title: upperbands barcode 7 calu-6

value: WT


title: whole-cell RNA, endoplasmic reticulum, Lsg1 siRNA, biol rep 3

status: Public on Mar 05 2025

type: SRA

city: Palo Alto

first: Maria

last: Barna

state: CA

address: 240 Pasteur Dr, BMI 4500

department: Genetics

country: USA

institute: Stanford University

description: Library name: ALIBi_Lsg1_KD_D3T

library_source: transcriptomic

data_processing:
For all RNA-seq analysis, the reference genome was generated using STAR/2.7.9a on the Mus musculus GRCm39 primary assembly with annotations from GENCODE vM27 and --sjdbOverhang 149. Alignment was performed with adapter sequences AGATCGGAAGAGCACA CGTCTGAACTCCAGTCAC and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAG ATCTCGGTGGTCGCCGTATCATT, and --clip3pAdapterMMp 0.1 0.1. Read counting was performed with htseq-count from htseq/0.11.2 -m intersection-nonempty -s reverse -i gene_id with annotations from GENCODE vM27. Genes were included in downstream analysis if the mean raw count across all samples was at least 5.  For RNA-seq analysis comparing cytosolic and ER ALIBi, differential abundance of read counts was performed using DESeq2 with a design matrix of “~ organelle + fraction + replicate + organelle:fraction” where “organelle” has values of “cytoplasm” or “endoplasmic reticulum” and “fraction” has values of “lysate” (whole-cell RNA fraction) or “eluate” (ribosome-bound RNA fraction). GO-Slim Cellular Component gene ontology terms were mapped using the PANTHER database. For comparison to existing ER transcriptome and translatome datasets from HEK293 cells, mouse gene IDs were converted based on the corresponding ENSEMBL gene ID or UCSC ID in each species, and mouse genes with no human homologs were excluded.  For RNA-seq analysis of ER ALIBi with Lsg1, Nmd3, or Gnl3 siRNA knockdown, differential abundance of read counts was analyzed separately for the whole-cell RNA fractions and for the ER ribosome-bound RNA fractions from cells transfected with ER-ALIBi using DESeq2 with a design matrix of “~replicate + sirna” where “sirna” has values representing either the siRNA-targeted gene or “scramble” (non-targeting control siRNA). For the Nmd3 and Gnl3 whole-cell RNA fractions, one out of three replicates for each condition was excluded from analysis because it appeared as an outlier in principle component analysis (PCA). Uniprot subcellular location codes were used to identify genes encoding membrane proteins or secreted/lumenal proteins.  For all RNA-seq analysis, adjusted p-values reflect multiple comparison correction using the Benjamini-Hochberg method, as implemented in DESeq2.
Assembly: Mus musculus GRCm39 primary assembly with annotations from GENCODE vM27
Supplementary files format and content: Tab-delimited HTSeq output files containing raw counts

molecule: polyA RNA

organism: Mus musculus

source_name: Rpl31-FTA E14Tg2a.4 mESCs

growth_protocol: E14Tg2a.4 mESCs were a gift from Thom Saunder’s lab (University of Michigan). Cell line identity was verified via short tandem repeat profiling performed by the American Type Culture Collection (ATCC, 137-XV, Manassas, VA). Cells were cultured in Knockout DMEM (ThermoFisher 10829-018) supplemented to a final concentration of 15% ES-qualified fetal bovine serum (MilliporeSigma ES-009-B), 1% non-essential amino acids (MilliporeSigma TMS-001-C), 2 mM L-glutamine (MilliporeSigma TMS-002-C), 1% penicillin/streptomycin (ThermoFisher 15140-122), 55 μM beta-mercaptoethanol (ThermoFisher 21985-023), and 1000 U/mL mouse leukemia inhibitory factor (mLIF, Gemini 400-495 10^7). Media was changed daily and cells were passaged every two days. Mycoplasma testing was performed according to the manufacturer’s instructions using the PromoKine PCR Mycoplasma Test Kit (PK-CA91-1096, Heidelberg, Germany).

extract_protocol:
Prior to affinity purification, an aliquot of cell lysate was reserved and mixed at a volume ratio of 1:9 with TRIzol (Thermo 15596-018) in an RNA non-stick tube. After affinity purification, eluate was mixed at a volume of 1:3 with TRIzol LS (Thermo 10296010) in an RNA non-stick tube. RNA was extracted using the DirectZol kit (R2060), following the manufacturer protocol without the on-column DNAse treatment. Extracted RNA was treated with Turbo DNAse (AM2239) per the manufacturer protocol and re-purified with an RNA Clean & Concentrator-5 column (R1016) per the manufacturer protocol. RNA concentration was estimated by Nanodrop 2000 (Thermo), and RNA integrity number (RIN) was assessed on an Agilent 2100 Bioanalyzer (total RNA pico) at the Stanford Protein and Nucleic Acid Facility.
For each sample, 750 ng of RNA was used as input for the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs E7760S) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs E7490) and indices from the NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and 2) (New England Biolabs E7335S, E7500S), per the manufacturer protocol with 9 cycles of PCR amplification. Libraries were assessed on an Agilent 2100 Bioanalyzer (DNA 1000) to have an amplicon size of ~300 bp. Libraries were sequenced by Novogene on a Novaseq X or X Plus with paired-end 150 bp reads to a total target depth of 20 - 26 million read pairs per sample.

treatment_protocol: Lysis buffer: 20 mM Tris pH 7.5 (ThermoFisher 15567027), 15 mM MgCl2 (ThermoFisher AM9530G), 150 mM NaCl (ThermoFisher AM9760G), 0.5 mM DTT (MilliporeSigma 43815), 2% n-dodecyl b-d-maltoside (MilliporeSigma W53094), 100 µg/mL cycloheximide, 1X Halt EDTA-Free Protease Inhibitor (ThermoFisher 78425), 0.1 U/µL Superase RNAse Inhibitor (ThermoFisher AM2696), 0.014 U/µL Turbo DNAse (ThermoFisher AM2239), 1 U/mL apyrase (New England Biolabs M0398L) in Ultrapure distilled water (ThermoFisher 10977-015).  RNAse removal buffer: 100 mM NaOH (MilliporeSigma 72068), 50 mM NaCl (ThermoFisher AM9760G) in Ultrapure distilled water (ThermoFisher 10977-015).  Salt wash: 100 mM NaCl (ThermoFisher AM9760G) in Ultrapure distilled water (ThermoFisher 10977-015).  Wash I: 20 mM Tris pH 7.5 (ThermoFisher 15567027), 15 mM MgCl2 (ThermoFisher AM9530G), 150 mM NaCl (ThermoFisher AM9760G), 0.5 mM DTT (MilliporeSigma 43815), 0.05% n-dodecyl b-d-maltoside (MilliporeSigma W53094), 100 µg/mL cycloheximide in Ultrapure distilled water (ThermoFisher 10977-015).  Wash II: 20 mM Tris pH 7.5 (ThermoFisher 15567027), 15 mM MgCl2 (ThermoFisher AM9530G), 300 mM NaCl (ThermoFisher AM9760G), 0.5 mM DTT (MilliporeSigma 43815), 0.05% n-dodecyl b-d-maltoside (MilliporeSigma W53094), 100 µg/mL cycloheximide in Ultrapure distilled water (ThermoFisher 10977-015).  Elution buffer (ThermoFisher 12575015): 1X AcTEV buffer, 1 mM DTT, 1% v/v AcTEV protease in Ultrapure distilled water (ThermoFisher 10977-015).  General precautions: once cells were transfected, exposure to ambient light and temperatures below 37 °C was minimized. Lysis, centrifugation, pulldown, and wash steps were carried out in a dark room with samples and buffers chilled to 4 C. Protein low-binding microcentrifuge tubes were used unless otherwise specified.  For samples not treated with siRNA, Rpl31-FTA mESCs were transfected with plasmids encoding the appropriate N- and C-terminal ALIBi fragments. 1.5 µg of each ALIBi plasmid was diluted in 100 µL Opti-MEM. In parallel, 7.5 µL of Lipofectamine 2000 was diluted in 100 µL Opti-MEM. The plasmid/Opti-MEM and Lipofectamine/Opti-MEM mixes were combined and incubated for 20 minutes at room temperature. For each condition, 3 million trypsinized cells were resuspended in 300 µL Opti-MEM, mixed with the plasmid-Lipofectamine complexes for 2 minutes at room temperature, and plated into one well of a 6-well plate containing 1.5 mL warmed media. Plates were incubated at 37 °C for 4 hours to allow reattachment before changing to fresh media. Media was changed 24 hours after transfection. At 48 hours after transfection, cells were changed to media containing 100 µg/mL cycloheximide and 50 uM biotin. Plates were immediately placed on a blue light transilluminator inside a 37 °C incubator for 15 minutes. Plates were washed once with ice-cold DPBS containing 100 µg/mL CHX, before adding 500 µL ice-cold lysis buffer per well. After incubating plates with lysis buffer on ice for 5 minutes, lysate was pipetted up and down six times in the plate with a P1000 pipet to fully dislodge cells and transferred to a 1.5 mL microcentrifuge tube. The lysate was further incubated for 15 minutes on ice, then clarified by centrifuging at 17,000 g for 3 minutes at 4 C. A 300 µL aliquot of the clarified lysate was added to pre-washed beads for affinity purification. For each sample, a 150 µL aliquot of beads was pre-washed as follows: the storage buffer was removed and the beads were washed twice with 500 µL of RNAse removal buffer, once with 500 µL of salt wash, and twice with 500 µL of Wash I. After adding clarified lysate, beads were rotated at 4 °C for 1 h, then washed once with a double bead volume of Wash I and twice with a double bead volume of Wash II. The beads were then incubated in one bead volume of elution buffer at room temperature for 1 h on a thermomixer at 800 rpm.  For samples with Lsg1, Nmd3, or Gnl3 siRNA knockdown and subsequent RNA-seq, a modified transfection was performed: 0.625 µg of each ALIBi plasmid and 26.7 pmol of Lsg1 siRNA (Horizon Discovery M-057491-01-0005), Nmd3 siRNA (Horizon Discovery M-051297-01-0005), Gnl3 siRNA (Horizon Discovery M-051664-01-0005), or control siRNA (Horizon Discovery D-001206-14-05) were diluted in 41.7 µL Opti-MEM. In parallel, 3.13 µL of Lipofectamine 2000 was diluted in 41.7 µL Opti-MEM. The plasmid/Opti-MEM and Lipofectamine/Opti-MEM mixes were combined and incubated for 20 minutes at room temperature. For each condition, 1.25 million trypsinized cells were resuspended in 125 µL Opti-MEM, mixed with the plasmid-Lipofectamine complexes for 10 minutes at room temperature, and plated into one well of a 6-well plate containing 2 mL warmed media. The remaining steps were performed as described above, with the modification that ALIBi activation, cell lysis, and affinity purification were performed 24 h after transfection.

tag: cell line

value: Rpl31-FTA E14Tg2a.4 mESCs

tag: cell type

value: mouse embryonic stem cells

tag: organelle

value: endoplasmic reticulum

tag: fraction

value: whole-cell

tag: sirna

tag: replicate

value: biol rep 3


title: Control_H4K16ac_ChIP_2

city: Al Ain

first: Suraiya

last: Ansari

address: Tawam

country: United Arab Emirates

institute: United Arab Emirates University

description:
rat embryo cortex  Control H4K16ac pulldown
H4K16Ac_CTRL_broad_peaks.broadPeak
H4K16Ac_CTRL.bw

library_source: genomic

data_processing:
Raw data checked for quality and aligned against rn6 genome using bowtie2 then peaks were called using macs2, visualised enriched regiongs with the help of deeptools
Assembly: rn6
Supplementary files format and content: .bw, narrowpeaks, broadpeaks

molecule: genomic DNA

organism: Rattus norvegicus

source_name: rat embryo brain cortex

extract_protocol:
The ChIP (Chromatin Immunoprecipitation) assay was carried following established protocols with minor modifications. Briefly, cells were crosslinked using 1% formaldehyde, and chromatin was fragmented by sonication. Immunoprecipitation was performed using specific antibodies (list of antibodies with catalogues) against H3K27me3, H3K4me3, H4K16Ac, total H3 and pan H4. Protein-DNA complexes were captured using protein A/G magnetic beads, washed, and eluted.
ChIP-seq libraries were prepared using NEBNext® Ultra™ II for DNA Library Prep (NEB #E7645) as per the manufacturer’s instructions. A final cleanup step was carried out using AMPure XP beads to ensure the library's quality. The DNA was then eluted from the beads and then subjected to quality control using a bioanalyzer before proceeding with the Next-Generation Sequencing (NGS

