title: KCS mouse pancreas, Ad5 cre, rep1

city: Shanghai

first: Yuli

last: Lin

address: 上海市徐汇区东安路130号

institute: Fudan University

data_processing:
BGISEQ platform was used to averagely generate about 1.22G Gb bases per sample.
The average mapping ratio with reference genome is 95.32%, the average mapping ratio with gene is 89.67%; 19395 genes were identified.
The raw data contains reads of low quality, reads with adaptor sequences and reads with high levels of N base.
We used HISAT to align the clean reads to the reference genome.
Assembly: mm10
Supplementary files format and content: excel file includes normalized data across 6 examples and differential gene analysis between 2 groups.

source_name: pancreas

extract_protocol:
RNA was harvested using kit(Tiangen).
Randomly break the qualified genomic DNA samples into 300bp to 400bp fragments using physical methods;  Perform end repair on broken DNA fragments and connect the A base at the 3 'end; DNA single stranded cyclization; Remove non cyclized sequences and purify them; Conduct quality checks on the constructed library; Make DNB; Sequencing the quality tested library on the machine

value: pancreas

value: Acinar cells

value: KCS

tag: infection

value: Ad5 cre


title: SMC3-AID-15min-S4-R1-AN-SPnAa

status: Public on Jan 25 2025

type: SRA

city: Worcester

first: Johan

middle: Harmen

last: Gibcus

state: MA

address: 368 Plantation Street, Dekker Lab HHMI, AS5.1015,

department: Department of Systems Biology

country: USA

institute: UMass Chan Medical School

description: DT-40-CDK1 knockout , transfected with Xenops laevis CDK1as and TIR1, has a CRISPR derived mAID-clover knockin at SMC3. These cells will synchronize at mitotic entrance after addition of 1NM-PP1. Addition of auxin will deplete SMC3-clover via TIR1 proteasome degradation.

library_source: genomic

data_processing:
Fastq files were processed with the distiller pipeline (https://github.com/mirnylab/distiller-nf)
Reads were mapped to bGalGal1.mat.broiler.GRCg7b (GCA_016699485.1) using bwa mem with flags-SP.
To get pairs files, mapped reads were parsed and classified using  pairtools (https://github.com/mirnylab/pairtools).
PCR and optical duplicates were removed by matching the positions of aligned reads with 2bp flexibility.
Pairs were filtered using mapping quality scores (MAPQ > 30) on each side of aligned chimeric reads and binned into multiple resolutions before low coverage bins were removed.
Multiresolution cooler files were created with the cooler package (https://github.com/mirnylab/cooler.git)
Assembly: bGalGal1.mat.broiler.GRCg7b (GCA_016699485.1)
Supplementary files format and content: HDF5, Multiresolution cooler files (https://github.com/open2c/cooltools)
Supplementary files format and content: Mapping statistics for cooler files generated by pairtools (https://github.com/mirnylab/pairtools)
Supplementary files format and content: Compartment EV1 track (https://github.com/open2c/cooltools)
Supplementary files format and content: Eigen vectors (https://github.com/open2c/cooltools)
Supplementary files format and content: Insulation track (https://github.com/open2c/cooltools)
Supplementary files format and content: Insulation boundaries (https://github.com/open2c/cooltools)

molecule: genomic DNA

organism: Gallus gallus

source_name: Bursa

growth_protocol: Chicken DT40 cells were cultured in RPMI 1640 medium supplemented with 10 % fetal bovine serum and 1% chicken serum at 39°C in 5% CO2 in air.

extract_protocol:
Following Hi-C 2.0 protocol steps 2.1 - 2.12 from supplemental material of Belaghzal et al., Methods 2017 Jul 1:123:56-65; PMID: 28435001
Following Hi-C 2.0 protocol steps 3.1 - 16.3 from supplemental material of Belaghzal et al., Methods 2017 Jul 1:123:56-65; PMID: 28435001

treatment_protocol: 1% formaldehyde for 10 minutes before glycine quenching (128 mM final) for 5 minutes at room temperature followed by 15 minutes on ice and wash with PBS before storing at -80°C

tag: tissue

value: Bursa

tag: cell line

tag: cell type

value: lymphoblast

tag: genotype

tag: treatment

value: Palbociclib 11+3 h (auxin), washed  (10 min). Release 7h. 1NMPP1 for 5 + 9 h (No auxin), washed (10 min), release for 15 min, after cross-linking, cells were GFP sorted (negative)


title: KCS mouse pancreas, Ad5 cre, rep2

address: 上海市徐汇区东安路130号

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus


title: SMC3-AID-G2-S4-R1-AN-SPnAa

value: Palbociclib 11+3 h (auxin), washed  (10 min). Release 7h. 1NMPP1 for 5 + 9 h (No auxin), washed (10 min) and cross-linking, cells were GFP sorted (negative)


title: KCS mouse pancreas, Ad5 cre, rep3

address: 上海市徐汇区东安路130号


title: KC mouse pancreas, Ad5 cre, rep3

address: 上海市徐汇区东安路130号

value: KC


title: SMC3-AID-30min-S4-R1-NN-SPnaa

value: Palbociclib 11+3 h (No auxin), washed  (10 min). Release 7h. 1NMPP1 for 5 + 9 h (No auxin), washed (10 min), release for 30 min, after cross-linking, cells were GFP sorted (negative)


title: SMC3-AID-15min-S4-R1-NN-SPnaa

value: Palbociclib 11+3 h (No auxin), washed  (10 min). Release 7h. 1NMPP1 for 5 + 9 h (No auxin), washed (10 min), release for 15 min, after cross-linking, cells were GFP sorted (negative)


title: KC mouse pancreas, Ad5 cre, rep2

address: 上海市徐汇区东安路130号


title: RNA-seq - Wild type organoid day 105, repeat #1

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

data_processing:
True SEQ Long RNA libraries were trimmed from their adapter with cutadapt and aligned to hg38 with STAR v2.5.2b
DEseq2 was applied to test for the differential expression between the conditions.
smallRNA libraries were also trimmed from the adapter with cutadapt, and ligned to the genome with STAR
using outFilterMatchNmin=16, alignSJDBoverhangMin=1000, alignIntronMax=1, alignEndsType EndToEnd, and outFilterMismatchNmax 3
The number of read count per gene was calculated with bedtools. The read count for mirRNAs that appear more than once in the genome was divided by the number of their copies in the genome.
Assembly: hg38
Supplementary files format and content: Supplementary_Table_2_RNAseq_CorticOs_D_105.xlsx,Supplementary_Table_3_SmallRNAseq_CorticOs_D105.xlsx,Supplementary_Table_5_RNAseq_brainOs_D_18_mmp9_treat.xlsx
Supplementary files format and content: raw read counts, normalized read count, DEseq2 statistics

organism: Homo sapiens

source_name: Cortical organoids

growth_protocol: hESCs were cultured in naïve media and then dissociated and aggregated in V-shaped low-adhesion wells. Days 0 -17: Dulbecco's Modified Eagle's Medium (DMEM), 20% KSR, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol, non-essential amino acids (NEAA) and Perstrep. 3uM SB-431542 and 5uM IWR-1 were freshly added. Days 18-35: aggregates moved to 10cm bacterial plates. The media used was DMEM-F12, Penstrep, Glutamax, and chemically defined lipid concentrate (CDLC). Days 35-70: B27 without vitamin A, 5ug/ml heparin, and N2 supplement were added to the media. Media was changed once in three days

extract_protocol:
Total RNA was extracted using the Direct-zol RNA Miniprep Plus kit (Zymo Research) following the manufacturer's protocols
Libraries were prepared using TrueSeq standard mRNA library kit NOVASeq6000, 100PE, 40~50m for mRNA and NEBNext Small RNA Prep Kit for small RNA

treatment_protocol: Control and LIS1+/- brain organoids were either treated with MMP9 Catalytic domain for 10min at 37'c or with an equa volume of PBS (sham). RNA extraction followed the treatment.

value: Cortical organoids

value: NIHhESC-10-0079 WIBR3

value: hESC

value: Wild type


title: SMC3-AID-30min-S4-R1-NA-SPnaA

value: Palbociclib 11+3 h (No auxin), washed  (10 min). Release 7h. 1NMPP1 for 5 + 9 h (auxin), washed (10 min), release for 30 min, after cross-linking, cells were GFP sorted (negative)


title: KC mouse pancreas, Ad5 cre, rep1

address: 上海市徐汇区东安路130号


title: SMC3-AID-G2-S4-R1-NN-SPnaa

value: Palbociclib 11+3 h (No auxin), washed  (10 min). Release 7h. 1NMPP1 for 5 + 9 h (No auxin), washed (10 min) and cross-linking, cells were GFP sorted (negative)


title: dTAG13-8hr-2

city: ANN ARBOR

first: Yuanhao

last: Huang

state: MI

address: 1418 McIntyre st

institute: University of Michigan

description:
Library name: 12204-JX-4
PE150 on a 300 cycle S4 flow cell

data_processing:
m6a modification sites were called using GLORI toolkit
Assembly: mm10
Supplementary files format and content: called m6a modification sites with annotations

molecule: polyA RNA

source_name: organoids

growth_protocol: The Rx:GFP harboring FKBP12F36V-HA knocked into c-terminal of Mettl3 were differentiatied with GMEM supplemented with 5% KSR, 1% NEAA, 1% β-ME, 1% Sodium Pyruvate) and AGN (0.1µM) at 37°C.

extract_protocol:
RNA extraction was performed by combination of Trizol reagent (ThermoFisher Scientific) and RNeasy mini kit (QIAGEN).100 µg of total RNA passed QC ( < 200nt of RNA) using MEGA clear transcription clean-up kit (Ambion, AM1908), and then underwent PolyA+ selection using Dynabeads Oligo(dT)25 kit (Invitrogen, 61006). After polyA+ selection, QC for mRNA purity and quantity by nanodrop, ~800-1,000ng mRNA went through fragmentation using NEB next Magnesium RNA Fragmentation Module (NEB, E6150S). 400-500ng of fragmented RNA with 5% of spike-in probes were added into 40 μl reaction buffer containing 6 μl glyoxal solution (8.8 M in H2O, Sigma-Aldrich, 50649), 20 μl DMSO and nuclease-free water. The mixture was incubated in a preheated thermocycler for 30 min at 50 °C. The tubes were placed at room temperature after incubation, then 10 μl saturated H3BO3 (Sigma-Aldrich, B0394) solution was added and the incubation continued at 50 °C for 30 min. Fifty microliters of deamination buffer was prepared per sample containing 750 mM NaNO2 (Sigma-Aldrich, 31443), 40 mM MES (pH 6.0), 10 μl glyoxal solution (8.8 M in H2O) and nuclease-free water. The 50 μl sample was added to premixed deamination buffer and gently pipetted ten times. The tubes were incubated for 8 h at 16 °C. RNA was purified by ethanol precipitation. The pellets were dissolved by 50 μl deprotection buffer (20ml deprotection buffer combined 10 ml 1 M triethylammonium acetate solution pH 8.6 with 9.5 ml deionized formamide and nuclease-free water to 20 ml). The mixture was incubated at 95 °C for 10 min. RNA was purified by ethanol precipitation and twice clean-up by RNA Clean & Concentrator kit.
The RNAs were sent to University of Michigan DNA Sequencing Core for direct RT and library construction, and sequencing using Illumina NovaSeq S4 Libraries platform with PE read lengths of 2 ×150 base pairs.

treatment_protocol: The differentiatied RPCs with or without dTAG13 (125nM) at day 6 for 8 hr. Collecting the cells at the same time.

value: organoids

value: Rx:GFP with FKBP12F36V-HA knocking into c-termincal of endogenous Mettl6

value: dTAG13 treated

tag: batch


title: SMC3-AID-30min-S4-R1-AA-SPnAA

value: Palbociclib 11+3 h (auxin), washed  (10 min). Release 7h. 1NMPP1 for 5 + 9 h (auxin), washed (10 min), release for 30 min, after cross-linking, cells were GFP sorted (negative)


title: dTAG13-0hr-2

description:
Library name: 12204-JX-2
PE150 on a 300 cycle S4 flow cell

value: Rx:GFP with FKBP12F36V-HA knocking into c-termincal of endogenous Mettl4

value: No


title: dTAG13-8hr-1

description:
Library name: 12204-JX-3
PE150 on a 300 cycle S4 flow cell

value: Rx:GFP with FKBP12F36V-HA knocking into c-termincal of endogenous Mettl5


title: Jurkat cells, A694T-1

city: Jinan

first: Maoxiao

last: Feng

address: Beiyuan Street 247

institute: Department of Clinical Laboratory

data_processing:
Qualified reads were then mapped to reference genome using STAR. SAM files were converted to BAM format using samtools. Gene expression matrix is generated with HTSeq software. Differential analysis of gene expression was performed by using DESeq2 package.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

source_name: Jurkat

extract_protocol:
RNA was extracted using TRIzol from the Jurkat cells recombinantly expressing EV (Empty Vector), KDM6AWT or KDM6AA694T.
RNA-seq libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, #E7775) and sequenced on an Illumina platform with 125bp/150bp paired-end reads. FastQC was used to perform quality control, and then adapter sequences and poor-quality reads were removed.

