title: Fer1_0-1.5_BS1

description: Drosophila embryos RNAi, shFer1, replicate 1, 0-1.5 hours


title: 210322_TFmap_S10

status: Public on Jan 05 2023

type: SRA

city: Cambridge

first: Julia

last: Joung

state: MA

address: 75 Ames St

country: USA

institute: Broad Institute

description:
TF mapping results for 210322_TFAtlas_S10
library strategy: amplicon

library_source: transcriptomic

data_processing:
Custom SHARE-seq pipeline
Scanpy v1.7.2
Custom Python script for mapping cells to transcription factor ORFs
Assembly: hg38
Supplementary files format and content: Raw count matrix generated by SHARE-seq pipeline (csv) and annotated processed data generated by Scanpy (h5ad). Map of cells to transcription factor ORFs produced by a custom Python script (csv)

molecule: polyA RNA

organism: Homo sapiens

source_name: H1 human embryonic stem cells

extract_protocol:
RNA was extracted using SHARE-seq
single-cell RNA-Seq libraries were prepared using SHARE-seq. Cells were mapped to their respective transcription factor perturbations by PCR amplifying the transcription factor and cell barcodes from the cDNA prior to tagmentation

tag: cell type

value: H1 human embryonic stem cells

tag: differentiation protocol

value: overexpression of a library with 3,550 transcription factors

tag: time point

value: 7 days


title: 190830_cardiomyocyte_Atrial_S1L

library_source: genomic

data_processing:
bcl2fastq 2.20.0
custom Python script to determine barcode distribution (see Methods)
Assembly: TF barcode sequences
Supplementary files format and content: Aggregated TF barcode counts determined using custom Python script for each condition
Library strategy: amplicon

molecule: genomic DNA

extract_protocol:
Genomic DNA was extracted using the Quick-DNA Midiprep Plus Kit (Zymo D4075)
Libraries were prepared by PCR amplification of TF barcodes using custom primers (see Methods)

value: cardiomyocytes

value: overexpression of a library with 80 transcription factors

value: 4 weeks

tag: screen condition

value: atrial sample 1 sorted low bin


title: Ets65A_CG32006_mCherry_16-18_BS2

city: Berkeley

first: Benjamin

middle: Wendell

last: Booth

state: CA

address: 1 Cyclotron Road

department: BioSciences

institute: Lawrence Berkeley National Laboratory

description: Drosophila embryos RNAi, shmCherry (Control for Ets65A, CG32006), replicate 2, 16-18 hours

data_processing:
Raw FASTQ files were aligned to the Drosophila melanogaster reference genome (Release 6)  using STAR aligner 2.7.3a  with default settings and up to 20 multiple alignments to produce BAM files.
HTSeq htseq-count v0.12.4 was used to determine read counts overlapping genes.
Differential gene expression in the RNAi experimental samples compared to the mCherry controls was determined using DESeq2 1.24.0.
bigWig files were created using a custom tool called bam2bedgraph to convert bam files into bedgraph files, then UCSC's bedGraphToBigWig to convert the bedgraph files to bigWig format.
Assembly: dm6
Supplementary files format and content: BAM alignment files aligning FASTQ read files to dm6 assembly using STAR 2.7.3a.
Supplementary files format and content: HTSeq htseq-count files produced with HTSeq v0.12.4
Supplementary files format and content: DESeq csv files produced using DESeq2 v1.24.0
Supplementary files format and content: bigWig files produced using custom bam2bedgraph script and UCSC bedGraphToBigWig tool

organism: Drosophila melanogaster

source_name: embryos

extract_protocol:
Frozen embryos were homogenized using the Pellet Pestle Cordless Motor (Kimble Cat. No. 749540-0000; Pellet Pestles Sigma Cat. No. Z359947). RNA was extracted from the homogenate using TRIzol Reagent (Thermo Fisher, Cat. No. 15596026), chloroform extraction and isopropanol precipitation.  RNA was resuspended in Nuclease Free Water (Ambion AM9930) and incubated over night before purification using the RNeasy Mini Kit (QIAGEN Cat. No. 74106).  After Qiagen clean up, RNA was quantified using NanoDrop ND1000v 3.5.2.
Libraries for sequencing were made using TruSeq Stranded mRNA Library Prep (llumina 20020594).

tag: tissue

value: embryos

tag: treatment

value: shmCherry (Control for Ets65A, CG32006)

tag: timepoint

value: 16-18 hours


title: 210322_TFmap_S09

description:
TF mapping results for 210322_TFAtlas_S09
library strategy: amplicon


title: 190830_cardiomyocyte_Mature_S1L

value: mature sample 1 sorted low bin


title: 190830_cardiomyocyte_Atrial_S1H

value: atrial sample 1 sorted high bin


title: Ets65A_CG32006_mCherry_16-18_BS1

description: Drosophila embryos RNAi, shmCherry (Control for Ets65A, CG32006), replicate 1, 16-18 hours


title: 210322_TFmap_S07

description:
TF mapping results for 210322_TFAtlas_S07
library strategy: amplicon


title: 210322_TFmap_S08

description:
TF mapping results for 210322_TFAtlas_S08
library strategy: amplicon


title: 190712_media_M7_Unsorted_S2

extract_protocol:
Lentivirus RNA was extracted using the QIAmp Viral RNA Mini Kit (Qiagen 52906). Genomic DNA was extracted using the Quick-DNA Midiprep Plus Kit (Zymo D4075)
Lentivirus RNA was reverse transcribed using the qScript Flex cDNA Kit (VWR 95049-100) with a custom primer (see Methods). Libraries were prepared by PCR amplification of TF barcodes using custom primers (see Methods)

value: overexpression of a library with 3,548 transcription factors

value: M7 media sample 2 unsorted


title: Ets65A_CG32006_mCherry_12-14_BS2

description: Drosophila embryos RNAi, shmCherry (Control for Ets65A, CG32006), replicate 2, 12-14 hours

value: 12-14 hours


title: 190712_media_M7_Unsorted_S1

value: M7 media sample 1 unsorted


title: 190712_media_M7_Stem_S2

value: M7 media sample 2 sorted high bin


title: 210322_TFmap_S11

description:
TF mapping results for 210322_TFAtlas_S11
library strategy: amplicon

value: H1 human embryonic stem cells


title: 190830_cardiomyocyte_Mature_S2L

value: mature sample 2 sorted low bin


title: 210322_TFmap_S06

description:
TF mapping results for 210322_TFAtlas_S06
library strategy: amplicon

value: overexpression of a library with 3,550 transcription factors

value: 7 days


title: 190712_media_M7_Stem_S1

value: M7 media sample 1 sorted high bin


title: 210322_TFmap_S05

description:
TF mapping results for 210322_TFAtlas_S05
library strategy: amplicon


title: 190712_media_M7_Diff_S1

value: M7 media sample 1 sorted low bin


title: 210322_TFmap_S04

description:
TF mapping results for 210322_TFAtlas_S04
library strategy: amplicon


title: Ets65A_CG32006_mCherry_0-1.5_BS2

description: Drosophila embryos RNAi, shmCherry (Control for Ets65A, CG32006), replicate 2, 0-1.5 hours

value: 0-1.5 hours


title: 190712_media_M7_Diff_S2

value: M7 media sample 2 sorted low bin


title: 190830_cardiomyocyte_Atrial_S2H

value: cardiomyocytes

value: overexpression of a library with 80 transcription factors

value: 4 weeks

value: atrial sample 2 sorted high bin


title: 190712_media_M6_Unsorted_S2

value: overexpression of a library with 3,548 transcription factors

value: M6 media sample 2 unsorted


title: 210322_TFmap_S03

description:
TF mapping results for 210322_TFAtlas_S03
library strategy: amplicon


title: 190712_media_M6_Unsorted_S1

value: M6 media sample 1 unsorted


title: 190712_media_M6_Stem_S2

value: M6 media sample 2 sorted high bin


title: 190712_media_M6_Stem_S1

value: M6 media sample 1 sorted high bin


title: 190712_media_M6_Diff_S2

value: H1 human embryonic stem cells

value: M6 media sample 2 sorted low bin


title: Ets65A_16-18_BS2

description: Drosophila embryos RNAi, shEts65A, replicate 2, 16-18 hours

value: embryos

value: 16-18 hours


title: 210322_TFmap_S02

description:
TF mapping results for 210322_TFAtlas_S02
library strategy: amplicon

value: overexpression of a library with 3,550 transcription factors

value: 7 days


title: Ets65A_CG32006_mCherry_0-1.5_BS1

description: Drosophila embryos RNAi, shmCherry (Control for Ets65A, CG32006), replicate 1, 0-1.5 hours

value: shmCherry (Control for Ets65A, CG32006)

value: 0-1.5 hours


title: Ets65A_16-18_BS1

description: Drosophila embryos RNAi, shEts65A, replicate 1, 16-18 hours


title: 190712_media_M6_Diff_S1

value: M6 media sample 1 sorted low bin


title: 190712_media_M5_Unsorted_S2

value: M5 media sample 2 unsorted


title: Ets65A_12-14_BS2

description: Drosophila embryos RNAi, shEts65A, replicate 2, 12-14 hours

value: 12-14 hours


title: 190712_media_M5_Unsorted_S1

value: M5 media sample 1 unsorted


title: 190712_media_M5_Stem_S2

value: overexpression of a library with 3,548 transcription factors

value: M5 media sample 2 sorted high bin


title: Ets65A_12-14_BS1

description: Drosophila embryos RNAi, shEts65A, replicate 1, 12-14 hours


title: Ets65A_CG32006_mCherry_12-14_BS1

description: Drosophila embryos RNAi, shmCherry (Control for Ets65A, CG32006), replicate 1, 12-14 hours


title: 190712_media_M5_Stem_S1

value: M5 media sample 1 sorted high bin


title: 190712_media_M5_Diff_S2

value: M5 media sample 2 sorted low bin


title: 210322_TFAtlas_S23

value: overexpression of a library with 897 transcription factors


title: Ets65A_0-1.5_BS2

description: Drosophila embryos RNAi, shEts65A, replicate 2, 0-1.5 hours


title: 190712_media_M5_Diff_S1

value: H1 human embryonic stem cells

value: M5 media sample 1 sorted low bin


title: 190712_media_M4_Unsorted_S1

value: M4 media sample 1 unsorted


title: 190712_media_M4_Unsorted_S2

value: M4 media sample 2 unsorted


title: 210322_TFAtlas_S21


title: Ets65A_0-1.5_BS1

description: Drosophila embryos RNAi, shEts65A, replicate 1, 0-1.5 hours

value: embryos


title: 190712_media_M4_Stem_S2

value: 7 days

value: M4 media sample 2 sorted high bin


title: 190712_media_M4_Stem_S1

value: M4 media sample 1 sorted high bin


title: 210322_TFAtlas_S20

value: overexpression of a library with 3,550 transcription factors


title: 210322_TFmap_S01

description:
TF mapping results for 210322_TFAtlas_S01
library strategy: amplicon


title: ERR_16-18_BS2

description: Drosophila embryos RNAi, shERR, replicate 2, 16-18 hours

value: shERR

value: 16-18 hours


title: 190712_media_M4_Diff_S2

value: M4 media sample 2 sorted low bin


title: ERR_16-18_BS1

description: Drosophila embryos RNAi, shERR, replicate 1, 16-18 hours


title: 190712_media_M4_Diff_S1

value: overexpression of a library with 3,548 transcription factors

value: M4 media sample 1 sorted low bin


title: 190712_media_M3_Unsorted_S2

value: M3 media sample 2 unsorted


title: 210322_TFAtlas_S24


title: ERR_10-12_BS1

description: Drosophila embryos RNAi, shERR, replicate 1, 10-12 hours

value: 10-12 hours


title: 190712_media_M3_Stem_S2

value: M3 media sample 2 sorted high bin


title: 190712_media_M3_Unsorted_S1

value: H1 human embryonic stem cells

value: M3 media sample 1 unsorted


title: 210322_TFAtlas_S19


title: 210322_TFAtlas_S18


title: 210322_TFAtlas_S17


title: 190712_media_M3_Stem_S1

value: M3 media sample 1 sorted high bin


title: 210322_TFAtlas_S22

value: overexpression of a library with 897 transcription factors


title: 210322_TFAtlas_S16


title: ERR_0-1.5_BS2

description: Drosophila embryos RNAi, shERR, replicate 2, 0-1.5 hours

value: embryos

value: 0-1.5 hours


title: 190712_media_M3_Diff_S2

value: 7 days

value: M3 media sample 2 sorted low bin


title: 210322_TFAtlas_S15

value: overexpression of a library with 3,550 transcription factors


title: 190712_media_M3_Diff_S1

value: M3 media sample 1 sorted low bin


title: 210322_TFAtlas_S14


title: ERR_10-12_BS2

description: Drosophila embryos RNAi, shERR, replicate 2, 10-12 hours

value: shERR


title: E5_da-Gal4_16-18_BS1

description: Drosophila embryos RNAi, shda-Gal4 (Control for E5), replicate 1, 16-18 hours

value: shda-Gal4 (Control for E5)

value: 16-18 hours


title: 190712_media_M2_Unsorted_S2

value: overexpression of a library with 3,548 transcription factors

value: M2 media sample 2 unsorted


title: 210322_TFAtlas_S13


title: 190712_media_M2_Unsorted_S1

value: M2 media sample 1 unsorted


title: LV free wall, adult non-operated heart No 14

type: RNA

city: Ota-ku

first: Hiroko

last: Izumi-Nakaseko

state: Tokyo

address: 5-21-16 Omori-Nishi

department: Faculty of Medicine

country: Japan

institute: Toho University

description: Gene expression data from free wall of left ventricule in adult non-operated heart of Macaca fascicularis

hyb_protocol: The biotin-tagged aRNA was hybridized to GeneChip® Rhesus Macaque Genome Array (Affymetrix).