tag: tissue

value: rat embryo brain cortex

tag: strain

value: Wistar-rat

tag: chip antibody

tag: treatment

value: Control


title: upperbands barcode 6 H1299 cells

city: Ann Arbor

first: Andrew

last: Ludlow

state: Education

address: 830 N University Ave

institute: University of Michigan

data_processing:
Base-calling was performed by Guppy (v 3.1.5). Fastq files which were classified as passed (Phred score of 8) by the MinKNOW software were subsequently processed and analyzed.
Passed fastq files were aligned to human genome (GRCh38.p13) using minimap2 (v 2.14; [19, 20]) in SAM MD-tag aware mode. Sam files were sorted with SAMtools (v 1.13; [21]) followed by transcriptClean (v 2.0.2; [22]) for correction of read microindels (< 5 bp), mismatches, and noncanonical splice junctions (< 5 bp). Read annotation was performed with TALON (v 5.0; [23]), using the human Gencode v.38 reference annotation gtf with minimum alignment identity = 0.5 and coverage = 0.5. Identified transcripts were subsequently filtered using a minimum count threshold of N = 35 reads in K = 2 samples.
Assembly: human genome (GRCh38.p13)
Supplementary files format and content: The processed data files are .tsv count matrix files generated by TALON (Talon abundance)

molecule: total RNA

organism: Homo sapiens

source_name: lung cancer

extract_protocol:
RNA was extracted (Qiazol) from four human cell lines (iPSCs CHiPs 22 Takara, H1299, Calu-6, A549).
cDNAs were synthesized (SuperScript IV Thermo Fisher). Sequencing libraries were prepared following ONT kit instructions with TERT specific primers and ONT sequences with a total 30 cycles. DNA bands in the 2.5 kb – 4 kb range (upper bands; upper TERT) and bands below 2.5 kb to 0.5 kb (lower bands; lower TERT) were excised and purified via gel extraction (Qiagen). Next, size binned fractions were amplified with ONT barcoded primers 1-12 (4 cells lines by 3 replicates by 2 size bins) for 20 cycles. Barcoded libraries from each cell line were pooled at equal molar ratios for each size bin (upper bands or lower bands). The pooled libraries for each size bin were sequenced on its own flow cell (two R9.4.1 flowcells). Sequencing was performed with the standard 72 h sequencing protocol run on the MinION Mk1C, using the MinKNOW software (v 3.3.2). From lower TERT, 21.8 million reads were obtained and 16.4 million reads passed from all 12 samples. From upper TERT, 14.1 million reads were obtained, and 12.2 million reads were passed from all 12 samples. Base-calling was performed by Guppy (v 3.1.5). Fastq files which were classified as passed (Phred score of 8) by the MinKNOW software were subsequently processed and analyzed.

value: lung cancer

tag: genotype

value: untreated


title: Control_H4K16ac_ChIP_1


title: ribosome-bound RNA, endoplasmic reticulum, Lsg1 siRNA, biol rep 3

description: Library name: ALIBi_Lsg1_KD_D3E

value: ribosome-bound


title: Qu1-39_ZT1_100-2

city: St. Paul

first: kathleen

last: Greenham

state: MN

address: 1445 Gortner Avenue

institute: University of Minnesota

data_processing:
Raw reads were mapped to a concatenated reference consisting of B. rapa R500 v1.2 (Lou et al., 2020) and B. olerarcea TO1000 (Parkin, I.A.P. et al. (2014). Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biol. 15: R77)  genomes.
The reads were trimmed and filtered by quality using Trimmomatic v0.33, and alignment was performed using HISAT2 2.1.0.
Raw counts were normalized using the R package edgeR
Genes with no variance in expression across the time series were removed and are referred to as 'Processed Genes' which are available on the GreenhamLab GitHub.
We further filtered out lowly expressed genes by retaining those with a mean log2 FPKM greater than zero in at least one time point.
Gene expression for any missing replicate (See MetaData table) was imputed as the median of the two remaining replicates for that time point.
Assembly: We used a concatenated genome consisting of B. rapa R500 v1.2 (Lou, P. et al. (2020). Genetic and genomic resources to study natural variation in Brassica rapa. Plant Direct 4: e00285) and B. oleracea TO1000 (Parkin, I.A.P. et al. (2014). Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biol. 15: R77.) genomes.
Supplementary files format and content: Raw counts for each gene (rows) at every timepoint and treatment (columns). ZT refers to number of hours since lights on. Well watered plants are described as 100 and water limited plants are described at 20. Column names identify the 'accession'_'ZT'_'well watered/water limited'-'biological replicate'.
Supplementary files format and content: Normalized counts for each gene (rows) at every timepoint and treatment (columns). We require at least one sample (where a sample is a full time course for a single plant) to have mean FPKM greater than zero to be kept as a "processed gene". ZT refers to number of hours since lights on. Well watered plants are described as 100 and water limited plants are described at 20. Column names identify the 'accession'_'ZT'_'well watered/water limited'-'biological replicate'.

organism: Brassica napus

source_name: leaf

growth_protocol: Seeds were inbibed on wet whatman paper for five days before sowing into 4inch wide pots filled with MetroMix360. Growth conditions were 28C/22C day/night temperatures, 14 hour day lengths with 400 umol/m2/s light intensity and 40% relative humidity for the duration of the four week experiment.

extract_protocol:
Leaf tissue from the apex of the youngest leaf from three individual plants was collected at_ZT (Zeitgeber; hours after dawn) 1, 7, 13, and 19. RNA was isolated using the MagMAX Plant RNA Isolation Kit (Thermo Fisher Scientific, Waltham MA).
Illumina TruSeq Stranded mRNA HT

treatment_protocol: Plants were equally separated into two treatments for the duration of the experiment: 100% watering (well-watered) and 20% watering (water limited). The target watering weights were determined as described in Fahlgren et al. (Fahlgren et al., 2015). All pots were watered once to 100% capacity on the first day of the experiment, and then weighed twice per day to maintain a target water weight through day seven on the Bellwether phenotyping platform. Starting on day eight, water limited plants were allowed to dry down to 20% capacity and maintained at 20% capacity until day 14 (seven days after water limitation treatment began). At this point all watering amounts were increased by 10% for the rest of the experiment.

value: leaf

tag: temperature

tag: photoperiod

tag: timepoint (zt_=_hours_after_dawn)

value: Quantum NE011

value: Well watered, 100% full capacity


title: whole-cell RNA, endoplasmic reticulum, Lsg1 siRNA, biol rep 2

description: Library name: ALIBi_Lsg1_KD_D2T

value: biol rep 2


title: Qu1-39_ZT13_100-1


title: Control_H3K4me3_ChIP_3

description:
rat embryo cortex  Control H3K4me3 pulldown
H3K4me3_CTRL_narrow_peaks.narrowPeak
H3K4me3_CTRL.bw


title: upperbands barcode 11 iPSCs

source_name: iPSCs

value: iPSCs

value: iPS


title: ribosome-bound RNA, endoplasmic reticulum, Lsg1 siRNA, biol rep 2

description: Library name: ALIBi_Lsg1_KD_D2E

value: Rpl31-FTA E14Tg2a.4 mESCs


title: upperbands barcode 4 H1299 cells

value: WT


title: Control_H3K4me3_ChIP_2


title: whole-cell RNA, endoplasmic reticulum, Lsg1 siRNA, biol rep 1

description: Library name: ALIBi_Lsg1_KD_D1T

value: mouse embryonic stem cells

value: endoplasmic reticulum

value: biol rep 1


title: Qu1-39_ZT19_100-1


title: Control_H3K4me3_ChIP_1

value: rat embryo brain cortex


title: upperbands barcode 2 A549 cells

value: Lung cancer


title: ribosome-bound RNA, endoplasmic reticulum, Lsg1 siRNA, biol rep 1

description: Library name: ALIBi_Lsg1_KD_D1E


title: Control_H3K27me3_ChIP_3

description:
rat embryo cortex  Control H3K27me3 pulldown
H3K27me3_CTRL_broad_peaks.broadPeak
H3K27me3_CTRL.bw

value: Wistar-rat

value: Control


title: upperbands barcode 3 A549 cells

value: lung cancer

value: untreated


title: upperbands barcode 9 calu-6


title: Qu1-39_ZT1_20-1

value: leaf

value: Water limited, 20% full capacity


title: whole-cell RNA, endoplasmic reticulum, scramble siRNA, biol rep 3

description: Library name: ALIBi_Lsg1_KD_B3T

value: whole-cell

value: scramble

value: biol rep 3


title: Qu1-39_ZT1_20-2

value: Quantum NE011


title: Control_H3K27me3_ChIP_2


title: Control_H3K27me3_ChIP_1


title: 100 ng/mL TNF S8

city: Livermore

first: Aimy

last: Sebastian

address: 7000 East Ave

department: BBTD

institute: LLNL

description: Cell cultures treated with TNF

data_processing:
Sequence reads were aligned against human reference genome (hg38) using STAR.  After read alignment, the number of reads per gene locus was summarized with ‘featureCounts’ from Rsubread package, using hg38 gene annotation.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes read counts for each sample .

source_name: human iPSC derived glutamatergic and GABAergic neuron co-cultured with primary human astrocytes

extract_protocol:
Co-cultures were  untreated (0 pg/ml) or treated with TNF (25 pg/mL, 10 ng/mL, and 100 ng/mL ) for 7 days, and cell were lysed using RLT buffer containing β-mercaptoethanol, and the supernatant collected. Total RNA was extracted and purified from the collected supernatant using the RNAeasy mini spin columns (Qiagen).
Poly(A)+-enriched cDNA libraries were generated using the Illumina TruSeq RNA Library Prep kit v2 (Illumina Inc., Hayward, CA, USA).

treatment_protocol: Co-cultures were untreated (0 pg/ml) or treated with TNF (25 pg/mL, 10 ng/mL, and 100 ng/mL) for 7 days. TNF was replaced during normal half-media changes at Day 2 and 4 of exposure.

value: Treated with 100 ng/mL TNF


title: Qu1-39_ZT13_20-3


title: upperbands barcode 5 H1299 cells

value: WT


title: Qu1-39_ZT13_20-1


title: whole-cell RNA, endoplasmic reticulum, scramble siRNA, biol rep 2

description: Library name: ALIBi_Lsg1_KD_B2T

value: Rpl31-FTA E14Tg2a.4 mESCs

value: mouse embryonic stem cells

value: biol rep 2


title: 100 ng/mL TNF S7

description: Cell cultures treated with TNF

value: human iPSC derived glutamatergic and GABAergic neuron co-cultured with primary human astrocytes


title: upperbands barcode 1 A549 cells

value: Lung cancer


title: Qu1-39_ZT1_100-1

value: Well watered, 100% full capacity


title: ribosome-bound RNA, endoplasmic reticulum, scramble siRNA, biol rep 2

description: Library name: ALIBi_Lsg1_KD_B2E

value: endoplasmic reticulum

value: ribosome-bound


title: 100 ng/mL TNF S6

description: Cell cultures treated with TNF


title: ChIRP NCI-H460 ZFAS1

city: Houston

first: Hua-Sheng

last: Chiu

state: TX

address: 1102 Bates Avenue

institute: Baylor College of Medicine

description: Library name: Sample7

data_processing:
Sequencing data were processed according to the procedure published by Hwang et al. (PMID: 38132125).
Assembly: GRCh38
Supplementary files format and content: narrowPeak files adhering to the standard narrowPeak format specification

source_name: lung

extract_protocol:
The CHIP DNA was assessed by Agilent 2200 TapeStation (Agilent Technologies, USA) and Qubit (Thermo Fisher Scientific, USA).
The ChIRP-Seq libraries were constructed following the Illumina ChIRP-Seq library generation protocol.

value: lung

tag: Sex

value: male

value: large cell lung carcinoma


title: ChIRP NCI-H460 Input

description: Library name: Sample5


title: Qu1-39_ZT1_100-3

value: leaf


title: 100 ng/mL TNF S5

description: Cell cultures treated with TNF


title: Qu1-39_ZT7_20-2

value: Water limited, 20% full capacity


title: ChIRP ECC1 Input

description: Library name: Sample1

source_name: endometrial

value: endometrial

value: female

value: endometrial adenocarcinoma


title: Qu1-39_ZT13_100-3

value: Quantum NE011


title: 100 ng/mL TNF S4

description: Cell cultures treated with TNF

value: Treated with 100 ng/mL TNF


title: ribosome-bound RNA, endoplasmic reticulum, scramble siRNA, biol rep 3

description: Library name: ALIBi_Lsg1_KD_B3E

value: Rpl31-FTA E14Tg2a.4 mESCs

value: mouse embryonic stem cells

value: scramble

value: biol rep 3


title: 100 ng/mL TNF S3

description: Cell cultures treated with TNF

value: human iPSC derived glutamatergic and GABAergic neuron co-cultured with primary human astrocytes


title: Mouse tumor tissue, 14 days later, rAAV8-NC treatment dissociated mouse 3

city: changsha

first: Muqi

last: Liu

state: Hunan

address: No.138 Tongzipo Road, Yuelu District, Changsha

department: Institute for Cell Transplantation and Gene Therapy

country: China

institute: the 3rd Xiangya Hospital of Central South University

library_source: transcriptomic single cell

data_processing:
Raw reads were processed to generate gene expression profiles using CeleScope v1.5.2 (Singleron Biotechnologies) with default parameters. Briefly, Barcodes and UMIs were extracted from R1 reads and corrected. Adapter sequences and poly A tails were trimmed from R2 reads and the trimmed R2 reads were aligned against the GRCm38 (mm10) transcriptome using STAR(v2.6.1b). Uniquely mapped reads were then assigned to exons with FeatureCounts(v2.0.1). Successfully Assigned Reads with the same cell barcode, UMI and gene were grouped together to generate the gene expression matrix for further analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

extract_protocol:
The fresh tissues were stored in the sCelLiveTM Tissue Preservation Solution (Singleron) on ice after the surgery within 30 mins. The specimens were washed with Hanks Balanced Salt Solution (HBSS) for three times, minced into small pieces, and then digested with 3 mL sCelLiveTM Tissue Dissociation Solution (Singleron) by Singleron PythoN™ Tissue Dissociation System at 37 °C for 15 min. The cell suspension was collected and filtered through a 40-micron sterile strainer. Afterwards, the GEXSCOPE® red blood cell lysis buﬀer (RCLB, Singleron) was added, and the mixture[Cell: RCLB=1:2 (volume ratio)] was incubated at room temperature for 5-8 min to remove red blood cells. The mixture was then centrifuged at 300 × g 4 ℃ for 5 mins to remove supernatant and suspended softly with PBS.
Single-cell suspensions (2×105 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron) (Ref). Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: tumor


title: MKD 7_8_ROI_012

city: La Jolla

first: Maayan

last: Baron

address: 9500 Gilman Dr.

