title: pDC_KO_rep3


title: E19_B2_81

status: Public on May 07 2020

type: SRA

city: shenzhen

first: CNSA

last: CNGB

address: BGI

country: China

institute: BGI

library_source: transcriptomic

data_processing:
BGI-seq basecalling software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Macaca_fascicularis_5.0.91 whole genome using STAR v2.3.4 with default parameters
Reads of exon  were calculated using RSEM
Genome_build: Macaca_fascicularis_5.0.91
Supplementary_files_format_and_content: tab-delimited text files include mapped reads values for each Sample

molecule: total RNA

organism: Macaca fascicularis

source_name: embryo

extract_protocol:
After washing with phosphate buffered saline (PBS) (MA0008, meilunbio), the embryo was digested with 0.1% trypsin (25200-072, Gibco) at 37°C for 5 to 10 min. Then the trypsin was neutralized with 2% FBS (04-002-1A, Biological Industries) and FBS was washed off with cold PBS with 0.1 to 1% bovine serum albumin (BSA). Finally, individual cells were picked into a lysis medium on ice with a mouth pipette. All procedures were performed under stereomicroscope
RNA libraries were prepared for sequencing using standard SMART-seq2 protocols for BGISEQ-500

tag: tissue

value: embryo


title: E19_B2_82


title: E19_B2_80


title: cDC2_WT_rep2

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

country: USA

institute: Washington University in St.Louis

data_processing:
Second mate was used for sample demultiplexing.
Individual single-end fastqs were aligned to mm10 genome using STAR with following options --outFilterMultimapNmax 15 --outFilterMismatchNmax 6 --outReadsUnmapped Fastx --outSAMstrandField All.
Gene expression was obtained via ht-seq and DESeq2 for differential expression.
Gene expression was obtained using in-house scripts bassed on MACS and HTSeq (https://github.com/ctlab/quant3p).
Genome_build: mm10

organism: Mus musculus

source_name: Dendritic cells

growth_protocol: Itgax-cre Stk11 fl/fl (LKB1) (17591855; 12226664) and WT male and female mice, all on a C57BL/6 background, were purchased from The Jackson Laboratory and crossed, housed and bred at the LUMC, Leiden, The Netherlands, under SPF conditions.

extract_protocol:
mRNA was extracted from cell lysates using oligo-dT beads (Invitrogen).
cDNA synthesis was carrid out using custom oligo-dT primer with a barcode and adaptor-linker sequence (CCTACACGACGCTCTTCCGATCT-XXXXXXXX-T15). After first-strand synthesis, samples were pooled together based on Actb qPCR values and RNA-DNA hybrids were degraded with consecutive acid-alkali treatment. Subsequently, a second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated with T4 ligase (NEB) followed by SPRI-beads (Agencourt AMPure XP, BeckmanCoulter) clean-up. The mixture was enriched by PCR for 12 cycles and SPRI-beads (Agencourt AMPure XP, BeckmanCoulter) purified to yield final strand-specific RNA-seq libraries.

treatment_protocol: To expand the number of Thymic DCs in mice, Flt3L-secreting B16 melanoma cells were harvested and washed using phenol red-free HBSS (Gibco) before subcutaneous injection of 2 × 106 cells in 100 µL of HBSS into the flank of 8 to 12 week old mice. Nine to twelve days later, thymi were harvested, placed in 500 µL medium (with Ca2+), mechanically disrupted, digested by addition of 50 µL medium (with Ca2+) supplemented with Collagenase D (Roche, Woerden, The Netherlands, end concentration of 1 mg/mL) and DNase I (Sigma, end concentration of 2000 U/mL) and incubation for 20 min at 37 °C. Upon completion of digestion, single-cell suspensions were subjected to red blood cell lysis (inhouse; 0.15 M NH4Cl, 1 mM KHCO3, 0.1 mM EDTA [Sigma] in ddH2O) and filtered with a 100 µm sterile filter before counting. From these suspensions, DC populations were further enriched by positive isolation with CD11c-Microbeads (Miltenyi, Leiden, The Netherlands) and sorting in cDC1 (CD8a+CD11c+MHCII+), cDC2 (CD11b+CD11c+MHCII+) and pDC (Siglec-H+CD11cint) subsets on a BD FACSAria using a 85 μm nozzle at 45 PSI.

tag: strain

tag: genotype

value: WT

tag: cell subtype


title: cDC1_KO_rep2

value: KO


title: cDC2_KO_rep2


title: cDC2_KO_rep3


title: pDC_KO_rep1

value: pDC


title: E19_B2_86


title: E19_B2_83


title: E19_B2_85


title: E19_B2_89


title: E19_B2_87


title: E19_B2_88


title: cDC1_KO_rep1


title: cDC2_WT_rep1


title: E19_B2_84


title: E19_B2_90


title: E19_B2_91


title: Bmal1 CT 16 ChIP

city: Beijing

first: wang

last: jiawen

address: 7 Science Park Road ZGC Life Science Park

institute: National institute of biological sciences

description:
CT16_Bm
Time-course harvest samples

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 1.0.0 with parameters -p 30 -m 1 -S -q
Peaks were called using MACS2 version 2.1.1 with parameters callpeak -g mm -B --SPMR
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigWig files were converted from bdg files generated by MACS2 version 2.1.1, representing fold enrichment for each site.

molecule: genomic DNA

source_name: Mouse liver

growth_protocol: WT C57BL/6J mice at age of 2~4 months old were entrained under a 12 h light (~ 50 lux light intensity)/ 12 h dark cycle at 25°C for two weeks.

extract_protocol:
Mouse liver was homogenized with tissue grinder (kimble) in PBS buffer containing complete protease inhibitor cocktail on ice, then cells were collected by centrifugation at 1500×g at 4 °C. Collected cells were sequentially cross-linked in 20 ml PBS buffer containing 1.5 mM EGS for 20 min, and followed by cross-linked in 20 ml PBS buffer containing 1% formaldehyde for 15 min at room temperature. The cross-link was stopped by adding glycine to a final concentration of 125 mM and incubate at room temperature for 5 min. ChIP assay and DNA sample preparation were performed strictly following the ChIP-IT High Sensitivity Kit (Active Motif). Eluted DNA was analyzed with high-throughput sequencings.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: After the synchronization of mouse clock to ambient light dark cycle, animals were transferred into constant darkness condition. 36 hours after light off, mouse liver (N=5) were collected at 4 hours interval. All experiments with mice were performed following the guidelines of the NIBS Institutional Animal Care and Use Committee (IACUC).

tag: strain/background

tag: genotype/variation

value: Liver

tag: time point

value: CT 16

tag: chip-grade antibody

value: Anti-Bmal1 (Abcam, Cat #ab3350, Lot# GR241928-12)

tag: 2nd antibody

value: anti-rabbit IgG


title: Ruvbl2 CT 4 ChIP

description:
CT4_R2
Time-course harvest samples

value: CT 4

value: Anti-Ruvbl2 (Novus Biologicals, NBP-40354)


title: E19_B2_93


title: Bmal1 CT 8 ChIP

description:
CT8_Bm
Time-course harvest samples

value: CT 8


title: E19_B2_09


title: Ruvbl2 CT 8 ChIP

description:
CT8_R2
Time-course harvest samples


title: Ruvbl2 CT 20 ChIP

description:
CT20_R2
Time-course harvest samples

value: CT 20


title: E19_B2_92


title: Ruvbl2 CT 16 ChIP

description:
CT16_R2
Time-course harvest samples


title: Bmal1 CT 4 ChIP

description:
CT4_Bm
Time-course harvest samples


title: Bmal1 CT 20 ChIP

description:
CT20_Bm
Time-course harvest samples


title: Ruvbl2 CT 12 ChIP

description:
CT12_R2
Time-course harvest samples

value: CT 12


title: Input

description:
0
Time-course harvest samples


title: Bmal1 CT 12 ChIP

description:
CT12_Bm
Time-course harvest samples


title: cDC2_KO_rep1


title: E19_B2_95


title: Bmal1 CT 0 ChIP

description:
CT0_Bm
Time-course harvest samples

value: CT 0


title: E19_B2_96


title: Ruvbl2 CT 0 ChIP

description:
CT0_R2
Time-course harvest samples


title: E09_B2_01


title: H3K27ac_E12.5_ChIPSeq_Rep2

city: Berlin

first: Denes

last: Hnisz

state: Berlin

address: Ihnestraße 63-73

department: Genome Regulation

country: Germany

institute: Max Planck Institute for Molecular Genetics

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 1.0.0 with parameters  ‘-n 2 -e 70 -m 1 -k 1 --best -l 200’
peaks were called using macs version 1.4.2 with parameters ‘-w -S --space=50 --keep-dup=auto –pvalue=1e-4’, The pvalue cutoff has been set individually lower depending on the datasets as described in the methods to get around 11k peaks.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were produced by macs output

source_name: limb buds mouse embryo

growth_protocol: Limb buds (stage E12.5) were micro-dissected from mouse embryos

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the respective antibody.
We sheared chromatin using Bioruptor until reaching a fragment size of 200-500bp. 10-15μg of chromatin was then used for each replicate H3K27ac ChIP and 30μg for CTCF ChIP. Antibodies: H3K27ac (Diagenode, C15410174) and CTCF (Active motif: 613111) was then performed as in Ibrahim et al. 2013.
Libraries were prepared using the Nextera adaptors and sequenced

treatment_protocol: Dissected tissue from embryos was pooled and turned into a single-cell suspension by digestion with Trypsin-EDTA 0.05% (Gibco) for 10 min at 37°C shaking at 900 RPM.The cells were mixed with 10%FCS/PBS and homogenized using a 40 µm cell strainer (Falcon). After centrifugation, cells were fixed in 1% PFA/10%FCS/PBS for 10’ at room temperature. Cells were then lysed 3C-Lysis buffer and nuclei pelleted by centrifugation. Then, nuclei were resuspended in buffer 3 for sonication (Lee et al. 2006).

value: limb bud

tag: age

tag: chip antibody

value: H3K27ac (Diagenode, C15410174)


title: E09_B2_18


title: E09_B2_19


title: H3K27ac_E12.5_ChIPSeq_Rep1


title: E09_B2_20


title: E09_B2_26


title: E19_B2_94


title: E09_B2_35


title: E09_B2_27


title: E09_B2_28


title: E09_B2_34


title: ChIP-seq_siID4 rep3

city: Darlinghurst

first: Alexander

last: Swarbrick

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
Reads were aligned to the mouse reference genome Mm10 using Bwa
Sam-to-Bam conversion was performed using Bwa
Alignment statistics generatied using Samtools Flagstat
peak calling was performed using MACS
blacklist regions removed
Genome_build: mm10
Supplementary_files_format_and_content: .bed files of consensus peaks (txt, tab delimited)

source_name: Mammary epithelial cells

growth_protocol: Comma-Dβ cells were maintained in DMEM/F12 media (Gibco) supplemented with 2% FBS (HyClone), 10 mM HEPES (Gibco), 0.125 IU/mL Insulin (Novo Nordisk) and 5 ng/mL mEGF (Life Technologies).

extract_protocol:
chromatin was immunoprecipitated from cross-linked nuclear extracts using antibodies and DNA was purified.
Illumina TruSeq ChIP library prep kit (Illumina)

treatment_protocol: Comma-Dβ cells were seeded at a density of 1.5x104 cells/cm2 into 100 mm dishes (Corning)  in antibiotic-free media. The following day siRNA constructs (Dharmacon) were transfected into the cells using Dharmafect-4 transfection reagent (Dharmacon) as per the manufacturer’s instructions at 20 nM. siRNA used were siGENOME Mouse Id4 SMARTpool (M-043687) and ON-TARGETplus Non-targeting Control Pool (D-001810). Media was changed the following day and cells were harvested 48 hr post-transfection.