scan_protocol: The amount of bound aRNA was measured by staining and scanning fluorescence intensity according to Affymetrix protocols.

data_processing: The obtained data was analyzed by Affymetrix® GeneChip® Command Console® Software and Affymetrix® Expression ConsoleTM with MAS5 algorithm.

label: biotin

molecule: total RNA

organism: Macaca fascicularis

source_name: heart

label_protocol: 100 ng of total RNA was used to generate biotin-tagged aRNA using GeneChip® 3' IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: The tissue samples at the weight of ≥50 mg of the left ventricular free wall were isolated from non-operated heart (n=4) or chronic atrioventricular block one (n=2) in male cynomolgus monkeys aging 4-6 years

extract_protocol: Total RNA was isolated from those samples using RNeasy Fibrous Tissue Mini Kit (QIAGEN, Valencia, CA, USA).

treatment_protocol: The animals were anesthetized with thiopental sodium (25 mg/kg, i.v.). After exsanguination, the heart was excised and plunged into saline. After the heart was rinsed with saline, the transmural specimen was obtained from the left ventricular free wall.

value: heart (left ventricular free wall)

tag: developmental stage

value: adult

tag: Sex

value: male

value: non-operated


title: 210322_TFAtlas_S12

value: H1 human embryonic stem cells


title: E5_da-Gal4_10-12_BS2

description: Drosophila embryos RNAi, shda-Gal4 (Control for E5), replicate 2, 10-12 hours

value: embryos

value: 10-12 hours


title: 5'-Seq Replicate 1

city: Boston

first: Zlata

last: Gvozdenov

address: 240 Longwood Ave

department: BCMP

institute: Harvard Medical School

description: Random DNA is at ChrXVII from 3911 to 21878 bp.

data_processing:
The reads were aligned with following command: bowtie2 -x sacCer3random_spombe -5 4 -3 16 --no-mixed --no-discordant --dovetail -X 1000 (-5 4 -3 16 was used for 37 nt read length, -5 4 -3 55 was used for 76 nt long reads).
bedtools bamtobed
Bed files were used to compute fragment locations for correctly aligned paired-end reads.
Duplicates based on both read pairs and fragment location were removed from the aligned reads.
5’ isoform location was derived by trimming fragment to obtain first nt position past the 5’ adapter (or the first nucleotide of the insert between the adapters) and by computing 5’ reads per genomic coordinates. Negative control values per genomic coordinate were normalized using internal S. pombe control and subtracted from the MDE treated sample (5’ isoform samples) to obtain true 5’ isoforms.
Assembly: sacCer3 (for spike-in: S. pombe ASM294v2)
Supplementary files format and content: Replicates were analyzed individually (every MDE treated, i.e. de-capped sample has its specific control that comes from the same experiment). Normalized per nucleotide counts were combined into one file, which has 3 columns: chromosome name, position, and counts (separated into two files for two DNA strands; plus bed file aligns to the minus strand, and minus 5seq file aligns to the plus strand).
Library strategy: 5'-Seq

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: Yeast were grown in SD his- medium at 30˚C to OD(595)=~0.55.

extract_protocol:
Hot phenol RNA extraction.
1 µg mRNA was obtained from DNased, total RNA (from the strain with random sequence artificial chromosome) via oligo d(T)25 magnetic bead enrichment. RNA was fragmented with NEBNext® Magnesium RNA Fragmentation Module and purified with ethanol precipitation. RNA was dephosphorylated with Quick CIP (NEB), heat inactivated and pre-adenylated 3’ adapter (Jin et al., 2015) was ligated with concentrated T4 RNA Ligase 1 (NEB). Reaction was split in two – mRNA deccaping enzyme (MDE, NEB) was added to one reaction, the other served as a control. 5’ adapter (Jin et al., 2015) was ligated with T4 RNA ligase 2 truncated (NEB), reaction was reverse transcribed, and the library was PCR amplified.

tag: strain


title: 190712_media_M2_Stem_S2

value: 7 days

value: M2 media sample 2 sorted high bin


title: 190712_media_M2_Stem_S1

value: M2 media sample 1 sorted high bin


title: 210322_TFAtlas_S11

value: overexpression of a library with 3,550 transcription factors


title: LV free wall, adult chronic atrioventricular block heart No 2

description: Gene expression data from free wall of left ventricule in adult pathological heart 8 months after the production of atrioventricular block of Macaca fascicularis

value: chronic atrioventricular block


title: LV free wall, adult non-operated heart No 13


title: E5_da-Gal4_0-1.5_BS2

description:
Drosophila embryos RNAi, shda-Gal4 (Control for E5), replicate 2, 0-1.5 hours
Sequencing Instruments: Illumina NextSeq 500; Illumina HiSeq 4000

value: shda-Gal4 (Control for E5)

value: 0-1.5 hours


title: HCC827 _CBX5 G7C (Replicate_3)

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

description: Processed data file: raw_counts.txt

data_processing:
The base calling was performed using RTA 1.18.64.0.
Reads were aligned to HG38 genome index and HG38 annotations using tophat version 2.1.0.
Aligned read counts are estimated from alignment file and HG38 gtf using Htseq-count version 0.6.0.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: raw_counts.txt: Raw read counts in tab-delimited text format.

source_name: Human HCC827 cells, CBX5 shRNA2 (G7) Transformed

growth_protocol: HCC827 cells stably expressing either CBX5 shRNAs or NS shRNA were grown in DMEM medium with 10% Fetal bovine serum and Penicilline and Streptomycin at 37 C under 5% CO2 condition.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacturer and then purified using RNeasy mini columns (Qiagen) as per the manufacturer's instructions.
mRNA is purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C. Following first-strand synthesis with random primers, second strand synthesis is performed with dUTP for generating strand-specific sequencing libraries. The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: HCC827 cells that expressed either CBX5 shRNAs or NS shRNA were used for preparing the total RNA and to perform gene expression array.

tag: cell line

value: Lung cancer cell line

tag: shRNA

value: CBX5 (G7)


title: ERR_0-1.5_BS1

description: Drosophila embryos RNAi, shERR, replicate 1, 0-1.5 hours

value: shERR


title: HCC827 _CBX5 G7B (Replicate_2)

description: Processed data file: raw_counts.txt


title: LV free wall, adult non-operated heart No 12

value: heart (left ventricular free wall)


title: 190712_media_M2_Diff_S2

value: overexpression of a library with 3,548 transcription factors

value: M2 media sample 2 sorted low bin


title: LV free wall, adult chronic atrioventricular block heart No 8

value: adult

value: male


title: 210322_TFAtlas_S09

value: H1 human embryonic stem cells


title: E5_da-Gal4_16-18_BS2

description: Drosophila embryos RNAi, shda-Gal4 (Control for E5), replicate 2, 16-18 hours

value: embryos

value: 16-18 hours


title: E5_da-Gal4_0-1.5_BS1

description:
Drosophila embryos RNAi, shda-Gal4 (Control for E5), replicate 1, 0-1.5 hours
Sequencing Instruments: Illumina NextSeq 500; Illumina HiSeq 4000


title: HCC827 _CBX5 G7A (Replicate_1)

description: Processed data file: raw_counts.txt


title: 190712_media_M2_Diff_S1

value: 7 days

value: M2 media sample 1 sorted low bin


title: 210322_TFAtlas_S08

value: overexpression of a library with 3,550 transcription factors


title: E5_16-18_BS1

description: Drosophila embryos RNAi, shE5, replicate 1, 16-18 hours


title: 190712_media_M1_Unsorted_S2

value: M1 media sample 2 unsorted


title: HCC827 _CBX5 G1C (Replicate_3)

description: Processed data file: raw_counts.txt

source_name: Human HCC827 cells, CBX5 shRNA1 (G1) Transformed

value: CBX5 (G1)


title: E5_da-Gal4_10-12_BS1

description: Drosophila embryos RNAi, shda-Gal4 (Control for E5), replicate 1, 10-12 hours

value: shda-Gal4 (Control for E5)

value: 10-12 hours


title: 210322_TFAtlas_S10


title: 210322_TFAtlas_S07


title: HCC827 _CBX5 G1B (Replicate_2)

description: Processed data file: raw_counts.txt

value: Lung cancer cell line


title: 190712_media_M1_Unsorted_S1

value: M1 media sample 1 unsorted


title: E5_10-12_BS2

description: Drosophila embryos RNAi, shE5, replicate 2, 10-12 hours


title: 190712_media_M1_Stem_S2

value: M1 media sample 2 sorted high bin


title: 210322_TFAtlas_S05


title: 210322_TFAtlas_S06


title: HCC827 _CBX5 G1A (Replicate_1)

description: Processed data file: raw_counts.txt


title: 190712_media_M1_Stem_S1

value: overexpression of a library with 3,548 transcription factors

value: M1 media sample 1 sorted high bin


title: E5_10-12_BS1

description: Drosophila embryos RNAi, shE5, replicate 1, 10-12 hours


title: 210322_TFAtlas_S04


title: LV free wall, adult non-operated heart No 11

value: heart (left ventricular free wall)

value: adult

value: non-operated


title: E5_16-18_BS2

description: Drosophila embryos RNAi, shE5, replicate 2, 16-18 hours

value: embryos


title: 190712_media_M1_Diff_S2

value: H1 human embryonic stem cells

value: M1 media sample 2 sorted low bin


title: E5_0-1.5_BS2

description:
Drosophila embryos RNAi, shE5, replicate 2, 0-1.5 hours
Sequencing Instruments: Illumina NextSeq 500; Illumina HiSeq 4000

value: 0-1.5 hours


title: 190712_media_M1_Diff_S1

value: 7 days

value: M1 media sample 1 sorted low bin


title: HCC827 NS (Control shRNA) )_CBX5 NSB (Replicate_2)

description: Processed data file: raw_counts.txt

source_name: Human HCC827 cells, NS (Control shRNA) Transformed

value: Control


title: Camta_16-18_BS2

description: Drosophila embryos RNAi, shCamta, replicate 2, 16-18 hours

value: shCamta

value: 16-18 hours


title: 210322_TFAtlas_S02

value: overexpression of a library with 3,550 transcription factors


title: Camta_16-18_BS1

description: Drosophila embryos RNAi, shCamta, replicate 1, 16-18 hours


title: 210322_TFAtlas_S01


title: Sample_Foxo4-KO5

city: Stillwater,

first: Khursheed

last: Iqbal

state: OK

address: 310 N Monroe St,

institute: Oklahoma state university

data_processing:
Reads from *.fastq files were mapped to the rat reference genome (Ensembl Rnor_5.0.78) using CLC Genomics Workbench 12.0 (Qiagen, Redwood City, CA).
mRNA abundance was expressed in transcripts per million (TPM).
A P value of 0.05 was used as a cutoff for significant differential expression.
Pathway analysis was performed using Datbase for Annotation, Visualization, and Integrated Discovery (DAVID, Huang et al., 2009).
Assembly: rat reference genome (Ensembl Rnor_5.0.78)

organism: Rattus norvegicus

source_name: Rat Junctional zone 18.5

growth_protocol: Holtzman Sprague-Dawley rats were housed in an environmentally controlled facility at the University of Kansas Medical Center (KUMC) with lights on from 0600 to 2000 h and allowed free access to food and water. Female rats (8-10 weeks of age) were mated with adult male rats (>3 months of age).  Mating was assessed by inspection of vaginal lavages. The presence of sperm in the vagina was designated gd 0.5. Placentation sites were dissected on gestation day 18.5 and placental junctional zones were isolated. Dissected placental junctional zone tissues were snap-frozen in liquid nitrogen and stored at -80°C until processing for RNA isolation. Total RNA was isolated from tissues using TRIzol reagent (Thermo Fisher Scientific, catalog No. 15596018). All rats were maintained in accordance with institutional policies for the care and use of vertebrate animals in research using protocols approved by the KUMC Animal Care and Use Committee.