value: Jurkat

value: human T lymphocyte cell line

value: KDM6A A694T overexpression

value: PMA+Ionomycin


title: dTAGMTL3-8hr-2

description:
Library name: 11870-QL-6
PE150 on a 300 cycle S4 flow cell

data_processing:
data is processed by ENCODE ChIP-seq pipeline with ATAC seq parameters
Assembly: mm10
Supplementary files format and content: bigwig chromasome accessibility signals

extract_protocol:
5X104 cells were washed with cold D-PBS and resuspended in 50 μl of cold lysis buffer (CHP-118-C, Boston Bioproducts) and pelleted. Transposition reaction by Tn5 transposase was incubated in TD buffer at 37°C for 30 min. After purification with MinElute Kit (QIAGEN), transposed DNA fragments were amplified through PCR.
ATAC-Seq were performed using Nextera DNA sample prep kit (Illumina) by following a protocol described elsewhere.  using barcoded Nextera PCR primers. Extra number of PCR cycles were added by qPCR as described and amplified DNA products were subjected to another round of DNA purification using MinElute Kit. Libraries were sent to University of Michigan DNA Sequencing Core for quality control test based on Bioanalyzer and sequenced using Illuminia Nova-seq 6000 with pair-end reads.

treatment_protocol: At day 5 and day 6 treated the differentiatied RPCs with or without dTAG13 (125nM) for 1 hr, 2 hr, 8 hr and 24 hr. Collecting the cells at the same time.

value: Rx:GFP FKBP12F36V-HA KI

value: FKBP12F36V-HA knocked into the C-terminal end of the two endogenous Mettl3 alleles


title: dTAGMTL3-24hr-1

description:
Library name: 11870-QL-7
PE150 on a 300 cycle S4 flow cell


title: dTAGMTL3-24hr-2

description:
Library name: 11870-QL-8
PE150 on a 300 cycle S4 flow cell


title: SMC3-AID-G2-S4-R1-AA-SPnAA

value: Bursa

value: lymphoblast

value: Palbociclib 11+3 h (auxin), washed  (10 min). Release 7h. 1NMPP1 for 5 + 9 h (auxin), washed (10 min) and cross-linking, cells were GFP sorted (negative)


title: dTAG13-0hr-1

description:
Library name: 12204-JX-1
PE150 on a 300 cycle S4 flow cell

value: Rx:GFP with FKBP12F36V-HA knocking into c-termincal of endogenous Mettl3


title: SMC2-AID-15min-S4-R2-spNA

description: DT-40-CDK1 knockout , transfected with Xenops laevis CDK1as and TIR1, has a CRISPR derived mAID-clover knockin at SMC2. These cells will synchronize at mitotic entrance after addition of 1NM-PP1. Addition of auxin will deplete SMC2-clover via TIR1 proteasome degradation.

value: 1NMPP1 for 10 h + 3 h (auxin), washed twice (10.5 min), release for 15 min, after cross-linking, cells were NOT GFP sorted (negative)


title: SMC3-AID-5min-S4-R1-NN-SPnaa

value: Palbociclib 11+3 h (No auxin), washed  (10 min). Release 7h. 1NMPP1 for 5 + 9 h (No auxin), washed (10 min), release for 5 min, after cross-linking, cells were GFP sorted (negative)


title: SMC2-AID-30min-S4-R2-spNA

value: 1NMPP1 for 10 h + 3 h (auxin), washed twice (10.5 min), release for 30 min, after cross-linking, cells were NOT GFP sorted (negative)


title: SMC2-AID-10min-S4-R4-spNA

value: 1NMPP1 for 10 h + 3 h (auxin), washed twice (10.5 min), release for 10 min, after cross-linking, cells were NOT GFP sorted (negative)


title: dTAGMTL3-8hr-1

description:
Library name: 11870-QL-5
PE150 on a 300 cycle S4 flow cell

value: organoids

value: dTAG13 treated


title: SMC3-AID-15min-S4-R1-AA-SPnAA

value: Palbociclib 11+3 h (auxin), washed  (10 min). Release 7h. 1NMPP1 for 5 + 9 h (auxin), washed  (10 min), release for 15 min, after cross-linking, cells were GFP sorted (negative)


title: dTAGMTL3-1hr-2

description:
Library name: 11870-QL-4
PE150 on a 300 cycle S4 flow cell


title: dTAGMTL3-0hr-2

description:
Library name: 11870-QL-2
PE150 on a 300 cycle S4 flow cell

value: No


title: SMC2-AID-G2-S4-R5-spNA

value: 1NMPP1 for 10 h + 3 h (auxin), washed twice (10.5 min)  and cross-linked, cells were NOT GFP sorted (negative)


title: SMC3-AID-5min-S4-R1-AA-SPnAA

value: Palbociclib 11+3 h (auxin), washed  (10 min). Release 7h. 1NMPP1 for 5 + 9 h (auxin), washed (10 min), release for 5 min, after cross-linking, cells were GFP sorted (negative)


title: SMC2-AID-2.5min-S4-R2-spNA

value: 1NMPP1 for 10 h + 3 h (auxin), washed twice (10.5 min), release for 2.5 min, after cross-linking, cells were NOT GFP sorted (negative)


title: SMC2-AID-7.5min-S5-R3-spnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed twice (10 min), release for 7.5 min, after cross-linking, cells were NOT GFP sorted (negative)


title: dTAGMTL3-1hr-1

description:
Library name: 11870-QL-3
PE150 on a 300 cycle S4 flow cell

value: Rx:GFP FKBP12F36V-HA KI

value: FKBP12F36V-HA knocked into the C-terminal end of the two endogenous Mettl3 alleles


title: SMC2-AID-5min-S4-R2-spNA

value: Bursa

value: lymphoblast

value: 1NMPP1 for 10 h + 3 h (auxin), washed twice (10.5 min), release for 5 min, after cross-linking, cells were GFP NOT sorted (negative)


title: Mettl3 KO-2

description:
Library name: 9446-JX-4
PE150 on a 300 cycle S4 flow cell

growth_protocol: Rx:GFP and Mettl3 KO harboring Dox-inducible HA-METTL3 were differentiatied with GMEM supplemented with 5% KSR, 1% NEAA, 1% β-ME, 1% Sodium Pyruvate) and AGN (0.1µM) at 37°C.

extract_protocol:
RNA extraction was performed by combination of Trizol reagent (ThermoFisher Scientific) and RNeasy mini kit (QIAGEN).100 µg of total RNA from WT or Mettl3KO ROs (day 4) passed QC were deleted less than 200nt of RNA using MEGA clear transcription clean-up kit (Ambion, AM1908), and then underwent PolyA+ selection using Dynabeads Oligo(dT)25 kit (Invitrogen, 61006). After polyA+ selection, checked mRNA purity and quantity by nanodrop, about 800-1,000ng mRNA went through fragmentation using NEB next Magnesium RNA Fragmentation Module (NEB, E6150S). 400-500ng of fragmented RNA with 5% of spike-in probes were added into 40 μl reaction buffer containing 6 μl glyoxal solution (8.8 M in H2O, Sigma-Aldrich, 50649), 20 μl DMSO and nuclease-free water. The mixture was incubated in a preheated thermocycler for 30 min at 50 °C. The tubes were placed at room temperature after incubation, then 10 μl saturated H3BO3 (Sigma-Aldrich, B0394) solution was added and the incubation continued at 50 °C for 30 min. Fifty microliters of deamination buffer was prepared per sample containing 750 mM NaNO2 (Sigma-Aldrich, 31443), 40 mM MES (pH 6.0), 10 μl glyoxal solution (8.8 M in H2O) and nuclease-free water. The 50 μl sample was added to premixed deamination buffer and gently pipetted ten times. The tubes were incubated for 8 h at 16 °C. RNA was purified by ethanol precipitation. The pellets were dissolved by 50 μl deprotection buffer (20ml deprotection buffer combined 10 ml 1 M triethylammonium acetate solution pH 8.6 with 9.5 ml deionized formamide and nuclease-free water to 20 ml). The mixture was incubated at 95 °C for 10 min. RNA was purified by ethanol precipitation and twice clean-up by RNA Clean & Concentrator kit.
The RNAs were sent to University of Michigan DNA Sequencing Core for direct RT and library construction, and sequencing using Illumina NovaSeq S4 Libraries platform with PE read lengths of 2 ×150 base pairs.

treatment_protocol: 4 days of differentiation for both Rx:GFP and Mettl3 KO.

value: Mettl3 KO Rx:GFP

value: Mettl3 KO


title: SMC2-AID-30min-S3-R1-spnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed twice (10 min), release for 30 min, after cross-linking, cells were NOT GFP sorted (negative)


title: Mettl3 KO-1

description:
Library name: 9446-JX-3
PE150 on a 300 cycle S4 flow cell


title: SMC2-AID-15min-S3-R1-spnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed twice (10 min), release for 15 min, after cross-linking, cells were NOT GFP sorted (negative)


title: Rx-GFP WT-2

description:
Library name: 9446-JX-2
PE150 on a 300 cycle S4 flow cell

value: organoids

value: WT


title: SMC2-AID-10min-S3-R3-spnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed twice (10 min), release for 10 min, after cross-linking, cells were NOT GFP sorted (negative)


title: SMC2-AID-7.5min-S3-R1-spnA


title: Rx-GFP WT-1

description:
Library name: 9446-JX-1
PE150 on a 300 cycle S4 flow cell

value: No


title: WTMTL3-GRBD with Dex d6-2

description:
Library name: 7120-JX-32
PE150 on a 300 cycle S4 flow cell

data_processing:
data is mapped to reference genome using STAR and processed using cuffdiff toolkit
Assembly: mm10
Supplementary files format and content: FPKM tsv file

growth_protocol: Rx:GFP, Mettl3 KO, Mettl3 KO with WTMETTL3-GRBD overexpression cells were differentiatied with GMEM supplemented with 5% KSR, 1% NEAA, 1% β-ME, 1% Sodium Pyruvate) and AGN (0.1µM) at 37°C.

extract_protocol:
Total RNA extraction for RNA-seq was performed by combination of Trizol reagent (ThermoFisher Scientific) and RNeasy mini kit (QIAGEN)
RNAs were sent to University of Michigan DNA Sequencing Core for RNA quality analysis, PolyA+ mRNA selection and library construction, and sequencing using Illumina NovaSeq S4 Libraries platform. Duplicate samples for each group were subjected to two round of independent library preparation and sequencing to avoid sample and batch effect of mRNA-seq.

treatment_protocol: Mettl3 KO with WTMETTL3-GRBD overexpression ROs were treated with or without Dex(10µM) for 2 days, 4 days and 6 days.

value: WT MTL3-GRBD OE in Mettl3 KO

value: WT MTL3-GRBD OE

value: AGN+Dex treated


title: SMC2-AID-5min-S3-R1-spnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed twice (10 min), release for 5 min, after cross-linking, cells were GFP NOT sorted (negative)


title: WTMTL3-GRBD with Dex d4-1

description:
Library name: 7120-JX-29
PE150 on a 300 cycle S4 flow cell


title: SMC2-AID-G2-S3-R4-spnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed twice (10 min)  and cross-linked, cells were NOT GFP sorted (negative)


title: WTMTL3-GRBD with Dex d6-1

description:
Library name: 7120-JX-31
PE150 on a 300 cycle S4 flow cell


title: SMC2-AID-2.5min-S3-R1-spnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed twice (10 min), release for 2.5 min, after cross-linking, cells were NOT GFP sorted (negative)


title: SMC3-SMC2-AID-15min-S1-R1-SpnA

description: DT-40-CDK1 knockout , transfected with Xenops laevis CDK1as and TIR1, has a CRISPR derived mAID-clover knockin at SMC3 and SMC2. These cells will synchronize at mitotic entrance after addition of 1NM-PP1. Addition of auxin will deplete SMC3-clover and SMC2-clover via TIR1 proteasome degradation.