tag: cell line

value: Comma-Dbeta

tag: cell type

value: Mammary epithelial cells

tag: passage number

tag: sirna

value: siGENOME Mouse Id4 SMARTpool (M-043687)


title: ChIP-seq_NT rep2

value: ON-TARGETplus Non-targeting Control Pool (D-001810)


title: ChIP-seq_NT rep3


title: ChIP-seq_siID4 rep1


title: ChIP-seq_siID4 rep2


title: E09_B2_33

value: embryo


title: input rep3 for NT&siID4

value: none (input)


title: E09_B2_02


title: E09_B2_41


title: input rep2 for NT&siID4


title: input rep1 for NT&siID4


title: E09_B2_43


title: E09_B2_36


title: input rep4 for NT&siID4


title: E09_B2_42


title: ChIP-seq_NT rep1


title: input rep2


title: input rep3


title: input rep1


title: E09_B2_49


title: H3K27Me3 rep4

value: H3K27Me3 (Merck Millipore 07-449)


title: E09_B2_50


title: E09_B2_51


title: H3K27Me3 rep3


title: H3K27Me3 rep2


title: input rep4


title: E09_B2_58


title: E09_B2_65


title: H3K27ac rep3

value: H3K27Ac (Active Motif 39034)


title: E09_B2_59


title: H3K4Me3 rep3

value: H3K4Me3 (Active Motif 28431)


title: H3K27ac rep2


title: H3K27ac rep1


title: E09_B2_67


title: E09_B2_74


title: H3K4Me3 rep1


title: E09_B2_75


title: HEB rep4


title: H3K27ac rep4


title: HEB rep3


title: E09_B2_82


title: E09_B2_81


title: E09_B2_73


title: H3K4Me3 rep4


title: H3K27Me3 rep1


title: E09_B2_25


title: E09_B2_89


title: HEB rep1


title: E09_B2_57


title: E09_B2_83


title: E09_B2_03


title: siID4 rep3

data_processing:
Adapters trimmed using Cutadapt
Reads were aligned to the mouse reference genome Mm10 using STAR
Gene feature counting was performed with RSEM
Transcripts with expression counts of 0 across all samples were removed
Genome_build: mm10
Supplementary_files_format_and_content: gene filtered RSEM counts (txt, tab delimited)

molecule: polyA RNA

extract_protocol:
RNA was extracted using the Qiagen miRNease mini kit (Qiagen)
The Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina) was used with 1 μg of input RNA following the manufacturer’s instructions.

treatment_protocol: Comma-Dβ cells were seeded at a density of 1.5x104 cells/cm2 into 6 well plates (Corning) in antibiotic-free media. The following day siRNA constructs (Dharmacon) were transfected into the cells using Dharmafect-4 transfection reagent (Dharmacon) as per the manufacturer’s instructions at 20 nM. siRNA used were siGENOME Mouse Id4 SMARTpool (M-043687) and ON-TARGETplus Non-targeting Control Pool (D-001810). Media was changed the following day and cells were harvested 48 hr post-transfection.

value: mammary epithelial cells


title: E09_B2_04


title: siID4 rep1


title: siID4 rep2


title: H3K4Me3 rep2


title: E09_B2_91


title: E09_B2_66


title: E09_B2_90


title: E09_B2_09


title: NT rep2


title: E09_B2_10


title: HEB rep2


title: NT rep1


title: E09_B2_11


title: E09_B2_17


title: E09_B2_12


title: E13_B2_27


title: E13_B2_29


title: Scn1a_A1783V_Hippocampus_1

city: Storrs

first: Rahul

middle: N

last: Kanadia

state: CT

address: 75 N. Eagleville Road

department: Physiology and Neurobiology

institute: University of Connecticut

data_processing:
Reads were aligned to the mm10 genome using Hisat2.
Single nucleotide variations were called using SNVQ and used to create a new reference genome.
Reads were aligned to the new reference genome using Hisat2.
Isoform and gene expression were determined using IsoEM2.
Differential isoform and gene expression were determined using IsoDE2.
Genome_build: mm10 (Ens v84)/GRCm38
Supplementary_files_format_and_content: *.txt: Tab-delimited text files with TPM values for each condition.

source_name: Hippocampus

extract_protocol:
Total RNA was extracted using the ZymoResearch Kit, per the manufacturer's instructions.
Total RNA was depleted from rRNA using RiboZero, followed by construction of the cDNA library using the Illumina TruSeq Stranded Total RNA Library Sample Prep Kit.

value: Hippocampus


title: Kcnq2_cKO_Hippocampus_3


title: Scn1a_A1783V_Hippocampus_2


title: E13_B2_28


title: E13_B2_18


title: Scn1a_A1783V_Hippocampus_3


title: Scn1a_WT_Hippocampus_1


title: Scn1a_WT_Hippocampus_2


title: E13_B2_31


title: Scn1a_WT_Hippocampus_3


title: Kcnq2_cKO_Hippocampus_2


title: Kcnq2_cKO_Hippocampus_1


title: E13_B2_34


title: Kcnq2_WT_Hippocampus_3


title: E13_B2_30


title: E13_B2_35


title: NT rep3


title: E13_B2_36


title: Kcnq2_WT_Hippocampus_1


title: E13_B2_37


title: E13_B2_38


title: Kcnq2_cKO_Cortex_3

source_name: Cortex

value: Cortex


title: E13_B2_19


title: E13_B2_39


title: Kcnq2_cKO_Cortex_2


title: Kcnq2_cKO_Cortex_1


title: Kcnq2_WT_Cortex_3


title: Kcnq2_WT_Cortex_2


title: Kcnq2_WT_Cortex_1


title: E13_B2_43


title: E13_B2_41


title: E13_B2_44


title: E13_B2_40


title: Hoxb13_input_rep_5

city: Dallas

first: Hesham

last: Sadek

state: TX

address: 5323 Harry Hines Blvd

department: Internal Medicine: Cardiology

institute: UT Southwestern Medical Center

description: Input for Hoxb13-ChIPSeq sample 2

data_processing:
Reads were trimmed using fastq-mcf(ea-utils/bd148d4)
Reads were mapped using bowtie2 (v2.2.3)
Duplicate Reads were removed using Picard MarkDuplicates (v1.127)
Enriched regions (peaks) were identified using the IDR pipeline and spp package (vc2066e1)
Peak regions were annotated by Chipseeker
Bigwig files were made using deepTools (v1.6)6 and normalization method as CPM
Genome_build: mm10
Supplementary_files_format_and_content: Bigiwg files
Supplementary_files_format_and_content: Annotated Bed files

source_name: heart extract

extract_protocol:
Ventricles from three P15 mouse hearts were used as biological triplicates for the ChIP-seq experiments. Tissue samples were ground to powder and crosslinked with 2% formaldehyde in PBS for 30 min and quenched with 0.125 M glycine for 10 min at room temperature. Crosslinked samples were then washed with cold PBS and further homogenized with a Dounce tissue grinder. Samples were collected by a brief spin, and treated with 10 mM Tris-HCl (pH 8.0), 10mM NaCl and 0.2% NP-40 for 30 min to collect nuclei. After nuclear extraction, chromatin was sheared on a Bioruptor Pico (Diagenode) for 20 cycles (30 sec on/ 30 sec off for each cycle) at 4°C in sonication buffer (0.1% SDS, 1% Triton X-100, 10 mM Tris-HCl, 1 mM EDTA, 0.1% sodium deoxycholate, 0.25% sarkosyl, 1 mM DTT, 1x cOmplete Protease Inhibitor Cocktail (Roche), and 200 µM PMSF, pH 8.0). After sonication, 1% of the sonicated chromatin from each sample was taken out as “input” samples. The remaining sonicated chromatin was evenly split for Meis1 or Hoxb13 ChIP. Sonication buffer was added to make the final volume to 1 mL. NaCl was then added to a final concentration of 300 mM for each sample. Antibody (anti-Meis1 Santa Cruz, sc-10599X, 1:200 or anti-Hoxb13 GeneTex, GTX129245, 1:100) was added to each sample and incubated at 4°C overnight with gentle rotation. The next day, 30 µL of pre-washed Dynabeads Protein G (Invitrogen, 10004D) was added to each sample for a two-hour incubation. After that, the beads were washed twice with 1 mL RIPA 0 buffer (0.1% SDS, 1% Triton X-100, 10 mM Tris-HCl, 1 mM EDTA, 0.1% sodium deoxycholate, pH 8.0), twice with 1 mL RIPA 0.3 buffer (0.1% SDS, 1% Triton X-100, 10 mM Tris-HCl, 1 mM EDTA, 0.1% sodium deoxycholate, 300 mM NaCl, pH 8.0), twice with 1 mL LiCl wash buffer (250 mM LiCl, 0.5% IGEPAL CA-630, 0.5% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.0), and finally twice with 1 mL TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0). For each ChIP sample or input sample, 100 uL of SDS elution buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0) was added and incubation was done at 65°C overnight on a ThermoMixer (Eppendorf) at 1000 rpm. The next day, supernatant was collected and further treated with 0.5 µg RNaseA (Sigma, 11119915001) for 30 min at 37°C, followed by 20 µg Proteinase K (NEB, P8107S) treatment at 37°C for 2h. DNA was recovered using MinElute PCR Purification Kit (QIAGEN, 28004) according to manufacturer’s protocol.
ChIP-Seq libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L) according to manufacturer’s protocol. After adapter ligation DNA was PCR amplified with Illumina primers for 9-15 cycles. Final ChIP-Seq libraries were pooled and sequenced on an Illumina Nextseq 500 system using the 75bp high output sequencing kit for single-end sequencing


title: E13_B2_42


title: E13_B2_45


title: Kcnq2_WT_Hippocampus_2


title: E13_B2_46


title: E13_B2_50


title: E13_B2_47


title: E13_B2_51


title: Meis1_input_rep_2

description: Input for Meis1-ChIPSeq sample 2


title: Meis1_input_rep_3

description: Input for Meis1-ChIPSeq sample 3


title: Hoxb13_ChIPSeq_rep_4

description: ChIPSeq data for Hoxb13 in P15 heart-sample 1

value: Hoxb13 (GeneTex, GTX129245)


title: Hoxb13_ChIPSeq_rep_5

description: ChIPSeq data for Hoxb13 in P15 heart-sample 2


title: Meis1_input_rep_1

description: Input for Meis1-ChIPSeq sample 1


title: E13_B2_20


title: Hoxb13_ChIPSeq_rep_6

description: ChIPSeq data for Hoxb13 in P15 heart-sample 3


title: E13_B2_53


title: Meis1_ChIPSeq_rep_3

description: ChIPSeq data for Meis1 in P15 heart-sample 3

value: Meis1 (Santa Cruz, sc-10599X)


title: Meis1_ChIPSeq_rep_2

description: ChIPSeq data for Meis1 in P15 heart-sample 2


title: Hoxb13_input_rep_6

description: Input for Hoxb13-ChIPSeq sample 3


title: E13_B2_54


title: Hoxb13_input_rep_4

description: Input for Hoxb13-ChIPSeq sample 1


title: E13_B2_55


title: E13_B2_56


title: RNAseq_2_Nkx_LIN9wt_SAV1wt_rep3

city: Wuerzburg

first: Stefan

last: Gaubatz

address: Am Hubland

department: Biochemistry and Cell Biology

institute: University of Wuerzburg

description: RNAseq_2_Nkx_logFC.txt,RNAseq_2_Nkx_countmatrix.txt

data_processing:
For RNA-seq analysis, reads were aligned to the murine genome (mm10) with TopHat v2.1.0 (Kim et al., 2013) using  BOWTIE2 (Langmead, 2010) with default parameters and samples were normalized to the sample with the smallest number of sequenced reads.
Reads per gene (Ensembl database GRCm38.p6) were counted with the "summarizeOverlaps" function in the R package {GenomicFeatures}.
Non- or weakly expressed genes were removed (threshold: mean read count per gene over all samples >1).
Differential gene expression was called using EdgeR and adjusting the calculated p-value with the Benjamini-Höchberg procedure.
mm10
The countmatrix files contain raw reads per ensembl gene.The logFC files contain ensembl gene names, gene symbols, gene description, log2FC, log2CPM, p-value and Benjamini-Höchberg-adjusted p-value (FDR). Details are described in readme.txt.

source_name: E13.5 ventricular heart

growth_protocol: Sav1tm1.1Dupa/J mice were obtained from Jackson laboratories, in which LoxP sites flank exon 3 of the Sav1 gene (Cai et al. 2010). We have previously descripted Lin9fl mice, in which LoxP sites flank exon 7 of the Lin9 gene (Reichert et al. 2010). Cardiomyocyte-specific deletion of Sav1 and Lin9 was achieved by crossing mice to Nkx2.5-Cre mice (Stanley et al. 2002).

extract_protocol:
For whole transcriptome analysis, total RNA was isolated using peqGOLD TriFast (Peqlab) in triplicates from ventricular heart tissue with the desired genotype.
DNA libraries were generated using 1µg RNA with the magnetic mRNA isolation module and NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs). DNA library was amplified by 7 PCR cycles and quality was analyzed using the fragment analyzer (Advanced Analytical). Libraries were sequenced on the NextSeq 500 platform (Illumina).