extract_protocol:
Total RNA was isolated from cells and tissues using TRIzol reagent (cat no. 15596018, Thermo Fisher, Waltham, MA).
Complementary DNA libraries from total RNA samples were prepared with Illumina TruSeq RNA preparation kits (Illumina, San Diego, CA). Barcoded cDNA libraries were multiplexed and sequenced with the NovaSeq 6000 DNA sequencer (100-bp paired-end reads) using a TruSeq 200-cycle SBS kit (Illumina) at the KUMC Genome Sequencing Facility. Reads from *.fastq files were mapped to the rat reference genome (Ensembl Rnor_5.0.78) using CLC Genomics Workbench 12.0 (Qiagen, Redwood City, CA). mRNA abundance was expressed in transcripts per million (TPM).  A P value of 0.05 was used as a cutoff for significant differential expression.

value: Rat Junctional zone 18.5

value: Holtzman Sprague-Dawley


title: Sample_Foxo4-KO4


title: Camta_12-14_BS1

description: Drosophila embryos RNAi, shCamta, replicate 1, 12-14 hours

value: 12-14 hours


title: 180509_FlowFISH_2gene_S3L

data_processing:
library strategy: amplicon
bcl2fastq 2.20.0
custom Python script to determine barcode distribution (see Methods)
Assembly: TF barcode sequences
Supplementary files format and content: Aggregated TF barcode counts determined using custom Python script for each condition

source_name: HUES66 human embryonic stem cells

extract_protocol:
genomic DNA was extracted using the Quick-DNA Midiprep Plus Kit (Zymo D4075)
Libraries were prepared by PCR amplification of TF barcodes using custom primers (see Methods)

value: HUES66 human embryonic stem cells

value: overexpression of a library with 90 transcription factors

value: 2 genes sample 3 sorted low bin


title: 180509_FlowFISH_2gene_S3H

value: 2 genes sample 3 sorted high bin


title: Sample_Foxo4-KO3


title: HCC827 NS (Control shRNA) )_CBX5 NSC (Replicate_3)

description: Processed data file: raw_counts.txt

value: Lung cancer cell line


title: 201218_TFmap_S4

description: TF mapping results for 201218_ATAC_D7_S5-S8 and 201218_RNA_D7_S5-S8

data_processing:
Custom SHARE-seq pipeline
Scanpy v1.7.2
Seurat v4
Custom Python script for mapping cells to transcription factor ORFs
Assembly: hg38
Supplementary files format and content: For ATAC-seq, fragments generated by custom SHARE-seq pipeline (tsv). For RNA-seq, raw count matrix generated by SHARE-seq pipeline (csv). Both ATAC- and RNA-seq annotated processed data were generated by Scanpy (h5ad) and Seurat (rds). For map of cells to transcription factor ORFs, custom Python script (csv).
Library strategy: amplicon

extract_protocol:
DNA and RNA were extracted using SHARE-seq
single-cell ATAC- and RNA-Seq libraries were prepared using SHARE-seq. Cells were mapped to their respective transcription factor perturbations by PCR amplifying the transcription factor and cell barcodes from the cDNA prior to tagmentation

value: H1 human embryonic stem cells

value: overexpression of a library with 198 transcription factors


title: 180509_FlowFISH_2gene_S2L

value: 2 genes sample 2 sorted low bin


title: 210322_TFAtlas_S03

value: 7 days


title: HCC827 NS (Control shRNA) )_CBX5 NSA (Replicate_1)

description: Processed data file: raw_counts.txt


title: 201218_TFmap_S2

description: TF mapping results for 201218_ATAC_D4_S5-S8 and 201218_RNA_D4_S5-S8

value: 4 days


title: Sample_Foxo4-KO2


title: Sample_Foxo4-KO1


title: 201218_TFmap_S1

description: TF mapping results for 201218_ATAC_D4_S1-S4 and 201218_RNA_D4_S1-S4


title: CG9876_Hr51_mCherry_6-8_BS1

description: Drosophila embryos RNAi, shmCherry (Control for CG9876, Hr51), replicate 1, 6-8 hours

value: embryos

value: shmCherry (Control for CG9876, Hr51)

value: 6-8 hours


title: CG9876_Hr51_mCherry_6-8_BS2

description: Drosophila embryos RNAi, shmCherry (Control for CG9876, Hr51), replicate 2, 6-8 hours


title: CG9876_Hr51_mCherry_16-18_BS2

description: Drosophila embryos RNAi, shmCherry (Control for CG9876, Hr51), replicate 2, 16-18 hours

value: 16-18 hours


title: 201218_TFmap_S3

description: TF mapping results for 201218_ATAC_D7_S1-S4 and 201218_RNA_D7_S1-S4


title: E5_0-1.5_BS1

description:
Drosophila embryos RNAi, shE5, replicate 1, 0-1.5 hours
Sequencing Instruments: Illumina NextSeq 500; Illumina HiSeq 4000

value: 0-1.5 hours


title: Camta_0-1.5_BS1

description: Drosophila embryos RNAi, shCamta, replicate 1, 0-1.5 hours

value: shCamta


title: 180509_FlowFISH_2gene_S1H

value: 2 genes sample 1 sorted high bin


title: Sample_Foxo4-WT4

value: Rat Junctional zone 18.5

value: Holtzman Sprague-Dawley


title: Sample_Foxo4-WT5


title: 201218_RNA_D7_S8

data_processing:
Custom SHARE-seq pipeline
Scanpy v1.7.2
Seurat v4
Custom Python script for mapping cells to transcription factor ORFs
Assembly: hg38
Supplementary files format and content: For ATAC-seq, fragments generated by custom SHARE-seq pipeline (tsv). For RNA-seq, raw count matrix generated by SHARE-seq pipeline (csv). Both ATAC- and RNA-seq annotated processed data were generated by Scanpy (h5ad) and Seurat (rds). For map of cells to transcription factor ORFs, custom Python script (csv).


title: 180509_FlowFISH_10gene_S3L

value: HUES66 human embryonic stem cells

value: overexpression of a library with 90 transcription factors

value: 10 genes sample 3 sorted low bin


title: CG9876_Hr51_mCherry_16-18_BS1

description: Drosophila embryos RNAi, shmCherry (Control for CG9876, Hr51), replicate 1, 16-18 hours


title: CG9876_Hr51_mCherry_12-14_BS2

description: Drosophila embryos RNAi, shmCherry (Control for CG9876, Hr51), replicate 2, 12-14 hours

value: 12-14 hours


title: 180509_FlowFISH_10gene_S3H

value: 10 genes sample 3 sorted high bin


title: Sample_Foxo4-WT3


title: Sample_Foxo4-WT2


title: 201218_RNA_D7_S6

value: H1 human embryonic stem cells

value: overexpression of a library with 198 transcription factors


title: CG9876_Hr51_mCherry_12-14_BS1

description: Drosophila embryos RNAi, shmCherry (Control for CG9876, Hr51), replicate 1, 12-14 hours


title: 180509_FlowFISH_2gene_S2H

value: 7 days

value: 2 genes sample 2 sorted high bin


title: 201218_RNA_D7_S5


title: 180509_FlowFISH_10gene_S2L

value: 10 genes sample 2 sorted low bin


title: 180509_FlowFISH_2gene_S1L

value: 2 genes sample 1 sorted low bin


title: 180509_FlowFISH_10gene_S2H

value: 10 genes sample 2 sorted high bin


title: Sample_Foxo4-WT1


title: Sample_Foxo4-KD-2

source_name: Rat trophoblast stem cell

value: Trophoblast stem cell

value: Foxo4 shRNA


title: 180509_FlowFISH_10gene_S1H

value: 10 genes sample 1 sorted high bin


title: 201218_RNA_D7_S3


title: Sample_Foxo4-KD-1


title: 201218_RNA_D7_S7


title: 201218_RNA_D7_S1


title: CG9876_Hr51_mCherry_0-1.5_BS2

description: Drosophila embryos RNAi, shmCherry (Control for CG9876, Hr51), replicate 2, 0-1.5 hours

value: embryos

value: shmCherry (Control for CG9876, Hr51)

value: 0-1.5 hours


title: CG9876_6-8_BS1

description: Drosophila embryos RNAi, shCG9876, replicate 1, 6-8 hours

value: 6-8 hours


title: 180509_FlowFISH_10gene_S1L

value: HUES66 human embryonic stem cells

value: overexpression of a library with 90 transcription factors

value: 10 genes sample 1 sorted low bin


title: 201218_RNA_D7_S4

value: H1 human embryonic stem cells


title: CG9876_Hr51_mCherry_0-1.5_BS1

description: Drosophila embryos RNAi, shmCherry (Control for CG9876, Hr51), replicate 1, 0-1.5 hours


title: Sample_Scr-3_KK

value: Control shRNA

value: Holtzman Sprague-Dawley


title: CG9876_16-18_BS2

description: Drosophila embryos RNAi, shCG9876, replicate 2, 16-18 hours

value: 16-18 hours


title: 201218_RNA_D7_S2

value: overexpression of a library with 198 transcription factors

value: 7 days


title: 180726_RFX4_S2

data_processing:
Cell Ranger Single cell Software Suite v3.1.0
Scanpy v1.7.2
Assembly: hg38
Supplementary files format and content: Raw count matrix generated by Cell Ranger (mtx and tsv) and annotated processed data generated by Scanpy (h5ad)

extract_protocol:
RNA was extracted using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10X Genomics 120237)
single-cell RNA-Seq libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10X Genomics 120237)

value: RFX4 overexpression followed by spontaneous differentiation

value: 8 week


title: CG9876_6-8_BS2

description: Drosophila embryos RNAi, shCG9876, replicate 2, 6-8 hours


title: Sample_Scr-2_KK

value: Trophoblast stem cell


title: 201218_RNA_D4_S8

value: 4 days


title: 201218_RNA_D4_S7


title: CG9876_16-18_BS1

description: Drosophila embryos RNAi, shCG9876, replicate 1, 16-18 hours

value: embryos


title: Sample_Scr-1_KK


title: 180726_PAX6_S2

value: PAX6 overexpression followed by spontaneous differentiation


title: Sample_Foxo4-KD-3

value: Foxo4 shRNA


title: 180726_PAX6_S1


title: CG9876_12-14_BS2

description: Drosophila embryos RNAi, shCG9876, replicate 2, 12-14 hours

value: 12-14 hours


title: PD-1-CXCR5+_3

city: New Haven

first: Hiromitsu

last: Asashima

state: CT

address: 300George St

institute: Yele School of Medicine

data_processing:
low quality ends (less than phred score=30) and short read length (minimum length=30) was trimmed using PRINSEQ++(version1.2).
Trimmed reads were aligned to the hg38 genome reference using STAR(v2.7.1), and subsequently RSEM (RNA-Seq by Expectation-Maximization) was used to count reads mapping to the genes from Ensembl release 93.
limma was applied to model each gene as a linear combination of donor-specific effects.
Read count normalization were performed using DESeq2
Supplementary files format and content: hg38
Supplementary files format and content: A tables with raw gene counts for every gene and every sample

source_name: blood

extract_protocol:
RNAs were isolated using RNeasy Plus Micro Kit (QIAGEN)
cDNAs were generated using the SMART-Seq v4 Ultra Low Input RNA Kit for sequencing (Takara/Clontech) and barcoded libraries were generated by the Nextera XT DNA Library Preparation kit (Illumina)

value: blood

tag: time

value: ex vivo

value: CD45RA-CD4+T cells


title: 201218_RNA_D4_S6

value: H1 human embryonic stem cells


title: CG9876_12-14_BS1

description: Drosophila embryos RNAi, shCG9876, replicate 1, 12-14 hours


title: 201218_RNA_D4_S5


title: CG9876_0-1.5_BS2

description: Drosophila embryos RNAi, shCG9876, replicate 2, 0-1.5 hours

value: 0-1.5 hours


title: 201218_RNA_D4_S4


title: 201218_RNA_D4_S3


title: 180726_ASCL1_S2

value: HUES66 human embryonic stem cells

value: ASCL1 overexpression followed by spontaneous differentiation


title: 180726_RFX4_S1


title: PD-1intCXCR5+_3


title: PD-1intCXCR5-_3


title: PD-1highCXCR5+_3


title: CG9876_0-1.5_BS1

description: Drosophila embryos RNAi, shCG9876, replicate 1, 0-1.5 hours


title: 201218_RNA_D4_S2

value: overexpression of a library with 198 transcription factors


title: CG34376_rgr_slou_mCherry_16-18_BS1

description: Drosophila embryos RNAi, shmCherry (Control for CG34376, rgr, slou), replicate 1, 16-18 hours

value: 16-18 hours


title: 180525_GW_S2

value: small molecule inhibition of GSK and WNT

value: 4 week


title: CG34376_rgr_slou_mCherry_16-18_BS2

description: Drosophila embryos RNAi, shmCherry (Control for CG34376, rgr, slou), replicate 2, 16-18 hours


title: 180726_ASCL1_S1

value: 8 week


title: CG34376_rgr_slou_mCherry_10-12_BS2

description: Drosophila embryos RNAi, shmCherry (Control for CG34376, rgr, slou), replicate 2, 10-12 hours