value: Bursa

value: 1NMPP1 for 10 h + 3 h (auxin), washed twice (10 min), release for 15 min, after cross-linking, cells were GFP sorted (negative)


title: WTMTL3-GRBD with Dex d4-2

description:
Library name: 7120-JX-30
PE150 on a 300 cycle S4 flow cell


title: SMC3-SMC2-AID-30min-S1-R1-SpnA

value: lymphoblast

value: 1NMPP1 for 10 h + 3 h (auxin), washed twice (10 min), release for 30 min, after cross-linking, cells were GFP sorted (negative)


title: SMC3-SMC2-AID-7.5min-S1-R1-SpnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed twice (10 min), release for 7.5 min, after cross-linking, cells were GFP sorted (negative)


title: SMC3-SMC2-AID-5min-S1-R1-SpnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed twice (10 min), release for 5 min, after cross-linking, cells were GFP sorted (negative)


title: WTMTL3-GRBD with Dex d0-1

description:
Library name: 7120-JX-25
PE150 on a 300 cycle S4 flow cell

source_name: ESCs

value: ESCs

value: Dex treated


title: WTMTL3-GRBD with Dex d0-2

description:
Library name: 7120-JX-26
PE150 on a 300 cycle S4 flow cell


title: SMC3-SMC2-AID-2.5min-S1-R1-SpnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed twice (10 min), release for 2.5 min, after cross-linking, cells were GFP sorted (negative)


title: WTMTL3-GRBD no Dex d6-1

description:
Library name: 7120-JX-23
PE150 on a 300 cycle S4 flow cell

value: organoids

value: AGN treated


title: WTMTL3-GRBD no Dex d6-2

description:
Library name: 7120-JX-24
PE150 on a 300 cycle S4 flow cell

value: WT MTL3-GRBD OE in Mettl3 KO


title: SMC3-SMC2-AID-G2-S1-R1-SpnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed twice (10 min)  and cross-linked, cells were GFP sorted (negative)


title: CAPH2-AID-30min-S4-R4-spnA

description: DT-40-CDK1 knockout , transfected with Xenops laevis CDK1as and TIR1, has a CRISPR derived mAID-clover knockin at CAP-H2. These cells will synchronize at mitotic entrance after addition of 1NM-PP1. Addition of auxin will deplete CAP-H2-clover via TIR1 proteasome degradation.

value: CAPH-AID

value: 1NMPP1 for 10 h + 3 h (auxin), washed (10:00 min), release for 30 min, after cross-linking; cells were NOT GFP sorted (negative)


title: WTMTL3-GRBD with Dex d2-1

description:
Library name: 7120-JX-27
PE150 on a 300 cycle S4 flow cell

value: WT MTL3-GRBD OE

value: AGN+Dex treated


title: dTAGMTL3-0hr-1

description:
Library name: 11870-QL-1
PE150 on a 300 cycle S4 flow cell

value: Rx:GFP FKBP12F36V-HA KI

value: FKBP12F36V-HA knocked into the C-terminal end of the two endogenous Mettl3 alleles

value: No


title: WTMTL3-GRBD no Dex d4-2

description:
Library name: 7120-JX-22
PE150 on a 300 cycle S4 flow cell


title: SMC3-SMC2-AID-10min-S1-R1-SpnA

value: Bursa

value: lymphoblast

value: 1NMPP1 for 10 h + 3 h (auxin), washed twice (10 min), release for 10 min, after cross-linking, cells were GFP sorted (negative)


title: WTMTL3-GRBD no Dex d4-1

description:
Library name: 7120-JX-21
PE150 on a 300 cycle S4 flow cell


title: CAPH2-AID-15min-S4-R4-spnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (10:00 min), release for 15 min, after cross-linking; cells were NOT GFP sorted (negative)


title: CAPH2-AID-10min-S4-R4-spnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (10:00 min), release for 10 min, after cross-linking; cells were NOT GFP sorted (negative)


title: WTMTL3-GRBD no Dex d2-2

description:
Library name: 7120-JX-20
PE150 on a 300 cycle S4 flow cell


title: CAPH2-AID-5min-S4-R4-spnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (10:00 min), release for 5 min, after cross-linking; cells were NOT GFP sorted (negative)


title: WTMTL3-GRBD no Dex d2-1

description:
Library name: 7120-JX-19
PE150 on a 300 cycle S4 flow cell

value: organoids


title: WTMTL3-GRBD with Dex d2-2

description:
Library name: 7120-JX-28
PE150 on a 300 cycle S4 flow cell


title: WTMTL3-GRBD no Dex d0-2

description:
Library name: 7120-JX-18
PE150 on a 300 cycle S4 flow cell

value: ESCs

value: NO


title: WTMTL3-GRBD no Dex d0-1

description:
Library name: 7120-JX-17
PE150 on a 300 cycle S4 flow cell

value: WT MTL3-GRBD OE in Mettl3 KO


title: CAPH2-AID-G2-S4-R6-spnA

value: CAPH-AID

value: 1NMPP1 for 10 h + 3 h (auxin), washed (10:00 min)  and cross-linked, cells were NOT GFP sorted (negative)


title: Mettl3 KO d6-2

description:
Library name: 7120-JX-16
PE150 on a 300 cycle S4 flow cell

value: Mettl3 KO

value: AGN treated


title: Mettl3 KO d4-2

description:
Library name: 7120-JX-14
PE150 on a 300 cycle S4 flow cell


title: CAPH2-AID-15min-S3-R3-spnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (8:22 min), release for 15 min, after cross-linking; cells were NOT GFP sorted (negative)


title: CAPH2-AID-10min-S3-R3-spnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (8:22 min), release for 11:20 min, after cross-linking; cells were NOT GFP sorted (negative)


title: CAPH2-AID-7.5min-S3-R3-spnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (8:22 min), release for 7.5 min, after cross-linking; cells were NOT GFP sorted (negative)


title: CAPH2-AID-5min-S3-R3-spnA

value: Bursa

value: 1NMPP1 for 10 h + 3 h (auxin), washed (8:22 min), release for 5 min, after cross-linking; cells were NOT GFP sorted (negative)


title: Mettl3 KO d4-1

description:
Library name: 7120-JX-13
PE150 on a 300 cycle S4 flow cell


title: CAPH2-AID-2.5min-S3-R3-spnA

value: lymphoblast

value: 1NMPP1 for 10 h + 3 h (auxin), washed (8:22 min), release for 2.5 min, after cross-linking; cells were NOT GFP sorted (negative)


title: Mettl3 KO d0-2

description:
Library name: 7120-JX-10
PE150 on a 300 cycle S4 flow cell

value: No


title: Mettl3 KO d2-2

description:
Library name: 7120-JX-12
PE150 on a 300 cycle S4 flow cell


title: Rx-GFP d6-2

description:
Library name: 7120-JX-8
PE150 on a 300 cycle S4 flow cell

value: WT


title: CAPH-AID-15min-S3-R3-spnA

description: DT-40-CDK1 knockout , transfected with Xenops laevis CDK1as and TIR1, has a CRISPR derived mAID-clover knockin at CAP-H. These cells will synchronize at mitotic entrance after addition of 1NM-PP1. Addition of auxin will deplete CAP-H-clover via TIR1 proteasome degradation.

value: 1NMPP1 for 10 h + 3 h (auxin), washed (7:54 min), release for 15 min, after cross-linking; cells were NOT GFP sorted (negative)


title: Mettl3 KO d0-1

description:
Library name: 7120-JX-9
PE150 on a 300 cycle S4 flow cell

value: ESCs


title: CAPH-AID-10min-S3-R3-spnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (7:54 min), release for 10 min, after cross-linking; cells were NOT GFP sorted (negative)


title: Rx-GFP d6-1

description:
Library name: 7120-JX-7
PE150 on a 300 cycle S4 flow cell

value: organoids


title: CAPH-AID-5min-S3-R3-spnA

value: CAPH-AID

value: 1NMPP1 for 10 h + 3 h (auxin), washed (7:54 min), release for 5 min, after cross-linking; cells were NOT GFP sorted (negative)


title: Rx-GFP d4-2

description:
Library name: 7120-JX-6
PE150 on a 300 cycle S4 flow cell


title: Rx-GFP d4-1

description:
Library name: 7120-JX-5
PE150 on a 300 cycle S4 flow cell


title: CAPH2-AID-30min-S3-R3-spnA

description: DT-40-CDK1 knockout , transfected with Xenops laevis CDK1as and TIR1, has a CRISPR derived mAID-clover knockin at CAP-H2. These cells will synchronize at mitotic entrance after addition of 1NM-PP1. Addition of auxin will deplete CAP-H2-clover via TIR1 proteasome degradation.

value: 1NMPP1 for 10 h + 3 h (auxin), washed (8:22 min), release for 30 min, after cross-linking; cells were NOT GFP sorted (negative)


title: CAPH-AID-7.5min-S3-R3-spnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (7:54 min), release for 7.5 min, after cross-linking; cells were NOT GFP sorted (negative)


title: Mettl3 KO d6-1

description:
Library name: 7120-JX-15
PE150 on a 300 cycle S4 flow cell

value: Mettl3 KO

value: AGN treated


title: Rx-GFP d2-2

description:
Library name: 7120-JX-4
PE150 on a 300 cycle S4 flow cell


title: Rx-GFP d2-1

description:
Library name: 7120-JX-3
PE150 on a 300 cycle S4 flow cell


title: CAPH-AID-G2-S3-R5-spnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (7:54 min)  and cross-linked, cells were NOT GFP sorted (negative)


title: SMC3-CAPH2-AID-30min-S3-R2-SpnA

description: DT-40-CDK1 knockout , transfected with Xenops laevis CDK1as and TIR1, has a CRISPR derived mAID-clover knockin at SMC3 and CAP-H2. These cells will synchronize at mitotic entrance after addition of 1NM-PP1. Addition of auxin will deplete SMC3-clover and CAP-H2-clover via TIR1 proteasome degradation.

value: Bursa

value: 1NMPP1 for 10 h + 3 h (auxin), washed (9 min), release for 30 min, after cross-linking, cells were GFP sorted (negative)


title: Rx-GFP d0-2

description:
Library name: 7120-JX-2
PE150 on a 300 cycle S4 flow cell


title: Rx-GFP d0-1

description:
Library name: 7120-JX-1
PE150 on a 300 cycle S4 flow cell


title: Mettl3 KO d2-1

description:
Library name: 7120-JX-11
PE150 on a 300 cycle S4 flow cell


title: SMC3-CAPH2-AID-10min-S3-R2-SpnA

value: lymphoblast

value: 1NMPP1 for 10 h + 3 h (auxin), washed (9 min), release for 10 min, after cross-linking, cells were GFP sorted (negative)


title: SMC3-CAPH2-AID-15min-S3-R2-SpnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (9 min), release for 15 min, after cross-linking, cells were GFP sorted (negative)


title: SMC3-CAPH2-AID-7.5min-S3-R2-SpnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (9 min), release for 7.5 min, after cross-linking, cells were GFP sorted (negative)


title: CAPH2-AID-G2-S3-R5-spnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (8:22 min)  and cross-linked, cells were NOT GFP sorted (negative)


title: SMC3-CAPH2-AID-5min-S3-R2-SpnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (9 min), release for 5 min, after cross-linking, cells were GFP sorted (negative)


title: CAPH-AID-30min-S3-R3-spnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (7:54 min), release for 30 min, after cross-linking; cells were NOT GFP sorted (negative)


title: KO-Dox-HA-CHIP

description:
Library name: 3258-JX-5
PE150 on a 300 cycle S4 flow cell

data_processing:
ChIP-seq data was processed using ENCODE ChIP-seq pipeline
Assembly: mm10
Supplementary files format and content: bigwig foldchange signals

growth_protocol: Rx:GFP, Mettl3 KO harboring Dox-inducible HA-METTL3 were differentiatied with GMEM supplemented with 5% KSR, 1% NEAA, 1% β-ME, 1% Sodium Pyruvate) and AGN (0.1µM) at 37°C.

extract_protocol:
Day 6 ROs of Rx:GFP and Mettl3 KO with or without Dox (2 µg/ml) treatment were trypsinized into single cells and then total cell number 2×107 cells for each ChIP were fixed with 10% paraformaldehyde (Sigma) at room temperature for 10 min and quenched the reaction using glycine at final concentration of 0.125 M. The cells pellets were further sonicated to 300–500 bp in SDS lysis buffer by using a Qsonica Biorupter. 15 μg ChIP grade anti-HA antibody (Abcam, ab9110) and anti-METTL3 (Bethyl, A301-567A) were used for ChIP assay.
The ChIP-DNA were sent to University of Michigan DNA Sequencing Core for quality control, library preparation, and sequencing using Illumina NovaSeq S4 Libraries platform.