treatment_protocol: non

tag: antibody

tag: isolation day

value: wild-type


title: RNAseq_2_Nkx_LIN9wt_SAV1KO_rep3

value: knockout


title: E13_B2_59

tag: tissue


title: RNAseq_2_Nkx_LIN9wt_SAV1wt_rep1


title: RNAseq_2_Nkx_LIN9wt_SAV1KO_rep2


title: E13_B2_57


title: E13_B2_60


title: E13_B2_58


title: RNAseq_2_Nkx_LIN9wt_SAV1wt_rep2


title: E13_B2_21


title: RNAseq_2_Nkx_LIN9wt_SAV1KO_rep1


title: RNAseq_2_Nkx_LIN9KO_SAV1wt_rep3


title: E13_B2_52


title: E13_B2_61


title: RNAseq_2_Nkx_LIN9KO_SAV1KO_rep3


title: E13_B2_67


title: E13_B2_62


title: RNAseq_2_Nkx_LIN9KO_SAV1wt_rep2


title: Meis1_ChIPSeq_rep_1

description: ChIPSeq data for Meis1 in P15 heart-sample 1

tag: strain


title: E13_B2_66


title: E13_B2_63


title: E13_B2_69


title: RNAseq_2_Nkx_LIN9KO_SAV1KO_rep1


title: RNAseq_1_Nkx_LIN9wt_rep3

description: RNAseq_1_Nkx_logFC.txt,RNAseq_1_Nkx_countmatrix.txt


title: RNAseq_1_Nkx_LIN9wt_rep2


title: RNAseq_2_Nkx_LIN9KO_SAV1KO_rep2


title: E13_B2_71


title: E13_B2_73


title: E13_B2_72


title: E13_B2_74


title: E13_B2_22


title: SPDH_transfected_chicken

description: ChIPseq

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-Seq reads were aligned to the chicken genome (assembly gg3) using bowtie version 1.0.0 with parameters  ‘-n 2 -e 70 -m 1 -k 1 --best -l 200’
Mapped reads in bamfiles from lanes L001 and L002 of eah experiment were merged using the merge command from bamtools
peaks were called using macs version 1.4.2 with parameters ‘-w -S --space=50 –keep-dup=auto’
rpm per bp normalization for the union of peaks between samples were  created by using bamToGFF_turbo.py with options -s both -e 200 -m 1 getting a single value per peak
Genome_build: gg3
Supplementary_files_format_and_content: bed files were produced from macs output

organism: Gallus gallus

source_name: SPDH expressing chMM

growth_protocol: Mesenchymal stem cells were isolated from the HH24 chicken limb buds, infected with an RCASBP(A) virus carrying the transgene on interest. Cells were plated (10µl of 2*10^7 cells/ml) and cultured for 6 days with the DMEM:HAM F11 media (supplemented with 10% Fetal Bovine Serum, 0,2% Chicken Serum, 1% Penicilin-Streptomicin and 1% L-glutamine).

extract_protocol:
Nuclei were isolated with three different lysis buffers as in Lee et al., 2006 and sonicated in the lysis buffer 3 until the chromatin was disrupted to the size between 200 and 300bp. Antibody: FLAG (Sigma Mouse monoclonal M2; F3165)
Libraries were prepared using NEBNext ChIP-seq Library Prep Master Mix for Illumina (New England Biolabs), fragments between 300-450bp were selected and sequenced on a Illumina HiSeq 1500 using Illumina TruSeq v3 chemistry.

treatment_protocol: Cells were infected with RCASBP viruses carrying 3x-Flag tagged wildtype or mutant Hoxd13 transgenes.

value: chicken micromass

tag: genotype

value: SPDH expressing chMM

value: FLAG (Sigma Mouse monoclonal M2; F3165)


title: RNAseq_2_Nkx_LIN9KO_SAV1wt_rep1


title: RNAseq_1_Nkx_LIN9KO_rep2


title: RNAseq_1_Nkx_LIN9KO_rep3


title: WT_HOXD13_transfected_chicken_Rep1

description: ChIPseq

source_name: Hoxd13(wt) expressing chMM

value: Hoxd13(wt) expressing chMM


title: WT_HOXD13_transfected_chicken_Rep2

description: ChIPseq


title: E13_B2_75


title: E13_B2_68


title: E13_B2_76


title: E13_B2_77


title: VE-cadherin -/- plus CD5-2

city: Camperdown

first: Jennifer

middle: R

last: Gamble

state: New South Wales

address: Building 93, Royal Prince Alfred Hospital

department: Vascular Biology

institute: CENTENARY INSTITUTE

description:
transformed cell line
VE-cadherin null EC
Jial02

data_processing:
Library preparations were sequenced on an Illumina Hiseq4000 platform and 150 bp paired-end reads were generated
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indices of the reference genome were built using Bowtie (v2.2.3) and paired-end clean reads were aligned to the reference genome using TopHat (v2.0.12).
HTSeq (v0.6.1) was used to count the read numbers mapped of each gene, followed by calculation of RPKM (Reads Per Kilobase of exon model per Million mapped reads) of each gene based on the length of the gene and reads count mapped to that gene
Differentially expressed genes were then determined using DESeq R package (v1.12.0). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P-value<0.05 and FDR<0.005 were assigned as differentially expressed.
Genome_build: hg19; mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: VE-cadherin null EC

extract_protocol:
Total RNA was extracted from ECs using RNeasy Plus Mini Kit (Qiagen)
RNA-Seq libraries for mRNA profiling were prepared from 1.5-5  µg total RNA using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

treatment_protocol: ECs were treated with either control or CD5-2 for 24h prior to RNA extraction

value: VE-cadherin null EC

value: VE-cadherin -/-

tag: treatment


title: E13_B2_82

value: embryo


title: E13_B2_78


title: SPDH_H3K27ac_ChIPSeq_spikein_INPUT_Rep2

description: ChIPseq

data_processing:
Basecalls performed using CASAVA version 1.4
Paired-end ChIP-Seq reads were quality filtered and adapter trimmed by using cutadapt version 1.18 with minquality 20, minlength 25 and illumina adapter sequence AGATCGGAAGAGC
Reads were aligend to the mouse genome mm9 or fly (D. melanogaster) genome dm6 with bwa version 0.7.17-r1188 using the ‘mem’ command and default options. A sorted bam file and corresponding index was created with samtools version 1.9
Duplicate reads have been identified and filtered by using MarkDuplicates from the gatk suite version 4.1.4.0.
Deduplicated reads were kept if their MAPQ value was at least 15 by using samtools with option -q 15
Peaks for the mapped mouse reads/fly reads were called using the callpeak program from macs2 version 2.1.2 and using INPUT ChIP as control and the option ‘narrow’.
Technical replicates (samples 7,8 and 9,10) were merged using the merge program from bamtools version 2.5.1.
Genome wide rpm per bp normalized coverage profiles were created by using bamToGFF_turbo.py from https://github.com/BradnerLab/pipeline.git. The genome was divided into 3mb regions and the tool was run with options -s both -e 200 -m 60000 resulting in 50bp bins.
Wig files from the rpm per bp matrices were created with samtools and then multiplied with dm6 spikein normalization factors
Genome_ build: mm9, dm6
Supplementary_files_format_and_content: bigwig files with spikein normalized rpm per bp values were created using samtools

growth_protocol: E12.5 littermate embryos (wt and homozygous) were obtained from staged matings of heterozygous Spdh mice.

extract_protocol:
Dissected tissue from embryos was pooled and turned into a single-cell suspension by digestion with Trypsin-EDTA 0.05% (Gibco) for 10 min at 37°C shaking at 900 RPM. Drosophila melanogaster S2 cells were spiked in in a 1:3 ratio. The cells were mixed with 10%FCS/PBS and homogenized using a 40 µm cell strainer (Falcon). After centrifugation, cells were fixed in 1% PFA/10%FCS/PBS for 10’ at room temperature. Cells were then lysed 3C-Lysis buffer (50mM TRIS pH 7.5; 150mM NaCl; 5mM EDTA; 0.5% NP-40; 1.15% Triton X-100; Protease Inhibitors (Roche)) and nuclei pelleted by centrifugation. For sonication, nuclei were resuspended in buffer 3 (Lee et al. 2006). Chromatin was sheared using a Bioruptor until reaching a fragment size of 200-500bp. Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the respective antibody. 10-15μg of chromatin was used for each replicate ChIP.  Antibodies: H3K27ac (Diagenode, C15410174)  as in Ibrahim et al. 2013.
Sequencing libraries were prepared using Nextera adaptors.

treatment_protocol: Limb buds (stage E12.5) were micro-dissected from mouse embryos treatment protocol.

value: limb bud

tag: developmental state

value: SPDH mutant

value: H3K27ac (Diagenode, C15410174)


title: RNAseq_1_Nkx_LIN9KO_rep1


title: E13_B2_70


title: ChIPseq_E16_LIN9

data_processing:
For ChIP-seq analysis, reads were aligned to the murine (mm10) genome with BOWTIE v1.1.2 (Langmead, 2010) using default parameters and samples were normalized to the sample with the smallest number of sequenced reads.
Genome-wide read density files ("bedgraph") were generated with the genomeCoverageBed function from the bedtools suite v2.26.0 (Quinlan et al., 2010).
mm10
bedgraph files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).

source_name: E16.5 ventricular heart

extract_protocol:
Chromatin was isolated from ventricular heart tissue of E16.5 or P10 hearts. In brief, minced tissue was fixed with 1% formaldehyde for 20 minutes at RT. The reaction was stopped by adding 125mM glycine for additional 5 minutes. Tissue was incubated in lysis buffer (50mM Tris-HCl pH8, 10mM EDTA, 1% SDS) for 1 h at 4°C. Samples were sonicated for 1 minute at 25% amplitude (10s ON / 30s OFF) at 4°C, insoluble material was removed by centrifugation and chromatin was fragmented to an approximate size of 150 to 300bp by additional sonicating for 10 minutes at 25% amplitude (10s On / 30s OFF) at 4°C using a Branson sonifier. Afterwards chromatin was diluted ten times in ChIP dilution buffer (50mM Tris-HCl pH8, 0.167M NaCl, 1.1% Triton X-100, 0.11% sodium deoxycholate). For immunoprecipitation, 9µg of the antibody was coupled to protein G dynabeads (Thermo Fisher Scientific) for 6 h at 4°C and then incubated with fragmented chromatin over night at 4°C. Beads were washed in total twelve times with wash buffer I (50mM Tris-HCl pH8, 0.15M NaCl, 1mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate), wash buffer II (50mM Tris-HCl pH8, 0.5M NaCl, 1mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate), wash buffer III (50mM Tris-HCl pH8, 0.5M LiCl2, 1mM EDTA, 1% Nonidet P-40, 0.7% sodium deoxycholate) and wash buffer IV (10mM Tris-HCl pH8, 1mM EDTA). 1mM  PMSF and protease inhibitor cocktail were added freshly to all buffers. After washing chromatin was eluted in (10mM Tris-HCl pH8, 0.3M NaCl, 5mM EDTA, 0.5% SDS, 10µg/ml RNAseA) and crosslink was reversed at 65°C over night. Proteins were digested by adding 200µg/ml proteinase K at 55°C for 2 h. DNA was purified using the QIAquick PCR Purification Kit (QIAGEN) and eluted in 50 µl EB buffer. Purified ChIP-DNA was quantified using the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific).
DNA liberaries were generated using 10ng purified ChIP-DNA and the NEBNext®Ultra IIDNALibrary Prep Kit for Illumina® (New England Biolabs) according to the manufacturer’s instructions. DNA library was amplified by 12-15 PCR cycles and quality was analyzed using the fragment analyzer (Advanced Analytical). Libraries were sequenced on the NextSeq 500 platform (Illumina).

value: LIN9 (Bethyl A300-BL3981)


title: E13_B2_23


title: ChIPseq_P10_LIN9

source_name: P10 ventricular heart


title: RNAseq_1_Nkx_LIN9wt_rep1


title: SPDH_H3K27ac_ChIPSeq_spikein_INPUT_Rep1

description: ChIPseq


title: E13_B2_84


title: ChIPseq_P10_input

value: non


title: E13_B2_79


title: E13_B2_85


title: WT_H3K27ac_ChIPSeq_spikein_INPUT_Rep2

description: ChIPseq


title: E13_B2_86


title: ChIPseq_E16_input


title: E13_B2_87


title: SPDH_H3K27me3_ChIPSeq

extract_protocol:
Dissected tissue from embryos was pooled and turned into a single-cell suspension by digestion with Trypsin-EDTA 0.05% (Gibco) for 10 min at 37°C shaking at 900 RPM. The cells were mixed with 10%FCS/PBS and homogenized using a 40 µm cell strainer (Falcon). After centrifugation, cells were fixed in 1% PFA/10%FCS/PBS for 10’ at room temperature. Cells were then lysed 3C-Lysis buffer (50mM TRIS pH 7.5; 150mM NaCl; 5mM EDTA; 0.5% NP-40; 1.15% Triton X-100; Protease Inhibitors (Roche)) and nuclei pelleted by centrifugation. For sonication, nuclei were resuspended in buffer 3 (Lee et al. 2006). Chromatin was sheared using a Bioruptor until reaching a fragment size of 200-500bp. Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the respective antibody. 10-15μg of chromatin was used for each replicate ChIP.  Antibodies: H3K27ac (Diagenode, C15410174) and H3K27me3 (Active motif: 613111) was performed as in Ibrahim et al. 2013.
Sequencing libraries were prepared using Nextera adaptors.

