, Room 306B

department: Molecular & Cell Biology

institute: University of Connecticut

data_processing:
Library strategy: PRO-seq
PRO-seq and ATAC-seq raw reads were adapter-clipped, quality-trimmed (Q>=20), then trimmed to a max length of 36bp and reads less than 15bp were removed. PRO-seq reads were reverse complemented using the fastx_toolkit and ribosomal reads were removed by aligning to the human rDNA sequence with bowtie (with -v2 -k1 options). Remaining reads were aligned to a combined hg38-dm6 genome using bowtie (with -v2 -m1 options). BAM files were then converted to BED format using BEDtools. PRO-seq BED files were collapsed to single-bp 3' ends and ATAC-seq alignments were extended to a total length of 150bp for downstream analysis. BED files were converted to bedGraph files with BEDtools. BedGraphs were converted to bigWigs using KentUtils.
Genome_build: hg38,dm6

growth_protocol: HeLa-S3 and HEK293T cell lines were cultured in Dulbecco’s Modified Eagle’s Medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C and 5% CO2.

extract_protocol:
PRO-seq libraries were prepared as previously described (Mahat et al, 2016; Judd et al., 2020) with minor modifications. For each replicate timepoint, both floating cells in the growth medium and cells removed by scraping in 1x PBS were collected, pooled, and centrifuged at 1000xg for 5 min. Cells were resuspended in 1x PBS and 10% was removed for FACS analysis before completing the wash. 1mL of buffer P (10mM Tris-Cl pH 8.0, 10mM KCl, 250mM sucrose, 5mM MgCl2, 1mM EDTA, 0.05% Tween-20, 0.5mM DTT, 10% Glycerol) was used to gently resuspend cell pellets, before adding an additional 9mL of buffer P and incubating on a shaker for 5min. Permeabilization was assessed with trypan blue and samples not initially permeabilized were again incubated on a shaker with buffer P containing 0.05% NP-40 for 5min. Permeabilized cells were then centrifuged at 1000xg for 5min before resuspension in 1mL buffer F (50mM Tris-CL pH 8.0, 40% glycerol, 5mM MgCl2, 0.1 mM EDTA, 0.5mM DTT), transferred to a 1.5mL tube, and centrifuged at 1000xg for 5min. Finally, permeabilized cells were resuspended in 55µL of buffer F and 1µL of RNase-inhibitor was added before snap-freezing in liquid nitrogen and storage at -80°C.  0.9-4.5 x 106 permeabilized cells were mixed with permeabilized Drosophila S2 nuclei in all biotin-NTP run-ons (1 x 106 Dm nuclei in each A replicate and 5 x 104 in each B replicate). Run-on RNA was then base-hydrolyzed for 10min on ice and enriched with M280 streptavidin-beads. Full-length PRO-seq libraries were prepared as above with minor modifications. Nuclei were prepared in duplicate as above from asynchronous and 2hr mitotic-release cells, totaling ~1x107 nuclei per sample. Immediately following nuclei isolation, each sample was split into two separate run-on reactions. After nuclear run-on, TRIzol was added to stop the reaction and RNA was extracted. RNA was precipitated and resuspended in water, bound to streptavidin M280 beads and extensively washed. RNA was then eluted, extracted, bound to beads again, and washed. Nascent RNA was eluted from the beads and remaining ribosomal RNA was removed using riboZero Gold (Illumina). Samples split at the run-on step were then pooled and 0.01ng of total Drosophila RNA (rRNA-depleted) was added as a spike-in control. ATAC-seq was performed as previously described (Buenrostro, Giresi, et al, 2013) with minor modifications. 50,000 permeabilized cells were pelleted and then incubated for 30min in ATAC-seq reaction buffer at 37°C in a shaker at 1000rpm. DNA was then extracted with phenol-chloroform before size selection with AMPure beads.
PRO-seq libraries were prepared as previously described (Mahat et al, 2016; Judd et al., 2020) with minor modifications. Base-hydrolyzed run-on RNA underwent 3'-adapter ligation and a second bead binding. Both end-repair reactions and the 5’-ligation were all performed with nascent RNA still bound to the beads. These on-bead reactions were done in a total volume of 20µL with constant rotation before elution from the beads and the subsequent reverse transcription and PCR steps. Test amplifications were performed on 5% of the library and samples were amplified the ideal number of cycles. Following final amplification, libraries were PAGE-purified to remove adapter-dimers and select molecules below 650bp in size. Libraries were then sequenced on an Illumina NextSeq 550, producing single-end 75bp reads. Full-length PRO-seq libraries were constructed using the Illumina TRU-seq stranded low-input RNA-seq kit following the standard protocol and then sequenced on an Illumina NextSeq 550, producing paired-end 150bp reads. ATAC-seq libraries were test amplified using 5% of the sample following AMPure clean-up. Samples were amplified the ideal number of cycles and libraries were then sequenced on an Illumina NextSeq 550, producing single-end 75bp reads.