institute: University of California San Diego

description: Library name: DSP-1012550005121-B-E01

data_processing:
library strategy: GeoMx Seq. Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.
Supplementary files format and content: xlsx file: Segment Properties, Target Properties, Probe QC, Area Norm, Q3 Norm
Library strategy: Spatial Transcriptomics

source_name: skin

extract_protocol:
Samples were incubated with 1) DNA oligo-barcoded ISH probes containing a UV-photocleavable linker and 2) flourescently labeled antibodies for visualization of morphological structures. Regions of interest (ROI) within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform (see manual https://nanostring.com/wp-content/uploads/2022/06/MAN-10150-01-GeoMx-DSP-Manual-Slide-Preparation-User-Manual.pdf).
Each collection of oligo tags from one well (representing an ROI from the tissue section)  was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed ROIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio. Concentration and purity of the resulting libraries was measured using a Bioanalyzer high-sensitivity DNA  assay and Qubit high-sensitivity dsDNA kit. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x).

value: skin


title: Qu1-39_ZT19_100-3

value: Well watered, 100% full capacity


title: Mouse tumor tissue, 14 days later, rAAV8-NC treatment dissociated mouse 2


title: Qu1-39_ZT1_20-3


title: 100 ng/mL TNF S2

description: Cell cultures treated with TNF


title: 100 ng/mL TNF S1

description: Cell cultures treated with TNF


title: Mouse tumor tissue, 14 days later, rAAV8-NC treatment dissociated mouse 1


title: MKD 7_8_ROI_010

description: Library name: DSP-1012550005121-B-D11


title: 10 ng/mL TNF S8

description: Cell cultures treated with TNF

value: Treated with 10 ng/mL TNF


title: Qu1-39_ZT19_100-2


title: Mouse tumor tissue, 14 days later, rAAV8-Ccl3 treatment dissociated mouse 3


title: MKD 7_8_ROI_009

description: Library name: DSP-1012550005121-B-D10


title: Mouse tumor tissue, 14 days later, rAAV8-Ccl3 treatment dissociated mouse 2


title: whole-cell RNA, endoplasmic reticulum, scramble siRNA, biol rep 1

description: Library name: ALIBi_Lsg1_KD_B1T

value: endoplasmic reticulum

value: whole-cell

value: biol rep 1


title: 10 ng/mL TNF S7

description: Cell cultures treated with TNF


title: ChIRP ECC1 ZFAS1

description: Library name: Sample3

value: endometrial


title: MKD 7_8_ROI_008

description: Library name: DSP-1012550005121-B-D09


title: ribosome-bound RNA, endoplasmic reticulum, scramble siRNA, biol rep 1

description: Library name: ALIBi_Lsg1_KD_B1E

value: ribosome-bound


title: Qu1-39_ZT7_100-3

value: leaf


title: Mouse tumor tissue, 14 days later, rAAV8-Ccl3 treatment dissociated mouse 1


title: ATAC_KO_L1C_2

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

data_processing:
The raw reads were first cleaned with Trim Galore v0.6.7, and the cleaned reads were further mapped to mm10 genome by using bowtie2 v2.3.5.1. The duplicated reads were removed by using sambamba v1.0.0. After using samtools v1.10 for transfering BAM file to BED format, macs2 v2.2.8 was used for peak calling and bamCoverage v3.5.2 was used for constructing Bigwig files.
Assembly: mm10
Supplementary files format and content: Bigwig files

source_name: embryo

extract_protocol:
The growing oocytes (GO) were harvested from 12-day-old WT and Zar1/2 knockout female mice, GV stage oocytes were harvested from 4-week-old WT and Zar1/2 knockout female mice 32-48h after PMSG and the late 1-cell embryos were harvest from 4-week-old WT and Zar1/2 knockout female mice by IVF. All the oocytes/embryos were washed by 0.2% BSA containing PBS for 3 times after the zona pellucida being removed. Samples were used for the ATAC-seq library construction following the protocol of the High-Sensitivity Open Chromatin Profile Kit 2.0 (for Illumina®) (Novoprotein, cat#N248). For extraction in brief, cells were lysed by the lysis buffer for 10 minutes on ice, the washed by wash buffer by centrifuge at 4℃, 500g for 10min, and the nucleus were collected after removing the flow-up.
The nucleus were futher used for fragmentation at 37℃, 1000rpm for 30 minutes. After stopping the fragmentation, The DNA were cleaned by beads. Clean DNA fragments were further amplified and indexed in the same PCR reaction.

value: embryo

value: Zar1/2 knockout


title: Qu1-39_ZT13_20-2

value: Quantum NE011

value: Water limited, 20% full capacity


title: 10 ng/mL TNF S6

description: Cell cultures treated with TNF


title: MKD 7_8_ROI_007

description: Library name: DSP-1012550005121-B-D08


title: ATAC_KO_L1C_1


title: MKD 7_8_ROI_006

description: Library name: DSP-1012550005121-B-D07


title: Qu1-39_ZT19_20-1


title: 10 ng/mL TNF S5

description: Cell cultures treated with TNF


title: Qu1-39_ZT19_20-3


title: MKD 7_8_ROI_011

description: Library name: DSP-1012550005121-B-D12


title: MKD 7_8_ROI_005

description: Library name: DSP-1012550005121-B-D06


title: ATAC_WT_L1C_2

value: WT


title: 10 ng/mL TNF S4

description: Cell cultures treated with TNF


title: 10 ng/mL TNF S3

description: Cell cultures treated with TNF


title: MKD 7_8_ROI_004

description: Library name: DSP-1012550005121-B-D05


title: Qu1-39_ZT7_20-1


title: Qu1-39_ZT7_100-1


title: MKD 7_8_ROI_003

description: Library name: DSP-1012550005121-B-D04


title: ATAC_WT_L1C_1


title: 10 ng/mL TNF S2

description: Cell cultures treated with TNF


title: Qu1-39_ZT13_100-2


title: 10 ng/mL TNF S1

description: Cell cultures treated with TNF


title: ATAC_KO_GV_2

source_name: oocyte

value: oocyte


title: ATAC_KO_GV_1


title: MKD 7_8_ROI_001

description: Library name: DSP-1012550005121-B-D02


title: ATAC_WT_GV_2


title: st1-45_ZT13_100-3

value: Stellar DH JZ111


title: Qu1-39_ZT7_20-3


title: 25 pg/mL TNF S7

description: Cell cultures treated with TNF

value: human iPSC derived glutamatergic and GABAergic neuron co-cultured with primary human astrocytes

value: Treated with 25 pg/mL TNF


title: MKD 4_6_ROI_012

description: Library name: DSP-1012550005121-B-D01

value: skin


title: st1-45_ZT19_20-1


title: 25 pg/mL TNF S6

description: Cell cultures treated with TNF


title: ATAC_WT_GV_1


title: st1-45_ZT19_100-3

value: Well watered, 100% full capacity


title: MKD 4_6_ROI_011

description: Library name: DSP-1012550005121-B-C12


title: 25 pg/mL TNF S5

description: Cell cultures treated with TNF


title: MKD 4_6_ROI_009

description: Library name: DSP-1012550005121-B-C10


title: MKD 4_6_ROI_010

description: Library name: DSP-1012550005121-B-C11


title: 25 pg/mL TNF S3

description: Cell cultures treated with TNF


title: ATAC_WT_GO_2


title: MKD 7_8_ROI_002

description: Library name: DSP-1012550005121-B-D03


title: st1-45_ZT1_20-3


title: st1-45_ZT19_100-2


title: 25 pg/mL TNF S2

description: Cell cultures treated with TNF


title: ATAC_KO_GO_1


title: 25 pg/mL TNF S8

description: Cell cultures treated with TNF


title: 25 pg/mL TNF S4

description: Cell cultures treated with TNF


title: st1-45_ZT19_100-1


title: ATAC_WT_GO_1


title: MKD 4_6_ROI_008

description: Library name: DSP-1012550005121-B-C09


title: MKD 4_6_ROI_007

description: Library name: DSP-1012550005121-B-C08


title: Qu1-39_ZT7_100-2


title: MLO-Y4 cells, ASO_4

city: Hong Kong

first: Rongliang

last: WANG

address: PRINCE OF WALES HOSPITAL, DEPT OF Orthopaedics and Traumatology, RM 1003 LKS MEDICAL SCIENCE BLDG

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
Dr. Tom Data Visualisation Solution
Sequence reads were trimmed for adaptor sequence using Dr. Tom Data Visualisation Solution (parameter-Quality limit: 0.05)
Trimmed sequence read were mapped to Mus_musculus genome (GCF_000001635.26_GRCm38.p6) using HISAT, Bowtie2 of Dr. Tom Data Visualisation Solution
Read count extraction and normalization were performed using Dr. Tom Data Visualisation Solution
Assembly: mm10
Supplementary files format and content: tab-delimited rext files includes raw counts for each sample
Supplementary files format and content: tab-delimited rext files includes FPKM values for each sample

growth_protocol: MLO-Y4 cells were cultured in α-MEM supplemented with 2.5% fetal bovine serum (FBS), 2.5% calf serum (CS), and 1% penicillin/streptomycin/ glutamine.

extract_protocol:
RNA was harvested using Trizol. 1 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using the Qubit® ssDNA Assay Kit following manufacturer's protocols.

treatment_protocol: MLO-Y4 cells were seeded in a μ-Slide I Luer fluid chamber slide, treated with H19 silencing, and then exposed to a shear stress stimulation of 2 Pa for 4 cycles

value: Osteocyte cell line

value: H19 silenced

value: Fluid shear stress


title: MKD 4_6_ROI_006

description: Library name: DSP-1012550005121-B-C07


title: ATAC_KO_GO_2


title: 25 pg/mL TNF S1

description: Cell cultures treated with TNF


title: MLO-Y4 cells, ASO_3


title: st1-45_ZT13_100-2


title: st1-45_ZT1_100-2


title: MLO-Y4 cells, ASO_2


title: st1-45_ZT1_20-2


title: 0 pg/mL TNF S6

description: Cell cultures treated with TNF

value: Treated with 0 pg/mL TNF


title: MKD 4_6_ROI_004

description: Library name: DSP-1012550005121-B-C05


title: 0 pg/mL TNF S5

description: Cell cultures treated with TNF


title: MKD 4_6_ROI_003

description: Library name: DSP-1012550005121-B-C04


title: st1-45_ZT19_20-2


title: st1-45_ZT19_20-3


title: st1-45_ZT13_100-1


title: MKD 4_6_ROI_002

description: Library name: DSP-1012550005121-B-C03


title: 0 pg/mL TNF S4

description: Cell cultures treated with TNF


title: st1-45_ZT13_20-1


title: MLO-Y4 cells, control_4


title: MLO-Y4 cells, control_3


title: 0 pg/mL TNF S3

description: Cell cultures treated with TNF


title: 0 pg/mL TNF S2

description: Cell cultures treated with TNF


title: MKD 4_6_ROI_001

description: Library name: DSP-1012550005121-B-C02


title: MLO-Y4 cells, control_1


title: st1-45_ZT1_100-3


title: MKD 3_5_ROI_011

description: Library name: DSP-1012550005121-B-B12


title: 0 pg/mL TNF S1

description: Cell cultures treated with TNF


title: MKD 4_6_ROI_005

description: Library name: DSP-1012550005121-B-C06


title: 0 pg/mL TNF S7

description: Cell cultures treated with TNF


title: HFMsDM2D7

city: Utrecht

first: Frank

last: van Steenbeek

state: Select State/Province

address: Yalelaan 104

country: Netherlands

institute: Utrecht University

data_processing:
perform quality control on FastQ files (using FastQC)
align reads of each sample in a run against reference genome (using STAR) and add read groups (using Picard)
perform quality control on generated BAM files (using Picard)
count reads in features (using HTSeq-count)
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes raw count values for each Sample

source_name: hepatic organoid

extract_protocol:
RNeasy Mini Kit (Qiagen)
TruSeq Stranded mRNA Library Prep Kit (Illumina)

value: hepatic organoid

tag: group

value: liver organoids cultured on 3D hollow fiber membranes


title: MKD 3_5_ROI_010

description: Library name: DSP-1012550005121-B-B11


title: MLO-Y4 cells, control_2


title: shHMGA1-3

city: Kaifeng

first: Kaiyue

last: He

state: Henan

address: North section of Jinming Avenue, Longting District, Kaifeng City, Henan Province

institute: Henan University

data_processing:
SOAPnuke (V2.1.0) was used to filter the sequencing data
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Esophageal tissue

extract_protocol:
Total RNA was extracted using the Trizol(Invitrogen, CA, USA), RNA purity and integrity was monitored by NanoDrop 2000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and a Bioanalyzer 2100 system (Agilent Technologies, CA, USA). RNA contamination was assessed by 1.5% agarose gel.
The mRNA was purified from the total RNA using poly‐T oligo‐attached magnetic beads. Sequencing libraries were generated from the purified mRNA using the V AHTS Universal V6 RNA-seq Library Kit for MGI (V azyme, Nanjing, China) following the manufacturer's recommendations with unique index codes. The Library quantification and size was assessed using Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Subsequently, sequencing was performed on a MGI-SEQ 2000 platform by Frasergen Bioinformatics Co., Ltd. (Wuhan, China).