value: H3K27me3 (Active motif:613111)


title: E13_B2_88


title: WT_H3K27ac_ChIPSeq_spikein_INPUT_Rep1

description: ChIPseq


title: SPDH_H3K27ac_ChIPSeq_spikein_Rep2

description: ChIPseq


title: WT_H3K27me3_ChIPSeq_Rep1

description: H3K27me3-L-E125-Wt-Mm_merged_5_peaks.bed


title: E13_B2_90


title: SPDH_H3K27ac_ChIPSeq


title: E13_B2_92


title: SPDH_H3K27ac_ChIPSeq_spikein_Rep1

description: ChIPseq


title: E13_B2_93


title: SPDH_E12.5_scRNASeq

data_processing:
*R1_001.fastq.gz: contains the cell barcode (first 16 nt) and UMI (next 10 nt)
*R2_001.fastq.gz: contains the 98 nt RNA sequence.
*I1_001.fastq.gz: contains the 8 nt sample index.
Raw base call (BCL) files generated by Illumina sequencers were demultiplexed into FASTQ files using 10X Genomics' Single-Cell Gene Expression Software Cell Ranger version 3.0.0 ("mkfastq" pipeline, default parameters).
For each experiment FASTQ files were aligned, filtered, barcode and UMI counted using 10X Genomics' Single-Cell Gene Expression Software Cell Ranger ("count pipeline", default parameters). Genomic reference: "refdata-cellranger-mm10-3.0.0", prepared by 10x Genomics.
Genome_build: mm10
Supplementary_files_format_and_content: MEX-formatted UMI count matrices of each sample. Sample names consist of genotype (WT: wild-type, SPDH mutant: SPDH), developmental state (E12.5). 10x Genomics explains their MEX-formatted UMI counts as follows: "The cellranger pipeline generates a gene-barcode matrix...Each matrix is stored in Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively." More information on the formatting can be found at https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices.

growth_protocol: Littermate embryos (wt and homozygous) were obtained from staged matings of heterozygous Spdh mice.

extract_protocol:
DNA-was extracted from embryonic forebrain tissue of each embryo using QuickExtract (Epicentre, QE09050) and used for immediate PCR genotyping. Distal limb buds (hand plate) from 1 wildtype and 1 homozygous Spdh embryo were then dissected and trypsinized for a total of 30 minutes in 500µl pre-warmed 3T-trypsin and gently dissociated by pipetting after 10, 15 and 25 minutes. Trypsinization was stopped by addition of 10ml medium (DMEM, 10%FBS, 2mM L-Glutamine, 50U/ml Penicillin/Streptomycin). Cell dissociation and cell viability (trypan-blue) was controlled microscopically. The cell suspension was passed throw a Flowmi strainer (40um, Scienceware H13680-0040).
For single-cell RNA sequencing with a target cell recovery of about 5,000 cells 8,000 cells were used as input for the generation of a droplet emulation using the Chromium Controller. Single-cell libraries were generated following the manual instructions of 10x Genomic (Chromium™ Single Cell 3’ v2), with the exception of fewer PCR cycles in cDNA amplification (11 cycles) and sample index PCR (10 cycles) than recommended in order to increase complexity of libraries. Libraries were sequenced with a minimum of 300 Mio paired end reads and parameters as described in the manual.

treatment_protocol: Individual littermate embryos were separated and kept at 4°C in PBS during genotyping.


title: WT_H3K27ac_ChIPSeq_spikein_Rep1

description: ChIPseq


title: E13_B2_94


title: E13_B2_24


title: WT_E12.5_scRNASeq


title: MCF10A cells, IR rep1

city: Houston

first: Junjie

last: Chen

state: Texas

address: 6565 MD Anderson Blvd

department: ERO

institute: UT MD Anderson Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling
Reads were adapter-trimmed and preprocessed with the FastQC software for the purpose of quality control and data filtering
Genome mapping was carried out using hisat2 software (v2.0.4) and the human reference genome
The mapped reads were assembled into transcripts and genes with the human genome annotation file (genecode.v28.annotation.gtf) using StringTie software (v1.3.4d).
Expression of the transcripts or genes was normalized as FPKM (fragments per kilobase of transcript per million mapped reads) for quantification. Transcripts with an FPKM score below 1 were removed, resulting in a total of 14,944 gene IDs. Note: MSTRGs without Gene Names/Symbols are not qualified for functional enrichment, so they will not affect any conclusions drawn in the manuscript.
Genome_build: UCSC hg38
Supplementary_files_format_and_content: Excel file includes FPKM values for each Sample

organism: Homo sapiens

source_name: MCF10A cells, IR

growth_protocol: MCF10A cells were cultured in DMEM/F-12 medium with 5% horse serum, 20ng/mL human EGF, 0.5mg/ml hydrocortisone, 100ng/ml cholera toxin and 10μg/mL recombinant human insulin.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen, 74104) combined with RNase-Free DNase treatment (Qiagen, 79254) according to the manufacturer’s instructions.
The library was prepared with illumina TruSeq Stranded Total RNA Library Prep kit including rRNA depletion and sequencing at NextSeq 500 (illumina) to generate 75 bp from paired-ends.

treatment_protocol: DMSO or AZD6738 (250 nM) was added 2 hours before irradiation with 20 Gy and maintained for 3 days.

value: breast epithelial cells

value: IR


title: VE-cadherin +/+ plus CD5-2

description:
primary cells
VE-cadherin expressed EC
CD5-2

source_name: HUVEC

value: HUVEC

value: VE-cadherin +/+


title: MCF10A cells, IR rep2


title: E13_B2_95


title: E13_B2_83


title: MCF10A cells, AZD6738 rep1

source_name: MCF10A cells, AZD6738


title: E13_B2_26

source_name: embryo


title: pooled HiC

city: Stanford

first: Thomas

last: Quertermous

state: CA

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

description:
1238  1278  1346  1347  1369  1386  1401  1448  1483  1497  1508  1522  1559  1576  1587  1596  1795  1848  1858  1923  2102  2105  2109  2115  2139  2228  2282  2305  2135  2356  2435  2510  2989  2999  3141  10705  20805  112201  177089  200212  289727  313605  317155  1020301  1042702  1060602  1062201.3  2030801  2040401  3100203  3101801  61646600  7103002  8072501  8100901  9052004  9070202  9071501  9092401  9102101  59386145  59885590  397Z030  399Z015  400Z012
4-7

data_processing:
Pooled HiC paired-end reads were aligned to the HCASMC phasing data masked hg19 genome using the HiC-Pro pipeline. Default settings were used to remove duplicate reads, assign reads to MboI restriction fragments, filter for valid interactions, and generate binned interaction matrices. Aligned reads were assigned to a specific allele on the basis of phasing data.
HiC-Pro filtered reads were then processed using the hicpro2juicebox and hicpro2fithic functions.
FitHiC and HiCCUPS ware used to identify high-confidence loops using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: HIC, TEXT, BEDPE

growth_protocol: Primary human coronary artery smooth muscle cells (HCASMCs) derived from normal human donor hearts were purchased from three different manufacturers, Lonza, PromoCell and Cell Applications (all tested negative for mycoplasma contamination) at passage 2 and were maintained in growth-supplemented smooth muscle basal media (Lonza # CC-3182) according to the manufacturer’s instructions. All experiments were performed on HCASMCs between passages 4 and 7.

extract_protocol:
The cells were washed with PBS and then harvested in Hi-C lysis buffer (10 mM Tris-HCl, pH 8, 10 mM NaCl, 0.2 % NP-40). Nuclei pellet was incubated in 0.5% SDS at 62 °C for 10 min and then quenched by water and 10% Triton X-100. MboI (NEB, R0147) enzyme digested DNA for 2 hours at 37 °C. Biotin labeled dATP (Thermo,19524016) and Klenow (NEB, M0210) were used to fill restriction fragment overhangs. The DNA was re-ligated by T4 DNA ligase (NEB, M0202) at room temperature for 4 hours. Re-ligated nuclei were lysis by 0.5% SDS and sheared for 2 min by sonication before extensive centrifugation. Supernatant was incubated at 65 °C over-night with Protease K and the DNA was purified.
For libraries construction, set aside DNA by 150 ng to the biotin capture step. Biotin labeled DNA was pre-bound to Streptavidin C-1 beads (Thermo, 65-001) in biotin binding buffer. After Tween buffer and TD buffer washing, Tn5 transposition was performed on beads at 55 °C for 10 min. Libraries were generated by PCR amplification with Nextera adapters added after washing the beads. Samples were size selected by PAGE purification (300–700 bp) for effective paired end sequencing and adapter dimer removal.

treatment_protocol: not applicable

value: smooth muscle cells


title: WT_H3K27me3_ChIPSeq_Rep2

value: wild-type


title: VE-cadherin +/+ plus control

description:
primary cells
VE-cadherin expressed EC
CTRL

value: control


title: WT_H3K27ac_ChIPSeq_spikein_Rep2

description: ChIPseq


title: MCF10A cells, AZD6738 rep2


title: E13_B2_25

extract_protocol:
After washing with phosphate buffered saline (PBS) (MA0008, meilunbio), the embryo was digested with 0.1% trypsin (25200-072, Gibco) at 37°C for 5 to 10 min. Then the trypsin was neutralized with 2% FBS (04-002-1A, Biological Industries) and FBS was washed off with cold PBS with 0.1 to 1% bovine serum albumin (BSA). Finally, individual cells were picked into a lysis medium on ice with a mouth pipette. All procedures were performed under stereomicroscope
RNA libraries were prepared for sequencing using standard SMART-seq2 protocols for BGISEQ-500


title: MCF10A cells, AZD6738+IR rep1

source_name: MCF10A cells, AZD6738+IR


title: E13_B2_89


title: E13_B2_91


title: E19_B1_26


title: MCF10A cells, DMSO rep2

source_name: MCF10A cells, DMSO

value: DMSO


title: postnatal_day8_periphery

first: Yufeng

last: Lu

address: 15 Datun Road, Chaoyang District

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
Illumina Casava1.8 software used for basecalling
Reads were aligned to GRCh38 human genome by Cellranger(v2.0.1)
Filtered count matrix was merged by Seurat R Package(v2.1.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: Filtered count matrix was formatted by mtx, and barcode and gene information was with tsv format

source_name: human neonatal retina

extract_protocol:
Fetal retina tissue samples were collected in ice-cold artificial cerebrospinal fluid (ACSF), single cell was selected by FACS
Chromium™ Single Cell 3’ Reagent Kits v2

tag: developmental stage

value: retina

tag: region

value: periphery


title: MCF10A cells, DMSO rep1


title: E19_B1_17

data_processing:
BGI-seq basecalling software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Macaca_fascicularis_5.0.91 whole genome using STAR v2.3.4 with default parameters
Reads of exon  were calculated using RSEM
Genome_build: Macaca_fascicularis_5.0.91
Supplementary_files_format_and_content: tab-delimited text files include mapped reads values for each Sample

value: embryo


title: postnatal_day8_macula

value: macula


title: E19_B1_27


title: MCF10A cells, AZD6738+IR rep2


title: FUSCIP2

city: New York

first: Yueh-Lin

last: Tsai

address: 1212 Amsterdam Ave.

institute: Columbia University

description: Immunoprecipitation replicate 2

data_processing:
Trim low quality bases using fastx-trimmer
Reads were aligned using bowtie2
3'READS pipeline selects polyA sites supporting (PASS) reads.
Supplementary_files_format_and_content: hg19

source_name: Glioma

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS, 5% CO2 and 37C.

extract_protocol:
Total RNA from whole-cell inputs and RNAs co-IPed with FUS-R521C were extracted using TRIzol.
The RNAs were fragmented by sonication and were captured using CU5T45 chimeric magnetic beads. The captured RNAs were then eluted from the beads and poly (A) tails removal by RNase H treatment. Eluted RNAs were then subjected to 5’ and 3’ adaptor ligation, RT-PCR and sequencing (Illumina TruSeq LT library preparation kit).

treatment_protocol: Appropriate number of U87-MG cells were replated on 100 mm petridish and grow for 24 hours prior to plasmid transfection. Plasmid p3xFLAG-CMV14-FUS-R521C was transfected into U87-MG cells using Lipofectamine 2000.