treatment_protocol: HeLa-S3 cells at 25-30% confluency were treated with 2mM thymidine for 24 hours, released in fresh medium for 3 hours, then treated with 100ng/mL nocodazole for 12 hours (Whitfield, et al, 2002). Mitotic cells were collected by shake-off, centrifuged and washed in 1x PBS, and then either grown on 15cm dishes in fresh medium for the corresponding time or immediately permeabilized (mitotic sample). Synchronization of HEK293T CDK1-AS cells was carried out by incubation with 100uM 1NMPP-1 for 20 hours (Gravells, et al, 2013).  To release cells into mitosis, cells were carefully washed twice with pre-warmed untreated media and returned to incubation at 37°C.  Cells were harvested at indicated timepoints. Hyperosmotic stress was induced by treating cells with media containing an additional 80mM KCl for 2 hours (Vilborg et al., 2017). Nocodazole-stress treatments were carried out by treating cells with media containing 100ng/mL nocodazole for 2 hours.

value: Thy-noc arrest +12hr

value: Cervical adenocarcinoma

value: Epithelial

tag: cell line


title: M12_repB_PROseq

tag: tissue


title: M8_repB_PROseq

tag: treatment

value: Thy-noc arrest +8hr


title: M8_repA_PROseq


title: M6_repB_PROseq

value: Thy-noc arrest +6hr


title: 100_MN

value: Tubulointerstitial compartment from kidney biopsy


title: 114_FSGS


title: M6_repA_PROseq


title: 13_MN


title: M3_repB_PROseq

value: Thy-noc arrest +3hr


title: M4_repB_PROseq

value: Thy-noc arrest +4hr


title: M3_repA_PROseq


title: 265_Other


title: 225_Other


title: M4_repA_PROseq


title: 292_Other


title: 91_MN


title: M2_repB_PROseq

value: Thy-noc arrest +2hr


title: 156_MN


title: 256_Other


title: 183_Other


title: 145_MCD


title: 128_MCD


title: 116_FSGS


title: 153_FSGS


title: 213_Other


title: 136_MN


title: M1.5_repB_PROseq

value: Thy-noc arrest +1.5hr


title: 199_Other


title: M1.5_repA_PROseq


title: 50_FSGS


title: 180_Other


title: M1_repB_PROseq

value: Thy-noc arrest +1hr


title: Mitosis_repB_PROseq

value: Thy-noc arrest


title: 226_Other


title: M1_repA_PROseq


title: 247_Other


title: M2_repA_PROseq


title: Mitosis_repA_PROseq


title: Async_repA_PROseq


title: WT-levn-3

city: Gainesville

first: Robert

last: Burne

state: Fl

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

description:
1C
repeat 3 of 3

data_processing:
Galaxy on HiPerGator
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Galaxy
Trimmed sequence reads were mapped to S. mutans genome
Read count extraction and normalization were performed
Supplementary files format and content: csv files that include combined raw counts of sequencing reads for each Sample

organism: Streptococcus mutans

source_name: WT UA159 strain

growth_protocol: Cells were grown in TV medium supplemented with 0.2% levan and grown in 37C 5% CO2 aerobic incubator

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit For Illumina following manufacturer's protocols.

tag: strain

value: WT UA159 strain

value: Growth onTV-levan


title: ΔfruB -levan-1

description:
2A
repeat 1 of 3

source_name: fruB mutant strain

value: fruB mutant strain


title: ΔfruB -levan-2

description:
2B
repeat 2 of 3


title: ΔfruB -levan-3

description:
2C
repeat 3 of 3


title: WT-levn-2

description:
1B
repeat 2 of 3


title: WT-levn-1

description:
1A
repeat 1 of 3


title: Epic: GSC11 try1 sh2 HOXA as2

type: genomic

hyb_protocol: Hybridisation on the arrays was performed by Integragen, SA following the Illumina Infinium HD methylation protocol.

scan_protocol: Standard protocol defined by Illumina for EPIC BeadChip.