value: organoids

value: Mettl3 KO; Dox-inducilbe HA-METTL5

value: AGN+Dox treated


title: SMC3-CAPH2-AID-2.5min-S3-R2-SpnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (9 min), release for 2.5 min, after cross-linking, cells were GFP sorted (negative)


title: KO-HA-CHIP

description:
Library name: 3258-JX-3
PE150 on a 300 cycle S4 flow cell

value: Mettl3 KO; Dox-inducilbe HA-METTL3


title: SMC3-CAPH2-AID-G2-S3-R2-SpnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (9 min)  and cross-linked, cells were GFP sorted (negative)


title: SMC3-CAPH2-AID-30min-S2-R1-Spna

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (9 min), release for 30 min, after cross-linking, cells were GFP sorted (positive)


title: CAPH-AID-2.5min-S3-R3-spnA

value: CAPH-AID

value: 1NMPP1 for 10 h + 3 h (auxin), washed (7:54 min), release for 2.5 min, after cross-linking; cells were NOT GFP sorted (negative)


title: WT-Input

description:
Library name: 3258-JX-2
PE150 on a 300 cycle S4 flow cell

value: WT

value: AGN treated


title: WT-METTL3-CHIP

description:
Library name: 3258-JX-1
PE150 on a 300 cycle S4 flow cell


title: SMC3-CAPH2-AID-15min-S2-R1-Spna

value: Bursa

value: lymphoblast

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (9 min), release for 15 min, after cross-linking, cells were GFP sorted (positive)


title: SMC3-CAPH2-AID-10min-S2-R1-Spna

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (9 min), release for 10 min, after cross-linking, cells were GFP sorted (positive)


title: MC38 WT Sample 2 replicate 2

city: Frederick

first: Liping

last: Yang

state: MD

address: 1050 Boyles St

institute: NIH-NCI

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing and gene counting were made using Cell Ranger software. The analysis was done using Seurat package in R.
Assembly: mm10
Supplementary files format and content: RDS file with processed data. Filtering, normalization, scaling was done using Seurat. Cell annotation was done using a combination of ScType and manual annotation

source_name: Tumor

growth_protocol: Seven-month-old C57BL/6 mice were injected with 1x10^6 cells in 100 µL PBS per mouse

extract_protocol:
Tumors were excised from the mice when the size reached up to 250-500mm3. The tumor tissues were washed with cold sterile PBS. Fat and necrotic areas and blood vessels were removed from the samples
RNA isolation was done using the Miltenyi Tumor Dissociation Kit. Cells with viability lower than 70% were removed. Aiming to capture 10,000 cells, 16,000 cells per sample were used for generating scRNAseq libraries following the guidance of 10x Genomics Chromium Next GEM Single Cell 3’ Gene Expression version 3.1.

value: Tumor

tag: strain

tag: age

value: 7 month


title: MC38 WT Sample 1 replicate 1

description: 10x Genomics


title: MC38 WT Sample 2 replicate 1

description: 10x Genomics


title: SMC3-CAPH2-AID-7.5min-S2-R1-Spna

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (9 min), release for 7.5 min, after cross-linking, cells were GFP sorted (positive)


title: KPC850

city: Fukuoka

first: Yuki

last: Mochida

address: 3-1-1 Maidashi

department: Graduate School of Medical Sciences

country: Japan

institute: Kyushu University

description: pancreatic adenocarcinoma cells

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (v.0.36)
Trimmed sequence reads were mapped to GRCm39 using STAR (v.2.7.10b) and RSEM (v. 1.3.3)
Assembly: GRCm39
Supplementary files format and content: count_data.tsv

source_name: PDAC

extract_protocol:
The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing usingTruSeq stranded mRNA kit (illumina)  according manufacturer's protocols

value: PDAC

value: KPC mouse derived pancreatic adenocarcinoma cells

value: KPC


title: MC38 WT Sample 1 replicate 2

description: 10x Genomics


title: KO-Dox-Input

description:
Library name: 3258-JX-6
PE150 on a 300 cycle S4 flow cell

value: organoids

value: Mettl3 KO

value: Mettl3 KO; Dox-inducilbe HA-METTL6

value: AGN+Dox treated


title: SMC3-CAPH2-AID-5min-S2-R1-Spna

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (9 min), release for 5 min, after cross-linking, cells were GFP sorted (positive)


title: KPC142

description: pancreatic adenocarcinoma cells


title: SMC3-CAPH2-AID-2.5min-S2-R1-Spna

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (9 min), release for 2.5 min, after cross-linking, cells were GFP sorted (positive)


title: SMC3-CAPH2-AID-G2-S2-R1-Spna

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (9 min)  and cross-linked, cells were GFP sorted (positive)


title: KPC469

description: pancreatic adenocarcinoma cells


title: SMC3-CAPH2-AID-7.5min-S1-R1-SpnA

value: Bursa

value: 1NMPP1 for 10 h + 3 h (auxin), washed (9 min), release for 7.5 min, after cross-linking, cells were GFP sorted (negative)


title: B_2

city: Luzhou

first: lei

last: yang

state: Sichuan

address: Xianglin Road

institute: southwest medical university

data_processing:
step CLC Genomics Workbenchv11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters-mismath cost:2 insertion cost: 3 deletion cost:3 length fraction:0.8 similarity fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: BV2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS)and antibiotics in humidified atmosphere with 5% CO2 at 37C

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

treatment_protocol: cells treated with Oxy-Hb (10uM) , Oxy-Hb (10uM)+C3a(20ug/ul,  PBS) and Oxy-Hb (10uM)+C3aRA( 50uM, PBS)

value: microglia


title: KO-Input

description:
Library name: 3258-JX-4
PE150 on a 300 cycle S4 flow cell

value: Mettl3 KO; Dox-inducilbe HA-METTL4

value: AGN treated


title: KPC180

description: pancreatic adenocarcinoma cells


title: SMC3-CAPH2-AID-15min-S1-R1-SpnA

value: lymphoblast

value: 1NMPP1 for 10 h + 3 h (auxin), washed (9 min), release for 15 min, after cross-linking, cells were GFP sorted (negative)


title: SMC3-CAPH2-AID-10min-S1-R1-SpnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (9 min), release for 9 min, after cross-linking, cells were GFP sorted (negative)


title: SMC3-CAPH2-AID-5min-S1-R1-SpnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (9 min), release for 5 min, after cross-linking, cells were GFP sorted (negative)


title: KPC630

description: pancreatic adenocarcinoma cells

value: PDAC

value: KPC mouse derived pancreatic adenocarcinoma cells

value: KPC


title: B_3


title: SMC3-CAPH2-AID-2.5min-S1-R1-SpnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (9 min), release for 2.5 min, after cross-linking, cells were GFP sorted (negative)


title: SMC3-CAPH2-AID-30min-S1-R1-SpnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (9 min), release for 30 min, after cross-linking, cells were GFP sorted (negative)


title: KPC490

description: pancreatic adenocarcinoma cells


title: B_1


title: SMC3-CAPH-AID-30min-S3-R2-SpnA

description: DT-40-CDK1 knockout , transfected with Xenops laevis CDK1as and TIR1, has a CRISPR derived mAID-clover knockin at SMC3 and CAP-H. These cells will synchronize at mitotic entrance after addition of 1NM-PP1. Addition of auxin will deplete SMC3-clover and CAP-H-clover via TIR1 proteasome degradation.

value: 1NMPP1 for 10 h + 3 h (auxin), washed (8:20 min), release for 30 min, after cross-linking, cells were GFP sorted (negative)


title: SMC3-CAPH2-AID-G2-S1-R1-SpnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (9 min)  and cross-linked, cells were GFP sorted (negative)


title: A_3


title: SMC3-CAPH-AID-10min-S3-R2-SpnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (8:20 min), release for 10 min, after cross-linking, cells were GFP sorted (negative)


title: SMC3-CAPH-AID-15min-S3-R2-SpnA

value: Bursa

value: 1NMPP1 for 10 h + 3 h (auxin), washed (8:20 min), release for 15 min, after cross-linking, cells were GFP sorted (negative)


title: A_1

value: microglia


title: Hb_3

value: oxy-Hb


title: SMC3-CAPH-AID-7.5min-S3-R2-SpnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (8:20 min), release for 7.5 min, after cross-linking, cells were GFP sorted (negative)


title: SMC3-CAPH-AID-5min-S3-R2-SpnA

value: lymphoblast

value: 1NMPP1 for 10 h + 3 h (auxin), washed (8:20 min), release for 5 min, after cross-linking, cells were GFP sorted (negative)


title: SMC3-CAPH-AID-2.5min-S3-R2-SpnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (8:20 min), release for 2.5 min, after cross-linking, cells were GFP sorted (negative)


title: Hb_2


title: Hb_1


title: HPMEC donor 3: ROCKi (1h) + DMSO (6h)

city: Boston

first: Lillian

middle: Jessica

last: Horin

address: 200 Longwood Ave

department: Systems Biology

institute: Harvard Medical School

description: Library name: HPMEC.6.ROCK.ROCKi.DMSO

data_processing:
Adapter read trimming using Trim Galore (v0.6.6) and quality control performed with FastQC (v0.12.1).
Expression of RNA transcripts quantified using Salmon (v1.8.0) and aligned with STAR (2.7.9a). Quality control performed with Qualimap (v2.2.1).
Normalized count data was obtained by inputting Salmon quantification into DESeq2 (v.1.44.0) and using the median of ratios method of normalization.
Assembly: Genome assembly GRCh38
Supplementary files format and content: csv file contains normalized counts for all samples

source_name: Lung

growth_protocol: Primary HPMECs were grown in a humidified growth chamber at 37°C, 5% CO2. cultivated up to passage 8 in complete growth media from manufacturer, PromoCell. At least 12 hours before experiment, cells were serum-starved with assay medium (0.02 ml/ml fetal calf serum and 10 ng/ml human epidermal growth factor, with anti-inflammatories heparin and hydrocortisone excluded from medium).

extract_protocol:
Total RNA was isolated from cells using the RNeasy Qiagen Extraction kit. At least 1200 ng was provided to Azenta for sequencing.
Library construction and sequencing were conducted by Azenta Next-Generation Sequencing, standard RNA-seq with polyA selection.

treatment_protocol: Cells were pre-treated with either water (H2O) or 10 uM Y-27632  (ROCKi) for 1 hour in fresh assay medium. Afterwards, cells were treated with either DMSO or VB for 6 hours

value: Lung

value: Primary HPMEC-c

value: microvascular endothelial cells

tag: donor

tag: pre-treatment

value: 0.1% DMSO


title: SMC3-CAPH-AID-G2-S3-R2-SpnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (8:20 min)  and cross-linked, cells were GFP sorted (negative)


title: HPMEC donor 3: Control (1h) + DMSO (6h)

description: Library name: HPMEC.6.ROCK.H2O.DMSO

value: Water (H2O)


title: HPMEC donor 2: ROCKi (1h) + VB (6h)

description: Library name: HPMEC.4.ROCK.ROCKi.VB

value: 100 nM vinblastine


title: HPMEC donor 3: ROCKi (1h) + VB (6h)

description: Library name: HPMEC.6.ROCK.ROCKi.VB


title: Con_2

value: PBS


title: Akk,intestine,7-week rep3

city: Guangzhou

first: Shiqi

last: Jia

address: Huangpu Avenue West 613

institute: Jinan University

data_processing:
using biomaker clound
Assembly: mm10

source_name: intestinal epithelium

growth_protocol: Feed mice with regular feed and clean water

extract_protocol:
Use trizol to extract total RNA from mouse intestinal epithelial cells and store it at -80 degrees.
mRNA seq Library using illumina

treatment_protocol: Mice were given AKK by gavage every day, and the control group was given PBS.

value: intestinal epithelium

value: Epithelial Cells

value: WT

value: Akk


title: HPMEC donor 3: Control (1h) + VB (6h)

description: Library name: HPMEC.6.ROCK.H2O.VB


title: SMC3-CAPH-AID-7.5min-S2-R1-spna

value: Bursa

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (8 min), release for 7.5 min, after cross-linking, cells were NOT GFP sorted (positive)


title: SMC3-CAPH-AID-5min-S2-R1-spna

value: lymphoblast

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (8 min), release for 5 min, after cross-linking, cells were GFP sorted (positive)


title: SMC3-CAPH-AID-15min-S2-R1-spna

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (8 min), release for 15 min, after cross-linking, cells were NOT GFP sorted (positive)


title: Akk,intestine,7-week rep2


title: SMC3-CAPH-AID-10min-S2-R1-spna

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (8 min), release for 8 min, after cross-linking, cells were NOT GFP sorted (positive)


title: A_2

value: microglia


title: Con_3


title: HPMEC donor 2: ROCKi (1h) + DMSO (6h)

description: Library name: HPMEC.4.ROCK.ROCKi.DMSO

value: Lung

value: Primary HPMEC-c

value: microvascular endothelial cells


title: SMC3-CAPH-AID-2.5min-S2-R1-spna

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (8 min), release for 2.5 min, after cross-linking, cells were NOT GFP sorted (positive)


title: Con_1


title: HPMEC donor 2: Control (1h) + VB (6h)

description: Library name: HPMEC.4.ROCK.H2O.VB

value: Water (H2O)

value: 100 nM vinblastine


title: Stat3 shRNA CAFs

type: RNA

city: beijing

first: di

last: zhao

address: 52 Fucheng Road, Haidian District, Beijing

institute: beijng cancer hospital

description: whole gene exression

hyb_protocol: 1.5ug of Cy3-labelled cRNA (specific activity > 10.0 pmol Cy3/ug cRNA) was fragmented at 60 ℃ for 30 minutes in a reaction volume of 250 ml containing 1× Agilent fragmentation buffer and 2× Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2× Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Microarrays for 17 hours at 65 ℃ in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 ℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned using Agilent Scanner G2505C.

data_processing: Data was extracted and normalized using Feature Extraction v10.7.1.1 software. Further Data analysis was performed using Agilent GeneSpring v13.1 software.

source_name: Stat3 shRNA CAFs

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy  column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), penicillin (100U/ml), and streptomycin (100 μg/ml).

extract_protocol: Total RNA was extracted using mirVanaTM RNA Isolation Kit (ABI, AM1561).