value: Esophageal tissue

value: esophageal squamous cell carcinoma


title: st1-45_ZT7_100-1

value: leaf


title: shHMGA1-2


title: MLO-Y4 cells, ASO_1


title: HFMsDM2D21


title: st1-45_ZT7_100-2


title: MKD 3_5_ROI_009

description: Library name: DSP-1012550005121-B-B10


title: st1-45_ZT7_20-2

value: Water limited, 20% full capacity


title: shHMGA1-1


title: MKD 3_5_ROI_008

description: Library name: DSP-1012550005121-B-B09


title: st1-45_ZT13_20-3


title: HFMsEM3D4


title: HFMsDM3D21


title: st1-45_ZT1_100-1


title: MKD 3_5_ROI_012

description: Library name: DSP-1012550005121-B-C01


title: shNC-2

value: shNC


title: MKD 3_5_ROI_007

description: Library name: DSP-1012550005121-B-B08


title: Se2-40_ZT1_20-2


title: MKD 3_5_ROI_006

description: Library name: DSP-1012550005121-B-B07


title: shNC-1


title: HFMsEM5D5


title: MKD 3_5_ROI_005

description: Library name: DSP-1012550005121-B-B06


title: HFMsDM3D14


title: MyD88KO-Rag1KO_3

city: Hershey

first: Marina

last: Chulkina

state: Pennsylvania

address: 500 University dr department of medicine

department: Medicine

institute: Penn State Health Medical Center

description:
Library name: T5
Column name in RagCounts.csv T5

data_processing:
Raw data were aligned to mouse genome (mm39) using STAR (v2.7.3a).
Assembly: mm39
Supplementary files format and content: RagCounts.csv file includes raw data counts for each sample

source_name: colonic mucosa

extract_protocol:
RNA was harvested using Rnaeasy kit (Qiagen).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: colonic mucosa


title: HFMsEM2D7


title: MKD 3_5_ROI_004

description: Library name: DSP-1012550005121-B-B05


title: MyD88KO-Rag1KO_2

description:
Library name: T4
Column name in RagCounts.csv T4


title: Se2-40_ZT19_20-2


title: Se2-40_ZT13_20-3


title: MKD 3_5_ROI_003

description: Library name: DSP-1012550005121-B-B04


title: Se2-40_ZT13_100-2


title: HFMsDM5D14


title: shNC-3


title: MyD88KO-Rag1KO_1

description:
Library name: T3
Column name in RagCounts.csv T3


title: MKD 3_5_ROI_002

description: Library name: DSP-1012550005121-B-B03


title: HFMsDM5D7


title: Control_Rag1KO_2

description:
Library name: C5
Column name in RagCounts.csv C5


title: Se2-40_ZT1_100-1


title: HFMsDM2D14


title: Se2-40_ZT7_20-2


title: Control_Rag1KO_3

description:
Library name: C7
Column name in RagCounts.csv C7


title: MKD 3_5_ROI_001

description: Library name: DSP-1012550005121-B-B02


title: MKD 1_2_ROI_012

description: Library name: DSP-1012550005121-B-B01


title: HFMsDM3D7


title: Se2-40_ZT7_100-1


title: HFMsDM5D21


title: MKD 1_2_ROI_011

description: Library name: DSP-1012550005121-B-A12


title: MyD88KO-Fib_3

description:
Library name: G26
Column name in Counts.csv G26

data_processing:
Raw data were aligned to mouse genome (mm39) using STAR (v2.7.3a).
Assembly: mm39
Supplementary files format and content: Counts.csv file includes raw data counts for each sample


title: DM2p5

value: liver organoids


title: MKD 1_2_ROI_009

description: Library name: DSP-1012550005121-B-A10


title: DM5p5


title: MKD 1_2_ROI_010

description: Library name: DSP-1012550005121-B-A11


title: Se2-40_ZT19_20-3


title: EM5p6


title: Se2-40_ZT13_100-3


title: Se2-40_ZT19_100-3


title: MyD88KO-Fib_1

description:
Library name: G22
Column name in Counts.csv G22


title: MKD 1_2_ROI_007

description: Library name: DSP-1012550005121-B-A08


title: EM2p6


title: MyD88KO-Fib_2

description:
Library name: G24
Column name in Counts.csv G24


title: Se2-40_ZT13_100-1


title: Control_3

description:
Library name: G15
Column name in Counts.csv G15


title: liver4

source_name: liver tissue

value: liver tissue


title: Control_Rag1KO_1

description:
Library name: C3
Column name in RagCounts.csv C3


title: MKD 1_2_ROI_006

description: Library name: DSP-1012550005121-B-A07


title: MyD88KO-Fib_4

description:
Library name: G27
Column name in Counts.csv G27


title: DM3p5


title: Control_2

description:
Library name: G14
Column name in Counts.csv G14


title: Se2-40_ZT19_20-1


title: MKD 1_2_ROI_005

description: Library name: DSP-1012550005121-B-A06


title: Se2-40_ZT13_20-2


title: EM3p6


title: MKD 1_2_ROI_004

description: Library name: DSP-1012550005121-B-A05


title: liver1


title: Se2-40_ZT1_100-2


title: MyD88KO_LPS_3

description:
Library name: D6
Column name in Counts_MyD88KO_vitro.csv D6

data_processing:
Raw data were aligned to mouse genome (mm39) using STAR (v2.7.3a).
Assembly: mm39
Supplementary files format and content: Counts_MyD88KO_vitro.csv file includes raw data counts for each sample

source_name: colonic mucosa, primary fibroblsts culture

value: LPS


title: MKD 1_2_ROI_008

description: Library name: DSP-1012550005121-B-A09

value: skin


title: MKD 1_2_ROI_003

description: Library name: DSP-1012550005121-B-A04


title: Se2-40_ZT19_100-2

value: Well watered, 100% full capacity


title: liver3


title: MyD88KO_LPS_2

description:
Library name: D5
Column name in Counts_MyD88KO_vitro.csv D5

value: colonic mucosa, primary fibroblsts culture


title: Se2-40_ZT7_20-3


title: MKD 1_2_ROI_002

description: Library name: DSP-1012550005121-B-A03


title: chrRNA_ovary_DMSO_24h_rep2

city: Beijing

first: Ming

last: Wang

state: Beijing

address: #15 Datun Road, Chaoyang, Beijing 100101, China

department: Key Laboratory of RNA Biology

institute: Institute of Biophysics, Chinese Academy of Sciences

description: Library name: Sample-18

data_processing:
Paired-end reads were processed with cutadapt v4.11 to remove adapters and low quality bases. Furthermore, 9 bp from both ends of reads were further trimmed.
Trimmed reads were aligned to dm6 with hisat2 v2.2.1 with default parameters
Strand-specific PRO-seq metaplot figures were generated using deeptools v3.5.1.
Assembly: mm10
Supplementary files format and content: bigWig files were generated using deepTools

molecule: nuclear RNA

organism: Drosophila melanogaster

source_name: ovary

growth_protocol: All fly strains were maintained at 25 °C and used for analysis at the age of 3–5 days.

extract_protocol:
Total RNA was isolated from dissected ovaries with TRIzol (Thermo Fisher Scientific, 15596018) and treated with the RQ1 RNase-Free DNase (Promega, #M6101).
RNA library was generated using an NSR method as described (Armour, C. D., 2009).

treatment_protocol: DMSO or auxin analog (5-Ad-IAA) treatment for 6 hr, 24 hr.

value: ovary

value: DMSO, 24 hr


title: MKD 1_2_ROI_001

description: Library name: DSP-1012550005121-B-A02


title: Se2-40_ZT13_20-1


title: Se2-40_ZT1_20-1


title: no_template_control

description: Library name: DSP-1012550005121-B-A01


title: MyD88KO_LPS_1

description:
Library name: D4
Column name in Counts_MyD88KO_vitro.csv D4


title: Se2-40_ZT7_100-2


title: chrRNA_ovary_5AdIAA_6h_rep2

description: Library name: Sample-16

value: IAA, 6 hr


title: Control_1

description:
Library name: G11
Column name in Counts.csv G11


title: Run02_Repli-ATAC_16h_noIP

city: Irvine

first: Annie

last: Trinh

address: 419 S. Circle View Drive

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description: Library name: Run02_Repli-ATAC_16h_noIP

data_processing:
For Repli-ATAC samples: Fastq files were trimmed using Trim Galore v0.4.462 and aligned using BWA63. Samtools v1.15.1 was used to remove mitochondrial DNA, duplicate reads, and unmapped reads. BamTools64 was used to remove reads containing more than 4 mismatches and reads with insert size greater than 2 kb. Peak calling was performed using MACS265. To quantify insert sizes, the CollectInsertSizeMetrics function of Picard66 was used with M=0.5 for each bam file.
Assembly: GRCh37 (hg19)
Supplementary files format and content: bigwig

growth_protocol: HUES64 hESCs were cultured on Geltrex (Thermo Fisher Scientific, A1413302) coated tissue culture plates with mTeSR (STEMCELL Technologies) media. Cells were incubated at 37°C with 5% CO2. Media was changed daily and cells were passaged upon reaching 80% confluency using ReleSR (STEMCELL Technologies).

extract_protocol:
For samples labeled with 50 µM BrdU or nocodazole, cells were lysed via incubation in SDS-PK buffer (0.5% wt/vol) sodium dodecyl sulfate (SDS), 50mM Tris-HCl, 0.01M EDTA, 1M NaCl and 0.2mg/ml proteinase K) at 56°C for 2h. Genomic DNA was isolated using phenol-chloroform extraction and isopropanol precipitation. For samples labeled with 500 µM BrdU, genomic DNA was isolated using the Puregene Cell Kit (8 x 10^8) (Qiagen, 158043) or Monarch® Genomic DNA Purification Kit (NEB, T3010S) according to the manufacturer’s instructions.
For Repli-ATAC samples: Collected cells were resuspended in 1 mL ice-cold DPBS buffer and 100K cells were transferred to and pelleted in a 1.5 mL Eppendorf tube at 4°C. The pellet was resuspended in 50 uL cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Nuclei were spun down immediately at 500 x g for 10 minutes at 4°C, supernatant was discarded, and the pellet was stored on ice.  To initiate the transposition reaction, the nuclei were resuspended in transposition reaction mix: 50 µL TD (2x reaction buffer, Illumina, FC-121-1030), 5 µL TDE1 (Nextera Tn5 Transposase, Illumina, FC-121-1030), and 45 µL nuclease-free water (Invitrogen, 10977-015). The transposition reaction was incubated on a thermomixer at 37°C for 30 minutes. Then, tagmented DNA was purified using the MinElute PCR Purification kit (Qiagen, 28004). To amplify transposed DNA fragments from each sample, the following was combined in a 0.2 mL PCR tube: 20 µL transposed DNA, 5 µL nuclease-free water, 25 µL NEBNext High-Fidelity 2x PCR Master Mix (NEB, M0541). Samples were placed in a thermal cycler for 1 cycle of 72°C for 5 minutes to allow for extension of both ends of the primer after transposition. DNA was purified using the MinElute PCR Purification kit.  10 µL of each sample was used for BrdU immunoprecipitation (IP) and 10 µL was stored aside at 4°C as a non-IP control. To denature the DNA in the IP sample, 490 µL of TE buffer was added and the sample was incubated at 95°C for 5 minutes on a thermomixer before cooling in an ice bath. The denatured DNA was collected and added to 60 µL of 10x IP buffer (28.5 mL nuclease-free water, 5 mL of 1 M sodium phosphate, pH 7.0, 14 mL of 5 M NaCl, and 2.5 mL of 10% wt/vol Triton X-100). 40 µL of 12.5 µg/mL anti-BrdU antibody (BD Biosciences, 555627) was added, and the sample was incubated for 1 hour at room temperature with constant rotation. The sample was centrifuged at 17,000 x g for 5 minutes at 4°C and the supernatant was completely removed. 750 µL of ice-cold 1x IP buffer was added before centrifuging and removing the supernatant again. The pellet was then resuspended in 200 µL digestion buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 0.5% SDS) with 0.25 mg/mL Proteinase K and incubated overnight at 37°C, then for 60 minutes at 56°C. Next, the sample was purified using AMPure XP Beads (Beckman Coulter, A63881) (2x bead volume) and resuspended in 20 µL Elution Buffer. To amplify the transposed DNA fragments, the following was combined in a 0.2 mL PCR tube: 20 µL transposed DNA, 2.5 µL 25 µM Custom Nextera PCR Primer 1, 2.5 µL 25 µM Custom Nextera PCR Primer 2, 25 µL NEBNext High-Fidelity 2x PCR Master Mix. The following PCR conditions were used: 1 cycle of 72°C for 5 minutes, 98°C for 30 seconds, followed by 5 cycles of 98°C for 10 seconds, 63°C for 30 seconds, 72°C for 1 minute. The PCR reaction was monitored using qPCR to stop amplification before saturation, in order to reduce GC and size bias61. Finally, the amplified library was purified using the MinElute PCR Purification kit.