value: 10-12 hours


title: 201218_ATAC_D7_S8

value: 7 days


title: 180525_GW_S1


title: PD-1-CXCR5+_2


title: 201218_RNA_D4_S1

value: 4 days


title: CG34376_rgr_slou_mCherry_10-12_BS1

description: Drosophila embryos RNAi, shmCherry (Control for CG34376, rgr, slou), replicate 1, 10-12 hours

value: embryos


title: 201218_ATAC_D7_S7


title: 180525_EOMES_S1

value: EOMES overexpression


title: PD-1-CXCR5-_3

value: blood


title: 180726_NFIB_S2

value: NFIB overexpression followed by spontaneous differentiation


title: CG34376_rgr_slou_mCherry_0-1.5_BS2

description: Drosophila embryos RNAi, shmCherry (Control for CG34376, rgr, slou), replicate 2, 0-1.5 hours


title: PD-1highCXCR5-_3

value: ex vivo

value: CD45RA-CD4+T cells


title: PD-1-CXCR5-_2


title: 201218_ATAC_D7_S6

value: H1 human embryonic stem cells


title: 201218_ATAC_D7_S5


title: 180726_NFIB_S1

value: HUES66 human embryonic stem cells


title: CG34376_rgr_slou_mCherry_0-1.5_BS1

description: Drosophila embryos RNAi, shmCherry (Control for CG34376, rgr, slou), replicate 1, 0-1.5 hours

value: 0-1.5 hours


title: PD-1intCXCR5-_2


title: PD-1highCXCR5+_2


title: 201218_ATAC_D7_S4

value: overexpression of a library with 198 transcription factors


title: CG34376_16-18_BS2

description: Drosophila embryos RNAi, shCG34376, replicate 2, 16-18 hours

value: 16-18 hours


title: CG34376_16-18_BS1

description: Drosophila embryos RNAi, shCG34376, replicate 1, 16-18 hours


title: 180124_TFmap

data_processing:
Cell Ranger Single cell Software Suite v3.1.0
Scanpy v1.7.2
Custom Python script for mapping cells to transcription factor ORFs
Assembly: hg38
Supplementary files format and content: Raw count matrix generated by Cell Ranger (mtx and tsv) and annotated processed data generated by Scanpy (h5ad). Map of cells to transcription factor ORFs produced by a custom Python script (csv)
Library strategy: AMPLICON

extract_protocol:
RNA was extracted using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10X Genomics 120237)
single-cell RNA-Seq libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10X Genomics 120237). Cells were mapped to their respective transcription factor perturbations by PCR amplifying the transcription factor and cell barcodes from the cDNA prior to tagmentation

tag: perturbation

value: overexpression of a library with 90 transcription factors

tag: perturbation time point


title: 180124_perturb_S8

data_processing:
Cell Ranger Single cell Software Suite v3.1.0
Scanpy v1.7.2
Custom Python script for mapping cells to transcription factor ORFs
Assembly: hg38
Supplementary files format and content: Raw count matrix generated by Cell Ranger (mtx and tsv) and annotated processed data generated by Scanpy (h5ad). Map of cells to transcription factor ORFs produced by a custom Python script (csv)


title: 180124_perturb_S7


title: CG34376_10-12_BS2

description: Drosophila embryos RNAi, shCG34376, replicate 2, 10-12 hours


title: PD-1-CXCR5+_1


title: 180124_perturb_S6


title: PD-1intCXCR5+_2


title: 180525_EOMES_S2

value: 4 week


title: 201218_ATAC_D7_S2


title: 201218_ATAC_D7_S1


title: CG34376_10-12_BS1

description: Drosophila embryos RNAi, shCG34376, replicate 1, 10-12 hours


title: 180124_perturb_S5


title: PD-1-CXCR5-_1


title: 180124_perturb_S4


title: PD-1intCXCR5+_1


title: 201218_ATAC_D4_S8


title: CG34376_0-1.5_BS1

description: Drosophila embryos RNAi, shCG34376, replicate 1, 0-1.5 hours


title: CG34376_0-1.5_BS2

description: Drosophila embryos RNAi, shCG34376, replicate 2, 0-1.5 hours


title: 201218_ATAC_D4_S7


title: 180124_perturb_S3


title: PD-1intCXCR5-_1


title: 201218_ATAC_D4_S6


title: CG33557_dmrt99B_mCherry_6-8_BS2

description: Drosophila embryos RNAi, shmCherry (Control for CG33557, dmrt99B), replicate 2, 6-8 hours

value: 6-8 hours


title: 201218_ATAC_D4_S5


title: PD-1highCXCR5+_1


title: CG33557_dmrt99B_mCherry_6-8_BS1

description: Drosophila embryos RNAi, shmCherry (Control for CG33557, dmrt99B), replicate 1, 6-8 hours


title: PD-1highCXCR5-_1


title: 201218_ATAC_D4_S3


title: CG33557_dmrt99B_mCherry_16-18_BS1

description: Drosophila embryos RNAi, shmCherry (Control for CG33557, dmrt99B), replicate 1, 16-18 hours


title: 201218_ATAC_D4_S4


title: T17

city: Mol

first: Mohamed

last: Mysara

state: Belgium

address: Boeretang 200

country: Belgium

institute: Belgian nuclear research center (SCK-CEN)

data_processing:
CLC Genomics Workbench v 22.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05, max length: 55, min length: 15)
Trimmed sequence reads were mapped to miRBase release 22 using CLC genomic benchwork (parameters: Allowing length-base isomiRs and strand specific, minimum sequence length : 18 and maximum for 25, maximum mismath 2,  insertion cost: 2 deletion cost: 2)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: miRBase Homo sapiens Release 22
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: brain

extract_protocol:
Total RNA including microRNAs (miRNAs) was isolated from the glioblastoma tissues and normal controls using the miRNeasy Serum/Plasma kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. Total RNA was eluted in a volume of 30 μL RNase-free water. Concentration, purity and integrity for the RNA were de-termined by spectrophotometry (Little Lunatic, Unchained labs, CA, USA) and Agilent 2100 Bioanalyzer/Agilent RNA 6000 Nano Kit (Agilent, CA, USA).
Library preparation including size fractionation with adapter ligation to 5’ phosphate was performed by GENEWIZ Inc (GENEWIZ, NJ, USA).

value: brain

tag: disease state

value: Glioblastoma


title: T16


title: 201218_ATAC_D4_S2

value: 4 days


title: CG33557_dmrt99B_mCherry_0-1.5_BS2

description: Drosophila embryos RNAi, shmCherry (Control for CG33557, dmrt99B), replicate 2, 0-1.5 hours

value: embryos


title: T15


title: Susceptible_stressed_4 [Sus_stress_9]

city: Rehovot

first: Gil

last: Levkowitz

state: Israel

address: 234 Herzl St.

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200) (parameters: -a ADAPTER1 -A ADAPTER2 -a “A{10}” -a “T{10}” –times 2 -q 20 -m 25).
Reads were mapped to genome /shareDB/genomes/Danio_rerio/UCSC/danRer11/Star_index/ using STAR (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic).
Counting was done using STAR.
Normalization of the counts and differential expression analysis was performed using DESeq2 (DOI: 10.1186/s13059-014-0550-8)
Genome_build: danRer11
Supplementary_files_format_and_content: Raw counts, normalized measurements, fold change after Deseq2

organism: Danio rerio

source_name: Susceptible larva

growth_protocol: Wildtype zebrafish larvae were grown in uncrowded densities till 6 days post fertilization.

extract_protocol:
RNA was extracted by the basic Trizol-chloroform phase separation method, precipitated with isopropanol, washed with 80% ethanol and resuspended in water.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Zebrafish larvae were differentiated into resilient and susceptible groups at 6 dpf. They were let to rest for a day, and at 7 dpf, single larvae were collected in Trizol either at basal conditions or 30 minutes following a stressful event.

tag: source type

value: Whole larva

value: AB

tag: archetype

value: Susceptible

tag: age

value: 7 dpf


title: CG33557_dmrt99B_mCherry_0-1.5_BS1

description: Drosophila embryos RNAi, shmCherry (Control for CG33557, dmrt99B), replicate 1, 0-1.5 hours


title: Susceptible_stressed_2 [Sus_stress_7]


title: Susceptible_stressed_3 [Sus_stress_8]


title: Susceptible_stressed_5 [Sus_stress_10]


title: T14


title: CG33557_6-8_BS2

description: Drosophila embryos RNAi, shCG33557, replicate 2, 6-8 hours


title: T13


title: PD-1highCXCR5-_2

value: blood

value: ex vivo

tag: cell type

value: CD45RA-CD4+T cells


title: Susceptible_stressed_1 [Sus_stress_6]


title: 180124_perturb_S2

value: HUES66 human embryonic stem cells

value: 7 days


title: CG33557_6-8_BS1

description: Drosophila embryos RNAi, shCG33557, replicate 1, 6-8 hours


title: CG33557_dmrt99B_mCherry_16-18_BS2

description: Drosophila embryos RNAi, shmCherry (Control for CG33557, dmrt99B), replicate 2, 16-18 hours

value: 16-18 hours


title: T12


title: T11


title: CG33557_16-18_BS2

description: Drosophila embryos RNAi, shCG33557, replicate 2, 16-18 hours


title: CG33557_16-18_BS1

description: Drosophila embryos RNAi, shCG33557, replicate 1, 16-18 hours


title: Susceptible_basal_3 [Sus_basal_8]


title: Susceptible_basal_4 [Sus_basal_10]


title: 201218_ATAC_D4_S1

value: H1 human embryonic stem cells

tag: differentiation protocol

value: overexpression of a library with 198 transcription factors

tag: time point


title: CG33557_0-1.5_BS2

description: Drosophila embryos RNAi, shCG33557, replicate 2, 0-1.5 hours

tag: tissue

tag: treatment

value: 0-1.5 hours


title: Susceptible_basal_1 [Sus_basal_5]


title: T10

value: brain


title: T9

value: Glioblastoma


title: T8


title: Resilient_stressed_3 [Res_stress_7]

source_name: Resilient larva

value: Resilient


title: T7


title: Resilient_stressed_4 [Res_stress_8]


title: Susceptible_basal_2 [Sus_basal_7]


title: CG33557_0-1.5_BS1

description: Drosophila embryos RNAi, shCG33557, replicate 1, 0-1.5 hours

value: embryos

tag: timepoint


title: CG32006_16-18_BS1

description: Drosophila embryos RNAi, shCG32006, replicate 1, 16-18 hours


title: Resilient_stressed_5 [Res_stress_9]

value: Whole larva


title: Resilient_stressed_2 [Res_stress_6]

value: AB


title: CG32006_12-14_BS2

description: Drosophila embryos RNAi, shCG32006, replicate 2, 12-14 hours

value: 12-14 hours


title: CG32006_12-14_BS1

description: Drosophila embryos RNAi, shCG32006, replicate 1, 12-14 hours


title: C3

value: Control


title: Resilient_stressed_1 [Res_stress_1]

value: 7 dpf


title: CG32006_0-1.5_BS2

description: Drosophila embryos RNAi, shCG32006, replicate 2, 0-1.5 hours


title: Resilient_basal_4 [Res_basal_10]


title: C1


title: Resilient_basal_3 [Res_basal_9]


title: Resilient_basal_2 [Res_basal_8]


title: CG2120_Pdp1_mCherry_16-18_BS2

description: Drosophila embryos RNAi, shmCherry (Control for CG2120, Pdp1), replicate 2, 16-18 hours

value: shmCherry (Control for CG2120, Pdp1)


title: CG32006_0-1.5_BS1

description: Drosophila embryos RNAi, shCG32006, replicate 1, 0-1.5 hours


title: GFHD113, DAC-Pg20, 4h

city: Krakow

first: Aleksander

middle: M

last: Grabiec

address: Gronostajowa 7

country: Poland

institute: Jagiellonian University

data_processing:
The quality of the raw reads was verified using the FastQC software (v. 0.11.9).
Reads were aligned to the human reference genome GRCh38.p13 using the STAR software (v. 2.1.0).
Gene expression levels were determined using the featureCounts tool (v. 2.0.3) and the GTF file from Ensembl database (v. 104) as a reference.
Assembly: human reference genome GRCh38.p13
Supplementary files format and content: Tab-delimited file with raw counts produced with the featureCounts tool. It contains 21 columns: 1 column with Ensembl geneID and 20 columns with counts (one column per sample).

growth_protocol: PHGFs were cultured in DMEM (Lonza) containing 10% fetal bovine serum (FBS) (Biowest), gentamicin (50 U/ml) and penicillin/streptomycin (50 U/ml) (both from Gibco), and used for experiments between passages 4 and 9.