treatment_protocol: using transwell apparatus with 0.4 μm pore size to coculture KYSE150 cells and CAFs

value: CAF cells


title: PBS,intestine,7-week rep3

value: intestinal epithelium

value: Epithelial Cells

value: PBS


title: SMC3-CAPH-AID-G2-S2-R1-spna

value: Bursa

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (8 min)  and cross-linked, cells were NOT GFP sorted (positive)


title: Stat3 shRNA CAFs (KYSE150 cells in the upper chamber)

description: whole gene exression


title: SMC3-CAPH-AID-30min-S2-R1-spna

value: lymphoblast

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (8 min), release for 30 min, after cross-linking, cells were NOT GFP sorted (positive)


title: PAFR shRNA CAFs

description: whole gene exression

source_name: PAFR shRNA CAFs


title: HPMEC donor 2: Control (1h) + DMSO (6h)

description: Library name: HPMEC.4.ROCK.H2O.DMSO

value: 0.1% DMSO


title: SMC3-CAPH-AID-30min-S1-R1-spnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (8 min), release for 30 min, after cross-linking, cells were NOT GFP sorted (negative)


title: HPMEC donor 1: ROCKi (1h) + DMSO (6h)

description: Library name: HPMEC.1.ROCK.ROCKi.DMSO


title: SMC3-CAPH-AID-15min-S1-R1-spnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (8 min), release for 15 min, after cross-linking, cells were NOT GFP sorted (negative)


title: SMC3-CAPH-AID-10min-S1-R1-spnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (8 min), release for 8 min, after cross-linking, cells were NOT GFP sorted (negative)


title: Akk,intestine,7-week rep1

value: WT

value: Akk


title: HPMEC donor 1: ROCKi (1h) + VB (6h)

description: Library name: HPMEC.1.ROCK.ROCKi.VB

value: Lung

value: Primary HPMEC-c

value: microvascular endothelial cells


title: PBS,intestine,7-week rep2


title: PBS,intestine,7-week rep1


title: CAFs (KYSE150 cells in the upper chamber)

description: whole gene exression

value: CAF cells


title: HPMEC donor 1: Control (1h) + VB (6h)

description: Library name: HPMEC.1.ROCK.H2O.VB

value: Water (H2O)

value: 100 nM vinblastine


title: rok null late-log

city: Cambridge

first: Alan

middle: D

last: Grossman

address: 31 Ames St.

department: Biology

institute: Massachusetts Institute of Technology

description:
Library name: 11785
Processed data files are wigs that were created after combining the data from the two rok+ samples (11779 and 11785). 11779_11785_nocutoff_f.wig is for reads mapping to the top strand; 11779_11785_nocutoff_r.wig is for reads mapping to the bottom strand.

data_processing:
The first 10 sequencing cycles were run "dark" because the sequencing primer anneals 10 bp within Tn916, which would result in identical sequence for all reads
The first 10 bases of sequence data was trimmed, because Tn916 can change the host flanking bases when it inserts
The trimmed sequences were mapped to the AG174 genome using  SMALT version 0.7.6
Wiggle files were generated using in-house R scripts
Assembly: AG174 (GenBank #CP007800.1)
Supplementary files format and content: Wiggle track, variableStep format

organism: Bacillus subtilis subsp. subtilis

source_name: ELC42-based Tn916 insertion library

growth_protocol: Tn916 donor and recipient strains were grown in LB medium at 37˚C to mid- or late-exponential phase as indicated in the sample titles

extract_protocol:
Total DNA was extracted using a Qiagen 100 G tip purification kit
TraDIS protocol was followed as described in Barquist et al., Bioinformatics 32, no. 7 (2016): 1109–11

treatment_protocol: The Tn916 donor strain ELC43 was mixed with ∆rok or rok+ recipient strains to create a library of Tn916 transconjugants

value: ELC42-based Tn916 insertion library

value: ELC42 is delta-rok(unmarked) comK::spc ICEBs1-cured trpC2 pheA1


title: KYSE150 Stat3 shRNA cells

description: whole gene exression

source_name: KYSE150 Stat3 shRNA cells

value: KYSE150 cells


title: HPMEC donor 1: Control (1h) + DMSO (6h)

description: Library name: HPMEC.1.ROCK.H2O.DMSO


title: SMC3-CAPH-AID-7.5min-S1-R1-spnA

value: Bursa

value: lymphoblast

value: 1NMPP1 for 10 h + 3 h (auxin), washed (8 min), release for 7.5 min, after cross-linking, cells were NOT GFP sorted (negative)


title: KYSE150 Stat3 shRNA cells (CAFs in the upper chamber)

description: whole gene exression


title: CAFs

description: whole gene exression

source_name: CAFs


title: SMC3-CAPH-AID-5min-S1-R1-spnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (8 min), release for 5 min, after cross-linking, cells were NOT GFP sorted (negative)


title: KYSE150 PAFR shRNA cells (CAFs in the upper chamber)

description: whole gene exression


title: PAFR shRNA CAFs (KYSE150 cells in the upper chamber)

description: whole gene exression


title: rok+ late-log

description:
Library name: 11786
Processed data files are wigs that were created after combining the data from the two rok+ samples (11780 and 11786). 11780_11786_nocutoff_f.wig is for reads mapping to the top strand; 11780_11786_nocutoff_r.wig is for reads mapping to the bottom strand.

source_name: ELC38-based Tn916 insertion library

value: ELC38-based Tn916 insertion library

value: ELC38 is comK::spc ICEBs1-cured trpC2 pheA1


title: rok+ mid-log

description:
Library name: 11780
Processed data files are wigs that were created after combining the data from the two rok+ samples (11780 and 11786). 11780_11786_nocutoff_f.wig is for reads mapping to the top strand; 11780_11786_nocutoff_r.wig is for reads mapping to the bottom strand.


title: HPMEC donor 3: RHOi (4h) + VB (6h)

description: Library name: HPMEC.6.RHO.RHOi.VB

extract_protocol:
Total RNA was isolated from cells using the RNeasy Qiagen Extraction kit. At least 700 ng was provided to Azenta for sequencing.
Library construction and sequencing were conducted by Azenta Next-Generation Sequencing, standard RNA-seq with polyA selection.

treatment_protocol: Cells were pre-treated with either water (H2O) or 1 ug/ml of C3 transferase (RHOi) for 4 hours in fresh assay medium. Afterwards, cells were treated with a booster dose of RHOi and either DMSO or VB for 6 hours

value: 1 µg/ml C3 transferase (RHOi)

value: 100 nM vinblastine + 0.5 µg/ml C3 transferase (RHOi)


title: SMC3-CAPH-AID-G2-S1-R1-spnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (8 min)  and cross-linked, cells were NOT GFP sorted (negative)


title: HPMEC donor 3: Control (4h) + VB (6h)

description: Library name: HPMEC.6.RHO.H2O.VB

value: Lung

value: Primary HPMEC-c


title: manganese treatment_rep3

city: Yangzhou

first: Yu

last: Zhang

address: No. 48, Wenhui East Road

institute: Yangzhou University

description:
Library name: manganese-3
manganese-3_FPKM

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3. (Langmead, B. and S. L. Salzberg, 2012).
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Assembly: Vibrio parahaemolyticus RIMD2210633, complete genome (NC_004603.1; NC_004605.1)
Supplementary files format and content: gene expression (read counts and fpkm for each stra).

organism: Vibrio parahaemolyticus

growth_protocol: The Vibrio parahaemolyticus RIMD 2210633 strain was cultured with TSB at 37℃ until the early-exponential phase (OD600 of 0.6–0.8).

extract_protocol:
RNA was extracted using an Eastep Super Total RNA Isolation Kit (Promega, Shanghai, China), according to the manufacturer’s instructions. RNA integrity and concentration were evaluated by gel electrophoresis and spectrophotometric analysis, respectively.
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Two aliquots (1 mL) were removed, one was treated with 1mM MnSO4 and the other was treated with deionized water.


title: rok null mid-log

description:
Library name: 11779
Processed data files are wigs that were created after combining the data from the two rok+ samples (11779 and 11785). 11779_11785_nocutoff_f.wig is for reads mapping to the top strand; 11779_11785_nocutoff_r.wig is for reads mapping to the bottom strand.


title: KYSE150 PAFR shRNA cells

description: whole gene exression

source_name: KYSE150 PAFR shRNA cells


title: SMC3-CAPH-AID-2.5min-S1-R1-spnA

extract_protocol:
Following Hi-C 2.0 protocol steps 2.1 - 2.12 from supplemental material of Belaghzal et al., Methods 2017 Jul 1:123:56-65; PMID: 28435001
Following Hi-C 2.0 protocol steps 3.1 - 16.3 from supplemental material of Belaghzal et al., Methods 2017 Jul 1:123:56-65; PMID: 28435001

value: 1NMPP1 for 10 h + 3 h (auxin), washed (8 min), release for 2.5 min, after cross-linking, cells were NOT GFP sorted (negative)


title: HPMEC donor 3: RHOi (4h) + DMSO (6h)

description: Library name: HPMEC.6.RHO.RHOi.DMSO

value: microvascular endothelial cells

value: 0.1% DMSO + 0.5 µg/ml C3 transferase (RHOi)


title: HPMEC donor 3: Control (4h) + DMSO (6h)

description: Library name: HPMEC.6.RHO.H2O.DMSO

value: Water (H2O)

value: 0.1% DMSO


title: manganese treatment_rep2

description:
Library name: manganese-2
manganese-2_FPKM


title: SMC3-AID-90min-S3-R1-spnA

description: DT-40-CDK1 knockout , transfected with Xenops laevis CDK1as and TIR1, has a CRISPR derived mAID-clover knockin at SMC3. These cells will synchronize at mitotic entrance after addition of 1NM-PP1. Addition of auxin will deplete SMC3-clover via TIR1 proteasome degradation.

value: 1NMPP1 for 10 h + 3 h ( auxin), washed (8:38 min), release for 90 min, after cross-linking; cells were NOT GFP sorted


title: manganese treatment_rep1

description:
Library name: manganese-1
manganese-1_FPKM


title: SMC3-AID-60min-S3-R1-spnA

value: Bursa

value: 1NMPP1 for 10 h + 3 h ( auxin), washed (8:38 min), release for 60 min, after cross-linking; cells were NOT GFP sorted


title: KYSE150 cells (Stat3 shRNA CAFs in the upper chamber)

description: whole gene exression

value: KYSE150 cells


title: HPMEC donor 2: RHOi (4h) + DMSO (6h)

description: Library name: HPMEC.4.RHO.RHOi.DMSO


title: water treatment_rep3

description:
Library name: controi-3
control-3_FPKM


title: water treatment_rep2

description:
Library name: control-2
control-2_FPKM


title: HPMEC donor 2: RHOi (4h) + VB (6h)

description: Library name: HPMEC.4.RHO.RHOi.VB


title: HPMEC donor 2: Control (4h) + VB (6h)

description: Library name: HPMEC.4.RHO.H2O.VB

value: 100 nM vinblastine


title: KYSE150 cells (shRNA vector CAFs in the upper chamber)

description: whole gene exression


title: SMC3-AID-10min-S3-R3-spnA

value: lymphoblast

value: 1NMPP1 for 10 h + 3 h ( auxin), washed (8:38 min), release for 11:20 min, after cross-linking; cells were NOT GFP sorted


title: SMC3-AID-15min-S3-R3-spnA

value: 1NMPP1 for 10 h + 3 h ( auxin), washed (8:38 min), release for 15 min, after cross-linking; cells were NOT GFP sorted


title: KYSE150 cells

description: whole gene exression

source_name: KYSE150 cells


title: water treatment_rep1

description:
Library name: control-1
control-1_FPKM


title: HPMEC donor 2: Control (4h) + DMSO (6h)

description: Library name: HPMEC.4.RHO.H2O.DMSO


title: SMC3-AID-30min-S3-R3-spnA

source_name: Bursa

value: 1NMPP1 for 10 h + 3 h ( auxin), washed (8:38 min), release for 30 min, after cross-linking; cells were NOT GFP sorted


title: HPMEC donor 1: RHOi (4h) + VB (6h)

description: Library name: HPMEC.1.RHO.RHOi.VB

value: 1 µg/ml C3 transferase (RHOi)

value: 100 nM vinblastine + 0.5 µg/ml C3 transferase (RHOi)


title: Neutrophils HD5

city: Amsterdam

first: Iris

last: de Rink

address: Plesmanlaan 121

country: Netherlands

institute: NKI

description: 5605_12_Healthy_Donor_8_NB_CGATCAGT-TCTCTCCG_S36

data_processing:
Raw reads were mapped with Hisat 2.1.0 with default parameters using grch38_snp_tran as a reference
readcounts were generated with itreecount (https://github.com/NKI-GCF/itreecount) using ensemble version 87
Assembly: GRCh38
Supplementary files format and content: Tab-delimited raw and normalized readcounts were generated for each sample

source_name: Blood

growth_protocol: Samples were processed immediately after blood draw

extract_protocol:
Neutrophils were sorted directly into RLT-buffer and snap-frozen
2-7 ng of total RNA for each sample was prepared in a volume of 4 ul. Oligo dT primer hybridization was performed by the addition of Oligo dT mix (0.7ul H2O, 0.1 ul RNAse inhibitor (40U/ul), 0.1 ul dNTP mix (100mM) and 0.1 ul Oligo-dT30VN primer (100uM)). Reverse transcription was performed as described but the MgCl2 concentration was adjusted to 10 mM. Template switching and 10 (1-4 ng RNA input) or 11 (5-8ng RNA input) cycles pre-amplification of full length cDNAs with template switching oligo’s was performed using ISPCR primer at a final concentration of 0.08 uM. The amplified full length cDNA was used for NGS library construction by Tagmentation for Illumina sequencing, using the Illumina Nextera XT DNA sample preparation kit (Illumina).