value: U87-MG glioma

tag: rna-ip antibody

value: Anti-FLAG (Sigma; F3165)

tag: sample type

value: co-IPed with FUS-R521C


title: GW20_Retina_macula

source_name: human embryonic retina

tag: gestational week


title: E19_B1_28


title: GW20_Retina_periphery


title: FUSCIP1

description: Immunoprecipitation replicate 1


title: WC2

description: Whole-cell input replicate 2

value: whole cell input


title: pooled ATACseq

description:
1238  1278  1346  1347  1369  1386  1401  1448  1483  1497  1508  1522  1559  1576  1587  1596  1795  1848  1858  1923  2102  2105  2109  2115  2139  2161  2228  2282  2305  2135  2356  2435  2463  2477  2510  2989  2999  3003  3141  10705  20805  102901  112201  177089  200212  289727  313605  317155  1020301  1042702  1060602  1062201.3  2030801  2040401  3100203  3101801  61646600  7103002  8072501  8100901  9052004  9070202  9071501  9090701  9092401  9102101  59386145  59885590  397Z030  399Z015  400Z012
4-7

data_processing:
Quality control of ATAC-seq data was performed using Fastqc v0.11.5, and then low-quality bases and adaptor contamination were trimmed by cutadapt 1.15 with default configuration
ATAC-seq reads were aligned to the hg19 genome assembly using BOWTIE2  version 2.2.6 with the --local configuration
Duplicate reads were marked by Picard MarkDuplicates 2.18.0
Duplicate reads and unmapped reads were removed by samtools view -f 2 -F 1804 (1.7)
BAM files were loaded into MCAS2.1.1 for peaks calling with --broad parameters and input as control.
Genome_build: hg19
Supplementary_files_format_and_content: BED6+4. 1st: chromosome, 2nd: start position of peak, 3rd: end position of peak, 4th: peak name, 5th: integer score for display, 7th: fold-change, 8th: -log10pvalue, 9th: -log10qvalue, 10th: relative summit position to peak start

source_name: human coronary artery smooth muscle cells

extract_protocol:
Approximately 50k fresh cells were collected and nuclei-enriched fractions were extracted with cold resuspension buffer (0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin). Nuclei pellets were collected by centrifugation and resuspended with transposition reaction buffer containing Tn5 transposases (Illumina Nextera). Transposition reactions were incubated at 37 °C for 30 min, followed by DNA purification using the DNA Clean-up and Concentration kit (Zymo D4013).
Libraries were amplified using Nextera barcodes and High-Fidelity polymerase (NEB M0541S) and purified using Agencourt Ampure XP beads (Beckman Coulter A63880) double-side selection (0.5X:0.9X).


title: GW27_Retina

extract_protocol:
Fetal retina tissue samples were collected in ice-cold artificial cerebrospinal fluid (ACSF), single cell was selected by FACS
Chromium™ Single Cell 3’ Reagent Kits v2，sample1(indexB2),sample2(indexB8),sample3(indexC5),sample4(indexB6),sample5(indexB1),sample6(indexC9),sample7(indexC10),sample8(indexD3)


title: GW24_2_Retina


title: WC1

description: Whole-cell input replicate 1


title: GW24_1_Retina


title: hESC_betacells, DA296-25%AA

city: Jerusalem

first: Aharon

last: Helman

address: Ein-Kerem

country: Israel

institute: Hebrew university

data_processing:
Sequencing reads were mapped to the human GRCh38 reference genome using RSEM (Li, B et al., 2011) calling the STAR aligner (Dobin, A et al., 2013).
tab-delimited text files containing RSEM output for single sample
Genome_build: GRCh38
Supplementary_files_format_and_content: text file with expected_count, TPM, and FPKM

source_name: HUES 8 hESC line

growth_protocol: ES-derived beta cells were generated based on a protocol published in Pagliuca et al. (2014)

extract_protocol: RNAeasy minikit protocol

treatment_protocol: Stage 6 ES-derived beta cells were grown in CMRL/RPMI media  with different amino acid concentrations (100%, 50%, 25% of the original concentration) + 10% FBS

value: HUES 8 hESC line

value: stem cell-derived beta cell

tag: differentiation stage

value: stage 6

tag: protocol


title: GW22_Retina


title: E19_B1_31


title: E19_B1_33


title: E19_B1_29


title: hESC_betacells, DA295-25%AA

tag: cell line

tag: cell type


title: hESC_betacells, DA279-25%AA


title: GW18_Retina


title: E19_B1_30


title: E19_B1_34


title: hESC_betacells, DA296-50%AA


title: GW14_Retina


title: hESC_betacells, DA295-50%AA


title: E19_B1_36


title: E19_B1_18


title: E19_B1_35


title: GW12_Retina


title: hESC_betacells, DA291-50%AA


title: E19_B1_37


title: E19_B1_38


title: hESC_betacells, DA279-50%AA


title: control rep 3

city: Jena

first: Mona

last: Hoyos

address: Winzerlaer Straße 2

department: Institute for General Microbiology

institute: FSU Jena

data_processing:
Sequencing of the cDNA libraries was performed by the LAFUGA service unit (Gene Center, Munich, Blum group).
cDNA reads were imported into CLC Genomics Workbench v11.0.
adaptor- and quality trimming was performed using the trim reads command with the following settings: sequence=NEB P7:AGATCGGAAGAGCACACGTCTGAACTCCAGTCA, NEB P5:AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; reads: all; when an adapter is found: trim 3'end; for reads without adapters: keep the read; scores=mismatch:2, gapcost:3, cutoff:10; cutoff at end: 4
The trimmed reads were checked for quality and mapped with CLC Genomics Workbench v12.0.3 to the V. cholerae reference genome (NCBI Acc.number: NC_002505, NC_002506) using the following settings: Mismatch cost=2, Insertion cost=3, Deletion cost=3, Length fraction=0.8, Similarity fraction=0.8, Global alignment=yes, Strand specific=reverse, Maximum number of hits for a read=10
Reads mapping in CDS were counted, and genes with a total count cutoff of >15 in all samples were considered for analysis. Read counts were normalized (CPM), and transformed (log2). Differential expression was tested using the built in tool corresponding to edgeR in exact mode with tagwise dispersions. Genes with a fold-change of > 3.0 and a FDR adjusted p-value < 0.05 were considered to be differentially expressed.
Genome_build: NC_002505, NC_002506
Supplementary_files_format_and_content: Read count table and edgeR (exact mode) analysis

organism: Vibrio cholerae

source_name: whole bacterial cells

growth_protocol: V. cholerae C6706 wild-type strains carrying pBAD1K-ctrl or pBAD1K-rasR were cultivated to exponential phase (OD600=0.5) in 50 ml LB media containing 50 µg/ml kanamycin.

extract_protocol:
RNA was isolated using AGPC with EXTRAzol according to standard protocols. Prepared RNA was DNase digested and cleaned up using standard nucleic acid precipitation procedures. Depletion of ribosomal RNA was performed using the Ribo-Zero rRNA Removal kit (Epicentre) for gram-negative bacteria. Integrity of the prepared RNA was tested using a Bioanalyzer.
cDNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760), according to the manufacturer's instructions. Quality of the prepared libraries was tested using a Bioanalyzer.

treatment_protocol: L-arabinose (0.2% final conc.) was added when cells reached exponential phase (OD600=0.5). After 15 minutes of treatment, 4 OD600 units of cells were harvested in tubes containing 20% "stop-mix" (95% ethanol, 5% phenol) and snap-frozen in liquid nitrogen until further processing.

value: wt pBAD1K-ctrl

tag: growth phase

value: exponential phase

value: 0.2% L-arabinose


title: PRVABC59-infected UCMSC at 48hpi

city: Seoul

first: Ok Sarah

last: Shin

address: 148, Gurodongro, Gurogu

country: South Korea

institute: Korea Univ.

data_processing:
Sequencing Quality assessment refer to Wang L, Wang S, Li W., RSeQC: Quality Control of RNA-seq experiments. Bioinformatics. 2012 Jun 27 and Simon Andrews. FastQC: A quality control tool for high throughput sequence data.
Gene expression level was measured according to Wang L, Feng Z, Wang X, Wang X, Zhang X. Bioinformatics. 2010 Jan 1;26(1):136-8. Epub 2009 Oct 24. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data.
Alignment was performed according to Li H, Durbin R. Bioinformatics. 2010 Mar 1;26(5):589-95. Epub 2010 Jan 15. Fast and accurate long-read alignment with Burrows-Wheeler transform.
Known miRNAs were detected by miRDeep2; refer to Friedlander, M R and Mackowiak, S D and Li, N and Chen, W and Rajewsky, N, miRDeep2 accurately identifies known and hundreds of  novel microRNA genes in seven animal clades, Nucleic Acids Research:37-52 (2011)
Novel miRNAs were predicted by miRDeep2; refer to Friedlander, M R and Mackowiak, S D and Li, N and Chen, W and Rajewsky, N, miRDeep2 accurately identifies known and hundreds of  novel microRNA genes in seven animal clades, Nucleic Acids Research:37-52 (2011)
Supplementary_files_format_and_content: excel files include gene_id, a.value, m.value, p. value, q.value, rank, estimatedDEG

source_name: Umbilical cord

growth_protocol: hUCMSCs were cultured using growth medium supplemented with 10% fetal bovine serum (FBS) and 1% non-essential amino acids, and cells from passage numbers 3 to 10 were used

extract_protocol:
Total RNA was isolated using an RNA prep kit (Direct-zol™ RNA MiniPrep Plus)
NEXTflex Illumina Small RNA-Seq Kit

treatment_protocol: hUCMSCs were seeded using growth media and infected with the virus for 2 hours; virus was removed and growth medium was added Penicillin/Streptomycin)

value: Mesenchymal stem cell

tag: passages

value: UCMSC

tag: infection


title: PRVABC59-infected UCMSC at 4hpi


title: hESC_betacells, DA291-25%AA


title: E19_B1_39

tag: tissue


title: hESC_betacells, DA296-100%AA


title: MR766-infected UCMSC at 48hpi

tag: strain


title: control rep 2

tag: genotype


title: E19_B1_40


title: MR766-infected UCMSC at 4hpi


title: GW16_Retina


title: E19_B1_41


title: hESC_betacells, DA291-100%AA


title: Mock smRNA-seq

value: mock


title: E19_B1_42


title: iPSC_betacells, after Transplantation-S23

source_name: Human stem cell-derived beta cells

treatment_protocol: Stage 6 ES-derived beta cells were transplanted under the kidney capsule of Beige-Scid immunodeficient mice

value: Human stem cell-derived beta cells

tag: time

value: After Transplantation


title: E19_B1_43

value: embryo


title: rneTS 44 rep2

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

data_processing:
read clipping/trimming: cutadapt 2.5
read alignment: READemption 0.5.0 (subcommand align)
coverage calculation and normalization: READemption 0.5.0 (subcommand coverage)
Genome_build: NC_002505.1, NC_002506.1
Supplementary_files_format_and_content: wiggle and CSV with first base coverage

growth_protocol: V. cholerae C6706 wild-type and rneTS strains were grown in LB medium at 30°C to late exponential phase (OD600 = 1.0) in biological triplicates. At this point, cultures were splitted in half and either continously grown at 30°C or shifted to 44°C. Cells were harvested 1h after temperature shift.

extract_protocol:
Total RNA was isolated using the Hot Phenol method as described previously (Fröhlich et al., 2018). Prepared RNA was DNAse digested and cleaned up using standard nucleic acid precipitation procedures.
cDNA libraries were prepared by vertis Biotechnology AG: total RNA samples were poly(A)-tailed and 5’PPP structures were removed using RNA 5’Polyphosphatase (Epicentre). An RNA adapter was ligated to the 5’ monophosphate and first-strand cDNA synthesis was performed using an oligo(dT)-adapter and M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified, purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics).

treatment_protocol: Cultures were divided in half and shifted to 30 or 44°C at late exponential phase (OD600=1.0). After 1h,  4 OD600 units of cells were harvested in tubes containing 1/5 vol. "stop-mix" (95% ethananol, 5% phenol) and snap-frozen in liquid nitrogen until further processing.

value: late exponential phase

tag: temperature


title: rneTS 44 rep1


title: WT 44 rep3

value: wild-type


title: rneTS 44 rep3


title: Naive CD4 T cell, 24h activated

city: Bellinzona

first: Roger

last: Geiger

address: Via Francesco Chiesa 5

country: Switzerland

institute: Institute for Research in Biomedicine

data_processing: The CASAVA 1.8.2 version of the Illumina pipeline was used to process raw data for format conversion and de-multiplexing

source_name: Blood

extract_protocol:
Total RNA was isolated from flow sorted naïve CD4+ T cells from two healthy donors using the RNeasy Plus Mini Kit from Qiagen.
The TruSeq Stranded mRNA Sample Prep kit (Illumina, San Diego) was used for library preparation starting with 1-2 μg of RNA (R.I.N. >7) as input. The poly-A mRNA was fragmented 3 minutes at 94°C and every purification step was performed by using 1X Agencourt AMPure XP beads. Both RNA samples and final libraries were quantified using the Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and quality tested by Agilent 2100 Bioanalyzer RNA Nano assay (Agilent technologies, Santa Clara, CA). Libraries were processed with Illumina cBot for cluster generation on the flowcell and sequenced on single-end mode at the multiplexing level requested on HiSeq2500 (Illumina, San Diego, CA).