treatment_protocol: For Repli-ATAC samples: HUES64 hESCs were grown to ~70% confluency in a 6-well plate. Different chase timepoints were assigned to different wells. To label nascent DNA, cell culture medium was replaced with 2 mL/well of mTeSR containing 50 µM BrdU. Cells were incubated in labeled medium for 1 hour at 37°C with 5% CO2. Next, 0h chase samples were washed once with mTeSR, and cells were collected using Accutase. For later chase timepoints, two washes with mTeSR were done before incubating the cells at 37°C with 5% CO2 until the chase timepoint was reached. Then, cells were collected using Accutase.

value: human embryonic stem cells

value: 50 µM BrdU, 1h pulse, 16h chase, no IP


title: MyD88KO_2

description:
Library name: D2
Column name in Counts_MyD88KO_vitro.csv D2


title: Se2-40_ZT1_100-3


title: MyD88KO_1

description:
Library name: D1
Column name in Counts_MyD88KO_vitro.csv D1


title: Se2-40_ZT7_100-3


title: chrRNA_ovary_5AdIAA_6h_rep1

description: Library name: Sample-15


title: Control_LPS_3

description:
Library name: C2
Column name in Counts_MyD88KO_vitro.csv C2


title: chrRNA_ovary_5AdIAA_24h_rep2

description: Library name: Sample-14

value: IAA, 24 hr


title: Run02_Repli-ATAC_1h_noIP

description: Library name: Run02_Repli-ATAC_1h_noIP

value: 50 µM BrdU, 1h pulse, 1h chase, no IP


title: Se2-40_ZT7_20-1

value: leaf


title: Control_3

description:
Library name: C1
Column name in Counts_MyD88KO_vitro.csv C1


title: PRO_ovary_untether_rep2

description: Library name: Sample-08

data_processing:
the read of paired-end reads was processed using cutadapt v4.1 to remove adaptors and low-quality bases (-q 25 -a CTGTCTCTTATACA).
As described in ChIP-seq above the processed data were aligned to spike-in genome using hisat2 v2.2.1108 with default parameters. The remaining reads were aligned to reference genome using hisat2 v2.2.1 with default parameters.
Strand-specific PRO-seq metaplot figures were generated using deeptools v3.5.1.
Assembly: mm10, dm6
Supplementary files format and content: bigWig files
Library strategy: PRO-Seq

source_name: Ovary

extract_protocol: PRO-seq was performed essentially as described (Judd et al., 2020).

treatment_protocol: DMSO or dTAG treatment for 60 min.

value: Ovary

value: untether


title: Ne3-38_ZT7_20-3

value: Water limited, 20% full capacity


title: Control_LPS_2

description:
Library name: B2
Column name in Counts_MyD88KO_vitro.csv B2


title: Run02_Repli-ATAC_0h_noIP

description: Library name: Run02_Repli-ATAC_0h_noIP

value: 50 µM BrdU, 1h pulse, 0h chase, no IP


title: chrRNA_ovary_5AdIAA_24h_rep1

description: Library name: Sample-13


title: Run02_Repli-ATAC_16h_IP

description: Library name: Run02_Repli-ATAC_16h_IP

value: 50 µM BrdU, 1h pulse, 16h chase, IP


title: Ne3-38_ZT13_20-3


title: Control_2

description:
Library name: B1
Column name in Counts_MyD88KO_vitro.csv B1


title: MyD88KO_3

description:
Library name: D3
Column name in Counts_MyD88KO_vitro.csv D3


title: PRO_ovary_untether_rep1

description: Library name: Sample-07


title: chrRNA_ovary_DMSO_24h_rep1

description: Library name: Sample-17


title: Ne3-38_ZT7_100-2


title: PRO_ovary_pcf11E_rep2

description: Library name: Sample-06

value: tethering Pcf11


title: Run02_Repli-ATAC_1h_IP

description: Library name: Run02_Repli-ATAC_1h_IP

value: 50 µM BrdU, 1h pulse, 1h chase, IP


title: Run02_Repli-ATAC_4h_noIP

description: Library name: Run02_Repli-ATAC_4h_noIP

value: 50 µM BrdU, 1h pulse, 4h chase, no IP


title: Ne3-38_ZT13_100-3

value: Well watered, 100% full capacity


title: Control_LPS_1

description:
Library name: A2
Column name in Counts_MyD88KO_vitro.csv A2

value: colonic mucosa, primary fibroblsts culture

value: LPS


title: Run02_Repli-ATAC_4h_IP

description: Library name: Run02_Repli-ATAC_4h_IP

value: 50 µM BrdU, 1h pulse, 4h chase, IP


title: Control_1

description:
Library name: A1
Column name in Counts_MyD88KO_vitro.csv A1


title: chrRNA_mESC_dTAG_60min_rep2

description: Library name: Sample-12

source_name: mESC

value: mESC

value: dTAG, 60  min


title: Run02_Repli-ATAC_0h_IP

description: Library name: Run02_Repli-ATAC_0h_IP

value: human embryonic stem cells

value: 50 µM BrdU, 1h pulse, 0h chase, IP


title: ChIP_ovary_untether_pol2_rep2

description: Library name: Sample-16

data_processing:
the paired-end reads were processed with cutadapt v4. to remove adaptors and low-quality bases (-m 20 -q 25 -a AGATCGGAAGAGC -A AGATCGGAAGAGC). Subsequently, the reads were aligned to the spike-in genome using bowtie2 v2.4.5 with default parameters.
PCR duplicates were removed using Picard (https://broadinstitute.github.io/picard/). MACS2 v2.2.7.1 was used to detect significant enrichments (broad peaks, q-value < 0.01). Peak calling was performed on combined reads from two biological replicates for each antibody.
Deeptools v3.5.1110 facilitated downstream analysis and visualization.
Assembly: mm10, dm6
Supplementary files format and content: bigWig

growth_protocol: The mESCs were cultured with KnockOut DMEM (ThermoFisher, 10829018) containing 15% FBS (Gibco), 100 U/mL penicillin-streptomycin, 1% L-glutamine, 100 μM β-mercaptoethanol, 1% nonessential amino acids, 100 U leukemia inhibiting factor, two inhibitors (3 μM CHIR99021 and 1 μM PD0325901), at 37 °C with 5% CO2

extract_protocol: ChIP-seq was carried out essentially as described (Jiang et al., 2020)

treatment_protocol: DMSO, dTAG treatment for 120 min

value: untethered


title: Ne3-38_ZT19_20-3

source_name: leaf

value: leaf


title: PRO_ovary_pcf11E_rep1

description: Library name: Sample-05

value: Ovary


title: Run01_Repli-ATAC_16h_noIP

description: Library name: Run01_Repli-ATAC_16h_noIP

value: 50 µM BrdU, 1h pulse, 16h chase, no IP


title: Run01_Repli-ATAC_4h_noIP

description: Library name: Run01_Repli-ATAC_4h_noIP


title: ChIP_ovary_untether_input_rep2

description: Library name: Sample-14


title: Run01_Repli-ATAC_1h_noIP

description: Library name: Run01_Repli-ATAC_1h_noIP

value: 50 µM BrdU, 1h pulse, 1h chase, no IP


title: Ne3-38_ZT13_20-2

value: Water limited, 20% full capacity


title: ChIP_ovary_untether_pol2_rep1

description: Library name: Sample-15


title: chrRNA_mESC_dTAG_30min_rep2

description: Library name: Sample-10

value: dTAG, 30  min


title: chrRNA_mESC_dTAG_30min_rep1

description: Library name: Sample-09


title: Ne3-38_ZT1_20-2


title: Run01_Repli-ATAC_0h_noIP

description: Library name: Run01_Repli-ATAC_0h_noIP

value: 50 µM BrdU, 1h pulse, 0h chase, no IP


title: Ne3-38_ZT13_100-1


title: ChIP_ovary_untether_input_rep1

description: Library name: Sample-13


title: chrRNA_mESC_dTAG_15min_rep2

description: Library name: Sample-08

value: dTAG, 15 min


title: Run01_Repli-ATAC_16h_IP

description: Library name: Run01_Repli-ATAC_16h_IP

value: 50 µM BrdU, 1h pulse, 16h chase, IP


title: Ne3-38_ZT19_20-2


title: chrRNA_mESC_dTAG_15min_rep1

description: Library name: Sample-07


title: ChIP_ovary_pcf11E_pol2_rep2

description: Library name: Sample-12

value: tethering Pcf11


title: Ne3-38_ZT1_100-1

value: Well watered, 100% full capacity


title: Ne3-38_ZT19_20-1


title: ChIP_ovary_pcf11E_input_rep1

description: Library name: Sample-09


title: ChIP_ovary_pcf11E_pol2_rep1

description: Library name: Sample-11


title: Run01_Repli-ATAC_4h_IP

description: Library name: Run01_Repli-ATAC_4h_IP

value: 50 µM BrdU, 1h pulse, 4h chase, IP


title: chrRNA_mESC_dTAG_120min_rep1

description: Library name: Sample-05

value: mESC

value: dTAG, 120 min


title: chrRNA_mESC_dTAG_60min_rep1

description: Library name: Sample-11

value: dTAG, 60  min


title: Run01_Repli-ATAC_0h_IP

description: Library name: Run01_Repli-ATAC_0h_IP

value: human embryonic stem cells

value: 50 µM BrdU, 1h pulse, 0h chase, IP


title: ChIP_ovary_pcf11E_input_rep2

description: Library name: Sample-10


title: chrRNA_mESC_dTAG_120min_rep2

description: Library name: Sample-06


title: Ne3-38_ZT7_100-1

value: leaf


title: Ne3-38_ZT7_100-3


title: Run01_Repli-ATAC_1h_IP

description: Library name: Run01_Repli-ATAC_1h_IP

value: 50 µM BrdU, 1h pulse, 1h chase, IP


title: chrRNA_mESC_DMSO_60min_rep2

description: Library name: Sample-04

value: DMSO


title: Ne3-38_ZT19_100-2


title: RNC-NC-O1-1

first: Yingjie

address: Research Center C701,School of Medicine,Zhejiang University,866 Yuhangtang Road

department: Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine

institute: Zhejiang University

data_processing:
Library strategy: RNC-seq
FANSe used for basecalling.
Reads were mapped using FANSe3.
After reads were aligned onto the genome, we analysis the unique reads binding regions of genes were identified using “edgeR” strategy.
Genome_build: Human RefSeq-RNA hg19, 20190603.
Supplementary_files_format_and_content: Translation_Ratio.txt: Tab-delimited text file includes translation ratios.

source_name: H9 cells

growth_protocol: H9 cells were cultured in mTeSR1 feeder free medium, 5% CO2, 37℃.

extract_protocol:
Briefly, samples were collected as described (Lian, X., et al., PLoS Genet 2016).
Libraries were constructed as described (Lian, X., et al., PLoS Genet 2016).

treatment_protocol: Cells were treated with siOCT4 and hypoxia condition (1% O2).

value: NC

tag: condition

value: Hypoxia (1% oxygen)


title: panc_NC_3

city: 广州

first: li

last: xiaobai

address: 381 Wushan Road, Tianhe District, Guangzhou

institute: south china university of technology

description:
Library name: panc_NC_3_Clean_Data1.fq.gz
FPKM.panc_NC_3

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Homo sapiens reference genome using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: GRCh38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

tag: cell line

value: Human pancreatic cancer cells


title: RNC-NC-O1-2


title: chrRNA_mESC_DMSO_60min_rep1

description: Library name: Sample-03


title: Ne3-38_ZT19_100-1

data_processing:
Raw reads were mapped to a concatenated reference consisting of B. rapa R500 v1.2 (Lou et al., 2020) and B. olerarcea TO1000 (Parkin, I.A.P. et al. (2014). Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biol. 15: R77)  genomes.
The reads were trimmed and filtered by quality using Trimmomatic v0.33, and alignment was performed using HISAT2 2.1.0.
Raw counts were normalized using the R package edgeR
Genes with no variance in expression across the time series were removed and are referred to as 'Processed Genes' which are available on the GreenhamLab GitHub.
We further filtered out lowly expressed genes by retaining those with a mean log2 FPKM greater than zero in at least one time point.
Gene expression for any missing replicate (See MetaData table) was imputed as the median of the two remaining replicates for that time point.
Assembly: We used a concatenated genome consisting of B. rapa R500 v1.2 (Lou, P. et al. (2020). Genetic and genomic resources to study natural variation in Brassica rapa. Plant Direct 4: e00285) and B. oleracea TO1000 (Parkin, I.A.P. et al. (2014). Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biol. 15: R77.) genomes.
Supplementary files format and content: Raw counts for each gene (rows) at every timepoint and treatment (columns). ZT refers to number of hours since lights on. Well watered plants are described as 100 and water limited plants are described at 20. Column names identify the 'accession'_'ZT'_'well watered/water limited'-'biological replicate'.
Supplementary files format and content: Normalized counts for each gene (rows) at every timepoint and treatment (columns). We require at least one sample (where a sample is a full time course for a single plant) to have mean FPKM greater than zero to be kept as a "processed gene". ZT refers to number of hours since lights on. Well watered plants are described as 100 and water limited plants are described at 20. Column names identify the 'accession'_'ZT'_'well watered/water limited'-'biological replicate'.