data_processing:
GenomeStudio V2011.1
Matrix_signal_intensities.txt: Unmethylated and methylated signal intensities.
Matrix_Processed.txt: Normalized Average Beta (control normalization and background subtraction).

label: Cy5 and Cy3

source_name: Glioblastoma stem cell

label_protocol: Bisulfite conversion was performed by Integragen, SA.

extract_protocol: DNA was isolated from frozen cells using the QIAamp DNA Mini Kit (Qiagen), according to the manufacturer’s recommendations.

treatment_protocol: For glioblastoma stem cells, SMART vector targeting HOXA-AS2 (V3SH11246-245316977 or V3SH11246-245298993) was purchased from GE Healthcare (Little Chalfont, UK). Viral particles were produced and concentrated by the Vectorology platform of Montpellier (Biocampus, Montpellier, France). GSCs were infected using a multiplicity of infection of 10 and were snap frozen 120 h later. For H9NSC, Empty and HOXA-AS2 transcript containing pcDNA3.1 (+) vector (Invitrogen V79020, Illkrich, France) were transfected with Fugene HD (Promega, France) according manufacturer’s recommendations and stable integration selection made by adding geneticin in the culture medium (50ul/ml during 24h and then 200ul/ml).

value: Glioblastoma stem cells:GSC11


title: Epic: GSC11 try2 sh2 HOXA as2


title: Async_repB_PROseq


title: Epic: H9NSC try2 empty vector

source_name: Human Neural Stem Cells

value: Human Neural Stem Cells :H9NSC

value: empty vector


title: 155_MN


title: RAR-a derived AMs lactate purified 3 [LUMC-08-LactPur-D28-3]

city: Enschede

first: Carla

last: Cofiño Fabrés

address: Drienerlolaan 5

country: Netherlands

institute: University of Twente

description: rRNA depleted total RNA

data_processing:
Trimming of the reads and alignment was performed with seq2science (v0.4.0, https://doi.org/10.5281/zenodo.4451349).
Fastp (v0.20.1) trimmed the low quality 3’ ends and Salmon (v1.3.0) quant aligned the reads to the GRCh38.p13 genome from Ensembl, tximeta (v1.4.3) was used to generate the gene expression matrix.
Assembly: GRCh38.p13 (Ensembl)
Supplementary files format and content: "GRCh38.p13-counts.tsv" contains the raw gene counts

extract_protocol:
RNA (10^6 cells per sample) was extracted using the NucleoSpin RNA kit (Macherey-Nagel) according to manufacturer’s instructions.
Libraries were generated from 200 ng RNA using the KAPA-RNA HyperPrep kit with RiboErase (Roche) to remove ribosomal RNA, according to manufacturer’s instructions. Library amplification was performed with 11 cycles.
Libraries were multiplexed and sequenced on NextSeq500 Illumina to generate 38bp PE reads.

value: hESC-Atrial cardiomyocyte

tag: timepoint

value: Day 28 of differentiation

value: lactate purified


title: Epic: H9NSC try2 HOXA as2 expressing vector

value: HOXA as2 expressing vector


title: 138_MN

value: Tubulointerstitial compartment from kidney biopsy


title: 259_Other


title: 255_Other


title: 2_FSGS


title: Epic: H9NSC try1 HOXA as2 expressing vector


title: 125_MN


title: 209_Other


title: 120_FSGS


title: 113_MN


title: 159_MN


title: 88_FSGS


title: 275_Other


title: Epic: GSC11 try2 sh3 HOXA as2


title: RAR-a derived AMs lactate purified 2 [LUMC-07-LactPur-D28-2]

description: rRNA depleted total RNA


title: 77_FSGS


title: 97_MN


title: Epic: H9NSC try1 empty vector


title: U87 RNAseq IDHwt rep3

city: Warsaw

first: Adria-Jaume

last: Roura

address: Ludwika Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology, Polish Academy of Sciences