value: Blood

tag: sorting

value: CD4+ CCR7+ CD45RA+ CD8- CD25-

tag: activation

value: anti CD3/CD28; 24h


title: E19_B1_46

first: CNSA

last: CNGB

address: BGI

institute: BGI


title: E19_B1_45


title: WT 44 rep1


title: Naive CD4 T cell, resting

value: not activated


title: WT 44 rep2


title: Sample21_MF

city: Oxford

first: Supat

last: Thongjuea

department: The MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Sequencing data in the binary base call (BCL) format were demultiplexed. Unique molecular identifier (UMI) counts were obtained by aligning FASTQ files to the human reference genome (GRCh38 3.0.0) using Cell Ranger software (version 3.0.1) from 10x Genomics. The CellRanger “count” standard pipeline was used to obtain the expression matrix for each individual library for each donor. Cells meeting the following QC parameters were applied to determine which cells to include in analyses: UMI counts > 1,000 and ≤ maximum UMIs); number of detected genes > 500 and ≤ maximum number of detected genes); the percentage of mitochondrial gene expression < 15% per cell. Genes expressed in at least 10 cells were included. We scaled UMI counts by normalizing each library size to 10000. The normalized expression values were then log transformed.
R1 for Samples 1-16 contains the cell-barcodes and unique molecular identifier (UMI). Only 26bp will be used (16bp for cell barcodes and 10bp for UMI).  R2 for Samples 1-16 contains the fragments of cDNA. So, R2 for samples 1-16 is biological.
For Samples 17-20:
R1 for Sample  17-21 is the fragment of cDNA. So, R1 for samples 17-21 is biological.
R2 for Samples 17-21 is the cell barcodes. So, R2 for samples 17-21 is technical.
R3 for Samples 17-21 is the UMI. So, R2 for samples 17-21 is technical.
I1 for Samples 17-21 is the sequencing index, and thus is technical.
Genome_build: GRCh38
Supplementary_files_format_and_content: MEX files were generated from the cellranger software. Cell information and UMI count were stored in the R object files.

source_name: CD34+ lineage negative peripheral blood HSPC

extract_protocol:
Cryopreserved perhipheral blood mononuclear cells were thawed and CD34+ lineage negative cells isolated by FACS for single cell RNA sequencing using the 10x Genomics 3' single cell platform.
Libraries were prepared as per the 10x Genomics Chromium Single Cell 3' Reagent kit user guide. Samples 1-16 were done with version 2 of 10x Genomics Chromium Single Cell 3' Reagent kit and Samples 17-21 were done with version 1 of 10x Genomics Chromium Single Cell 3' Reagent kit.

tag: diagnosis

value: Myelofibrosis sample

value: CD34+Lineage- hematopoietic stem/progenitor cells (HSPCs)


title: E19_B1_44

city: shenzhen


title: iPSC_betacells, after Transplantation-S22

value: stage 6

value: transplanted under the kidney capsule of Beige-Scid immunodeficient mice


title: iPSC_betacells, after Transplantation-S16


title: iPSC_betacells, after Transplantation-S21


title: Sample20_MF


title: E19_B1_47


title: E19_B1_19


title: hESC_betacells, DA295-100%AA

value: HUES 8 hESC line

value: stem cell-derived beta cell


title: iPSC_betacells, after Transplantation-S12


title: rneTS 30 rep1


title: Sample18_Healthy

value: Healthy mobilized apheresis donor


title: hESC_betacells, DA279-100%AA


title: WT 30 rep3


title: E19_B1_49


title: rneTS 30 rep2


title: iPSC_betacells, before Transplantation-S9

value: Before Transplantation


title: Sample17_Healthy


title: E19_B1_50


title: Naive CD4 T cell, 6h activated

value: anti CD3/CD28; 6h


title: iPSC_betacells, after Transplantation-S24

value: Human stem cell-derived beta cells

value: After Transplantation


title: Sample19_MF


title: Input-CRY2

city: Beijing

first: wang

last: jiawen

address: 7 Science Park Road ZGC Life Science Park

institute: National institute of biological sciences

data_processing:
Basecalls performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie version 1.0.0 with parameters -p 30 -m 1 -S -q
Peaks were called using MACS2 version 2.1.1 with parameters callpeak -g hs -B --SPMR
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig files were converted from bdg files generated by MACS2 version 2.1.1; Scores represent signal per million reads for fragment pileup profiles.

source_name: U2OS cell

growth_protocol: U2OS cells (passage 15-20) were routinely grown till confluence (10% FBS with 1% Pen+Str antibiotics in DMEM).

extract_protocol:
Cells in 15 cm dish were sequentially cross-linked in 20 ml PBS buffer containing 1.5 mM EGS for 20 min, and followed by cross-linked in 20 ml PBS buffer containing 1% formaldehyde for 15 min at room temperature. The cross-link was stopped by adding glycine to a final concentration of 125 mM and incubate at room temperature for 5 min. ChIP assay and DNA sample preparation were performed strictly following the ChIP-IT High Sensitivity Kit (Active Motif). Eluted DNA was analyzed with high-throughput sequencings.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: When cells reached confluency, continued to grow for another day and then harvested cells for ChIP-seq.

tag: treatment

tag: chip-grade antibody

tag: 2nd antibody


title: iPSC_betacells, after Transplantation-S14

tag: differentiation stage

tag: protocol


title: iPSC_betacells, before Transplantation-S3

tag: cell type


title: WT 30 rep2

tag: growth phase

value: late exponential phase


title: rneTS 30 rep3


title: E19_B1_52

value: embryo


title: WT 30 rep1

value: wild-type


title: E19_B1_53


title: iPSC_betacells, before Transplantation-S4


title: Input-BMAL1-RUVBL2

tag: cell line


title: iPSC_betacells, before Transplantation-S2


title: ChIP-RUVBL2

value: Anti-RUVBL2 (Novus Biologicals, NBP-40354)

value: anti-rabbit IgG


title: oppB ATC BCM rep 3

data_processing:
Sequencing of the cDNA libraries was performed by vertis Biotechnology AG using a NextSeq 500 system in single-read mode for 75 cycles.
cDNA reads were imported into CLC Genomics Workbench v12.0.3.
adaptor- and quality trimming was performed using the trim reads command with the following settings: sequence=TruSeq_Antisense_primer:AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC; reads: all; when an adapter is found: trim 3'end; for reads without adapters: keep the read; scores=mismatch:2, gapcost:3, cutoff:10; cutoff at end: 4
The trimmed reads were checked for quality and mapped to the V.cholerae reference genome (NCBI Acc.number: NC_002505, NC_002506) with the 3xFLAG sequence inserted upstream of oppA and oppB stop codons. The following settings were used: Mismatch cost=2, Insertion cost=3, Deletion cost=3, Length fraction=0.8, Similarity fraction=0.8, Global alignment=yes, Strand specific=no, Maximum number of hits for a read=1
Reads mapping in CDS were counted, and genes with a total count cutoff of >8 in all samples were considered for analysis. Read counts were normalized (CPM), and transformed (log2). Differential expression was tested using the built in tool corresponding to edgeR in exact mode with tagwise dispersions. Genes with a fold-change of > 3.0 and a FDR adjusted p-value < 0.05 were considered to be differentially expressed.
Genome_build: NC_002505, NC_002506
Supplementary_files_format_and_content: Read count table and edgeR (exact mode) analysis

growth_protocol: V. cholerae C6706 strains carrying oppA::3xFLAG oppB::3xFLAG genes and either the wild-type oppB allele or the start codon of oppB mutated to ATC were cultivated to early stationary phase (OD600 of 1.5) in 20 ml LB media without antibiotics.

extract_protocol:
RNA was isolated using hot phenol as described previously (Fröhlich et al., 2018). Prepared RNA was DNase digested and cleaned up using standard nucleic acid precipitation procedures.
cDNA libraries were prepared by were prepared by vertis Biotechnology AG in a 3’ end-specific protocol: ribosomal RNA was depleted and the Illumina 5’ sequencing adaptor was ligated to the 3’ OH end of RNA molecules. First strand synthesis using M-MLV reverse transcriptase was followed by fragmentation and strand-specific ligation of the Illumina 3’ sequencing adaptor to the 3’ end of first-strand cDNA. Finally, 3’ cDNA fragments were amplified, purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics).

treatment_protocol: When cells reached early stationary phase (OD600=1.5), cultures were divided into 2x6ml and treated with either bicyclomycin (25 µg/ml final conc.) or the respective volume of H2O (mock treatment). After 2 hours of treatment, 4 OD600 units of cells were harvested in tubes containing 1/5 "stop-mix" (95% ethanol, 5% phenol) and snap-frozen in liquid nitrogen until further processing.

value: oppA::3xFLAG oppB::3xFLAG oppB ATC

value: stationary phase

value: 25 µg/ml bicyclomycin


title: control rep 1

value: wt pBAD1K-ctrl

value: exponential phase

value: 0.2% L-arabinose


title: oppB ATC BCM rep 2


title: E19_B1_54


title: ChIP-CRY2

value: Anti-CRY2 (Bethyl Laboratories, A302-615A)


title: ChIP-CRY1

value: Anti-CRY1 (Bethyl Laboratories, A302-614A)


title: 86 year old Adult retina scRNA-seq

city: St. Louis

first: Brian

middle: Stewart

last: Clark

state: Missouri

address: 660 S Euclid Ave; Campus Box #8096

department: Ophthalmology and Visual Sciences

institute: Washington University

description:
Single retinal cells from an 86 year old healthy adult retina processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
Read 1: 98bp, Read 2: 26bp; i7:8bp

data_processing:
fastq files were aligned to Hg38 using Cellranger 2.0.1 or newer versions using the refdata-cellranger-GRCh38-3.0.0 reference index provided by 10x. Count matrices were manually aggregated and used as input into Monocle2.99. single cell RNAseq framework
only retinal and potential RPE cells were included in the finalized matrix (Final_matrix.mtx), however, all cells on which sequencing profiles were obtained are included in the All_cells.mtx file.
Genome_build: Hg38 (refdata-cellranger-GRCh38-3.0.0)
Supplementary_files_format_and_content: Final_matrix.mtx: Expression data of the finalized retina matrix (118,555 cells)
Supplementary_files_format_and_content: genes.csv: Gene features for all expression matrices. Rownames of genes.tsv correspond to the rownames of Final_matrix.mtx and All_cells.mtx files
Supplementary_files_format_and_content: Final_barcodes.csv: Cell features of the final retina matrix (118,555 cells)
Supplementary_files_format_and_content: All_cells.mtx: Expression data of all sequenced cells (138,672 cells)
Supplementary_files_format_and_content: All_barcodes.csv: Cell features of all sequenced cells (138.672 cells)

source_name: Retinal Cells

extract_protocol: 10x Genomics 3' v2 Single Cell RNA-sequencing

value: dissociated retina

tag: cell source

value: primary tissue


title: Hgw19 replicate 2 retina scRNA-seq

description:
Single retinal cells from gestational week 19 human retinas processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
Read 1: 98bp, Read 2: 26bp; i7:8bp

tag: tissue


title: ChIP-BMAL1

value: Anti-BMAL1 (Abcam, Cat #ab3350, Lot# GR241928-12)


title: E19_B1_55


title: oppB ATC BCM rep 1

tag: strain


title: E19_B1_56


title: oppB ATC mock rep 2

tag: genotype


title: oppB ATC mock rep 3


title: Input-CRY1


title: E19_B1_51


title: Hgw19 replicate 1 retina scRNA-seq


title: RUVBL2 dmso input

description:
DMSO_Input
ChIP was performed using indicated antibody (CRY2, Bethyl Laboratories, A302-615A; RUVBL2, Novus Biologicals, NBP-40354) together with 10 µg chromatin. 50 ng spike-in chromatin (Active Motif, 53083) and 2 µg spike-in antibody (Active Motif, 61686) were added for normalization.

data_processing:
Basecalls performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the hg19 and BDGP6 genome assembly respectively using bowtie version 1.0.0 with parameters -p 40 -m 1 -S -q
Remove deduplicate reads using gatk MarkDuplicates version 4.0.12.0
Compare Drosophila tag counts from other samples to the sample containing the least tags and generate a normalization factor for each comparison.
Downsample the tag counts of datasets proportional to the normalization factor.
Peaks were called using MACS2 version 2.1.1 with parameters callpeak -g hs -B
Genome_build: hg19, BDGP6
Supplementary_files_format_and_content: bigWig files were converted from bdg files generated by MACS2 version 2.1.1; Scores represent signal for fragment pileup profiles.