title: panc_NC_2

description:
Library name: panc_NC_2_Clean_Data1.fq.gz
FPKM.panc_NC_2

tag: cell type


title: chrRNA_mESC_DMSO_0min_rep2

description: Library name: Sample-02


title: panc_NC_1

description:
Library name: panc_NC_1_Clean_Data1.fq.gz
FPKM.panc_NC_1


title: chrRNA_mESC_DMSO_0min_rep1

description: Library name: Sample-01


title: RNA-NC-O1-1

data_processing:
FANSe used for basecalling.
Reads were mapped using FANSe3.
After reads were aligned onto the genome, we analysis the unique reads binding regions of genes were identified using “edgeR” strategy.
Genome_build: Human RefSeq-RNA hg19, 20190603.
Supplementary_files_format_and_content: Translation_Ratio.txt: Tab-delimited text file includes translation ratios.


title: panc_lac_3

description:
Library name: panc_lac_3_Clean_Data1.fq.gz
FPKM.panc_lac_3

value: l-lactate


title: Ne3-38_ZT19_100-3


title: PRO_mESC_dTAG_60min_rep2

description: Library name: Sample-04

value: dTAG 60 min


title: RNC-siOCT4-O20-2

value: Normoxia (20% oxygen)


title: panc_lac_1

description:
Library name: panc_lac_1_Clean_Data1.fq.gz
FPKM.panc_lac_1


title: RNC-siOCT4-O20-1


title: PRO_mESC_DMSO_60min_rep2

description: Library name: Sample-02

value: DMSO 60 min


title: RNA-siOCT4-O20-2


title: RNA-siOCT4-O20-1


title: PRO_mESC_dTAG_60min_rep1

description: Library name: Sample-03


title: Ne3-38_ZT13_20-1

value: Water limited, 20% full capacity


title: Ne3-38_ZT1_20-3


title: PRO_mESC_DMSO_60min_rep1

description: Library name: Sample-01


title: Ne3-38_ZT1_20-1


title: ChIP_mESC_dTAG_120min_pol2_rep2

description: Library name: Sample-08

value: dTAG


title: RNC-NC-O20-2


title: Ne3-38_ZT7_20-2


title: RNA-NC-O1-2


title: MKN74 cells, Control2

city: Changsha

first: Fen

address: 138 Tongzipo Road

institute: The Third Xiangya Hospital, Central South University

description:
Library name: Sample 11
Column name in gene_count_matrix.txt: MNC2

data_processing:
Libraries were deeply sequenced on the Illumina Novaseq 6000 according to the activity and expected data volume.
The raw RNA-Seq sequence reads were trimmed using Trimmomatic (version 0.39) to remove low-quality reads and adapters.
Assembly: Trimmed data were first evaluated by the software “FastQC” (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) with the default parameter and then aligned with Hisat2 (version 2.1.0) against the human (hg38) genome guided by GENCODE gene annotation (version 34) with the default parameter.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

growth_protocol: RPMI-1640 mediu mcontaining 10% fetal bovine serum

extract_protocol:
Total RNA was isolated using RNAiso Plus (Total RNA extraction reagent, Thermo Fisher Scientific) according to the manufacturer’s instructions and quantified by the NanoDrop 2000 spectrophotometer.
TruSeq Stranded Total Sample Preparation Kit (Illumina, 20020596) was used for sequencing library construction.

value: gastric epithelial cells

value: WT

value: subculture


title: MKN74 cells, Control3

description:
Library name: Sample 12
Column name in gene_count_matrix.txt: MNC3


title: Ne3-38_ZT1_100-2

extract_protocol:
Leaf tissue from the apex of the youngest leaf from three individual plants was collected at_ZT (Zeitgeber; hours after dawn) 1, 7, 13, and 19. RNA was isolated using the MagMAX Plant RNA Isolation Kit (Thermo Fisher Scientific, Waltham MA).
Illumina TruSeq Stranded mRNA HT

value: Well watered, 100% full capacity


title: MKN74 cells, KD3

description:
Library name: Sample 9
Column name in gene_count_matrix.txt: MKD3

value: TRAF1 knockdown


title: RNC-NC-O20-1


title: Mu4-37_ZT7_20-2

value: leaf


title: ChIP_mESC_dTAG_120min_pol2_rep1

description: Library name: Sample-07

value: mESC


title: RNA-NC-O20-2


title: ChIP_mESC_dTAG_120min_input_rep2

description: Library name: Sample-06


title: MKN74 cells, KD2

description:
Library name: Sample 8
Column name in gene_count_matrix.txt: MKD2


title: Mu4-37_ZT13_100-2


title: ChIP_mESC_dTAG_120min_input_rep1

description: Library name: Sample-05


title: panc_lac_2

description:
Library name: panc_lac_2_Clean_Data1.fq.gz
FPKM.panc_lac_2


title: RNA-NC-O20-1


title: Mu4-37_ZT13_20-1


title: MKN74 cells, Control1

description:
Library name: Sample 10
Column name in gene_count_matrix.txt: MNC1


title: MKN74 cells, KD1

description:
Library name: Sample 7
Column name in gene_count_matrix.txt: MKD1


title: RNC-siOCT4-O1-2


title: HGC27 cells, OE3

description:
Library name: Sample 6
Column name in gene_count_matrix.txt: HOE3

value: TRAF1 overexpressing


title: ChIP_mESC_DMSO_pol2_rep1

description: Library name: Sample-03

value: DMSO


title: RNC-siOCT4-O1-1

value: Hypoxia (1% oxygen)


title: Mu4-37_ZT1_20-2


title: RNA-siOCT4-O1-2


title: Mu4-37_ZT19_100-1


title: ChIP_mESC_DMSO_input_rep1

description: Library name: Sample-01


title: HGC27 cells, OE2

description:
Library name: Sample 5
Column name in gene_count_matrix.txt: HOE2


title: ChIP_mESC_DMSO_input_rep2

description: Library name: Sample-02


title: HGC27 cells, OE1

description:
Library name: Sample 4
Column name in gene_count_matrix.txt: HOE1


title: Mu4-37_ZT19_100-3


title: Mu4-37_ZT13_20-2


title: CnT_mESC_dTAG_60min_pol2_rep2

description: Library name: Sample-12

data_processing:
the paired-end reads were processed with cutadapt v4. to remove adaptors and low-quality bases (-m 20 -q 25 -a AGATCGGAAGAGC -A AGATCGGAAGAGC). Subsequently, the reads were aligned to the spike-in genome using bowtie2 v2.4.5 with default parameters.
PCR duplicates were removed using Picard (https://broadinstitute.github.io/picard/). MACS2 v2.2.7.1 was used to detect significant enrichments (broad peaks, q-value < 0.01). Peak calling was performed on combined reads from two biological replicates for each antibody.
Deeptools v3.5.1110 facilitated downstream analysis and visualization.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol: CUT&Tag assays were performed as described (Kaya-Okur et al., 2019) with some modifications.

treatment_protocol: DMSO, dTAG treatment for 60 min or 120 min


title: HGC27 cells, Control3

description:
Library name: Sample 3
Column name in gene_count_matrix.txt: HNC3


title: HGC27 cells, Control1

description:
Library name: Sample 1
Column name in gene_count_matrix.txt: HNC1


title: CnT_mESC_dTAG_60min_pol2_rep1

description: Library name: Sample-11


title: Mu4-37_ZT7_20-1


title: aPD-1 Treatment, Totalseq

city: Chicago

first: Tony

last: Pan

address: 5801 S Ellis Ave

institute: University of Chicago

description:
10x Genomics
aPD1_1 Totalseq
pd1_1_matrix.mtx.gz
pd1_1_features.tsv.gz
pd1_1_barcodes.tsv.gz
pd1_2_matrix.mtx.gz
pd1_2_features.tsv.gz
pd1_2_barcodes.tsv.gz
pd1_3_matrix.mtx.gz
pd1_3_features.tsv.gz
pd1_3_barcodes.tsv.gz

library_source: other

data_processing:
Alignment, filtering, barcode counting, UMI counting, and demultiplexing was performed using CellRanger v. 6.1.2
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: protein

source_name: Tumor

extract_protocol:
Dissected primary tumors were washed with cold RPMI 1640 media (Cytiva, SH30027.01), then minced into 1-mm cubes. Tumor cubes were then resuspended in RPMI 1640 media (Cytiva, SH30027.01) containing 1 mg/mL collagenase IV (Sigma-Aldrich, C5138-100MG) and 20 µg/mL DNase I (Sigma-Aldrich, 10104159001). before incubated for 30 min at 37 °C. The tumor pieces were then ground and filtered through 70 µm cell strainers (Corning, 431751) to get single cells. Then the filtered cells were resuspended by Red Cell Lysis Buffer (eBioscience, 00-4300-54) and incubated for 5 min at room temperature to lyse red blood cells. Lysis was stopped by adding an equal volume of RPMI 1640 media (Cytiva, SH30027.01). Cells were washed twice with RPMI 1640 media (Cytiva, SH30027.01) and filtered through 70 cell strainers (Corning, 431751). Cells from the tumor suspension were washed with cold FACS buffer (PBS, 2% BSA, 0.05% sodium azide). Fc receptors were blocked with Mouse TruStain FcX (BioLegend, 101319) at 1:50 dilution for 5 minutes at 4°C. Then, cells were incubated for 30 minutes at 4°C in the dark with a staining solution containing Total-seq anti-mouse Hashtag antibodies (BioLegend, 155861 for Hash 1, 155863 for Hash 2, 155865 for Hash 3) and AF647-labeled anti-CD45 (clone 30-F11, BioLegend, 103124) for leukocyte detection. The three replicates for each experimental condition were each labeled with a different Hashtag antibody. Subsequently, stained cells were conjugated with LIVE/DEAD Fixable Near-IR viability dye (Invitrogen, L34975) at 1:1000 dilution in PBS for 5 minutes at room temperature. Finally, cells were washed three times in cold cell media (RPMI, 10 % FBS) before fluorescence-activated cell sorting (BD Biosciences, FACSAria Fusion). CD45+ sorting gates were drawn based on a fluorescence-minus-one control on the AF647 channel. Up to 13000 CD45+ live cells were sorted from each sample. Sequences for the hashtag antibodies are as follows: ACCCACCAGTAAGAC, GGTCGAGAGCATTCA, CTTGCCGCATGTCAT.
The Hashtag-labeled sorted cells from each replicate were pooled and partitioned into droplets for single-cell omics assays via Chromium Next GEM Single -Cell 5’ Reagent Kits v2 (10x Genomics, 1000263). RNA-seq libraries were prepared according to manufacturer protocols. Libraries for Hashtagging were prepared via the 5’ Feature Barcode Kit (10x Genomics, 1000256). All libraries were quantified via the Qubit dsDNA HS Assay Kit (Invitrogen, Q32851), quality-checked for fragment sizes via high-sensitivity D5000 screentapes (Agilent, 5067-5592), pooled, and sequenced (Illumina, NextSeq 550).
scRNA-seq, Total-seq

value: CD45+ cells

value: Tumor

value: BALB/c 4T1

tag: age

value: 11 weeks old

tag: library type

value: mux

tag: hashtags

value: aPD1_1 Totalseq - hashtag1, aPD1_2 Totalseq - hashtag2, aPD1_3 Totalseq - hashtag3


title: Combo (Sting + aPD-1) Treatment, Totalseq

description:
10x Genomics
Combo1 Totalseq
combo1_matrix.mtx.gz
combo1_features.tsv.gz
combo1_barcodes.tsv.gz
combo2_matrix.mtx.gz
combo2_features.tsv.gz
combo2_barcodes.tsv.gz
combo3_matrix.mtx.gz
combo3_features.tsv.gz
combo3_barcodes.tsv.gz

value: Combo (Sting + aPD-1)

value: Combo1 Totalseq - hashtag1, Combo2 Totalseq - hashtag2, Combo3 Totalseq - hashtag3