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit (Qiagen)
mRNA was enriched using oligo(dT) beads from NEBNext® Poly(A) mRNA Magnetic Isolation Module (cat# E7490L; NEB). Next, sequencing libraries were generated using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina® (cat# E7770L; NEB) according to the manufacturer’s instructions. Briefly, fragmentation was performed using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNaseH-) and random hexamer primer. Second strand cDNA was synthesized using DNA Polymerase I and RNase H  and the reaction buffer containing dUTP instead of dTTP. The remaining overhangs were converted into blunt ends by exonuclease/polymerase activities. Following adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP beads (cat# A63987; Beckman Coulter) to select cDNA fragments of 250-300 bp in length. Subsequently, 3 μl USER Enzyme (NEB) was incubated with size-selected, adaptor-ligated cDNA at 37° C for 15 min followed by 5 min incubation at 95°C. Next, PCR was performed using Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. Finally, PCR products were purified using AMPure XP beads and library quality was assessed using the Agilent High Sensitivity DNA Kit (cat# 5067-4626) on the Agilent Bioanalyzer 2100 system (Agilent Technologies).

treatment_protocol: One day prior to treatment with inhibitors, cells were seeded in 10 cm dishes in medium supplemented with 10% FBS and antibiotics. Cells were cultured for 12 days in the presence of DMSO (control) or decitabine (DAC; 5 μM). Every 4 days medium was replaced, and fresh portion of DAC was added. After 12-day culture with DMSO or DAC (5 μM), GFs (n=5, cell lines from individual healthy donors, indicated by biobank numbers GFHD06, 106, 102, 112, 113) were seeded in 6-well plates for 24 h and then were either left untreated or were infected with P. gingivalis (MOI 20) for 4 h.

value: primary human gingival fibroblast


title: T5


title: GFHD113, DAC-medium, 4h

value: DAC-medium


title: CG2120_Pdp1_mCherry_16-18_BS1

description: Drosophila embryos RNAi, shmCherry (Control for CG2120, Pdp1), replicate 1, 16-18 hours


title: CG2120_Pdp1_mCherry_14-16_BS2

description: Drosophila embryos RNAi, shmCherry (Control for CG2120, Pdp1), replicate 2, 14-16 hours

value: 14-16 hours


title: T2


title: GFHD113, DMSO-Pg20, 4h


title: CG2120_Pdp1_mCherry_14-16_BS1

description: Drosophila embryos RNAi, shmCherry (Control for CG2120, Pdp1), replicate 1, 14-16 hours


title: T1


title: T3


title: GFHD113, DMSO-medium, 4h

value: DMSO-medium


title: 200209_RFX4_S2

extract_protocol:
RNA was extracted using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10X Genomics 1000075)
single-cell RNA-Seq libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10X Genomics 1000075)

value: H1 human embryonic stem cells

value: RFX4 overexpression combined with dual SMAD inhibition

value: induced neural progenitors


title: 200209_RFX4_S1


title: CG2120_Pdp1_mCherry_0-1.5_BS2

description: Drosophila embryos RNAi, shmCherry (Control for CG2120, Pdp1), replicate 2, 0-1.5 hours

value: 0-1.5 hours


title: CG32006_16-18_BS2

description: Drosophila embryos RNAi, shCG32006, replicate 2, 16-18 hours

value: 16-18 hours


title: T6

value: brain

value: Glioblastoma


title: GFHD112, DAC-Pg20, 4h


title: 200209_EB_S2

value: embryoid body


title: C2


title: 200209_EB_S1


title: CG2120_Pdp1_mCherry_0-1.5_BS1

description: Drosophila embryos RNAi, shmCherry (Control for CG2120, Pdp1), replicate 1, 0-1.5 hours

value: embryos


title: GFHD112, DAC-medium, 4h


title: Sole-15

city: Ann Arbor

first: William

middle: R

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

data_processing:
FastQ file statistics were calculated using FastQC. Reads were trimmed based upon quality scores using TrimGalore. Ribosomal RNA was filtered out using SortMeRNA.
Read mapping was then done using Hisat2 and stringtie to the reference genome UCSC GRCh38/hg38.
Post-mapping quality statistics were calculated using RSeQC and RNA-SeQC. The differential expression testing was then performed using edgeR with normalization for library size.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKM for every gene and every sample

source_name: Skin

extract_protocol:
Skin biopsies were snap-frozen in liquid nitrogen and stored at -80°C until use. Samples were then pulverized and dissolved in complete RLT buffer (Qiagen, Valencia, CA) for RNA extraction. RNA was isolated using the RNeasy Mini kit (Qiagen).
Stranded mRNA libraries were prepared using the TruSeq RNA library prep kit (Illumina) and sequenced on the Illumina HiSeq 4000 sequencer by the University of Michigan Advanced Genomics Core using standard Illumina protocols.

value: Skin

tag: location

value: sole

tag: individual

value: subject 15


title: Hip-15

value: hip


title: T4


title: Resilient_basal_1 [Res_basal_7]

value: Whole larva

tag: strain

value: AB

value: Resilient

value: 7 dpf


title: 200209_DS_S2

value: H1 human embryonic stem cells

value: dual SMAD inhibition


title: CG15696_suHw_gfzf_cad_mCherry_2-4_BS2

description: Drosophila embryos RNAi, shmCherry (Control for CG15696, su(Hw), gfzf, cad), replicate 2, 2-4 hours

value: 2-4 hours


title: CG15696_suHw_gfzf_cad_mCherry_2-4_BS1

description: Drosophila embryos RNAi, shmCherry (Control for CG15696, su(Hw), gfzf, cad), replicate 1, 2-4 hours


title: Sole-14

value: subject 14


title: GFHD112, DMSO-Pg20, 4h

tag: cell line

value: primary human gingival fibroblast


title: CG15696_suHw_gfzf_cad_mCherry_16-18_BS2

description: Drosophila embryos RNAi, shmCherry (Control for CG15696, su(Hw), gfzf, cad), replicate 2, 16-18 hours

value: 16-18 hours


title: Hip-14


title: GFHD112, DMSO-medium, 4h

value: DMSO-medium


title: GFHD102, DAC-Pg20, 4h


title: 191108_TFv2d56_8w_S2

value: RFX4 overexpression combined with dual SMAD inhibition followed by spontaneous differentiation

value: 8 week


title: Sole-13

value: Skin

value: subject 13


title: 191108_TFv2d56_8w_S1


title: CG15696_suHw_gfzf_cad_mCherry_16-18_BS1

description: Drosophila embryos RNAi, shmCherry (Control for CG15696, su(Hw), gfzf, cad), replicate 1, 16-18 hours

value: embryos


title: CG15696_suHw_gfzf_cad_mCherry_0-1.5_BS2

description: Drosophila embryos RNAi, shmCherry (Control for CG15696, su(Hw), gfzf, cad), replicate 2, 0-1.5 hours

value: 0-1.5 hours


title: 191108_TFv2d56_4w_S2

value: 4 week


title: CG15696_suHw_gfzf_cad_mCherry_0-1.5_BS1

description: Drosophila embryos RNAi, shmCherry (Control for CG15696, su(Hw), gfzf, cad), replicate 1, 0-1.5 hours


title: GFHD102, DMSO-Pg20, 4h


title: 191108_TFv2d56_4w_S1


title: CG15696_2-4_BS2

description: Drosophila embryos RNAi, shCG15696, replicate 2, 2-4 hours


title: Sole-12

value: sole

value: subject 12


title: GFHD102, DAC-medium, 4h

value: DAC-medium


title: GFHD106, DAC-Pg20, 4h


title: GFHD102, DMSO-medium, 4h


title: HFD/ FGFR4_4

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp.
Trimmed sequence reads were pseudoaligned to mouse transcriptome (Ensembl version 94) using kallisto.
Transcript counts were collapsed into gene counts using tximport.
Assembly: GRCm38/Ensembl 94
Supplementary files format and content: CSV file includes gene counts for all samples

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNA was extracted from liver biopsies in a mix of Trizol and chloroform and then precipitated with 70% of ethanol. RNA purification was performed using RNeasy Mini Kit columns (QIAGEN, catalog 74106).
RNA libraries for RNA-seq were prepared using the KAPA mRNA HyperPrep  Kit following manufacturer's protocols.

value: Liver

tag: Sex

value: male

tag: diet

value: HFD


title: 200209_DS_S1

value: H1 human embryonic stem cells

value: dual SMAD inhibition

value: induced neural progenitors


title: Sole-11

value: subject 11


title: Hip-12

value: hip


title: 180124_perturb_S1

value: HUES66 human embryonic stem cells

tag: perturbation

value: overexpression of a library with 90 transcription factors

tag: perturbation time point

value: 7 days


title: HFD/ FGFR4_3


title: GFHD106, DAC-medium, 4h

value: primary human gingival fibroblast


title: Hip-11

value: Skin


title: 201218_ATAC_D7_S3

value: overexpression of a library with 198 transcription factors


title: GFHD106, DMSO-Pg20, 4h


title: HFD/ FGFR4_2


title: HFD/ FGFR4_1


title: CG15696_16-18_BS1

description: Drosophila embryos RNAi, shCG15696, replicate 1, 16-18 hours

data_processing:
Raw FASTQ files were aligned to the Drosophila melanogaster reference genome (Release 6)  using STAR aligner 2.7.3a  with default settings and up to 20 multiple alignments to produce BAM files.
HTSeq htseq-count v0.12.4 was used to determine read counts overlapping genes.
Differential gene expression in the RNAi experimental samples compared to the mCherry controls was determined using DESeq2 1.24.0.
bigWig files were created using a custom tool called bam2bedgraph to convert bam files into bedgraph files, then UCSC's bedGraphToBigWig to convert the bedgraph files to bigWig format.
Assembly: dm6
Supplementary files format and content: BAM alignment files aligning FASTQ read files to dm6 assembly using STAR 2.7.3a.
Supplementary files format and content: HTSeq htseq-count files produced with HTSeq v0.12.4
Supplementary files format and content: DESeq csv files produced using DESeq2 v1.24.0
Supplementary files format and content: bigWig files produced using custom bam2bedgraph script and UCSC bedGraphToBigWig tool

extract_protocol:
Frozen embryos were homogenized using the Pellet Pestle Cordless Motor (Kimble Cat. No. 749540-0000; Pellet Pestles Sigma Cat. No. Z359947). RNA was extracted from the homogenate using TRIzol Reagent (Thermo Fisher, Cat. No. 15596026), chloroform extraction and isopropanol precipitation.  RNA was resuspended in Nuclease Free Water (Ambion AM9930) and incubated over night before purification using the RNeasy Mini Kit (QIAGEN Cat. No. 74106).  After Qiagen clean up, RNA was quantified using NanoDrop ND1000v 3.5.2.
Libraries for sequencing were made using TruSeq Stranded mRNA Library Prep (llumina 20020594).

value: embryos

value: 16-18 hours


title: Hip-13

value: subject 13


title: Hip-10

value: subject 10


title: GFHD106, DMSO-medium, 4h

value: DMSO-medium


title: Palm-10

value: palm


title: HFD_4

value: Liver

value: male

value: HFD

value: Control


title: CG15696_0-1.5_BS1

description: Drosophila embryos RNAi, shCG15696, replicate 1, 0-1.5 hours

value: 0-1.5 hours


title: GFHD06, DAC-Pg20, 4h


title: Hip-9

value: hip

value: subject 9


title: CG10209_16-18_BS2

description: Drosophila embryos RNAi, shCG10209, replicate 2, 16-18 hours


title: HFD_3


title: Palm-9


title: GFHD06, DAC-medium, 4h

value: DAC-medium


title: CG15696_2-4_BS1

description: Drosophila embryos RNAi, shCG15696, replicate 1, 2-4 hours

value: 2-4 hours


title: Hip-8

value: Skin

value: subject 8


title: HFD_1


title: GFHD06, DMSO-Pg20, 4h

value: primary human gingival fibroblast


title: CG10209_12-14_BS2

description: Drosophila embryos RNAi, shCG10209, replicate 2, 12-14 hours

value: embryos

value: 12-14 hours


title: HFD_2


title: CG10209_16-18_BS1

description: Drosophila embryos RNAi, shCG10209, replicate 1, 16-18 hours

value: 16-18 hours


title: CG15696_16-18_BS2

description: Drosophila embryos RNAi, shCG15696, replicate 2, 16-18 hours


title: Chow/ FGFR4_4

value: Chow


title: Palm-8

value: palm


title: GFHD06, DMSO-medium, 4h

value: DMSO-medium


title: CG10209_12-14_BS1

description: Drosophila embryos RNAi, shCG10209, replicate 1, 12-14 hours


title: Hip-7

value: subject 7


title: Chow/ FGFR4_3

value: Liver

value: male


title: CG10209_0-1.5_BS1

description: Drosophila embryos RNAi, shCG10209, replicate 1, 0-1.5 hours

value: 0-1.5 hours


title: Exp5 THP1 DMs CRISPR KO IGSF8 b

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

institute: Weizmann Institute

description:
Bulk whole transcript RNA-seq
stat2_irf9.tsv.gz

data_processing:
Lab full transcript pipeline, UCSC based reference. Includes removing the linker AGATCGGAAGAGCACACGT, removing reads aligned to the r/tRNA, alignment to the genome and then (the unaligned) to the transcriptome.
tab-delimited text file with the number of reads per gene in each sample
Assembly: hg19 + TB40/E (NCBI accession EF999921.1)