extract_protocol:
Cells in 15 cm dish were sequentially cross-linked in 20 ml PBS buffer containing 1.5 mM EGS for 20 min, and followed by cross-linked in 20 ml PBS buffer containing 1% formaldehyde for 15 min at room temperature. The cross-link was stopped by adding glycine to a final concentration of 125 mM and incubate at room temperature for 5 min. DNA sample preparation and spike-in ChIP assay were performed strictly following the ChIP-IT High Sensitivity Kit (Active Motif). Eluted DNA was analyzed with high-throughput sequencings.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: When cells reached confluency, continued to grow for another day. Treated cells with cordycepin (100 uM) for 1 h as indicated, harvested cells for ChIP-seq.

tag: spike-in reference organism

value: Drosophila melanogaster

tag: spike-in antibody


title: E19_B1_57


title: oppB ATC mock rep 1


title: CRY2 dmso input

description:
Dm_input
ChIP was performed using indicated antibody (CRY2, Bethyl Laboratories, A302-615A; RUVBL2, Novus Biologicals, NBP-40354) together with 10 µg chromatin. 50 ng spike-in chromatin (Active Motif, 53083) and 2 µg spike-in antibody (Active Motif, 61686) were added for normalization.


title: E19_B1_20


title: Hgw17 retina scRNA-seq

description:
Single retinal cells from gestational week 17 human retinas processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
Read 1: 98bp, Read 2: 26bp; i7:8bp


title: wild-type BCM rep 3

value: oppA::3xFLAG oppB::3xFLAG


title: iPSC_betacells, before Transplantation-S1

value: Human stem cell-derived beta cells

value: stage 6

value: transplanted under the kidney capsule of Beige-Scid immunodeficient mice

tag: time

value: Before Transplantation


title: Hgw13 retina scRNA-seq

description:
Single retinal cells from gestational week 13 human retinas processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
Read 1: 98bp, Read 2: 26bp; i7:8bp


title: E19_B1_58

value: embryo


title: RUVBL2 cordycepin input

description:
Cordy_Input-2
ChIP was performed using indicated antibody (CRY2, Bethyl Laboratories, A302-615A; RUVBL2, Novus Biologicals, NBP-40354) together with 10 µg chromatin. 50 ng spike-in chromatin (Active Motif, 53083) and 2 µg spike-in antibody (Active Motif, 61686) were added for normalization.


title: wild-type BCM rep 2

value: stationary phase


title: E19_B1_59


title: Hgw15 retina scRNA-seq

description:
Single retinal cells from gestational week 15 human retinas processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
Read 1: 98bp, Read 2: 26bp; i7:8bp


title: wild-type BCM rep 1

value: 25 µg/ml bicyclomycin


title: Hgw11 retina scRNA-seq

description:
Single retinal cells from gestational week 11 human retinas processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
Read 1: 98bp, Read 2: 26bp; i7:8bp


title: RUVBL2 dmso ChIP

description:
DMSO_R2
ChIP was performed using indicated antibody (CRY2, Bethyl Laboratories, A302-615A; RUVBL2, Novus Biologicals, NBP-40354) together with 10 µg chromatin. 50 ng spike-in chromatin (Active Motif, 53083) and 2 µg spike-in antibody (Active Motif, 61686) were added for normalization.

value: DMSO

value: Anti-Ruvbl2 (Novus Biologicals, NBP-40354)

value: anti-rabbit IgG

value: Spike-in Antibody (Active Motif, 61686)


title: Hgw9 retina scRNA-seq

description:
Single retinal cells from gestational week 9 human retinas processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
Read 1: 98bp, Read 2: 26bp; i7:8bp


title: wild-type mock rep 3


title: E19_B1_61


title: wild-type mock rep 2


title: CRY2 dmso ChIP

description:
Cry2_Dm
ChIP was performed using indicated antibody (CRY2, Bethyl Laboratories, A302-615A; RUVBL2, Novus Biologicals, NBP-40354) together with 10 µg chromatin. 50 ng spike-in chromatin (Active Motif, 53083) and 2 µg spike-in antibody (Active Motif, 61686) were added for normalization.

value: Anti-Cry2 (Bethyl Laboratories, A302-615A)


title: wild-type mock rep 1


title: E19_B1_62


title: CRY2 cordycepin ChIP

description:
Cry2_Cordy4
ChIP was performed using indicated antibody (CRY2, Bethyl Laboratories, A302-615A; RUVBL2, Novus Biologicals, NBP-40354) together with 10 µg chromatin. 50 ng spike-in chromatin (Active Motif, 53083) and 2 µg spike-in antibody (Active Motif, 61686) were added for normalization.

value: Cordycepin


title: 59 days in culture human retinal organoid

description:
Day 59 in culture single cells from human retinal organoids processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
Read 1: 98bp, Read 2: 26bp; i7:8bp

value: dissociated retinal organoid

value: retinal cells from IMR-90 induced pluripotent stem cells


title: 42 days in culture human retinal organoid

description:
Day 42 in culture single cells from human retinal organoids processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
Read 1: 98bp, Read 2: 26bp; i7:8bp


title: E19_B1_65


title: CRY2 cordycepin input

description:
Cordy4_input
ChIP was performed using indicated antibody (CRY2, Bethyl Laboratories, A302-615A; RUVBL2, Novus Biologicals, NBP-40354) together with 10 µg chromatin. 50 ng spike-in chromatin (Active Motif, 53083) and 2 µg spike-in antibody (Active Motif, 61686) were added for normalization.

value: Drosophila melanogaster


title: RUVBL2 cordycepin ChIP

description:
Cordy_R2-2
ChIP was performed using indicated antibody (CRY2, Bethyl Laboratories, A302-615A; RUVBL2, Novus Biologicals, NBP-40354) together with 10 µg chromatin. 50 ng spike-in chromatin (Active Motif, 53083) and 2 µg spike-in antibody (Active Motif, 61686) were added for normalization.


title: E19_B1_63


title: 24 days in culture human retinal organoid

description:
Day 24 in culture single cells from human retinal organoids processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
Read 1: 98bp, Read 2: 26bp; i7:8bp


title: E19_B1_66


title: BMAL1 dmso input

description: Input-dmso

data_processing:
Basecalls performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie version 1.0.0 with parameters -p 40 -m 1 -S -q
Peaks were called using MACS2 version 2.1.1 with parameters callpeak -g hs -B --SPMR
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig files were converted from bdg files generated by MACS2 version 2.1.1, representing fold enrichment for each site.

treatment_protocol: When cells reached confluency, continued to grow for another day. Treated cells with cordycepin (100uM) for 1 h as indicated, harvested cells for ChIP-seq.


title: CRY1 dmso input


title: 30 days in culture human retinal organoid

description:
Day 30 in culture single cells from human retinal organoids processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
Read 1: 98bp, Read 2: 26bp; i7:8bp


title: LNCaPWNKSLUG2

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

description: WNK1 SLUG  overexpressed cell_2

data_processing:
Dara processing were performed with Partek Flow according to Manufactures Instruction
Supplementary_files_format_and_content: Excel File contain the gene list

source_name: WNK1 SLUG  overexpressed cell_2

growth_protocol: Cell are cultured in stnadared condition according to ATCC

extract_protocol:
Total RNA was extracted using the Direct-Zol RNA kit  (Zymo Research, Irvine, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: LNCaP

value: Human Prostate cancer Cell


title: E19_B1_67


title: E19_B1_60


title: Human embryo_beta cells_Day 1

data_processing:
Data were processed with 10X cellranger software version 3.0.1. Illumina data were demultiplexed with cellranger mkfastq.
Fastq formatted read data aligned to hg19-3.0.0 human genome reference with cellranger count script.
Genome_build: 10X cellranger human genome reference hg19-3.0.0
Supplementary_files_format_and_content: Filtered feature-barcode matrices containing only cellular barcodes in MEX format
Filtered feature-barcode matrices containing only cellular barcodes in HDF5 format

source_name: Human fetal pancreas

growth_protocol: Pancreatic islets were isolated from human fetal pancreas

extract_protocol: 10X genomics

treatment_protocol: islets were incubated for 1 day or for 4 days in CMRL/RPMI media with 100% or 25% of the original concentration of amino acids.

tag: developmental stage

value: fetal

value: pancreas

value: beta cells

tag: age

value: 120 embryonic day

value: Day 1


title: Human embryo_beta cells_Day 4 100%AA

value: Day 4


title: Human embryo_beta cells_Day 4 25%AA


title: Sample16_MF

tag: diagnosis

value: Myelofibrosis sample

value: CD34+Lineage- hematopoietic stem/progenitor cells (HSPCs)


title: E19_B1_68

source_name: embryo

extract_protocol:
After washing with phosphate buffered saline (PBS) (MA0008, meilunbio), the embryo was digested with 0.1% trypsin (25200-072, Gibco) at 37°C for 5 to 10 min. Then the trypsin was neutralized with 2% FBS (04-002-1A, Biological Industries) and FBS was washed off with cold PBS with 0.1 to 1% bovine serum albumin (BSA). Finally, individual cells were picked into a lysis medium on ice with a mouth pipette. All procedures were performed under stereomicroscope
RNA libraries were prepared for sequencing using standard SMART-seq2 protocols for BGISEQ-500

value: embryo


title: CRY1 cordycepin input

tag: treatment

tag: chip-grade antibody


title: BMAL1 cordycepin input

description: Input-cordy

tag: 2nd antibody


title: Sample15_MF


title: LNCaPCONT2

description: Vector Control Cell_2

source_name: Vector Control Cell_2


title: E19_B1_21


title: LNCaPWNKSLUG1

description: WNK1 SLUG  overexpressed cell_1

source_name: WNK1 SLUG  overexpressed cell_1


title: E19_B1_69


title: BMAL1 dmso ChIP

description: Dmso-Bm

value: DMSO

value: Anti-Bmal1 (Abcam, Cat #ab3350, Lot# GR241928-12)

value: anti-rabbit IgG


title: LNCaPCONT1

description: Vector Control Cell_1

source_name: Vector Control Cell_1


title: Sample14_MF


title: BMAL1 cordycepin ChIP

description: Cordy-Bm

value: Cordycepin


title: Sample13_Healthy

value: Healthy mobilized apheresis donor


title: LNCaP_BRCA2_RB1_2

description: BRCA2 RB1 Khoockdown cell _1

source_name: BRCA2 RB1 Khoockdown cell _1


title: E19_B1_70


title: Sample12_MF


title: LNCaP_BRCA2_RB1_1

description: BRCA2 RB1 Khoockdown cell _1


title: CRY1 dmso ChIP

value: Anti-Cry1 (Bethyl Laboratories, A302-614A)


title: E19_B1_72


title: E20_2-4

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Macaca_fascicularis_5.0.91 whole genome using STAR v2.3.4 with default parameters
Reads of exon  were calculated using RSEM
Genome_build: Macaca_fascicularis_5.0.91
Supplementary_files_format_and_content: tab-delimited text files include mapped reads values for each Sample

extract_protocol:
Monkey embryos with decidua were collected and embedded in optimal cutting temperature compound (OCT; 4583, Tissue-Tek OCT, skura). Embryos were cryo-sectioned along the anterior-posterior axis. Populations of approximately 20 cells from putative EPI, TE, EXMC or VE/YE were collected by laser microdissection and processed for low-input RNA sequencing based on Smart-seq2 method.
RNA libraries were prepared for sequencing using standard SMART-seq2 protocols for ILLUMINA

value: Day 20


title: E19_B1_71

data_processing:
BGI-seq basecalling software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Macaca_fascicularis_5.0.91 whole genome using STAR v2.3.4 with default parameters
Reads of exon  were calculated using RSEM
Genome_build: Macaca_fascicularis_5.0.91
Supplementary_files_format_and_content: tab-delimited text files include mapped reads values for each Sample


title: E19_B1_73


title: CRY1 cordycepin ChIP


title: E20_2-3


title: Sample10_MF


title: Sample11_MF


title: LNCaP_RB1_2

description: RB1 shRNA cell_2

source_name: RB1 shRNA cell_2

value: LNCaP

value: Human Prostate cancer Cell


title: Sample09_Healthy


title: E20_2-2


title: Sample08_MF


title: E19_B1_74


title: LNCaP_BCA2_1

description: BRCA2 CRISPR cell_1

source_name: BRCA2 CRISPR cell_1


title: E19_B1_76


title: LNCaP_SCR2

description: Scrambled Control Cell_2

source_name: Scrambled Control Cell_2


title: LNCaP_RB1_1

description: RB1 shRNA cell_1

source_name: RB1 shRNA cell_1


title: E20_1-4


title: LNCaP_Scr_1

description: Scrambled Control Cell_1

source_name: Scrambled Control Cell_1


title: E19_B1_77


title: LNCaP_BRCA2_2

description: BRCA2 CRISPR cell_2

source_name: BRCA2 CRISPR cell_2


title: E20_2-1


title: E20_1-3


title: E19_B1_78


title: Sample07_MF


title: E19_B1_75


title: Sample05_MF


title: Sample04_MF


title: E20_1-2


title: E19_B1_22


title: E20_1-1


title: E19_B1_79


title: Sample03_MF


title: E16

value: Day 16


title: Sample02_MF


title: S4-4

description:
others
bulk_Readcount_matix.txt

value: Day 18


title: Sample06_Healthy


title: Sample01_Healthy


title: H3K27me3-ChIPseq-Patski-WT

city: Seattle

first: Xinxian

last: Deng

state: WA

address: 1959 NE Pacific St.