treatment_protocol: No treatment

value: Blood

value: FACS sorted neutrophils

tag: disease state

value: healthy


title: TIR-1; dpy-27::AID; cec-4, auxin, rep3

city: Ann Arbor

first: Gyorgyi

last: Csankovszki

address: 1105 N University Ave

department: MCDB

data_processing:
The reads were trimmed using CutAdapt v2.3.FastQC v0.11.8 was used to ensure the quality of data.Reads were mapped to the reference genome WBcel235 and read counts were generated using Salmon v1.9.0. Differential gene expression analysis was performed using DESeq2 v1.42.0. Downstream analyses were performed using R scripts and packages.
Assembly: WS235
Supplementary files format and content: tab-delimited text files with FPKM values

organism: Caenorhabditis elegans

source_name: TIR-1; dpy-27::AID; cec-4, auxin, rep3

growth_protocol: Synced L1s were placed on HGM plates with or without auxin, and NA22 as a food source. They were grown at 20C and collected for RNA extraction after 24-hours.

extract_protocol:
Packed L3 larvae were resuspended in TRIzol. RNA was extracted and purified using the Qiagen RNeasy kit with on-column DNAse digestion.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (catalog number E7760L), and NEBNext Multiplex Oligos for Illumina Unique dual (catalog number E6448S) were used for library prep.The mRNA was fragmented and copied into first strand cDNA using reverse transcriptase and random primers. The 3' ends of the cDNA were then adenylated and adapters were ligated. The products were purified and enriched by PCR to create the final cDNA library.

treatment_protocol: Auxin treated samples were grown on 4mM auxin HGM plates with NA22. Samples without auxin treatment were grown on regular HGM plates with NA22.

tag: developmental stage

value: TIR-1; dpy-27::AID; cec-4

value: auxin


title: KYSE150 cells (PAFR shRNA CAFs in the upper chamber)

description: whole gene exression


title: Neutrophils HD7

description: 5605_14_Healthy_Donor_13_NB_TCGACGTC-TCTCTCCG_S38


title: SMC3-AID-7.5min-S3-R3-spnA

data_processing:
Fastq files were processed with the distiller pipeline (https://github.com/mirnylab/distiller-nf)
Reads were mapped to bGalGal1.mat.broiler.GRCg7b (GCA_016699485.1) using bwa mem with flags-SP.
To get pairs files, mapped reads were parsed and classified using  pairtools (https://github.com/mirnylab/pairtools).
PCR and optical duplicates were removed by matching the positions of aligned reads with 2bp flexibility.
Pairs were filtered using mapping quality scores (MAPQ > 30) on each side of aligned chimeric reads and binned into multiple resolutions before low coverage bins were removed.
Multiresolution cooler files were created with the cooler package (https://github.com/mirnylab/cooler.git)
Assembly: bGalGal1.mat.broiler.GRCg7b (GCA_016699485.1)
Supplementary files format and content: HDF5, Multiresolution cooler files (https://github.com/open2c/cooltools)
Supplementary files format and content: Mapping statistics for cooler files generated by pairtools (https://github.com/mirnylab/pairtools)
Supplementary files format and content: Compartment EV1 track (https://github.com/open2c/cooltools)
Supplementary files format and content: Eigen vectors (https://github.com/open2c/cooltools)
Supplementary files format and content: Insulation track (https://github.com/open2c/cooltools)
Supplementary files format and content: Insulation boundaries (https://github.com/open2c/cooltools)

value: 1NMPP1 for 10 h + 3 h ( auxin), washed (8:38 min), release for 7.5 min, after cross-linking; cells were NOT GFP sorted


title: TIR-1; dpy-27::AID; cec-4, auxin, rep2

source_name: TIR-1; dpy-27::AID; cec-4, auxin, rep2


title: Neutrophils HD4

description: 5605_11_Healthy_Donor_6_NB_CCTAAGAC-CGTCTAAT_S35


title: SMC3-AID-5min-S3-R3-spnA

value: 1NMPP1 for 10 h + 3 h ( auxin), washed (8:38 min), release for 5 min, after cross-linking; cells were NOT GFP sorted


title: TIR-1; dpy-27::AID; cec-4, auxin, rep1

source_name: TIR-1; dpy-27::AID; cec-4, auxin, rep1


title: HPMEC donor 1: Control (4h) + VB (6h)

description: Library name: HPMEC.1.RHO.H2O.VB

value: Lung

value: Primary HPMEC-c

value: microvascular endothelial cells

value: Water (H2O)


title: Neutrophils HD6

description: 5605_13_Healthy_Donor_12_NB_TGCAGCTA-TCTCTCCG_S37


title: HPMEC donor 1: RHOi (4h) + DMSO (6h)

description: Library name: HPMEC.1.RHO.RHOi.DMSO

value: 0.1% DMSO + 0.5 µg/ml C3 transferase (RHOi)


title: SMC3-AID-2.5min-S3-R3-spnA

value: Bursa

value: lymphoblast

value: 1NMPP1 for 10 h + 3 h ( auxin), washed (8:38 min), release for 2.5 min, after cross-linking; cells were NOT GFP sorted


title: TIR-1; dpy-27::AID; cec-4, no auxin, rep3


title: Neutrophils HD2

description: 5605_9_Healthy_donor_14_HG_TAGCGCTC-CGTCTAAT_S27


title: HPMEC donor 1: Control (4h) + DMSO (6h)

description: Library name: HPMEC.1.RHO.H2O.DMSO

value: 0.1% DMSO


title: SMC3-AID-G2-S3-R3-spnA

value: 1NMPP1 for 10 h + 3 h ( auxin), washed (8:38 min)  and cross-linked, cells were NOT GFP sorted


title: Neutrophils HD1

description: 5605_8_Healthy_donor_13_HG_ATGCGCAG-CTAAGCCT_S25

value: Blood


title: TIR-1; dpy-27::AID; cec-4, no auxin, rep2


title: SMC3-AID-30min-S2-R2-SpnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (20 min), release for 30 min, after cross-linking, cells were GFP sorted (negative)


title: RPE1 rep 3: CA4

description: Library name: RPE1.3.CA4

source_name: hTERT RPE1

growth_protocol: hTERT RPE1s were cultivated in a 37°C, 5% CO2 humidified chamber. After cells reached 100% confluency, and then maintained for 5 days to induce quiescence. Media was changed every 2-3 days to maintain nutrition of culture

extract_protocol:
Total RNA was isolated from cells using the RNeasy Qiagen Extraction kit. At least 2300 ng was provided to Azenta for sequencing.
Library construction and sequencing were conducted by Azenta Next-Generation Sequencing, standard RNA-seq with polyA selection.

treatment_protocol: After a full 5 days of quiescence, hTERT RPE1s were treated with baseline (0.1% DMSO) or treatment (100 nM CA4) for 6 hours in fresh medium.

value: hTERT RPE1

value: 100 nM CA4


title: Neutrophils mTNBC7

value: FACS sorted neutrophils

value: Triple-Negative Breast Cancer


title: TIR-1; dpy-27::AID; cec-4, no auxin, rep1

value: TIR-1; dpy-27::AID; cec-4


title: RPE1 rep 3: DMSO

description: Library name: RPE1.3.DMSO


title: Neutrophils HD3

description: 5605_10_Healthy_Donor_4_NB_ACTGAGCG-CGTCTAAT_S34

value: healthy


title: Neutrophils mTNBC6


title: SMC3-AID-10min-S2-R2-SpnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (20 min), release for 10 min, after cross-linking, cells were GFP sorted (negative)


title: TIR-1; dpy-27::AID, auxin, rep3

source_name: TIR-1; dpy-27::AID, auxin, rep3

value: TIR-1; dpy-27::AID

value: auxin


title: RPE1 rep 2: CA4

description: Library name: RPE1.2.CA4


title: TIR-1; dpy-27::AID, auxin, rep2

source_name: TIR-1; dpy-27::AID, auxin, rep2


title: RPE1 rep 2: DMSO

description: Library name: RPE1.2.DMSO


title: Neutrophils mTNBC5


title: Neutrophils mTNBC4

description: 5605_4_Tonic_82_HG_GGAGCTAC-AAGGAGTA_S30


title: SMC3-AID-7.5min-S2-R2-SpnA

value: 1NMPP1 for 10 h + 3 h (auxin), washed (20 min), release for 7.5 min, after cross-linking, cells were GFP sorted (negative)


title: TIR-1; dpy-27::AID, auxin, rep1

source_name: TIR-1; dpy-27::AID, auxin, rep1


title: Neutrophils mTNBC3

description: 5605_3_Tonic_83_HG_ACTCGCTA-AAGGAGTA_S28


title: RPE1 rep 1: DMSO

description: Library name: RPE1.1.DMSO


title: SMC3-AID-2.5min-S2-R2-SpnA

value: Bursa

value: 1NMPP1 for 10 h + 3 h (auxin), washed (20 min), release for 2.5 min, after cross-linking, cells were GFP sorted (negative)


title: RPE1 rep 1: CA4

description: Library name: RPE1.1.CA4


title: TIR-1; dpy-27::AID, no auxin, rep2

source_name: TIR-1; dpy-27::AID, no auxin, rep2


title: TIR-1; dpy-27::AID, no auxin, rep3

source_name: TIR-1; dpy-27::AID, no auxin, rep3


title: Neutrophils mTNBC2

description: 5605_2_Tonic_80_HG_ATCTCAGG-AAGGAGTA_S29


title: TIR-1; dpy-27::AID, no auxin, rep1

source_name: TIR-1; dpy-27::AID, no auxin, rep1


title: SMC3-AID-G2-S2-R2-SpnA

value: lymphoblast

value: 1NMPP1 for 10 h + 3 h (auxin), washed (20 min)  and cross-linked, cells were cells were GFP sorted (negative)


title: HPMEC donor 3: PL

description: Library name: HPMEC.6.PL

source_name: Lung

extract_protocol:
Total RNA was isolated from cells using the RNeasy Qiagen Extraction kit. At least 1800 ng was provided to Azenta for sequencing.
Library construction and sequencing were conducted by Azenta Next-Generation Sequencing, standard RNA-seq with polyA selection.

treatment_protocol: Cells were treated with baseline (DMSO) or treatment for 6 hours in fresh assay medium.

value: Lung

value: Primary HPMEC-c

value: microvascular endothelial cells

value: 100 nM plinabulin


title: Neutrophils mTNBC1

description: 5605_1_Tonic_74_HG_GCTCATGA-AAGGAGTA_S26

value: Blood


title: SMC3-AID-30min-S1-R1-spna

treatment_protocol: 1% formaldehyde for 10 minutes before glycine quenching (128 mM final) for 5 minutes at room temperature followed by 15 minutes on ice and wash with PBS before storing at -80°C

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (20 min), release for 30 min, after cross-linking, cells were NOT GFP sorted (positive)


title: L. albus 80 min 10 mM sucrose  replicate 3

city: Hayward

first: Claudia

last: Uhde-Stone

state: CA

address: 25800 Carlos Bee Blvd

department: Biological Sciences

institute: California State University, East Bay

description:
Library name: t80_rep3
150PE

data_processing:
Illumina bcl2fastq2(v2.20) Conversion Software was used to demultiplex the obtained sequencing data and to convert base call files into FASTQ files. We transferred demultiplexed FastQ files containing 527 million reads from the QB3 server to our storage allocation at the EXPANSE supercomputer housed at SDSC (San Diego Supercomputer Center). We checked sequence quality using FastQC (https://qubeshub.org/resources/fastqc). Next, we removed adaptors and any low-quality sequences with TRIMMOMATIC Version 0.32.
Sequence quality was again checked by FastQC to ensure TRIMMOMATIC properly removed all adaptors and low-quality regions. Then all paired RNA-seq reads were mapped with HiSat2 to the L. albus reference genome  (GCA_009771035.1)
We used the prepDE.py3 script (http://ccb.jhu.edu/software/stringtie/dl/prepDE.py3) to extract two CSV (comma separated value) files with transcript and gene count information. These files were explored further in RStudio. We used DESeq2 for time course analysis of differential expression. In addition, we extracted the normalized expression data FPKM (Fragment per kilobase and million) using Ballgown.
Assembly: CNRS_Lalb_1.0/GCA_009771035.1 assembly
Supplementary files format and content: csv file containing DESeq2 data for 20 min (t20), 40 min (t40) and 80 min (t80) of sucrose treatment (DESeq2_and_FPKM_all_genes_t20-t40-t80_annotated.csv)

organism: Lupinus albus

source_name: several ~4-5 cm root sections with tips

growth_protocol: White lupin (Lupinus albus, cultivar Amiga) seeds were sterilized by shaking for 3 minutes in 10% bleach, followed by several rinses with sterile water. Sterile seeds were then spread out on sterile petri dishes (10-20 seeds per dish) and covered about halfway with sterile water to germinate at room temperature in the dark for 3-4 days. Once the radicles reached a length of 2-3 cm, the seedlings were transferred to containers filled with 850 ml of Hoagland solution, which was changed about every 4 days. The temperature of the growth chamber was maintained at ~21°C with a light cycle of 16 hours and a dark cycle of 8 hours.