source_name: THP1 derived macrophages

growth_protocol: THP1 cells were grown in RPMI media with 15% heat-inactivated fetal bovine serum (FBS), 2 mM L-glutamine, and 100 units/ml penicillin and streptomycin

extract_protocol:
Cells were collected in TRI-reagent, RNA was extracted by phase separation followed by poly(A) selection using Dynabeads
RNA-seq as descibed in Shishkin et al. (2015). Nat. Methods  12 323–330

treatment_protocol: Cells were infected with HCMV strain TB40E with an SV40-GFP tag

value: THP1 monocyte derived macrophages

tag: infection

value: Uninfected

tag: time (hr)

tag: population

value: total

tag: expt


title: Hip-6

value: hip

value: subject 6


title: Palm-7

value: Skin


title: Chow/ FGFR4_2


title: Chow/ FGFR4_1


title: Blimp-1_kay_mCherry_16-18_BS2

description: Drosophila embryos RNAi, shmCherry (Control for Blimp-1, kay), replicate 2, 16-18 hours

value: shmCherry (Control for Blimp-1, kay)


title: Palm-6


title: Exp5 THP1 DMs CRISPR KO STAT2 a

extract_protocol:
Cells were collected in TRI-reagent, RNA was extracted by phase separation followed by poly(A) selection using Dynabeads
RNA-seq as descibed in Shishkin et al. (2015). Nat. Methods  12 323–327

tag: cell type


title: Blimp-1_kay_mCherry_16-18_BS1

description: Drosophila embryos RNAi, shmCherry (Control for Blimp-1, kay), replicate 1, 16-18 hours

value: embryos


title: Hip-5

value: subject 5


title: Chow_3

value: Control


title: Blimp-1_kay_mCherry_10-12_BS2

description: Drosophila embryos RNAi, shmCherry (Control for Blimp-1, kay), replicate 2, 10-12 hours

value: 10-12 hours


title: Chow_4

value: Chow


title: Chow_2


title: Blimp-1_kay_mCherry_10-12_BS1

description: Drosophila embryos RNAi, shmCherry (Control for Blimp-1, kay), replicate 1, 10-12 hours


title: Exp5 THP1 DMs CRISPR KO IGSF8 a

extract_protocol:
Cells were collected in TRI-reagent, RNA was extracted by phase separation followed by poly(A) selection using Dynabeads
RNA-seq as descibed in Shishkin et al. (2015). Nat. Methods  12 323–329


title: Palm-5

value: palm


title: Chow_1


title: Hip-4

value: subject 4


title: Exp5 THP1 DMs CRISPR KO IRF9 b

extract_protocol:
Cells were collected in TRI-reagent, RNA was extracted by phase separation followed by poly(A) selection using Dynabeads
RNA-seq as descibed in Shishkin et al. (2015). Nat. Methods  12 323–326


title: Palm-4


title: Blimp-1_kay_mCherry_0-1.5_BS2

description: Drosophila embryos RNAi, shmCherry (Control for Blimp-1, kay), replicate 2, 0-1.5 hours


title: Exp4 BAL macrophages mock 3dpi b

description:
Bulk 3' RNA seq
BAL.bulk.tsv.gz

data_processing:
MARS-seq pipeline, Ensembl based reference The UMIs is at the end of the read header (10 bps).
tab-delimited text file with the number of UMIs per gene in each sample
Assembly: hg19 + TB40/E (NCBI accession EF999921.1)

source_name: BAL macrophages

growth_protocol: BAL cells were grown in RPMI media with 10% heat-inactivated fetal bovine serum (FBS), 2 mM L-glutamine, and 100 units/ml penicillin and streptomycin

extract_protocol:
Sorted cell pellets were lysed in RLT buffer. Reverse transcription and template switching was performed with indexed poly(T) primers.
mcSCRB  as described in Bagnoli et al. (2018) Nat. Commun. 9, 2937 adapted for processing of bulk samples.

value: BAL macrophages

value: Mock


title: Exp5 THP1 DMs CRISPR KO STAT2 b

extract_protocol:
Cells were collected in TRI-reagent, RNA was extracted by phase separation followed by poly(A) selection using Dynabeads
RNA-seq as descibed in Shishkin et al. (2015). Nat. Methods  12 323–328


title: Blimp-1_kay_mCherry_0-1.5_BS1

description: Drosophila embryos RNAi, shmCherry (Control for Blimp-1, kay), replicate 1, 0-1.5 hours

source_name: embryos

value: 0-1.5 hours


title: CG10209_0-1.5_BS2

description: Drosophila embryos RNAi, shCG10209, replicate 2, 0-1.5 hours


title: Muscle_RORg_pos_Treg#4

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: raw read counts

source_name: RORγ+ Tregs isolated from cardiotoxin-injured skeletal muscle

extract_protocol: For MuSC samples, cells were isolated by enzymatic digestion of the indicated tissue and cells were purified by fluoresence activated cell sorting. 1000 cells were sorted in TCL buffer with 1% 2-mercaptoethanol and submitted for library construction and sequencing. For whole muscle and liver samples, tissue was homogenized in Trizol, and then RNA was isolated per the manufacterure protocol. 2ng of purified RNA were added to TCL buffer with 1% 2-mercaptoethanol and submitted for library construction and sequencing.

tag: genotype

value: Foxp3-Thy1.1x Rorc-GFP/wt

value: cardiotoxin-induced hindlimb skeletal muscle injury


title: Exp5 THP1 DMs CRISPR KO IRF9 a

extract_protocol:
Cells were collected in TRI-reagent, RNA was extracted by phase separation followed by poly(A) selection using Dynabeads
RNA-seq as descibed in Shishkin et al. (2015). Nat. Methods  12 323–325

value: THP1 monocyte derived macrophages

value: Uninfected

value: total


title: Exp4 BAL macrophages TB40/E 3dpi GFP-dim b

description:
Bulk 3' RNA seq
BAL.bulk.tsv.gz

value: HCMV-GFP

value: GFP-dim


title: Hip-3

tag: tissue

value: Skin

value: hip

value: subject 3


title: Bdp1_toe_dac_mCherry_6-8_BS2

description: Drosophila embryos RNAi, shmCherry (Control for Bdp1, toe, dac), replicate 2, 6-8 hours

value: embryos

tag: treatment

value: shmCherry (Control for Bdp1, toe, dac)

value: 6-8 hours


title: Palm-3

value: palm


title: Muscle_RORg_pos_Treg#2


title: Exp4 BAL macrophages TB40/E 3dpi GFP-bright

description:
Bulk 3' RNA seq
BAL.bulk.tsv.gz

value: BAL macrophages

value: GFP-bright


title: Hip-2

value: subject 2


title: Muscle_RORg_pos_Treg#1

value: Foxp3-Thy1.1x Rorc-GFP/wt


title: Exp4 BAL macrophages mock 3dpi a

description:
Bulk 3' RNA seq
BAL.bulk.tsv.gz

value: Mock


title: Exp3 BAL cells TB40/E 70hpi

description: Single cell 3' RNA seq

data_processing:
10x CellRanger, Ensembl based reference.
h5 output of Cell Ranger with number of UMIs per gene in each cell
Assembly: hg19 + TB40/E (NCBI accession EF999921.1)

source_name: BAL cells

extract_protocol:
cells were directly processed using the 10x Genomics protocol
10X Genomics Chromium Single Cell 3′ Gene Expression v3.1

value: BAL cells


title: Colon_RORg_pos_Treg#3

source_name: RORγ+ Tregs isolated from the colon

value: cardiotoxin-induced hindlimb skeletal muscle injury


title: Exp3 BAL cells TB40/E 20hpi

description: Single cell 3' RNA seq

value: total


title: Bdp1_toe_dac_mCherry_16-18_BS2

description: Drosophila embryos RNAi, shmCherry (Control for Bdp1, toe, dac), replicate 2, 16-18 hours

tag: timepoint

value: 16-18 hours


title: Colon_RORg_pos_Treg#2


title: Hip-1

tag: location

value: subject 1


title: Palm-1

value: Skin

tag: individual


title: Bdp1_toe_dac_mCherry_16-18_BS1

description: Drosophila embryos RNAi, shmCherry (Control for Bdp1, toe, dac), replicate 1, 16-18 hours


title: UM-UC-3_siTotal-AR_Rep3

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

data_processing:
Data analysis was performed with a TopHat2-Cufflinks-Cuffdiff pipeline (1,2) for mapping/alignment of raw sequence reads (FASTQ format) to the reference human genome assembly (GRCh37/hg19), transcript assembly, and quantitation of gene and transcript expression as FPKM (Fragments Per Kilobase of transcript per Million mapped reads). Data were annotated for unique genes/transcripts with Ensembl Release 82 (GRCh37/hg19).
Assembly: GRCh37/hg19
Supplementary files format and content: Processed data is provided as a text file (Mudryj_siAR_UMUC3_Transcript_FPKM.txt) consisting of a matrix of FPKM expression values. Each column contains feature information (Transcript_id, Gene_id, Official_Symbol, Gene_type) and then FPKM data for each sample. Each row contains the gene count data for each feature across the sample panel.

growth_protocol: UM-UC-3 epithelial 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). 2.0 ug of total RNA was subjected to ribo-depeltion and enriched RNA was used for the construction of sequencing libraries.
RNA-Seq libraries were prepared using using a library preparation protocol to capture both mRNA and lncRNA transcripts following manufacturer's protocols.

treatment_protocol: Cells were treated with 50nM siC, siFL-AR or siAR-v19, and were harvested after 3 days

value: epithelial cells

value: WT

value: si total AR


title: UM-UC-3_siTotal-AR_Rep2


title: KO mouse intestinal organoids treated with 4OHT

city: Illkirch-Graffenstaden

first: Guillaume

last: Davidson

address: 1 Rue Laurent Fries

country: France

institute: I.G.B.M.C. - Institut de génétique et de biologie moléculaire et cellulaire

library_source: transcriptomic single cell

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment to reference genome mm10 and gene quantification for each cell was done using CellRanger v3.1.
Data are imported into R and analyzed using the Seurat package v3.1.4.
Assembly: mm10
Supplementary files format and content: TSV files containing raw UMI counts for cells used in Seurat analysis.

source_name: Captured single cell RNA

growth_protocol: Organoid cultures were established from ileal crypts of 4-month-old mice, grown in 20 µl of Matrigel® (Corning®, #356231) in 48-wells plates (Greiner Bio-one, 677180) in 250 µl Mouse IntestiCult™ Organoid Growth Medium (STEMCELL™, 06005) treated for 3 days with 1 µM (Z)-4-hydroxytamoxifen (4-OHT, Sigma-Aldrich, H7904) in EtOH or with EtOH alone for control experiments

extract_protocol:
Organoids were dissociated with Accutase (A6964, Sigma) at 27 °C for 5 min and the cells were suspended in culture medium. Cells were then sorted by flow cytometry to select live cells and captured using 10X Genomics Chromium Analyzer.
Single Cell 3ʹ Gene Expression libraries comprise standard Illumina paired-end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1, while 8 bp sample index sequences are incorporated as the i7 index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired-end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 12 bp UMI.

tag: strain

value: ileum-derived Intestine organoid


title: Muscle_RORg_pos_Treg#3


title: Lung_old_NaCl_miRNA_SK1.1.162

city: Biberach

first: Sergio

last: Picart-Armada

address: Birkendorfer Straße 65

country: Germany

institute: Boehringer Ingelheim

description:
miRNA_READS_727.txt
727_29

data_processing:
Illumina reads were converted to the industry standard FASTQ format and aligned to the mouse reference genome from Ensembl 70 using the STAR v2.5.2a aligner on default settings. For increased alignment accuracy, the STAR genome index was generated to include splice junction annotations with the options ‘—sjdbGTFfile’ and ‘—sjdbOverhang 49’.
The quality of the RNA-Seq samples was verified with FASTQC 0.11.2 and RNASeQC version 1.1.8. The featureCounts tool of the subRead package v1.5.0 was used to quantify the per-gene read counts with the “-s 2” parameter.
Cufflinks v2.2.1  was used to calculate the FPKM values with the following parameters “--max-bundle-frags 1000000000 --max-bundle-length 5000000 --library-type fr-firststrand --no-effective-length-correction --compatible-hits-norm --max-frag-multihits 1”.
The matrix of read counts and were imported into R and per-sample read count normalization factors were calculated using trimmed mean of M-values (TMM) and subsequently normalized using the Bioconductor LIMMA-Voom analysis R package for differential expression analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: RPKM_685.txt: counts for mRNAs. miRNA_READS_727.txt: counts for microRNAs

source_name: Lung

extract_protocol:
Lung tissue was perfused twice with 10ml 1x PBS (Sigma, city, country) through the right side of the heart entering the pulmonary vasculature. Subsequently, lung was removed from the chest cavity, each lobe was separated and thereafter immediately flash frozen in liquid nitrogen. Lungs were then stored at -80°C until homogenized in 2ml Eppendorf tubes (Eppendorf, Hamburg, Germany) using a TissueLyser LT (Qiagen, Hilden, Germany). Samples remained frozen throughout the entire procedure. Lung powder was generated for next generation sequencing (NGS; 20mg tissue).
Total RNA was isolated using the Qiazol procedure according to manufacturer´s protocol (Qiagen, Hilden, Germany). A total of 20mg tissue was used for RNA isolation. Quality of RNA was assessed by the Fragment Analyzer (Agilent Technologies, Santa Clara, CA, USA) using the SS RNA Kit (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Male mice were randomized before the study. Mice were instilled intratracheally (i.t.) under 3-4% isoflurane anesthesia once on day 0. Bleomycin administration was performed in a hanging position with a Vasofix-Braunüle 22G (B.Braun, Melsungen, Germany). Mice were instilled using 0.7 and 0.63 mg/kg of bleomycin sulphate (Merck, Darmstadt, Germany) in saline solution for the young and old mice, respectively. Control mice received saline solution only. Mice were analyzed 21 days after bleomycin administration.