title: HGC27 cells, Control2

description:
Library name: Sample 2
Column name in gene_count_matrix.txt: HNC2

value: gastric epithelial cells

value: WT


title: Mu4-37_ZT19_100-2

value: Well watered, 100% full capacity


title: ChIP_mESC_DMSO_pol2_rep2

description: Library name: Sample-04


title: Sting Treatment, Totalseq

description:
10x Genomics
Sting1 Totalseq
sting1_matrix.mtx.gz
sting1_features.tsv.gz
sting1_barcodes.tsv.gz
sting2_matrix.mtx.gz
sting2_features.tsv.gz
sting2_barcodes.tsv.gz
sting3_matrix.mtx.gz
sting3_features.tsv.gz
sting3_barcodes.tsv.gz

value: Sting

value: Sting1 Totalseq - hashtag1, Sting2 Totalseq - hashtag2, Sting3 Totalseq - hashtag3


title: PBS Control Treatment, Totalseq

description:
10x Genomics
PBS1 Totalseq
pbs1_matrix.mtx.gz
pbs1_features.tsv.gz
pbs1_barcodes.tsv.gz
pbs2_matrix.mtx.gz
pbs2_features.tsv.gz
pbs2_barcodes.tsv.gz
pbs3_matrix.mtx.gz
pbs3_features.tsv.gz
pbs3_barcodes.tsv.gz

value: PBS Control

value: PBS1 Totalseq - hashtag1, PBS2 Totalseq - hashtag2, PBS3 Totalseq - hashtag3


title: N3

city: Guangzhou

first: Fang

last: Zhou

address: No. 106 Zhongshan Second Road

institute: Guangdong Provincial People's Hospital

description:
Library name: Sample 6
N3

data_processing:
Disembarkation data quality control
Matching genome
Modification site recognition
Differential site recognition
Functional enrichment analysis
Assembly: HG19
Supplementary files format and content: The table contains the circRNA information identified by each sample

source_name: PDAC tissue

extract_protocol:
total RNA was extracted from tissue samples and RNA samples were detected in three main ways: (1) Nanodrop performs preliminary concentration and purity detection of RNA (2) Qubit accurately quantified RNA concentration (3) Agilent 2100 accurately detects RNA integrity (RIN value)
ncRNA-Seq

value: PDAC tissue


title: Mu4-37_ZT7_20-3

first: kathleen

address: 1445 Gortner Avenue

institute: University of Minnesota

value: leaf

value: Water limited, 20% full capacity


title: CnT_mESC_dTAG_60min_pcf11E-FLAG_rep2

description: Library name: Sample-10

value: mESC

value: dTAG 60 min


title: CnT_mESC_dTAG_60min_pcf11E-FLAG_rep1

description: Library name: Sample-09


title: Mu4-37_ZT19_20-1


title: N2

description:
Library name: Sample 5
N2


title: RNA-siOCT4-O1-1

tag: sirna

value: Hypoxia (1% oxygen)


title: CnT_mESC_dTAG_120min_pol2_rep2

description: Library name: Sample-08

value: dTAG 120 min


title: Mu4-37_ZT13_100-3

tag: tissue


title: Mu4-37_ZT19_20-3


title: N1

description:
Library name: Sample 4
N1


title: CnT_mESC_dTAG_120min_pol2_rep1

description: Library name: Sample-07


title: T3

description:
Library name: Sample 3
T3


title: Sting Treatment, RNA

description:
10x Genomics
Sting1 RNA
sting1_matrix.mtx.gz
sting1_features.tsv.gz
sting1_barcodes.tsv.gz
sting2_matrix.mtx.gz
sting2_features.tsv.gz
sting2_barcodes.tsv.gz
sting3_matrix.mtx.gz
sting3_features.tsv.gz
sting3_barcodes.tsv.gz

value: CD45+ cells

value: Tumor

tag: strain

value: BALB/c 4T1

value: 11 weeks old

value: gex

value: Sting1 RNA - hashtag1, Sting2 RNA - hashtag2, Sting3 RNA - hashtag3


title: CnT_mESC_DMSO_60min_pol2_rep2

description: Library name: Sample-06

value: DMSO 60 min


title: Mu4-37_ZT13_20-3


title: T2

description:
Library name: Sample 2
T2


title: Mu4-37_ZT7_100-2

value: Well watered, 100% full capacity


title: T1

description:
Library name: Sample 1
T1


title: Mu4-37_ZT7_100-3


title: PBS Control Treatment, RNA

description:
10x Genomics
PBS1 RNA
pbs1_matrix.mtx.gz
pbs1_features.tsv.gz
pbs1_barcodes.tsv.gz
pbs2_matrix.mtx.gz
pbs2_features.tsv.gz
pbs2_barcodes.tsv.gz
pbs3_matrix.mtx.gz
pbs3_features.tsv.gz
pbs3_barcodes.tsv.gz

value: PBS Control

value: PBS1 RNA - hashtag1, PBS2 RNA - hashtag2, PBS3 RNA - hashtag3


title: CnT_mESC_DMSO_60min_pcf11E-FLAG_rep2

description: Library name: Sample-04


title: Mu4-37_ZT1_100-2


title: CnT_mESC_DMSO_60min_pcf11E-FLAG_rep1

description: Library name: Sample-03


title: 211 e1

city: Philadelphia

first: Sydney

last: Shaffer

state: PA

address: 421 Curie Boulevard

department: Penn Medicine

institute: University of Pennsylvania

description:
Library name: 211_e1
10X Genomics

data_processing:
Raw Illumina base call files were demultiplexed and converted into FASTQ files using CellRanger mkfastq v5.0.0. The resulting FASTQ files were loaded into STARsolo v2.7.9a for alignment to the 10x reference GRCh38-2020-A53. Count matrices generated with the –soloFeatures GeneFull argument were used for downstream analyses.
For Sample A211, CellRanger v5.0.0 was used to align and process reads
Assembly: GRCh38-2020-A53
Supplementary files format and content: *barcodes.tsv: 10X cell barcodes
Supplementary files format and content: *features.tsv: Tab-separated list of features (genes or clone) and identifiers for type of feature.
Supplementary files format and content: *matrix.mtx: Sparse count matrix

source_name: Esophagus

extract_protocol:
Fresh pinch biopsies were washed twice in DPBS before being coarsely chopped with a scalpel and transferred into 0.5 mL DPBS solution containing 0.1 WU ml-1 Liberase TH (Roche, 5401151001) and 0.5 U ml-1 RQ1 DNase I (Promega, M6101). The samples were incubated at 37 °C in successive 10-minute rounds with gentle vortexing every 2 minutes and trituration every 5 minutes. At the end of each round of incubation, large tissue pieces were spun down in a microcentrifuge and the supernatant containing single cells was passed through a 70-um cell strainer fitted onto a 50-mL conical tube containing 8 mL DPBS + 1% bovine serum albumin (BSA; Sigma-Aldrich, A7906) in DPBS on ice. 0.5 mL fresh dissociation solution was added to the tissue at the beginning of each incubation step. The samples were further filtered through the 0.35 um cell-strainer cap of a FACS tube and single cells were pelleted by centrifugation at 400g for 4 minutes at 4 °C. Samples were washed twice in 1 mL DPBS + 0.04% BSA and finally resuspended in 50 uL DPBS + 0.04% BSA, at which point they were counted in 0.2% trypan blue (Gibco, 15250061) in preparation for 10x Genomics Chromium Next GEM Single Cell 3’ v3.1 library preparation. For the frozen BE biopsy from Patient 2, the tissue was quickly thawed at 37 °C and rinsed three times in DPBS + 10% fetal bovine serum (GE, SH30396.03) before being dissociated and filtered as described above. After the final filtering step, dead cells were removed with the Dead Cell Removal Kit (Miltenyi Biotec, 130-090-101) following the manufacturer’s protocol.
Single-cell suspensions were loaded onto a 10x Chromium Controller for GEM generation of approximately 5,000-10,000 cells for each sample. 10x Genomics Chromium Next GEM Single Cell 3’ v3.1 Dual Index library preparation was performed following the manufacturer’s protocol. Library quality was confirmed on an Agilent 2100 Bioanalyzer Instrument using the High Sensitivity DNA Kit (Agilent). Libraries were paired-end sequenced on an Illumina NextSeq 550 with 28 cycles for Read 1 and 43 cycles for Read 2, as well as 10 cycles for both indices.

value: Esophagus


title: Combo (Sting + aPD-1) Treatment, RNA

description:
10x Genomics
Combo1 RNA
combo1_matrix.mtx.gz
combo1_features.tsv.gz
combo1_barcodes.tsv.gz
combo2_matrix.mtx.gz
combo2_features.tsv.gz
combo2_barcodes.tsv.gz
combo3_matrix.mtx.gz
combo3_features.tsv.gz
combo3_barcodes.tsv.gz

value: Combo (Sting + aPD-1)

value: Combo1 RNA - hashtag1, Combo2 RNA - hashtag2, Combo3 RNA - hashtag3


title: Donor 6 Cas9  post tumor rechallenge

city: Los Angeles

first: Yiqian

last: Gu

address: 5000D Terasaki Life Sciences Building

institute: University of California Los Angeles

description:
Library name: CB3-CAS9
Libraries were sequenced 2 X 50

data_processing:
Paired-end sequencing reads were aligned to the hg38 reference genome using Bowtie2 (v2.4.2). Alignments were converted to BAM format, sorted, and indexed using samtools (v1.15).
Mitochondrial reads were excluded using samtools, followed by removal of multi-mapped reads.
Blacklisted genomic regions (ENCODE hg38 blacklist) were filtered using bedtools (v2.30.0). The resulting BAM files were re-sorted and indexed.
For ATAC-seq peak calling, MACS2 (v2.2.9.1) was employed.
Peaks from all samples were concatenated, merged using bedtools merge, and read counts per peak were quantified using bedtools multicov.
Assembly: hg38
Supplementary files format and content: .bed file

source_name: Cord blood

growth_protocol: Freshly isolated Cord blood derived NK cells were grown with exogenous human interleukin-2 (IL-2; 200 U/ml) and K562-based feeder cells (1:2; E:T ratio). The day 6 expanded NK cells were electroporated with either Cas9 alone or DNMT3a sgRNAs or TET2KO sgRNAs to generate respective gene(s) KO cells. After KO conformation, the day 13 expanded Cas9 or KO NK cells were rechallenged (n=5 times) with THP1-GFP+ AML cells (2:1;E:T ratio) over 10 days. The  NK cells were flow sorted after tumor rechallenge completion and used for bulk ATAC sequencing.

extract_protocol:
50,000 nuclei from NK cells were subjected to tagmentation using Tagment DNA enzyme (Illumina) followed by library preparation.
Libraries from tagmented DNA were prepared using NEBNext High-Fidelity 2x PCR Master Mix and indexing Primers followed by DNA cleanup using SPRISelect beads (Beckman Coulter).

value: Cord blood

value: Primary Human cells

value: Human  Cord blood derived NK

value: Cas9  WT

value: Tumor rechallenged with THP1 cells


title: CnT_mESC_DMSO_120min_pol2_rep2

description: Library name: Sample-02

value: mESC

value: DMSO 120 min


title: aPD-1 Treatment, RNA

description:
10x Genomics
aPD1_1 RNA
pd1_1_matrix.mtx.gz
pd1_1_features.tsv.gz
pd1_1_barcodes.tsv.gz
pd1_2_matrix.mtx.gz
pd1_2_features.tsv.gz
pd1_2_barcodes.tsv.gz
pd1_3_matrix.mtx.gz
pd1_3_features.tsv.gz
pd1_3_barcodes.tsv.gz

value: CD45+ cells

value: Tumor

value: BALB/c 4T1

value: 11 weeks old

value: aPD1_1 RNA - hashtag1, aPD1_2 RNA - hashtag2, aPD1_3 RNA - hashtag3


title: 211 c10

description:
Library name: 211_c10
10X Genomics

source_name: Stomach

value: Stomach


title: Donor 6 DNMT3a KO post tumor rechallenge

description:
Library name: CB3-DNMT3KO
Libraries were sequenced 2 X 50

value: DNMT3a KO


title: Mu4-37_ZT1_100-3

city: St. Paul

last: Greenham

value: leaf

value: Well watered, 100% full capacity


title: Mu4-37_ZT7_100-1


title: CnT_mESC_DMSO_120min_pol2_rep1

description: Library name: Sample-01


title: 211 be7

description:
Library name: 211_be7
10X Genomics

source_name: Barrett's Esophagus

value: Barrett's Esophagus


title: Donor 5 DNMT3a KO post tumor rechallenge

description:
Library name: CB122-DNMT3KO
Libraries were sequenced 2 X 50

value: Cord blood


title: 199 s10

description:
Library name: 199_s10
10X Genomics

value: Esophagus


title: CnT_mESC_DMSO_60min_pol2_rep1

description: Library name: Sample-05

value: DMSO 60 min


title: Mu4-37_ZT1_20-3

value: Water limited, 20% full capacity


title: Mu4-37_ZT19_20-2


title: Donor 5 Cas9. post tumor rechallenge

description:
Library name: CB122-CAS9
Libraries were sequenced 2 X 50

value: Primary Human cells

value: Human  Cord blood derived NK

value: Cas9  WT

value: Tumor rechallenged with THP1 cells


title: SL2i, SLC16A1 clone 1, rep2

city: New York

first: Lydia

last: Finley

state: NY

address: 430 E 67th St

department: Cell Biology Program

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: SL2i_SLC16A1-1_2
MCT1_RNA-seq_raw_counts.csv

data_processing:
FASTQ files were aligned to the reference genome using DRAGEN v3.10 (Illumina) to generate BAM files.
Raw counts matrix was generated using featureCounts/subread.
Assembly: GRCm39
Supplementary files format and content: Processed data files include raw counts for each sample in CSV format.