extract_protocol:
RNA from frozen root samples was isolated using the RNeasy Plant Mini kit (Qiagen, Valencia, CA, USA). TapeStation (Agilent, Santa Clara, CA, USA) was used to assess both quantity and quality of each sample; only RNA samples with RIN (RNA integrity Numbers) above 8 were used for RNA-seq.
The Stranded mRNA Kit (Illumina, Foster City, CA, USA) was used to convert the extracted RNA to cDNA, following the manufacturer’s instructions. Unique dual bar-coding for each cDNA library was done using the IDT for Illumina RNA UD Indexes Set A (Illumina). Quantity and quality of cDNA libraries were assessed via TapeStation (Agilent, Santa Clara, CA, USA) and remaining adaptors were cleaned up where necessary using AMPure XP magnetic beads (New England Biolabs, Ipswich, MA, USA) at a ratio of 1 volume DNA to 0.8 volumes of beads. Exact quantification, pooling, and sequencing of the 12 barcoded cDNA libraries was performed at QB3 (Institute for Quantitative Biosciences at UC Berkeley). Sequencing of the pooled cDNA libraries was performed on one flowcell lane on the Illumina No-vaSeq6000 SP 150PE (paired-end) next-generation sequencing platform.

treatment_protocol: For treatment, the plant roots of selected pots were exposed to sucrose by adding 8.5 ml of 1 M sucrose (prepared in Hoagland solution) directly to the hydroponic solution, for a final concentration of 10 mM sucrose. Harvesting was done after exposing the plants to sucrose for different periods: 0 minutes (control), 20, 40, and 80 minutes. All time points were done in 3 biological replications (1 plant for each biological replication). For harvesting, about 100 mg of the root tip sections with a length of about 4-5 cm were harvested in liquid nitrogen from each plant and stored immediately at -80 deg C

value: several ~4-5 cm root sections with tips

value: wildtype

value: 80 min 10 mM sucrose


title: HPMEC donor 3: DTXL

description: Library name: HPMEC.6.DTXL

value: 100 nM docetaxel


title: dpy-27::AID, auxin, rep3

source_name: dpy-27::AID, auxin, rep3


title: SMC3-AID-5min-S2-R2-SpnA

growth_protocol: Chicken DT40 cells were cultured in RPMI 1640 medium supplemented with 10 % fetal bovine serum and 1% chicken serum at 39°C in 5% CO2 in air.

value: 1NMPP1 for 10 h + 3 h (auxin), washed (20 min), release for 5 min, after cross-linking, cells were GFP sorted (negative)


title: dpy-27::AID, auxin, rep2

source_name: dpy-27::AID, auxin, rep2

value: auxin


title: HPMEC donor 3: VB

description: Library name: HPMEC.6.VB

value: 100 nM vinblastine


title: SMC3-AID-15min-S1-R1-spna

value: Bursa

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (20 min), release for 15 min, after cross-linking, cells were NOT GFP sorted (positive)


title: L. albus 80 min 10 mM sucrose  replicate 2

description:
Library name: t80_rep2
150PE


title: HPMEC donor 3: CA4

description: Library name: HPMEC.6.CA4

value: 100 nM combretastatin A4


title: dpy-27::AID, no auxin, rep3

source_name: dpy-27::AID, no auxin, rep3


title: HPMEC donor 3: DMSO

description: Library name: HPMEC.6.DMSO

value: 0.1% DMSO


title: SMC3-AID-10min-S1-R1-spna

source_name: Bursa

value: lymphoblast

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (20 min), release for 10 min, after cross-linking, cells were NOT GFP sorted (positive)


title: L. albus 20 min 10 mM sucrose  replicate 3

description:
Library name: t20_rep3
150PE

value: 20 min 10 mM sucrose


title: SMC3-AID-G2-S1-R1-spna

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (20 min)  and cross-linked, cells were NOT GFP sorted (positive)


title: L. albus 40 min 10 mM sucrose  replicate 1

description:
Library name: t40_rep1
150PE

value: 40 min 10 mM sucrose


title: WT-90min-S5-R1-spMa

description: DT-40-CDK1 knockout , transfected with Xenops laevis CDK1as and TIR1

value: WT-CDK1as (Z11)

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (9 min), release for 60 min, after cross-linking; cells were NOT GFP sorted


title: dpy-27::AID, no auxin, rep1

source_name: dpy-27::AID, no auxin, rep1


title: dpy-27::AID, auxin, rep1

source_name: dpy-27::AID, auxin, rep1


title: SMC3-AID-7.5min-S1-R1-spna

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (20 min), release for 7.5 min, after cross-linking, cells were NOT GFP sorted (positive)


title: dpy-21; cec-4, no auxin, rep2

source_name: dpy-21; cec-4, no auxin, rep2

value: dpy-21; cec-4


title: HPMEC donor 2: CA4

description: Library name: HPMEC.4.CA4

value: Lung

value: Primary HPMEC-c

value: microvascular endothelial cells


title: L. albus 20 min 10 mM sucrose  replicate 1

description:
Library name: t20_rep1
150PE

value: several ~4-5 cm root sections with tips

value: wildtype


title: HPMEC donor 2: PL

description: Library name: HPMEC.4.PL

value: 100 nM plinabulin


title: SMC3-AID-2.5min-S1-R1-spna

value: Bursa

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (20 min), release for 2.5 min, after cross-linking, cells were  GFP sorted (positive)


title: dpy-27::AID, no auxin, rep2

source_name: dpy-27::AID, no auxin, rep2


title: SMC3-AID-5min-S1-R1-spna

value: lymphoblast

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (20 min), release for 5 min, after cross-linking, cells were NOT GFP sorted (positive)


title: HPMEC donor 2: VB

description: Library name: HPMEC.4.VB

value: 100 nM vinblastine


title: L. albus 40 min 10 mM sucrose  replicate 3

description:
Library name: t40_rep3
150PE


title: HPMEC donor 2: DTXL

description: Library name: HPMEC.4.DTXL

value: 100 nM docetaxel


title: dpy-21; cec-4, no auxin, rep3

source_name: dpy-21; cec-4, no auxin, rep3


title: L. albus 80 min 10 mM sucrose  replicate 1

description:
Library name: t80_rep1
150PE

value: 80 min 10 mM sucrose


title: L. albus 40 min 10 mM sucrose  replicate 2

description:
Library name: t40_rep2
150PE

value: 40 min 10 mM sucrose


title: HPMEC donor 2: TNF-α

description: Library name: HPMEC.4.TNFa

value: 1 ng/ml TNF-α


title: L. albus no sucrose (control) replicate 3

description:
Library name: t0_rep3
150PE

value: control


title: WT-60min-S5-R4-spMa

value: WT-CDK1as (Z11)

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (9 min), release for 60 min, after cross-linking; cells were NOT GFP sorted


title: WT-30min-S5-R5-spna

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (9 min), release for 30 min, after cross-linking; cells were NOT GFP sorted


title: WT-15min-S5-R4-spna

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (9 min), release for 15 min, after cross-linking; cells were NOT GFP sorted


title: HPMEC donor 3: TNF-α

description: Library name: HPMEC.6.TNFa

value: Lung

value: Primary HPMEC-c

value: microvascular endothelial cells


title: dpy-21; cec-4, no auxin, rep1

source_name: dpy-21; cec-4, no auxin, rep1

value: dpy-21; cec-4


title: L. albus no sucrose (control) replicate 1

description:
Library name: t0_rep1
150PE

value: several ~4-5 cm root sections with tips

value: wildtype


title: dpy-21, no auxin, rep2

source_name: dpy-21, no auxin, rep2


title: WT-7.5min-S5-R3-spna

value: Bursa

value: lymphoblast

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (9 min), release for 7.5 min, after cross-linking; cells were NOT GFP sorted


title: dpy-21, no auxin, rep3

source_name: dpy-21, no auxin, rep3


title: HPMEC donor 1: DTXL

description: Library name: HPMEC.1.DTXL

value: 100 nM docetaxel


title: L. albus no sucrose (control) replicate 2

description:
Library name: t0_rep2
150PE


title: dpy-21, no auxin, rep1

source_name: dpy-21, no auxin, rep1


title: HPMEC donor 1: VB

description: Library name: HPMEC.1.VB

value: 100 nM vinblastine


title: 14 days post infection mouse brain 2

city: Port St. Lucie

first: Shan

last: Zhou

state: FL

address: 9801 Southwest Discovery Way

institute: Cleveland Clinic

description: Library name: 14dpi_2

data_processing:
IGV
Assembly: IGV
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: whole brain

extract_protocol:
RNA was harvested using RNeasy Lipid Tissue Mini Kit (Qiagen). 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep, Ligation Kit following manufacturer's protocols.

value: whole brain

value: primary brain cells

value: WT

value: 14 days post infected with 10000 PFU SARS-Cov-2-MA30


title: HPMEC donor 2: DMSO

description: Library name: HPMEC.4.DMSO

value: 0.1% DMSO


title: WT-10min-S5-R4-spna

value: WT-CDK1as (Z11)

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (9 min), release for 10 min, after cross-linking; cells were NOT GFP sorted


title: cec-4, auxin, rep1

source_name: cec-4, auxin, rep1

value: auxin


title: cec-4, auxin, rep3

source_name: cec-4, auxin, rep3


title: WT-5min-S5-R4-spna

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (9 min), release for 5 min, after cross-linking; cells were NOT GFP sorted


title: cec-4, auxin, rep2

source_name: cec-4, auxin, rep2


title: WT-15min-S4-R3-spna

value: Cells were treated with 1NMPP1 for 10 h, release after 15 min


title: 4 days post infection mouse brain 3

description: Library name: 4dpi_3

value: 4 days post infected with 10000 PFU SARS-Cov-2-MA30


title: HPMEC donor 1: PL

description: Library name: HPMEC.1.PL

source_name: Lung

value: Lung

value: Primary HPMEC-c

value: microvascular endothelial cells

value: 100 nM plinabulin


title: HPMEC donor 1: CA4

description: Library name: HPMEC.1.CA4

value: 100 nM combretastatin A4


title: WT-2.5min-S5-R3-spna

value: Bursa

value: lymphoblast

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (9 min), release for 2.5 min, after cross-linking; cells were NOT GFP sorted


title: 14 days post infection mouse brain 3

description: Library name: 14dpi_3

value: whole brain

value: primary brain cells

value: WT


title: cec-4, no auxin, rep3

source_name: cec-4, no auxin, rep3


title: L. albus 20 min 10 mM sucrose  replicate 2

description:
Library name: t20_rep2
150PE

source_name: several ~4-5 cm root sections with tips

value: several ~4-5 cm root sections with tips

value: wildtype

value: 20 min 10 mM sucrose


title: 14 days post infection mouse brain 1

description: Library name: 14dpi_1

value: 14 days post infected with 10000 PFU SARS-Cov-2-MA30


title: WT-G2-S5-R8-spna

source_name: Bursa

value: WT-CDK1as (Z11)

value: 1NMPP1 for 10 h + 3 h (no auxin), washed (9 min)  and cross-linked, cells were NOT GFP sorted


title: cec-4, no auxin, rep2

source_name: cec-4, no auxin, rep2


title: HPMEC donor 1: DMSO

description: Library name: HPMEC.1.DMSO

value: Lung

value: 0.1% DMSO


title: HPMEC donor 1: TNF-α

description: Library name: HPMEC.1.TNFa

value: Primary HPMEC-c

value: microvascular endothelial cells

value: 1 ng/ml TNF-α


title: WT, no auxin, rep3

source_name: WT, no auxin, rep3


title: HCC - T

city: fuzhou

first: xiaoyun

last: chen

address: 福建省福州市闽侯县上街镇学园路1号

institute: Fujian Medical University

data_processing:
After quality control, the reads were 3’5'-adaptor trimmed and filtered 15 bp reads with cutadapt software.
The trimmed reads were aligned to reference genome with bowtie software.
For each sample, known miRNAs, and predicted novel miRNAs were identified and enumerated using miRDeep2 software package (Freedlander et al. Nature Biotechnology, 26, 407-415 (2008) ).
Raw reads were normalized by calculated CPM value.
Assembly: miRBase Release 22
Supplementary files format and content: The xlsx format file contains the CPM value of gene in every sample.