tag: age

value: old

value: NaCl

tag: day

tag: animal id

value: Male

value: Lung


title: Colon_RORg_pos_Treg#1


title: Exp4 BAL macrophages TB40/E 3dpi GFP-dim a

description:
Bulk 3' RNA seq
BAL.bulk.tsv.gz

value: BAL macrophages

value: HCMV-GFP

value: GFP-dim


title: UM-UC-3_siTotal-AR_Rep1

tag: cell line


title: WT mouse intestinal organoids treated with Ethanol.

treatment_protocol: Organoid cultures were established from ileal crypts of 4-month-old mice, grown in 20 µl of Matrigel® (Corning®, #356231) in 48-wells plates (Greiner Bio-one, 677180) in 250 µl Mouse IntestiCult™ Organoid Growth Medium (STEMCELL™, 06005) treated for 3 days with 1 µM (Z)-4-hydroxytamoxifen (4-OHT, Sigma-Aldrich, H7904) in EtOH or with EtOH alone for control experiments


title: Bdp1_6-8_BS2

description: Drosophila embryos RNAi, shBdp1, replicate 2, 6-8 hours

value: embryos

value: 6-8 hours


title: Bdp1_toe_dac_mCherry_6-8_BS1

description: Drosophila embryos RNAi, shmCherry (Control for Bdp1, toe, dac), replicate 1, 6-8 hours

value: shmCherry (Control for Bdp1, toe, dac)


title: Lung_old_Bleo_miRNA_SK1.1.153

description:
miRNA_READS_727.txt
727_28

value: Bleo

tag: Sex


title: Palm-2

value: palm

value: subject 2


title: Lung_old_NaCl_miRNA_SK1.1.150

description:
miRNA_READS_727.txt
727_27


title: DtTam_Rep3

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were preprocessed in order to remove adapter and low-quality sequences (Phred quality score below 20) using cutadapt version 1.10.
Reads were mapped to rRNA sequences using bowtie version 2.2.8, and reads mapping to rRNA sequences were removed for further analysis. Reads were mapped to spike sequences using bowtie2 version 2.2.8, and reads mapping to spike sequences were removed for further analysis.
Reads were mapped to reference genome mm9 using STAR v2.5.3a. Only uniquely aligned reads were retained for further analyses.
Gene expression quantification was performed from uniquely aligned reads using htseq-count version v0.6.1 with annotations from Ensembl version 67.
Data normalization and fold-change across conditions computation were performed using the DESeq2 Bioconductor package. Significantly deregulated genes were selected using a log2 fold change >1 and <1 and adjusted p-value cutoff of 0.05.
Assembly: mm9
Supplementary files format and content: Excel file containing normalized (by sequencing depth and gene length) average expression for each condition and log2(fold-change) with adjusted p-values for each DESeq2 comparisons. Mice and organoids data are in two sheets.

source_name: mouse intestinal organoids treated with 4OHT

extract_protocol: P2586 : RNA-Seq libraries were generated from --- ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and IDT for Illumina - TruSeq RNA UD Indexes (96 Indexes, 96 Samples) (Illumina, San Diego, USA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using SPRI select beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: Organoid cultures were established from ileal crypts of 4-month-old mice, grown in 20 µl of Matrigel® (Corning®, #356231) in 48-wells plates (Greiner Bio-one, 677180) in 250 µl Mouse IntestiCult™ Organoid Growth Medium (STEMCELL™, 06005)  treated for 3 days with 1 µM (Z)-4-hydroxytamoxifen (4-OHT, Sigma-Aldrich, H7904) in EtOH or with EtOH alone for control experiments


title: Bdp1_16-18_BS2

description: Drosophila embryos RNAi, shBdp1, replicate 2, 16-18 hours

value: 16-18 hours


title: Bdp1_16-18_BS1

description: Drosophila embryos RNAi, shBdp1, replicate 1, 16-18 hours


title: UM-UC-3_siAR-v19_Rep2

value: epithelial cells

value: WT

value: si AR-v19


title: DtTam_Rep2

value: ileum-derived Intestine organoid


title: Bdp1_toe_dac_mCherry_0-1.5_BS1

description: Drosophila embryos RNAi, shmCherry (Control for Bdp1, toe, dac), replicate 1, 0-1.5 hours

value: 0-1.5 hours


title: DtTam_Rep1

treatment_protocol: Organoid cultures were established from ileal crypts of 4-month-old mice, grown in 20 µl of Matrigel® (Corning®, #356231) in 48-wells plates (Greiner Bio-one, 677180) in 250 µl Mouse IntestiCult™ Organoid Growth Medium (STEMCELL™, 06005)


title: Lung_old_Bleo_miRNA_SK1.1.144

description:
miRNA_READS_727.txt
727_26

value: old

value: Male


title: Bdp1_toe_dac_mCherry_0-1.5_BS2

description: Drosophila embryos RNAi, shmCherry (Control for Bdp1, toe, dac), replicate 2, 0-1.5 hours


title: UM-UC-3_siAR-v19_Rep1


title: UM-UC-3_siFL-AR_Rep3

value: si FL-AR


title: UM-UC-3_siFL-AR_Rep2


title: Lung_old_NaCl_miRNA_SK1.1.131

description:
miRNA_READS_727.txt
727_25

value: NaCl

value: Lung


title: CtrlTam_Rep2

source_name: mouse intestinal organoids treated with Ethanol.


title: Bdp1_0-1.5_BS1

description: Drosophila embryos RNAi, shBdp1, replicate 1, 0-1.5 hours

value: embryos


title: Bdp1_6-8_BS1

description: Drosophila embryos RNAi, shBdp1, replicate 1, 6-8 hours

value: 6-8 hours


title: 3'READS Replicate 6

description:
Random DNA is at ChrXVII from 3911 to 21878 bp.
3reads_plus.bed
3reads_minus.bed

data_processing:
bowtie2 -5 25 -3 25 --no-mixed --no-discordant --dovetail -X 1000
Duplicates based on both read pairs were removed generating new fastq file with filtered, non-duplicate reads from which Ts (3’ As) were shortened.
The filtered reads were aligned with bowtie -p24 -n0 -l17 -m1.
Only reads with polyTs, i.e. reads that come from the truthful polyadenylation were considered. The reads ending with T, such that it is not clear whether the T comes from the genomes or is a part of the polyadenylation process, were excluded.
Assembly: sacCer3 (for spike-in: S. pombe ASM294v2)
Supplementary files format and content: Replicate fastq were combined into one file after removing duplicates. Final file contains per nucleotide polyA read count with 3 columns: chromosome name, position, and count. Two separate files mapping to two strands were provided (plus file maps to minus strand and vice versa).
Library strategy: 3'READS

source_name: Yeast

extract_protocol:
Hot phenol RNA extraction.
3'READS library was prepared as described by Jin et al., 2015.


title: UM-UC-3_siFL-AR_Rep1


title: 3'READS Replicate 5


title: CtrlTam_Rep3


title: Bdp1_0-1.5_BS2

description: Drosophila embryos RNAi, shBdp1, replicate 2, 0-1.5 hours


title: Lung_old_NaCl_miRNA_SK1.1.119

description:
miRNA_READS_727.txt
727_23


title: Lung_old_Bleo_miRNA_SK1.1.130

description:
miRNA_READS_727.txt
727_24


title: UM-UC-3_siControl_Rep3

value: siC


title: CtrlTam_Rep1


title: UM-UC-3_siAR-v19_Rep3


title: Lung_old_Bleo_miRNA_SK1.1.117

description:
miRNA_READS_727.txt
727_22

value: Bleo


title: AdultKO_Rep3

source_name: Mouse injected tamoxifen

value: 8 week adult ileum


title: 3'READS Replicate 4


title: UM-UC-3_siControl_Rep2


title: AdultKO_Rep2


title: Lung_old_Bleo_miRNA_SK1.1.105

description:
miRNA_READS_727.txt
727_20


title: UM-UC-3_siControl_Rep1


title: 3'READS Replicate 3


title: AdultKO_Rep1


title: 3'READS Replicate 2


title: Lung_old_NaCl_miRNA_SK1.1.99

description:
miRNA_READS_727.txt
727_19


title: UM-UC-3_AR-v19_Rep3


title: AdultWT_Rep3

source_name: Mouse injected sunflower oil


title: Lung_old_Bleo_miRNA_SK1.1.98

description:
miRNA_READS_727.txt
727_18


title: UM-UC-3_AR-v19_Rep1


title: Lung_old_Bleo_miRNA_SK1.1.92

description:
miRNA_READS_727.txt
727_17


title: UM-UC-3_pcDNA_Rep3


title: UM-UC-3_AR-v19_Rep2


title: 4tU-Seq Replicate 3

description: Random DNA is at ChrXVII from 3911 to 21878 bp.

data_processing:
bowtie2 -5 25 -3 25 –no-mixed –no-discordant –dovetail
bedtools bamtobed
Bed files were used to compute fragment locations for correctly aligned paired-end reads.
Duplicate fragments were eliminated based on the adapter-contained random nucleotide combinations and genomic locations of the fragments.
Per nucleotide coverage from the fragment locations were derived.
Spike-in normalized nt coverages were used to subtract background (DMSO treated samples) from the 4tU sample to obtain active transcription measurement.
Assembly: sacCer3 (for spike-ins: K. lactis ASM251v1, S. pombe ASM294v2)
Supplementary files format and content: Per nucleotide coverage/count has 3 columns: chromosome name, position, and count (directionality files are separated; plus counts align to minus strand and vice versa, minus counts correspond to plus genes).
Library strategy: 4tU-RNA

extract_protocol:
Hot phenol RNA extraction.
4tU-RNA enrichment was performed similarly as previously described (Duffy and Simon, 2016) with minor modifications. Briefly, polyA RNA was obtained from hot-phenol extracted RNA, fragmented with Magnesium RNA Fragmentation Module (NEB) and biotinylated with activated disulfide methane thiosulfonate (MTS) biotin (Biotium Biotin-XX MTSEA). Alternatively, 4tU-RNA was purified from hot-phenol extracted RNA and then subjected to polyA enrichment and magnesium fragmentation.
Fragments of mRNA were ligated to a linker and a cDNA library was prepared as described (Jin et al., 2015).

treatment_protocol: Yeast cells containing ChrXVII were treated with either 4-thiouracil (4tU, Sigma Aldrich; 5 mM final concentration) or DMSO as a control for 5 min. (Spike-in control cells were prepared by treating K. lactis cells with 4tU for 5 min; S. pombe cells were not treated).


title: AdultWT_Rep2


title: 4tU-Seq Replicate 4


title: Lung_old_Bleo_miRNA_SK1.1.85

description:
miRNA_READS_727.txt
727_15


title: Lung_old_Bleo_miRNA_SK1.1.114

description:
miRNA_READS_727.txt
727_21


title: 4tU-Seq Replicate 5


title: Lung_old_NaCl_miRNA_SK1.1.89

description:
miRNA_READS_727.txt
727_16


title: AdultWT_Rep1


title: UM-UC-3_pcDNA_Rep2


title: EmbryoKO_Rep2

value: E17.5 Intestine


title: UM-UC-3_pcDNA_Rep1


title: 4tU-Seq Replicate 2


title: EmbryoKO_Rep1


title: 4tU-Seq Replicate 1


title: Exp2 Macrophage TB40/E 144hpi dim population

description:
exp2.cells.tsv.gz
exp2.reads.tsv.gz

data_processing:
The MARS-seq pipeline scripts with a genome of hg19 + TB40/E were used.
The fastq files, include in the header, the barcodes and the quality of the barcodes coming from the other read, and the cell name.
It is first the quality of the batch barcode, the cell barcode and the read UMI, and then the barcodes in the same order, all separated by -
Genome_build: hg19 + TB40/E (NCBI accession EF999921.1)
Supplementary_files_format_and_content: tab-delimited text files. Include number of umis for all genes, per cell, and a TOC  cell name, plate name, plate coordinate, cell barcode, plate barcode, etc.