description:
data_norm_DESeq2_2.xlsx
RAG_F11_0010_P01_V11

data_processing:
In the RNAseq primary analysis, Illumina-specific adapters, low-quality 5’ and 3’ bases and short reads were removed in the FASTQ files using Trimmomatic tool.
RNA sequencing reads were aligned to a reference human genome sequence (hg38) using the STAR aligner.
Duplicates were identified and marked using Picard Tools and the resulting RNAseq mapped reads were summarized and counted by gene using HTseq, in paired-end mode, reverse-stranded mode and considering only reads with MAPQ values of 3 or higher and primary aligment.
Low-expressed genes were prefiltered and an a analysis of differentially expressed genes was performed using DESeq2.
In the ChIPseq primary analysis, reads with phred values >30 were retained for downstream analysis.
PCR duplicates were marked and removed using Picard Tools and the resulting reads were mapped to the human genome with the BWA-MEM algorithm.
Peaks were called with MACS2 software using default parameters, and secondary peak analysis was performed with the R libraries ChipSeeker and clusterProfiler.
Genome_build: hg38
Supplementary_files_format_and_content: DESeq2 normalized abundance measurements ouput
Supplementary_files_format_and_content: MACS2 narrow peaks files

source_name: U87 RNAseq IDHwt

extract_protocol:
RNA libraries were prepared using KAPA Stranded mRNAseq protocol
DNA libraries for ChIPseq were prepared using Qiaseq Ultra Low Input protocol

value: U87 human glioma cell line

value: brain

tag: genotype

value: wild type

tag: sample type

value: U87 MG

tag: transfection

value: untreated


title: RAR-a derived AMs lactate purified 1 [LUMC-05-LactPur-D28-1]

description: rRNA depleted total RNA


title: U87 RNAseq IDHwt rep2

description:
data_norm_DESeq2_2.xlsx
RAG_F11_0008_P01_V11


title: Sample_111 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

data_processing:
fastQC 0.11.5
fastqScreen 0.11.4
cutadapt 1.14 -m 50 -A CTGTCTCTTATA -a CTGTCTCTTATA
STAR 2.5.2.a --bamRemoveDuplicatesType UniqueIdentical --twopassMode Basic --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif
htseq-count --stranded=no --order=pos --mode=union
Genome_build: GRCh 38.86

source_name: Tubulointerstitium from kidney biopsy

extract_protocol:
Qiagen Allprep DNA/RNA Micro Kit (cat# 80284)
Takara SMART-Seq v4 Ultra Low Input RNA Kit (cat# 634891)
oligo(dT)

value: Tubulointerstitium from kidney biopsy

tag: disease

value: Focal Segmental Glomerulosclerosis


title: U87 RNAseq IDHmut rep2

description:
data_norm_DESeq2_2.xlsx
RAG_F31_0007_P01_V11

source_name: U87 RNAseq IDHmut

value: IDH1 knockdown

value: IDH1 mutant-U-87 isogenic cell line


title: U87 siCTRL RNAseq IDHmut rep3

description:
data_norm_DESeq2_1.xlsx
SRT_F31_0017_P01_V11

source_name: U87 siCTRL RNAseq IDHmut

value: REST-targeting siRNA


title: Sample_20 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Other Nephrotic Syndrome


title: 56_Other


title: Sample_37 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Membranous Nephropathy


title: U87 siREST RNAseq IDHwt rep3

description:
data_norm_DESeq2_1.xlsx
SRT_F11_0016_P01_V21

source_name: U87 siREST RNAseq IDHwt

value: siCTRL


title: U87 siREST RNAseq IDHmut rep3

description:
data_norm_DESeq2_1.xlsx
SRT_F31_0018_P01_V21

source_name: U87 siREST RNAseq IDHmut


title: U87 siCTRL RNAseq IDHwt rep3

description:
data_norm_DESeq2_1.xlsx
SRT_F11_0015_P01_V11

source_name: U87 siCTRL RNAseq IDHwt


title: U87 siREST RNAseq IDHwt rep2

description:
data_norm_DESeq2_1.xlsx
SRT_F11_0012_P01_V21


title: U87 RNAseq IDHmut rep3

description:
data_norm_DESeq2_2.xlsx
RAG_F31_0009_P01_V11


title: U87 siREST RNAseq IDHmut rep2

description:
data_norm_DESeq2_1.xlsx
SRT_F31_0014_P01_V21


title: Sample_55 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: U87 siCTRL RNAseq IDHmut rep2

description:
data_norm_DESeq2_1.xlsx
SRT_F31_0013_P01_V11


title: Sample_145 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Sample_72 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 211_Other


title: 282_Other


title: 68_FSGS

source_name: Tubulointerstitial RNA from kidney biopsy of patient with Focal Segmental Glomerulosclerosis


title: U87 siREST RNAseq IDHmut rep1

description:
data_norm_DESeq2_1.xlsx
SRT_F31_0010_P01_V21


title: 151_FSGS