source_name: liver cancer

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen/Life Technologies) following the manufacturer’s protocol. RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE).Small RNA libraries were constructed using New England Biolabs (NEB) NEBNext Multiplex Small RNA Library Prep Set for Illumina sequencers and the NEB standard protocol. Individual libraries were constructed using 1µg of total RNA isolated from each sample.
1) 3’-adaptor ligation;2) 5’-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) size selection of 135   155 bp PCR amplified fragments (corresponding to 15   35 nt small RNAs).

value: hepatocellular carcinoma

value: liver cancer


title: WT-7.5min-S4-R2-spna

city: Worcester

first: Johan

last: Gibcus

value: Bursa

value: lymphoblast

value: Cells were treated with 1NMPP1 for 10 h, release after 7.5 min


title: cec-4, no auxin, rep1

source_name: cec-4, no auxin, rep1


title: WT-5min-S4-R3-spna

value: Cells were treated with 1NMPP1 for 10 h, release after 5 min


title: Mock infection mouse brain 3

description: Library name: Ctrl_3

value: whole brain

value: primary brain cells

value: WT

value: Mock infection


title: HCC - N

address: 福建省福州市闽侯县上街镇学园路1号

source_name: adjacent normal tissue

value: adjacent normal tissue


title: Mock infection mouse brain 2

description: Library name: Ctrl_2


title: WT, no auxin, rep1

source_name: WT, no auxin, rep1


title: 4 days post infection mouse brain 1

description: Library name: 4dpi_1

value: 4 days post infected with 10000 PFU SARS-Cov-2-MA30


title: HCC - HePG2

address: 福建省福州市闽侯县上街镇学园路1号

source_name: cell line

value: cell line


title: HCC - 97H

address: 福建省福州市闽侯县上街镇学园路1号


title: WT-10min-S4-R3-spna

value: WT-CDK1as (Z11)

value: Cells were treated with 1NMPP1 for 10 h, release after 10 min


title: WT, no auxin, rep2

source_name: WT, no auxin, rep2


title: KP4_FOCAD_0h_DoxPos_3

status: Public on Jan 24 2025

first: Patricia

middle: C

last: Borck

address: 415 Main St

department: Cancer Program

institute: Broad Institute

description: Library name: KP4_FOCAD_0h_DoxPos_3

data_processing:
BCL files demultiplexed with bcl2fastq then aligned to hg28 using STAR
Quality control checked with RNA-SeQ2
Expected counts derived with RSEM
Supplementary files format and content: comma-delimited file with rows for each sample and Ensembl Genes as columns, containing RSEM expected counts
Assembly: hg38

extract_protocol:
Total RNA was purified according to the Qiagen RNeasy Mini Kit protocol
Libraries were prepared according to the NEBNext® Ultra™ II Directional RNA Library Prep Kit

treatment_protocol: All cells were transduced with a DOX-inducible PELO gRNA and later engineered to constitutively express dCas9-KRAB-MeCP2 and enAsCasd12a. These cells were subsequently transduced with a gRNA for enAsCasd12a against FOCAD or a control gRNA (Ch2). After confirming FOCAD knockout cell were treated with DOX or vehicle (DMSO) for 4 days and then collected for the expression profiling.

value: DOX+

tag: time


title: KP4_FOCAD_0h_DoxPos_2

description: Library name: KP4_FOCAD_0h_DoxPos_2


title: Mock infection mouse brain 1

description: Library name: Ctrl_1


title: WT-G2-S4-R5-spna

address: 368 Plantation Street, Dekker Lab HHMI, AS5.1015,

institute: UMass Chan Medical School

value: Cells were treated with 1NMPP1 for 10 h, released immediately


title: KP4_FOCAD_0h_DoxNeg_3

description: Library name: KP4_FOCAD_0h_DoxNeg_3

value: DOX-


title: KP4_FOCAD_0h_DoxPos_1

description: Library name: KP4_FOCAD_0h_DoxPos_1


title: KP4_FOCAD_0h_DoxNeg_2

description: Library name: KP4_FOCAD_0h_DoxNeg_2


title: KP4_Chr2_0h_DoxPos_3

description: Library name: KP4_Chr2_0h_DoxPos_3


title: KP4_FOCAD_0h_DoxNeg_1

description: Library name: KP4_FOCAD_0h_DoxNeg_1


title: KP4_Chr2_0h_DoxPos_1

description: Library name: KP4_Chr2_0h_DoxPos_1


title: A549-dCas9-VP64 Parental Replicate 2

first: Evan

middle: Stuart

last: Bradley

address: 55 N Lake Avenue

department: Microbiology

description: Library name: P8_S8_L001

data_processing:
Base calling by Illumina basespace v7.28.1
quality control with FastQC v0.12.0
alignment with STAR 2.7.11b
transcript quantification with RSEM 2.0.1
Assembly: human hg38_genecode_v44
Supplementary files format and content: transcript counts in tab-delimited spread sheet

source_name: lung

extract_protocol:
Trizol total RNA extraction
Illumina Stranded mRNA library prepartion

value: lung

value: Bronchial Epithelial


title: A549-dCas9-VP64-B4GALNT2

description: Library name: PL2_S18_L001


title: KP4_Chr2_0h_DoxNeg_1

description: Library name: KP4_Chr2_0h_DoxNeg_1


title: KP4_Chr2_0h_DoxPos_2

description: Library name: KP4_Chr2_0h_DoxPos_2


title: KP4_Chr2_0h_DoxNeg_2

description: Library name: KP4_Chr2_0h_DoxNeg_2


title: ChIP-seq-05_GFP_ARMC5-GFP-FL_SPT5-AID_NVP2_rep1

city: Chicago

last: Aoi

state: IL

address: 303 E Superior St. SQBRC 7-300

department: Biochemistry & Molecular Genetics

institute: Northwestern University

description: ChIP-seq

data_processing:
Following the quality-trimming using trimmomatic 0.39, the reads were aligned to the genome using bowtie 2.4.5 and convereted to genome coverage file in bigwig format using deepTools 3.5.1.
Assembly: hg38
Supplementary files format and content: bigwig files containing genome coverage data

extract_protocol:
Cells were crosslinked in 1% formaldehyde/PBS and sonicated using Covaris to solubilize chromatin fraction. Following immunoprecipitation, elution fraction was reverse crosslinked and DNA was purified using PCR purification kit (QIAGEN).
Libraries were constructed using KAPA HyperPrep kit (Roche).

value: Colorectal adenocarcinoma


title: A549-dCas9-VP64 Parental Replicate 3

description: Library name: PL1_S17_L001


title: KP4_Chr2_0h_DoxNeg_3

description: Library name: KP4_Chr2_0h_DoxNeg_3


title: ChIP-seq-05_GFP_ARMC5-GFP-FL_SPT5-AID_NVP2-Aux_rep1

description: ChIP-seq


title: A549-dCas9-VP64 Parental Replicate 1

description: Library name: P15_S15_L001


title: ChIP-seq-06_GFP_ARMC5-GFP-FL_SPT5-AID_Aux_rep2

description: ChIP-seq

value: Aux


title: ChIP-seq-06_GFP_ARMC5-GFP-FL_SPT5-AID_NVP2-Aux_rep2

description: ChIP-seq


title: ChIP-seq-06_GFP_ARMC5-GFP-FL_SPT5-AID_NVP2_rep2

description: ChIP-seq


title: ChIP-seq-04_GFP_ARMC5-GFP-FL_SPT5-AID_H2O-90m_rep2

description: ChIP-seq


title: ChIP-seq-05_GFP_ARMC5-GFP-FL_SPT5-AID_Aux_rep1

description: ChIP-seq


title: 4 days post infection mouse brain 2

description: Library name: 4dpi_2

source_name: whole brain


title: ChIP-seq-06_GFP_ARMC5-GFP-FL_SPT5-AID_DMSO_rep2

description: ChIP-seq

value: DMSO


title: ChIP-seq-04_GFP_noGFP_SPT5-AID_Aux-90m_rep2

description: ChIP-seq


title: ChIP-seq-05_GFP_ARMC5-GFP-FL_SPT5-AID_DMSO_rep1

description: ChIP-seq


title: ChIP-seq-03_GFP_noGFP_SPT5-AID_H2O-90m_rep1

description: ChIP-seq


title: ChIP-seq-04_GFP_noGFP_SPT5-AID_H2O-90m_rep2

description: ChIP-seq


title: ChIP-seq-04_GFP_ARMC5-GFP-dB_SPT5-AID_Aux-90m_rep2

description: ChIP-seq


title: ChIP-seq-04_GFP_ARMC5-GFP-dB_SPT5-AID_H2O-90m_rep2

description: ChIP-seq


title: ChIP-seq-02_Pol2_SPT5AID_shNT_Aux-180m

description: ChIP-seq


title: ChIP-seq-03_GFP_noGFP_SPT5-AID_Aux-90m_rep1

description: ChIP-seq


title: ChIP-seq-02_Pol2_SPT5AID_shNT_Aux-90m

description: ChIP-seq


title: ChIP-seq-03_GFP_ARMC5-GFP-dB_SPT5-AID_Aux-90m_rep1

description: ChIP-seq


title: ChIP-seq-04_GFP_ARMC5-GFP-FL_SPT5-AID_Aux-90m_rep2

description: ChIP-seq


title: ChIP-seq-02_Pol2_SPT5AID_shARMC5_Aux-90m

description: ChIP-seq


title: ChIP-seq-03_GFP_ARMC5-GFP-FL_SPT5-AID_H2O-90m_rep1

description: ChIP-seq


title: ChIP-seq-02_Pol2_SPT5AID_shARMC5_Aux-0m

description: ChIP-seq


title: Zebrafish, scRNAseq, shield-sibling-2

city: qingdao

first: yizhuang

last: zhang

state: shandong

address: No.72 Binhai Road  Jimo District

department: school of life sciences

institute: shandong university

description:
10X Genomics GemCode Single-cell
s98

data_processing:
To remove any remaining biochemical reagents and primers from the post GEM reaction mixture, silane magnetic beads were employed. The full-length, barcoded cDNAs were subsequently amplified by PCR to generate sufficient mass for library construction. During GEM incubation, the molecules had R1 (Read 1 primer sequence) added to them. P5, P7, a sample index, and R2 (Read 2 primer sequence) were added during library construction through processes such as End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contained the P5 and P7 primers required for Illumina bridge amplification. The Single Cell 3' Protocol generated Illumina-ready sequencing libraries. Each Single Cell 3' Library consisted of standard Illumina paired-end constructs that began and ended with P5 and P7. The Single Cell 3' 16 bp 10x Barcode and 10 bp UMI were encoded in Read 1, while Read 2 was utilized to sequence the cDNA fragment. Sample index sequences were incorporated as the i7 index read. Read 1 and Read 2 corresponded to the standard Illumina® sequencing primer sites used in paired-end sequencing.
Assembly: GRCz10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: whole embryo

growth_protocol: Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C

extract_protocol:
For the preparation of single-cell suspensions, a total of thirty-three mutant embryos of Mrbm24a or wild-type embryos at the shield stage were collected. These cellular suspensions were then loaded onto a 10X Genomics GemCode Single-cell instrument, which generates single-cell Gel Bead-In-EMulsion (GEMs).
Libraries were generated and sequenced from the cDNAs using Chromium Next GEM Single Cell 3' Reagent Kits v3.1. Upon dissolution of the Gel Bead within a GEM, primers containing an Illumina® R1 sequence (Read 1 sequencing primer), a 16 nt 10x Barcode, a 10 nt Unique Molecular Identifier (UMI), and a poly-dT primer sequence were released. These primers were mixed with the cell lysate and Master Mix. Full-length, barcoded cDNAs were then reverse-transcribed from poly-adenylated mRNA

value: whole embryo

value: shield stage

value: embryonic cell

value: wild type


title: Zebrafish, scRNAseq, shield-Mrbm24a-2

description:
10X Genomics GemCode Single-cell
s96


title: ChIP-seq-02_Pol2_SPT5AID_shNT_Aux-0m

description: ChIP-seq


title: ChIP-seq-03_GFP_ARMC5-GFP-FL_SPT5-AID_Aux-90m_rep1

description: ChIP-seq


title: RNA-seq_shARMC5_Rep3

description: polyA+ RNA-seq

data_processing:
Following the quality-trimming using cutadapt 4.2, the reads were applied to transcript quantification using salmon 1.9.0 with --gcBias option and summarization using tximeta.
Assembly: hg38
Supplementary files format and content: sf file containing transcript quantification from Salmon

extract_protocol:
Total RNA was extracted using RNeasy mini kit (QIAGEN).
Libraries were constructed using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB# E7490) and NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770).


title: ChIP-seq-02_Pol2_SPT5AID_shARMC5_Aux-180m

description: ChIP-seq


title: RNA-seq_shARMC5_Rep2

description: polyA+ RNA-seq


title: RNA-seq_shARMC5_Rep1

description: polyA+ RNA-seq


title: A549-dCas9-VP64-ADAR

description: Library name: P16_S16_L001


title: Zebrafish, scRNAseq, shield-Mrbm24a-1

description:
10X Genomics GemCode Single-cell
s95