source_name: mouse ESC

growth_protocol: Mouse ESC lines were maintained in Knockout DMEM with 10% fetal bovine serum. Cells were mainted either with leukemia ininhibitory factor (LIF) or LIF + inhibitors against GSK3B and MEK (2i).

extract_protocol:
RNA was isolated using TRIzol (Thermo Fisher Scientific, 15596018) according to the manufacturer’s instructions.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500 ng of total RNA with RIN values of 9.3-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR.

treatment_protocol: For experiments, medium was switched to a mixture of DMEM and NB with 10% dialyzed fetal bovine serum and 0.2 mM sodium pyruvate.

value: mouse ESC


title: 199 s8

description:
Library name: 199_s8
10X Genomics


title: 199 s6

description:
Library name: 199_s6
10X Genomics


title: Gr2-35_ZT13_20-3

value: Gruener Schnittrohl_BnASSYST-219


title: Donor 5 TET2 KO post tumor rechallenge

description:
Library name: CB122-TET2KO
Libraries were sequenced 2 X 50


title: 211 be4

description:
Library name: 211_be4
10X Genomics


title: Donor 4 DNMT3a KO  post tumor rechallenge

description:
Library name: CB121-DNMT3KO
Libraries were sequenced 2 X 50


title: 199 s4

description:
Library name: 199_s4
10X Genomics


title: Donor 3 TET2 KO. post tumor rechallenge

description:
Library name: CB120-TET2KO
Libraries were sequenced 2 X 50


title: SL2i, chr8A, rep1

description:
Library name: SL2i_CHR8A_1
MCT1_RNA-seq_raw_counts.csv


title: Donor 4 Cas9. post tumor rechallenge

description:
Library name: CB121-CAS9
Libraries were sequenced 2 X 50


title: Gr2-35_ZT13_100-3


title: 199 s3

description:
Library name: 199_s3
10X Genomics


title: SL2i, SLC16A1 clone 2, rep2

description:
Library name: SL2i_SLC16A1-2_2
MCT1_RNA-seq_raw_counts.csv


title: 199 s5

description:
Library name: 199_s5
10X Genomics


title: SL2i, SLC16A1 clone 1, rep1

description:
Library name: SL2i_SLC16A1-1_1
MCT1_RNA-seq_raw_counts.csv


title: Gr2-35_ZT13_100-2


title: Gr2-35_ZT1_100-1


title: Donor 3 DNMT3a KO post tumor rechallenge

description:
Library name: CB120-DNMT3KO
Libraries were sequenced 2 X 50


title: SL2i, chr8A, rep2

description:
Library name: SL2i_CHR8A_2
MCT1_RNA-seq_raw_counts.csv


title: 199 s1

description:
Library name: 199_s1
10X Genomics


title: Gr2-35_ZT1_20-2


title: Donor 4 TET2 KO. post tumor rechallenge

description:
Library name: CB121-TET2KO
Libraries were sequenced 2 X 50


title: SL, SLC16A1 clone 2, rep3

description:
Library name: SL_SLC16A1-2_3
MCT1_RNA-seq_raw_counts.csv


title: Donor 3 Cas9. post tumor rechallenge

description:
Library name: CB120-CAS9
Libraries were sequenced 2 X 50


title: 198 s10

description:
Library name: 198_s10
10X Genomics


title: SL, SLC16A1 clone 2, rep2

description:
Library name: SL_SLC16A1-2_2
MCT1_RNA-seq_raw_counts.csv


title: Gr2-35_ZT7_20-3


title: SL, SLC16A1 clone 2, rep1

description:
Library name: SL_SLC16A1-2_1
MCT1_RNA-seq_raw_counts.csv


title: 198 s8

description:
Library name: 198_s8
10X Genomics


title: SL2i, SLC16A1 clone 2, rep1

description:
Library name: SL2i_SLC16A1-2_1
MCT1_RNA-seq_raw_counts.csv


title: SL, SLC16A1 clone 1, rep2

description:
Library name: SL_SLC16A1-1_2
MCT1_RNA-seq_raw_counts.csv


title: Gr2-35_ZT7_100-3


title: Donor 2 Cas9 post tumor rechallenge

description:
Library name: CB116-CAS9
Libraries were sequenced 2 X 50


title: Donor 2 DNMT3a KO. post tumor rechallenge

description:
Library name: CB116-DNMT3KO
Libraries were sequenced 2 X 50


title: Gr2-35_ZT19_100-2


title: 198 s6

description:
Library name: 198_s6
10X Genomics


title: SL, SLC16A1 clone 1, rep1

description:
Library name: SL_SLC16A1-1_1
MCT1_RNA-seq_raw_counts.csv


title: Gr2-35_ZT7_20-2


title: Donor 1 Ca9 post tumor rechallenge

description:
Library name: CB1-CAS9
Libraries were sequenced 2 X 50


title: SL, SLC16A1 clone 1, rep3

description:
Library name: SL_SLC16A1-1_3
MCT1_RNA-seq_raw_counts.csv


title: 198 s5

description:
Library name: 198_s5
10X Genomics


title: 196 scj2

description:
Library name: 196scj2
10X Genomics

source_name: Squamocolumnar Junction

value: Squamocolumnar Junction


title: SL, chr8A, rep2

description:
Library name: SL_CHR8A_2
MCT1_RNA-seq_raw_counts.csv


title: Donor 2 TET2 KO. post tumor rechallenge

description:
Library name: CB116-TET2KO
Libraries were sequenced 2 X 50


title: 198 s1

description:
Library name: 198_s1
10X Genomics


title: SL, chr8A, rep3

description:
Library name: SL_CHR8A_3
MCT1_RNA-seq_raw_counts.csv


title: Gr2-35_ZT1_100-3


title: 196 scj1

description:
Library name: 196scj1
10X Genomics


title: 198 s4

description:
Library name: 198_s4
10X Genomics


title: SL, chr8A, rep1

description:
Library name: SL_CHR8A_1
MCT1_RNA-seq_raw_counts.csv


title: Gr2-35_ZT7_100-1


title: Gr2-35_ZT7_100-2


title: 5'-NRXN1-973-iGLUT-Vehicle-BiolRep-2

first: GANG

last: FANG

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: Library name: 973-DIV21-iGLUT-Veh-R2

data_processing:
Reads were first mapped by STAR v2.7.2a to a hg38/mm10 hybrid reference.
All reads unique mapped to hg38 were exracted.
Read counts of each gene were counted by featureCounts v2.0.3.
Assembly: hg38
Supplementary files format and content: CSV file of raw read counts

growth_protocol: For iGLUT neurons, at day -1 hiPSCs expanded in 10cm dishes were dissociated with accutase (StemCell Technologies, #07920), washed and pelleted with a 1:4 ratio of accutase to DMEM for 5 min at 1000 rcf, and re-suspended with StemFlex media containing ROCK inhibitor, THX (10µM/mL; Sigma Aldrich, SML1045). The hiPSCs are then co-transduced with TetO-Ngn2-Puro (Addgene #79049) or TetO-Ngn2-Neo (Addgene# 99378) and UCb-rtTA (legacy vector from the lab of Fred Gage) and seeded at 1.0-1.5x106 cells in 1.5mL per well on 6-well plates were coated with 2x Matrigel for at least one hour at 37°C. The hiPSC-viral mixture was then incubated overnight. The following morning (day 0), a full media change with iGLUT induction media was performed with the following recipe: Neurobasal Media: 1x N2 (Life technologies #17502-048), 1x B-27 minus Vitamin A (Life technologies #12587-010), 1x Antibiotic-Antimycotic, 1x Sodium Pyruvate, 1x GlutaMax (Life technologies #35050), 500µg/mL cyclic-AMP (Sigma #D0627), 200µM L-ascorbic acid (Sigma #A0278), 20ng/ml BDNF (Peprotech #450-02), 20ng/ml GDNF (Peprotech #450-10), 1µg/ml natural mouse laminin (Life technologies #23017015). On days 1-2, iGLUT cells were treated with respective antibiotic concentrations at 1µg/mL puromycin (Sigma# P7255) or 0.5µg/mL neomycin (Life technologies #11811-031). On day 3, antibiotic medium was withdrawn and iGLUT cells were treated with 4µM Ara-C. On Day 4, iGLUT cells were dissociated with accutase for 15 min, washed and pelleted with a 1:4 ratio of accutase to DMEM for 5 min at 800 rcf, and re-suspended with iGLUT media containing ROCK inhibitor, Ara-C and 2% low-hemoglobin FBS (R&D systems #S11510). iGLUT neurons were distributed among wells (500-750k cells per 24wp or 0.75-1.5E6 cell per 12wp) pre-seeded with confluent mouse glia. The following day, iGLUT neurons received a full media change with Brainphys maturation media (Brainphys, 1x N2, 1x B-27 minus Vitamin A, 1x Antibiotic-Antimycotic, 500µg/mL cyclic-AMP, 200µM Ascorbic Acid, 20ng/ml BDNF, 20ng/ml GDNF, 2% low-hemoglobin FBS, 1µg/ml Mouse Laminin) supplemented with Ara-C and were subsequently monitored for growth of non-neuronal/glial cells. Ara-C treatment was tittered down with half-media changes (without Ara-C) every 3-4 days until used for experiments.  iGABA production paralleled the methods aforementioned. hiPSCs were instead co-transduced with TetO-Ascl1-puro (Addgene #97330) or TetO-Ascl1-neo, TetO-Dlx2-hygro (Addgene #97329) and UCb-rtTA and seeded at 0.8-1.2x106 cells in 1.5mL per well on 6-well plates similarly prepared. The following morning (day 0), a full media change with iGABA induction media (DMEM/F-12 + Glutamax, 1x N2, 1x B-27 minus Vitamin A, 1x Antibiotic-Antimycotic) was performed. On days 1-2 iGABA cells were selected with respective antibiotic concentrations at 1µg/mL puromycin or 0.5µg/mL neomycin and 0.25µg/mL hygromycin (Life Technologies #10687010), followed by antibiotic withdrawal and Ara-C treatment on day 3. iGABA neurons were re-seeded identically to iGLUT cells, at 150-250k cells per 24wp well. iGABA cultures were morphologically QC’ed prior to all experiments, with uncharacteristic batches being discarded.

extract_protocol:
For the isolation of RNA, 2D cells were lysed using TRIzol (Life Technologies #15596026) and purified using the Qiagen miRNeasy Kit (Qiagen Cat# 74106) according to the manufacturer’s instructions.
Libraries were prepared via the Kapa Hyper library prep with ribo-erase (Roche #KK8541), according to the manufacturer's instructions.

treatment_protocol: beta-estradiol was reconstituted in DMSO and subsequently diluted in Brainphys maturation media for a final concentration of 30nM. Neurons were treated daily (in half media changes). iGLUT and iGABA neurons were treated starting from ~DIV14-18. Chronic treatments for functional experiments extended daily beta-estradiol replenishments for ~14 days and harvested on DIV21 ~4 hours post final dosage. ASOs were delivered using Lipofectamine RNAiMAX Transfection Reagent (Thermo, #13778075). The Lipofectamine RNAiMAX was diluted in Opti-MEM Medium (Thermo, #31985070). ASO was then diluted in Opti-MEM Medium at 1µM. The diluted ASO was added in a 1:1 ratio to the diluted Lipofectamine RNAiMAX and incubated at room temperature for 5 minutes. The ASO-lipid complex was added to cells, and incubated for 72 hours post-transfection, until RNA harvest. ASO samples for RNA-Seq were harvested on DIV17.

value: hiPSC-derived-GLUT

value: Vehicle

tag: time

tag: experimental batch


title: 5'-NRXN1-973-iGLUT-Vehicle-BiolRep-1

description: Library name: 973-DIV21-iGLUT-Veh-R1

tag: genotype

tag: treatment


title: 5'-NRXN1-973-iGLUT-Vehicle-BiolRep-3

description: Library name: 973-DIV21-iGLUT-Veh-R3


title: Gr2-35_ZT19_100-1

tag: temperature

tag: photoperiod


title: Donor 1 DNMT3a KO post tumor rechallenge

description:
Library name: CB1-DNMT3KO
Libraries were sequenced 2 X 50

value: DNMT3a KO


title: 5'-NRXN1-973-iGLUT-Best-BiolRep-3

description: Library name: 973-DIV21-iGLUT-Best-R3

value: Beta-estradiol


title: 196 be

description:
Library name: 196be
10X Genomics


title: SL, LbNOX, rep2

description:
Library name: LBNOX_2
LbNOX_RNA-seq_raw_counts.csv


title: Gr2-35_ZT19_20-2

value: leaf

tag: timepoint (zt_=_hours_after_dawn)