source_name: PMA-induced monocyte-derived macrophages HCMV-GFP infected 144hpi sorted GFP-dim

growth_protocol: Primary human CD14+ monocytes were maintained in X-vivo-15 media (Lonza) supplemented with 2.25mM L-glutamine. PMA-induced monocyte-derived macrophages were grown in RPMI supplemented with 10% FBS, 1%pen-strep and 1% glutamine.

extract_protocol:
Single cells were sorted into lysis buffer in 384 well plates and RT was carried out with oligo dT primers.
Single cell 3' RNA seq

tag: infection

value: HCMV-GFP

tag: time

value: dim

tag: experiment


title: EmbryoWT_Rep3


title: 3'READS Replicate 1


title: EmbryoWT_Rep2


title: Exp2 Macrophage TB40/E 72hpi dim population

description:
exp2.cells.tsv.gz
exp2.reads.tsv.gz

source_name: PMA-induced monocyte-derived macrophages HCMV-GFP infected 72hpi sorted GFP-dim

tag: population


title: Lung_young_NaCl_miRNA_SK1.1.62

description:
miRNA_READS_727.txt
727_12

value: young


title: EmbryoKO_Rep3


title: RNA-Seq Replicate 1

description:
Random DNA is at ChrXVII from 3911 to 21878 bp.
RNA_Seq_per_nt_count.bed

data_processing:
bowtie2 -5 25 -3 25 –no-mixed –no-discordant –dovetail
bedtools bamtobed
Bed files were used to compute fragment locations for correctly aligned paired-end reads.
Per nucleotide coverage from fragment locations and counts per defined intervals were derived.
Assembly: sacCer3
Supplementary files format and content: Per nucleotide coverage/count joined from two replicates (RNA_Seq_per_nt_count.bed) has 4 columns: chromosome name, position, count, directionality (plus counts align to minus strand and vice versa, minus counts correspond to plus genes).

extract_protocol:
Hot phenol RNA extraction.
Total RNA was subjected to polyA selection and fragmentation using Magnesium RNA Fragmentation Module (NEB).
mRNA fragments were ligated to a linker and a cDNA library was prepared as described (Jin et al., 2015).


title: RNA-Seq Replicate 2


title: Lung_young_Bleo_miRNA_SK1.1.80

description:
miRNA_READS_727.txt
727_14


title: Lung_young_Bleo_miRNA_SK1.1.56

description:
miRNA_READS_727.txt
727_11


title: ΔntrC cytosine 2 (RNA-seq)

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

data_processing:
Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
Transcripts Per kilobase Megabase of library size (TPM) were calculated using DEseq2.0
Assembly: NC_000913.2
Supplementary files format and content: comma-delimited text files include TPM values for each Sample.

organism: Escherichia coli K-12

source_name: bacteria cells

growth_protocol: E. coli K-12 MG1655 nac and ntrC mutant cells were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, or W2 minimal media with 0.2% glucose and 2 g/L glutamine, cytidine or cytosine.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a Qubit 4.0 (Thermo Scientific Inc., Wilmington, DE, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cell culture was treated with the RNAprotect reagent (Qiagen).

tag: nitrogen source

value: cytosine

value: delta ntrC

tag: phase

value: mid-log phase

tag: medium

value: W2 minimal media


title: EPZ_Rep3

source_name: mouse intestinal organoids treated with 4OHT + EPZ-6438 and grown ex vivo for 11 days.

treatment_protocol: Organoid cultures were treated for 3 days with 1 µM (Z)-4-hydroxytamoxifen (4-OHT, Sigma-Aldrich, H7904) + EPZ6438 at 1 µM

tag: tissue

value: ileum-derived Intestine organoid


title: Exp1 Monocyte TB40/E 72hpi

description:
exp1.cells.tsv.gz
exp1.reads.tsv.gz

source_name: Primary CD14+ monocytes HCMV-GFP infected 72hpi

tag: cell type

value: Primary CD14+ monocytes

value: total


title: ΔntrC cytosine 1 (RNA-seq)

tag: genotype


title: Exp1 Monocyte TB40/E 144hpi

description:
exp1.cells.tsv.gz
exp1.reads.tsv.gz

source_name: Primary CD14+ monocytes HCMV-GFP infected 144hpi


title: ΔntrC cytidine 2 (RNA-seq)

value: cytidine


title: Lung_young_Bleo_miRNA_SK1.1.44

description:
miRNA_READS_727.txt
727_8

tag: treatment

value: Male

value: Lung


title: Lung_young_Bleo_miRNA_SK1.1.46

description:
miRNA_READS_727.txt
727_9

tag: strain


title: EmbryoWT_Rep1


title: ΔntrC cytidine 1 (RNA-seq)


title: EPZ_Rep2


title: Lung_young_NaCl_miRNA_SK1.1.70

description:
miRNA_READS_727.txt
727_13

tag: age

value: NaCl


title: EPZ_Rep1


title: Exp1 Monocyte TB40/E 24hpi

description:
exp1.cells.tsv.gz
exp1.reads.tsv.gz

source_name: Primary CD14+ monocytes HCMV-GFP infected 24hpi


title: Exp1 Monocyte TB40/E 48hpi

description:
exp1.cells.tsv.gz
exp1.reads.tsv.gz

source_name: Primary CD14+ monocytes HCMV-GFP infected 48hpi


title: ΔntrC glutamine 2 (RNA-seq)

value: glutamine


title: Lung_young_Bleo_miRNA_SK1.1.32

description:
miRNA_READS_727.txt
727_6

value: Bleo

tag: day


title: DT_TAM

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm9 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Peaks were called using MACS 2.1.1 with ‘--nomodel --shift -100 --extsize 200 --broad’ parameters
Assembly: mm9
Supplementary files format and content: Peaks called by MACS2 in broadPeak format.

source_name: ATAC-seq fragmented chromatin

extract_protocol: ATAC-seq was performed by standard procedures

tag: genotype/variation

value: KO


title: Exp1 Monocyte TB40/E 12hpi

description:
exp1.cells.tsv.gz
exp1.reads.tsv.gz

source_name: Primary CD14+ monocytes HCMV-GFP infected 12hpi

value: HCMV-GFP


title: ctrl_TAM

value: WT


title: ΔntrC glutamine 1 (RNA-seq)


title: Lung_young_Bleo_miRNA_SK1.1.28

description:
miRNA_READS_727.txt
727_5

value: young

tag: animal id


title: Exp1 Monocyte TB40/E 5hpi

description:
exp1.cells.tsv.gz
exp1.reads.tsv.gz

source_name: Primary CD14+ monocytes HCMV-GFP infected 5hpi


title: Exp2 Macrophage TB40/E 24hpi

description:
exp2.cells.tsv.gz
exp2.reads.tsv.gz

source_name: PMA-induced monocyte-derived macrophages HCMV-GFP infected 24hpi


title: Lung_young_NaCl_miRNA_SK1.1.49

description:
miRNA_READS_727.txt
727_10

source_name: Lung

tag: Sex


title: ΔntrC ammonia 2 (RNA-seq)

value: ammonia

value: M9 minimal media


title: Exp1 Monocyte Mock 144hpi

description:
exp1.cells.tsv.gz
exp1.reads.tsv.gz

source_name: Primary CD14+ monocytes mock-infected 144hpi

tag: infection

value: mock-infected


title: Lung_young_NaCl_miRNA_SK1.1.25

description:
miRNA_READS_727.txt
727_4


title: Lung_young_Bleo_miRNA_SK1.1.22

description:
miRNA_READS_727.txt
727_3


title: ΔntrC ammonia 1 (RNA-seq)

value: delta ntrC

value: mid-log phase


title: Exp1 Monocyte Mock 5hpi

description:
exp1.cells.tsv.gz
exp1.reads.tsv.gz

source_name: Primary CD14+ monocytes mock-infected 5hpi

value: Primary CD14+ monocytes

tag: time


title: Lung_young_NaCl_miRNA_SK1.1.16

description:
miRNA_READS_727.txt
727_2


title: mice fed a nomal diet

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: epididymal adipose tissue

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: 8-week-old male C57BL/6J mice were randomized into experimental groups and fed either a normal diet with 5% fat (ND) or 60% kcal high fat diet (HFD) for 8 weeks

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Qiagen).

value: epididymal adipose tissue

tag: diet

value: normal


title: Δnac cytosine 2 (RNA-seq)

value: cytosine

value: delta nac

value: W2 minimal media


title: mice fed a high-fat diet

value: high-fat


title: Exp1 Macrophage TB40/E 144hpi

description:
exp1.cells.tsv.gz
exp1.reads.tsv.gz

source_name: PMA-induced monocyte-derived macrophages HCMV-GFP infected 144hpi

tag: population

value: total

tag: experiment


title: M82-HS-1h ChIP-seq_H3K27ac Rep2

city: Paris

first: Jing

last: An

address: 630 Rue Noetzlin

institute: Universite Paris Saclay

description: Bio rep 2

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar SE $input $output ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads data were mapped using bowtie2 v 2.3.5 with the following setting "bowtie2 --very-sensitive" against the genome of SollycM82_v1.0.
Filtering step: Mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30  "mapping_quality >= 30"
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the command "samtools fixmate -m  and samtools markdup -r "
Peak calling: peaks of read density were called with macs2 2.2.7.1 with the command "macs2 callpeak  -t sample.bam   -c Input.bam -g 829069930 -p 0.05 --extsize 150 --bw 500 -B -n --outdir
Bigwig generation: read density was scored with s3norm with the default paramaters
Assembly: SollycM82_v1.0
Supplementary files format and content: s3norm normalized bigwig for plots generated with ComputeMatrix plotprofile of Deeptools

organism: Solanum lycopersicum

source_name: Leaf

growth_protocol: Plants were grown in pots in growth chambers at 24 °C under long-day (16 h of light) conditions.

extract_protocol:
ChIP-seq assays were performed on 4-week-old tomato fourth branch of leaves according to Bio-protocol of Ramirez-Prado, J.S. et al (2021) by using anti-H3K27me1 (Millipore, 07-448), anti-H3K9ac (Millipore, 07-352), anti-H3K14ac (Millipore, 07-353), anti-H3K18ac (Millipore, 07-354), anti-H3K27ac (Abcam, ab4729), anti-H3K4me3 (Millipore, 07-473) and anti-polymerase II (Abcam, ab26721) antibodies.
ChIP-seq libraries were prepared from 10ng of DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s instructions. Two independently biological replicates were generated for each time point of heat stress. DNA libraries were checked for quality and quantified using an Agilent 2100 Bioanalyzer (Agilent) and subjected to 1 × 75 bp high-throughput sequencing by NextSeq 500 (Illumina).

treatment_protocol: 4 weeks old plants were treated at 45°C 0h, 1h and 6h in the climatic chamber (aralab).

tag: cultivar

value: cv. M82 (Tomato cultivar M82)

value: Leaf

value: Heat stress 1h


title: Δnac cytosine 1 (RNA-seq)

tag: nitrogen source

tag: phase

tag: medium


title: M82-HS-6h ChIP-seq_H3K27ac Rep2

description: Bio rep 2

tag: genotype

value: WT

tag: tissue

value: Heat stress 6h


title: NC3 [miRNA-seq]

city: Shanghai

first: Zheyu

last: Zhang

address: Yueyang Road

country: China

institute: CAS

data_processing:
the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads.
Cutadapt was used to trim the adapters for short reads.
miRDeep2 was used for the prediction of new miRNAs and the quantification of miRNAs.
Based on CPM standardized miRNAs, the DE miRNAs were calculated and screened by R software edgeR.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

source_name: microglial cells

growth_protocol: BV2 microglial cells were cultured in Dulbecco’s modified Eagle medium high glucose media containing 10% fetal bovine serum.

extract_protocol:
Total RNA in the BV2 cells was isolated using TRIzol reagent. The quality and quantity of the RNA was assessed using a NanoDrop ND-1000.
We constructed the small RNA library using the  NEB Multiplex Small RNA Library Prep Set for Illumina.
The sequencing libraries of samples were denatured with 0.1 M NaOH to produce single-stranded DNA and sequenced by an Illumina NextSeq 500 sequencer.

treatment_protocol: Half the cells of this subline provided the negative control group (Ad-NC). The other half were then infected with adenovirus for 48 hours to give the experimental group (Ad-shGCH1).

value: negative control


title: Exp1 Macrophage TB40/E 72hpi

description:
exp1.cells.tsv.gz
exp1.reads.tsv.gz

source_name: PMA-induced monocyte-derived macrophages HCMV-GFP infected 72hpi

tag: cell type

value: HCMV-GFP