department: Laboratory Medicine and Pathology

institute: University of Washington

data_processing:
H3K27me3 ChIP-seq paired-end reads were mapped to the BL6 genome using the NCBI build v38/mm10 reference genome assembly obtained from the UCSC Genome Browser46 using BWA-MEM (v0.7.3) in paired-end mode using default parameters.
Primary mapped valid paired reads with MAPQ>=10 were de-duplicated and used for calling H3K27me3 peaks based on biallelic reads using MACS2.  Peaks were called using all reads (unsegregated).
Genome_build: mm10

organism: Mus musculus x Mus spretus

source_name: H3K27me3 ChIP-seq experiment in wild-type Patski cells

growth_protocol: Standard cell culturing protocol using 10% FBS in DMEM.

extract_protocol:
ChIP was performed using fixed chromatin from Patski cells. DNA from ChIP pull-down chromatin fractions were de-crosslinked and purified using QIAquick PCR purification kit.
Sequencing libraries were prepared each from three or  four pooled independent ChIP samples from Patski cells using the Illumina seq sample prep kit. Size selection of the library was done by gel excision or two-step Ampure bead purification and purification of DNA in the 300-600bp range.

value: Fibroblasts derived from hybrid embryonic kidney

value: Patski cells

tag: chip antibody

value: Anti-H3K27me3 Antibody (Rabbit Polyclonal Antibody; Upstate/Millipore, #07-449)


title: E19_B1_81


title: E19_B1_82


title: H3K27me3-ChIPseq-Patski-ΔFirreXa

source_name: H3K27me3 ChIP-seq experiment in CRISPR/cas9-modified Patski cells

tag: cell type


title: S4-3

description:
others
bulk_Readcount_matix.txt


title: E19_B1_84


title: MIF-KO MM.1S cells

type: RNA

first: Qiang

last: Wang

address: 6550 FANNIN STREET

institute: HOUSTON METHODIST RESEARCH INSTITUTE

description: Gene expression data from MIF-KO MM.1S cells

hyb_protocol: Fragmented and labeled ss-cDNA was hybridyzed for 16 hr at 45°C on GeneChip Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: All GeneChips were scanned on an Affymetrix GeneChip Scanner 3000.

data_processing: Normalization was performed using the Robust Multiarray Average and differentially expressed genes between two groups were identified by R/Bioconductor using limma package.

label: biotin

source_name: Human MM cell line MM.1S

label_protocol: Total RNA was labeled using the GeneChip WT PLUS Reagent Kit.

growth_protocol: ARP-1 and MM.1S MM cells were cultured in RPMI1640 medium containing 10% fetal bovine serum and 100 U penicillin / 0.1 mg/ml streptomycin.

extract_protocol: Total RNA were extracted using Rneasy mini kit (Qiagen).

treatment_protocol: CTR-KO and MIF-KO MM cell lines were established by infecting lentivirus carrying CTR or MIF shRNA and sorting GFP+ cells.

value: multiple myeloma cell line

tag: genotype/variation

value: MIF-KO


title: S4-1

description:
others
bulk_Readcount_matix.txt

value: embryo


title: CTR-KO MM.1S cells

description: Gene expression data from CTR-KO MM.1S cells

tag: cell line

value: control-knockout


title: CTR-KO ARP-1 cells

description: Gene expression data from MIF-KO ARP-1 cells

source_name: Human MM cell line ARP-1


title: S3-6

description:
exmc
bulk_Readcount_matix.txt


title: E19_B1_90


title: S3-5

description:
exmc
bulk_Readcount_matix.txt


title: E19_B1_91


title: S3-4

description:
exmc
bulk_Readcount_matix.txt


title: S3-3

description:
exmc
bulk_Readcount_matix.txt


title: S4-2

description:
others
bulk_Readcount_matix.txt


title: E19_B1_83


title: E19_B1_23


title: pooled TCF21 ChIPseq

description:
1238  1278  1346  1347  1369  1386  1401  1448  1483  1497  1508  1522  1559  1576  1587  1596  1795  1848  1858  1923  2102  2105  2109  2115  2139  2228  2282  2305  2135  2356  2435  2510  2989  2999  3141  10705  20805  112201  177089  200212  289727  313605  317155  1020301  1042702  1060602  1062201.3  2030801  2040401  3100203  3101801  61646600  7103002  8072501  8100901  9052004  9070202  9071501  9092401  9102101  59386145  59885590  397Z030  399Z015  400Z012
4-7

data_processing:
Quality control of ChIP-seq data was performed using Fastqc v0.11.5, and then low-quality bases and adaptor contamination were trimmed by cutadapt 1.15 with default configuration
ChIP-seq reads were aligned to the hg19 genome assembly using BWA mem version 0.7.17-r1188 with the default configuration
Duplicate reads were marked by Picard MarkDuplicates 2.18.0
Duplicate reads and unmapped reads were removed by samtools view -f 2 -F 1804 (1.7)
BAM files were loaded into MCAS2.1.1 for peaks calling with --broad parameters and input as control.
Genome_build: hg19
Supplementary_files_format_and_content: BED6+4. 1st: chromosome, 2nd: start position of peak, 3rd: end position of peak, 4th: peak name, 5th: integer score for display, 7th: fold-change, 8th: -log10pvalue, 9th: -log10qvalue, 10th: relative summit position to peak start

source_name: human coronary artery smooth muscle cells

extract_protocol:
Cells were lysis by 0.5% SDS and the lysates were clarified from sonicated cells and protein-DNA complexes were isolated with TCF21 antibody (HPA013189).
Libraries were prepared with KAPA Hyper Prep kit (KK8502) per standrad instruction.

tag: antibody

value: smooth muscle cells


title: E19_B1_24

tag: tissue


title: S3-2

description:
exmc
bulk_Readcount_matix.txt


title: E19_B1_89


title: E19_B1_25


title: MIF-KO ARP-1 cells

description: Gene expression data from CTR-KO ARP-1 cells


title: CAR 3

data_processing:
BasecallVersion 0.5.6.153 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: ARP-1 MM cells were cultured in RPMI1640 medium containing 10% fetal bovine serum and 100 U penicillin / 0.1 mg/ml streptomycin.

extract_protocol:
RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 2 x 10^6 ARP-1 MM cells were treated with DMSO or Cfz for 16 hours.

value: Human multiple myeloma (MM)  cell line

tag: passage

value: carfilzomib (Cfz)


title: Hippocampus intact memory. Biological replicate 4

city: Pamplona

first: Ana

last: Garcia Osta

state: Navarra

address: Juslarrocha 10, 3H

department: neuroscience

country: Spain

institute: Cima

description: B6.Cg-Tg(APPswe)E1-2Dbo/J  mice 18-20 mont-old

hyb_protocol: Labeled sense cDNA was hybridized to the GeneChip® Mouse Clariom S Arrays, washed and stained on a GeneChip® Fluidics 450 workstation (Affymetrix) according to the manufacturer protocols.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000 7G

data_processing: Data were normalized with Bioconductor software using RMA algorithm.

source_name: Mouse hippocampi after morris water maze

label_protocol: The sense cDNA was prepared from 1 ng of total RNA using the Affymetrix GeneChip® WT Pico Kit (PN902623). The sense strand cDNA was then fragmented and biotinylated according to the manufacturer's instructions.

growth_protocol: Hippocampus of mouse  that underwent  Morris water maze test before sacrificed.

extract_protocol: The RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: Mice were sacrificed by cervical dislocation, brain was extracted and the hippocampus was dissected and kept in dry ice immediately. Tissue was stored at -80 C until RNA extraction.

value: hippocampus

tag: memory status

value: intact

tag: genotype

value: 18-20 months


title: S2-3

description:
epiblast
bulk_Readcount_matix.txt

source_name: embryo


title: Hippocampus intact memory. Biological replicate 3


title: S2-2

description:
epiblast
bulk_Readcount_matix.txt


title: CAR 2


title: Hippocampus intact memory. Biological replicate 2


title: CAR 1


title: DMSO 3

value: DMSO and


title: ΔB11 + pSMT3-Phsp60-B11 R2

city: Shanghai

first: Chuan

address: 131 # Dong An Road

institute: Fudan University

data_processing:
RNA-seq was performed by BGI Group, Shenzhen, Guangdong, China. Briefly, a strand-specific cDNA library was constructed for each sample to keep the direction of RNA transcription. The obtained cDNA libraries were sequenced on an Illumina HiSeq 4000 machine.
Joints were removed and quality of RNA-Seq data was filtered by Scythe and Sickle software (the Phred mass of the base group was required to be greater than 20). High-quality reads were mapped to the reference sequence of Mycobacterium marinum M (NC_010612.1) using Tophat software with default parameters.  The relative expression of the individual genes in each sample was obtained by counting fragments per kilobase of transcript per million mapped reads (FPKM) with the Cuffnorm tool in the Cufflinks software package.
Genome_build: mycobacterium marinum M starin  https://www.ncbi.nlm.nih.gov/nuccore/NC_010612.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Mycobacterium marinum M

source_name: ΔB11 + pSMT3-Phsp60-B11

growth_protocol: cultures were grown from a single colony, n fresh 7H9-OADC（10%） medium, and grown to the OD600 ~ 2.0 at 30°C  with shaking at 105 rpm

extract_protocol:
Bacterial cultures at OD600~2.0 were mixed with 0.2 volumes of stop solution (95% ethanol and 5% phenol) and immediately frozen in liquid nitrogen. Total RNA was isolated using the Trizol method. Briefly, 4.0 OD600 of cells were resuspended with 1mL Trizol (#15596018, Invitrogen) and 0.2 mL 0.1mm Zirconia/Silica beads (#11079101z, Biospec).   Bacteria cells were lysed with a Precellys 24 homogenizer (4500 rpm, 3x30s, separated by 5min intervals on ice,). After mixing with 400 μl chloroform and centrifugation in a Phase Lock Gel tube (#WM5-2302820, TIANGEN Biotech) at 13,000 rpm for 15 min, 500 ul of the aqueous phase was mixed with 450 μl isopropanol and precipitated at room temperature for 30 min. After centrifugation at 13,000 rpm for 30min, RNA pellets were washed with 80% ethanol, dissolved in ultra-pure water (#10977, Thermo Fisher Scientific), and the RNA concentration was determined using NanoDrop 2000.
Ribosomal RNAs was removed by Biotin-labled rRNA probe. Purified and fragmentated RNA was then treated by Illumina TruSeq Standard Kit: Fragmented RNA was reverse transcribed to first chain cDNA random oligo and reverse transcriptase. Second chain cDNA was generated with DNA polymerase I and RNase H. dTTP was replaced by dUTP when Second chain cDNA was generated to increase the chain-specificity. Double chain cDNA was then poly A tailed and ligated with adaptor. After PCR application , samples were sequenced in illumine Hi-seq platform

treatment_protocol: Cells were collected without treatment

tag: strain

value: M strain with B11 deletion

value: with B11-overexpressed plasmid pSMT3-Phsp60-B11

tag: sample type

value: Bacterial cells


title: ΔB11 + pSMT3 (Mock)-R2

source_name: ΔB11 + pSMT3 (Mock)

value: with empty plasmid pSMT3 (Mock)


title: Hippocampus memory impaired. Biological replicate 3

value: impaired


title: Hippocampus intact memory. Biological replicate 1


title: S2-1

description:
epiblast
bulk_Readcount_matix.txt

value: Day 18


title: Hippocampus memory impaired. Biological replicate 2


title: DMSO 2


title: S1-2

description:
hypoblast
bulk_Readcount_matix.txt


title: DMSO 1


title: S3-1

description:
exmc
bulk_Readcount_matix.txt


title: ΔB11 + pSMT3-Phsp60-B11 R1


title: ΔB11 + pSMT3 (Mock)-R1